ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Ihre E-Mail wurde erfolgreich gesendet. Bitte prüfen Sie Ihren Maileingang.

Leider ist ein Fehler beim E-Mail-Versand aufgetreten. Bitte versuchen Sie es erneut.

Vorgang fortführen?

Exportieren
Filter
  • Annual Reviews
  • BioMed Central
  • 2015-2019  (43.755)
  • 2005-2009  (17.552)
  • 1980-1984  (4.446)
  • 1965-1969  (2.421)
  • 1945-1949  (614)
  • 1935-1939  (300)
Sammlung
Schlagwörter
Verlag/Herausgeber
Sprache
Erscheinungszeitraum
Jahr
  • 1
    facet.materialart.
    Unbekannt
    Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms (2018)
    BioMed Central
    Details
    Publikationsdatum: 2021-03-29
    Schlagwort(e): 551
    Sprache: Englisch
    Materialart: article , publishedVersion
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    CITATION GEO-LEO
  • 2
    facet.materialart.
    Unbekannt
    Spatial compartmentalization of free radical formation and mitochondrial heterogeneity in bivalve gills revealed by live-imaging techniques (2016)
    BioMed Central
    In:  EPIC3Frontiers in Zoology, BioMed Central, 13(4)
    Details
    Publikationsdatum: 2016-02-05
    Beschreibung: Background: Reactive oxygen (ROS) and nitrogen (RNS) species are produced during normal unstressed metabolic activity in aerobic tissues. Most analytical work uses tissue homogenates, and lacks spatial information on the tissue specific sites of actual ROS formation. Live-imaging techniques (LIT) utilize target-specific fluorescent dyes to visualize biochemical processes at cellular level. Results: Together with oxidative stress measurements, here we report application of LIT to bivalve gills for ex-vivo analysis of gill physiology and mapping of ROS and RNS formation in the living tissue. Our results indicate that a) mitochondria located in the basal parts of the epithelial cells close to the blood vessels are hyperpolarized with high Δψm, whereas b) the peripheral mitochondria close to the cilia have low (depolarized) Δψm. These mitochondria are densely packed (mitotracker Deep Red 633 staining), have acidic pH (Ageladine-A) and collocate with high formation of nitric oxide (DAF-2DA staining). NO formation is also observed in the endothelial cells surrounding the filament blood sinus. ROS (namely H2O2, HOO• and ONOO− radicals, assessed through C-H2DFFDA staining) are mainly formed within the blood sinus of the filaments and are likely to be produced by hemocytes as defense against invading pathogens. On the ventral bend of the gills, subepithelial mucus glands contain large mucous vacuoles showing higher fluorescence intensities for O2 •- than the rest of the tissue. Whether this O2 •- production is instrumental to mucus formation or serves antimicrobial protection of the gill surface is unknown. Cells of the ventral bends contain the superoxide forming mucocytes and show significantly higher protein carbonyl formation than the rest of the gill tissue. Conclusions: In summary, ROS and RNS formation is highly compartmentalized in bivalve gills under unstressed conditions. The main mechanisms are the differentiation of mitochondria membrane potential and basal ROS formation in inner and outer filament layers, as well as potentially antimicrobial ROS formation in the central blood vessel. Our results provide new insight into this subject and highlight the fact that studying ROS formation in tissue homogenates may not be adequate to understand the underlying mechanism in complex tissues. Keywords: Bivalve, Gill, Live-imaging, Fluorescence, Mitochondria, ROS, RNS * Correspondence:
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 3
    facet.materialart.
    Unbekannt
    The environmental toxicant 2,3,7,8-tetrachlorodibenzo-p-dioxin disrupts morphogenesis of the rat pre-implantation embryo (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Hutt et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Developmental Biology 8 (2008): 1, doi:10.1186/1471-213X-8-1.
    Beschreibung: Environmental toxicants, whose actions are often mediated through the aryl hydrocarbon receptor (AhR) pathway, pose risks to the health and well-being of exposed species, including humans. Of particular concern are exposures during the earliest stages of development that while failing to abrogate embryogenesis, may have long term effects on newborns or adults. The purpose of this study was to evaluate the effect of maternal exposure to the AhR-specific ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the development of rat pre-implantation embryos with respect to nuclear and cytoskeletal architecture and cell lineage allocation. We performed a systematic 3 dimensional (3D) confocal microscopy analysis of rat pre-implantation embryos following maternal exposure to environmentally relevant doses of TCDD. Both chronic (50 ng/kg/wk for 3 months) and acute (50 ng/kg and 1 μg/kg at proestrus) maternal TCDD exposure disrupted morphogenesis at the compaction stage (8–16 cell), with defects including monopolar spindle formation, f-actin capping and fragmentation due to aberrant cytokinesis. Additionally, the size, shape and position of nuclei were modified in compaction stage pre-implantation embryos collected from treated animals. Notably, maternal TCDD exposure did not compromise survival to blastocyst, which with the exception of nuclear shape, were morphologically similar to control blastocysts. We have identified the compaction stage of pre-implantation embryogenesis as critically sensitive to the effects of TCDD, while survival to the blastocyst stage is not compromised. To the best of our knowledge this is the first in vivo study to demonstrate a critical window of pre-implantation mammalian development that is vulnerable to disruption by an AhR ligand at environmentally relevant doses.
    Beschreibung: This research was supported by NIH/NIEHS-012916 (BKP), ESHE Fund (DFA), Hall Family Foundation (DFA and KJH) and Biomedical Research Training Grant KUMC (KJH).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: video/quicktime
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 4
    facet.materialart.
    Unbekannt
    New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria (2007)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2007 Ioannidis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 8 (2007): 182, doi:10.1186/1471-2164-8-182.
    Beschreibung: Background: The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). Identifying the ori of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria. Results: Using features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori boundary genes were found to be hemE and COG1253 protein (CBS domain protein). Comparisons of the putative ori region among related Wolbachia strains showed higher conservation of bases within binding sites. Conclusion: The sequences of the ori regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the ori region in genome sequencing projects.
    Beschreibung: PI, PS, SS, GT and KB acknowledge support of their work from intramural funding from the University of Ioannina. SB, JDH, LB and JW acknowledge support of their work from the U.S. National Science Foundation grant EF-0328363. SB also acknowledges the support from the NASA Astrobiology Institute (NNA04CC04A)
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 5
    facet.materialart.
    Unbekannt
    Accuracy and quality of massively parallel DNA pyrosequencing (2007)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2007 Huse et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R143, doi:10.1186/gb-2007-8-7-r143.
    Beschreibung: Additional data file 1 is a fasta file of the 43 known sequences used. Additional data file 2 is a gzip-compressed fasta file of the sequences output by the GS20. These sequences correspond to those included in Additional data files 3, 4, 5 but include only the final sequence information. Additional data files 3, 4, 5 are three compressed text files representing the text translations of the original GS20 binary output (sff) files for all of the sequencing used in the analysis, including sequence, flowgram and other run information. GS20 data are reported by region of the PicoTiterPlate™; we sequenced three plate regions.
    Beschreibung: Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that catalogue differences between PCR amplicons of ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage of consensus assemblies to detect and minimize incorrect base calls. We performed an empirical study of the per-base error rate for the Roche GS20 system using sequences of the V6 hypervariable region from cloned microbial ribosomal DNA (tag sequencing). We calculated a 99.5% accuracy rate in unassembled sequences, and identified several factors that can be used to remove a small percentage of low-quality reads, improving the accuracy to 99.75% or better. By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods.
    Beschreibung: This work was supported by National Aeronautics and Space Administration Astrobiology Institute Cooperative Agreement NNA04CC04A (to MLS), subcontracts from the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J Stegeman PI to HGM and MLS), grants from the WM Keck Foundation and the G Unger Vetlesen Foundation (to MLS), and a National Research Council Research Associateship Award (to JAH).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Format: application/zip
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 6
    facet.materialart.
    Unbekannt
    Atypical properties of a conventional calcium channel β subunit from the platyhelminth Schistosoma mansoni (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Salvador-Recatalà et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Physiology 8 (2008): 6, doi:10.1186/1472-6793-8-6.
    Beschreibung: The function of voltage-gated calcium (Cav) channels greatly depends on coupling to cytoplasmic accessory β subunits, which not only promote surface expression, but also modulate gating and kinetic properties of the α1 subunit. Schistosomes, parasitic platyhelminths that cause schistosomiasis, express two β subunit subtypes: a structurally conventional β subunit and a variant β subunit with unusual functional properties. We have previously characterized the functional properties of the variant Cavβ subunit. Here, we focus on the modulatory phenotype of the conventional Cavβ subunit (SmCavβ) using the human Cav2.3 channel as the substrate for SmCavβ and the whole-cell patch-clamp technique. The conventional Schistosoma mansoni Cavβ subunit markedly increases Cav2.3 currents, slows macroscopic inactivation and shifts steady state inactivation in the hyperpolarizing direction. However, currents produced by Cav2.3 in the presence of SmCavβ run-down to approximately 75% of their initial amplitudes within two minutes of establishing the whole-cell configuration. This suppressive effect was independent of Ca2+, but dependent on intracellular Mg2+-ATP. Additional experiments revealed that SmCavβ lends the Cav2.3/SmCavβ complex sensitivity to Na+ ions. A mutant version of the Cavβ subunit lacking the first forty-six amino acids, including a string of twenty-two acidic residues, no longer conferred sensitivity to intracellular Mg2+-ATP and Na+ ions, while continuing to show wild type modulation of current amplitude and inactivation of Cav2.3. The data presented in this article provide insights into novel mechanisms employed by platyhelminth Cavβ subunits to modulate voltage-gated Ca2+ currents that indicate interactions between the Ca2+ channel complex and chelated forms of ATP as well as Na+ ions. These results have potentially important implications for understanding previously unknown mechanisms by which platyhelminths and perhaps other organisms modulate Ca2+ currents in excitable cells.
    Beschreibung: This work was supported by NIH grant #s R01 AI-40522 and R01 AI-73660 to RMG and by NIH-NCRR grant # P41 RR001395 to the Biocurrents Research Center (BRC) at MBL.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 7
    facet.materialart.
    Unbekannt
    Genomics of an extreme psychrophile, Psychromonas ingrahamii (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Riley et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 9 (2008): 210, doi:10.1186/1471-2164-9-210.
    Beschreibung: The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.
    Beschreibung: MR acknowledges support from DE-FG02-04ER63940. JTS acknowledges the support from the University of Washington NASA NAI program and the NSF Astrobiology IGERT program. TZW acknowledges support from a grant from the Fondation Fourmentin-Guilbert and AD acknowledges support from the European Union BioSapiens Network of Excellence, Grant LSHG CT-2003-503265
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/vnd.ms-excel
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 8
    facet.materialart.
    Unbekannt
    Comparative proteome analysis of psychrophilic versus mesophilic bacterial species : insights into the molecular basis of cold adaptation of proteins (2009)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 10 (2009): 11, doi:10.1186/1471-2164-10-11.
    Beschreibung: Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are underrepresented in the helical regions of proteins of psychrophiles. The patterns of amino acid substitutions between the orthologous proteins of psychrophiles versus mesophiles are significantly different for several amino acids when compared to their substitutions in orthologous proteins of within the mesophiles or psychrophiles. Current results provide quantitative substitution preferences (or avoidance) of amino acids that lead to the adaptation of proteins to cold temperatures. These finding would help future efforts in selecting mutations for rational design of proteins with enhanced psychrophilic properties.
    Beschreibung: This work was supported by a grant from Howard Hughes Medical Institute to Queens College, CUNY, and Queens College Research Enhancement Grant.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 9
    facet.materialart.
    Unbekannt
    GenBank and PubMed : how connected are they? (2009)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2009 Sarkar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 2 (2009): 101, doi:10.1186/1756-0500-2-101.
    Beschreibung: GenBank(R) is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs). Here we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences. Our analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.
    Beschreibung: INS and HM are funded in part by a research grant from the Ellison Medical Foundation and National Library of Medicine award R01LM009725 to INS.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 10
    facet.materialart.
    Unbekannt
    Nuclear receptor complement of the cnidarian Nematostella vectensis : phylogenetic relationships and developmental expression patterns (2009)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2009 Reitzel and Tarrant. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 9 (2009): 230, doi:10.1186/1471-2148-9-230.
    Beschreibung: Nuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes. Sequenced genomes from an increasing number of bilaterians have provided a more complete picture of duplication and loss of nuclear receptors in protostomes and deuterostomes but have left open the question of which nuclear receptors were present in the cnidarian-bilaterian ancestor. In addition, nuclear receptor expression and function are largely uncharacterized within cnidarians, preventing determination of conserved and novel nuclear receptor functions in the context of animal evolution. Here we report the first complete set of nuclear receptors from a cnidarian, the starlet sea anemone Nematostella vectensis. Genomic searches using conserved DNA- and ligand-binding domains revealed seventeen nuclear receptors in N. vectensis. Phylogenetic analyses support N. vectensis orthologs of bilaterian nuclear receptors in four nuclear receptor subfamilies within nuclear receptor family 2 (COUP-TF, TLL, HNF4, TR2/4) and one putative ortholog of GCNF (nuclear receptor family 6). Other N. vectensis genes grouped well with nuclear receptor family 2 but represented lineage-specific duplications somewhere within the cnidarian lineage and were not clear orthologs of bilaterian genes. Three nuclear receptors were not well-supported within any particular nuclear receptor family. The seventeen nuclear receptors exhibited distinct developmental expression patterns, with expression of several nuclear receptors limited to a subset of developmental stages. N. vectensis contains a diverse complement of nuclear receptors including orthologs of several bilaterian nuclear receptors. Novel nuclear receptors in N. vectensis may be ancient genes lost from triploblastic lineages or may represent cnidarian-specific radiations. Nuclear receptors exhibited distinct developmental expression patterns, which are consistent with diverse regulatory roles for these genes. Understanding the evolutionary relationships and developmental expression of the N. vectensis nuclear receptor complement provides insight into the evolution of the nuclear receptor superfamily and a foundation for mechanistic characterization of cnidarian nuclear receptor function.
    Beschreibung: We are grateful for financial support from the Woods Hole Oceanographic Institution (WHOI) through the Tropical Research Initiative, the Ocean Life Institute (AMT), the Academic Programs Office, and to the Beacon Institute for Rivers and Estuaries (AMR).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/postscript
    Format: application/pdf
    Format: application/msword
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 11
    facet.materialart.
    Unbekannt
    Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Biology 13 (2015): 105, doi:10.1186/s12915-015-0213-6
    Beschreibung: The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth ~3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines. We report observations from sediments of three DHAB (Urania, Discovery, L’Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTrackerTM Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L’Atalante normoxic control sediments were fit, while specimens from L’Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L’Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions. We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time.
    Beschreibung: Supported by NSF grants OCE-0849578 to VPE and JMB, OCE-1061391 to JMB and VPE, and The Investment in Science Fund at WHOI.
    Schlagwort(e): Athalassohaline ; Bryozoa ; CellTrackerTM Green ; Discovery ; L’Atalante ; Loricifera ; Meiofauna ; Nematoda ; Ultrastructure ; Urania
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 12
    facet.materialart.
    Unbekannt
    Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 5 (2017): 50, doi:10.1186/s40168-017-0270-x.
    Beschreibung: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. We used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients. Our analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8 weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems. The analytical strategy adopted in our study can provide genomic insights into bacterial populations that may be critical to the efficacy of FMT due to their success in gut colonization and metabolic properties, and guide cultivation efforts to investigate mechanistic underpinnings of this procedure beyond associations.
    Beschreibung: AME was supported by the Frank R. Lillie Research Innovation Award and startup funds from the University of Chicago. This project was supported by the Mutchnik Family Charitable Fund and the University of Chicago Gastro-Intestinal Research Foundation.
    Schlagwort(e): Fecal microbiota transplantation ; Colonization ; Metagenomics ; Metagenome-assembled genomes
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 13
    facet.materialart.
    Unbekannt
    The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae (2018)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbial Cell Factories 17 (2018): 170, doi:10.1186/s12934-018-1018-4.
    Beschreibung: Ammonium assimilation is linked to fundamental cellular processes that include the synthesis of non-essential amino acids like glutamate and glutamine. In Saccharomyces cerevisiae glutamate can be synthesized from α-ketoglutarate and ammonium through the action of NADP-dependent glutamate dehydrogenases Gdh1 and Gdh3. Gdh1 and Gdh3 are evolutionarily adapted isoforms and cover the anabolic role of the GDH-pathway. Here, we review the role and function of the GDH pathway in glutamate metabolism and we discuss the additional contributions of the pathway in chromatin regulation, nitrogen catabolite repression, ROS-mediated apoptosis, iron deficiency and sphingolipid-dependent actin cytoskeleton modulation in S.cerevisiae. The pleiotropic effects of GDH pathway in yeast biology highlight the importance of glutamate homeostasis in vital cellular processes and reveal new features for conserved enzymes that were primarily characterized for their metabolic capacity. These newly described features constitute insights that can be utilized for challenges regarding genetic engineering of glutamate homeostasis and maintenance of redox balances, biosynthesis of important metabolites and production of organic substrates. We also conclude that the discussed pleiotropic features intersect with basic metabolism and set a new background for further glutamate-dependent applied research of biotechnological interest.
    Beschreibung: The writing of the manuscript was supported by the European Union (European Social Fund – ESF) and by the Greek National Strategic Reference Framework (NSRF) THALIS: – UOC “Mitochondrial dysfunction in neurodegenerative diseases” (Grant Code 377226).
    Schlagwort(e): Glutamate dehydrogenase ; GDH1 ; GDH2 ; GDH3 ; Ammonium assimilation ; GABA shunt ; ROS-mediated apoptosis ; Chromatin regulation ; Nitrogen catabolite repression ; S. cerevisiae
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 14
    facet.materialart.
    Unbekannt
    Role of carbon cycle observations and knowledge in carbon management (2005)
    Annual Reviews
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Beschreibung: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Beschreibung: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Schlagwort(e): Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 406392 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 15
    facet.materialart.
    Unbekannt
    A functional update of the Escherichia coli K-12 genome (2005)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.
    Beschreibung: Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.
    Beschreibung: This work was supported by NIH grant RO1 RR07861, the NASA Astrobiology Institute grant NCC2-1054, grants from the Edward Mallinckrodt, Jr Foundation and the Sinsheimer Foundation, and NSF grants NSF DBI - 9984882 and NSF IIS - 9996304.
    Schlagwort(e): Escherichia coli K-12
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 89280 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 16
    facet.materialart.
    Unbekannt
    Long nonlinear internal waves (2006)
    Annual Reviews
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Beschreibung: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Beschreibung: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Schlagwort(e): Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 1034976 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 17
    facet.materialart.
    Unbekannt
    EGenBio : a data management system for evolutionary genomics and biodiversity (2006)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006.
    Beschreibung: © 2006 Nahum et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Beschreibung: EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs.
    Beschreibung: This work was partly funded by the National Institutes of Health (R22/R33 Innovation and Development grant to David Pollock), the National Science Foundation (CBM2/EPSCOR), and the State of Louisiana (Biological Computation and Visualization Center, Governor's iotechnology Initiative, and startup funds to David Pollock).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 358631 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 18
    facet.materialart.
    Unbekannt
    Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing (2007)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2006 Erdner and Anderson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 7 (2006): 88, doi:10.1186/1471-2164-7-88.
    Beschreibung: Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endosymbionts of marine invertebrates and are well known for their involvement in "red tides". Dinoflagellates are also notable for their unusual genome content and structure, which suggests that the organization and regulation of dinoflagellate genes may be very different from that of most eukaryotes. To investigate the content and regulation of the dinoflagellate genome, we performed a global analysis of the transcriptome of the toxic dinoflagellate Alexandrium fundyense under nitrate- and phosphate-limited conditions using Massively Parallel Signature Sequencing (MPSS).
    Beschreibung: This work was funded by National Science Foundation OCE-0136861 and OCE-0430724, National Institute of Environmental Health Sciences 1 P50 ES012742-01, and a grant from the Woods Hole Oceanographic Institution Ocean Life Institute.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 370083 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 19
    facet.materialart.
    Unbekannt
    Extending knowledge of Escherichia coli metabolism by modeling and experiment (2007)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2003 BioMed Central. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 4 (2003): 235, doi:10.1186/gb-2003-4-11-235.
    Beschreibung: One of the challenges for ‘post-genomic’ biology is the integration of data from many different sources. Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 65636 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 20
    facet.materialart.
    Unbekannt
    Clinical applications and limitations of current ovarian stem cell research : a review (2007)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2006 Hutt and Albertini. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Journal of Experimental & Clinical Assisted Reproduction 3 (2006): 6, doi:10.1186/1743-1050-3-6.
    Beschreibung: The publication of a report in Nature in 2004 by the Tilly group suggesting that mouse ovaries are capable of generating oocytes de novo post-natally, has sparked interest in a problem long thought to have been resolved from classical studies in a variety of mammalian species. Within a nearly two year time period, laboratories around the world have taken up the challenge to dogma raised by this initial report, either to test this concept in an experimental basic science setting or give direction to clinical applications that could result, were the original premises of this work in the mouse valid for extrapolation to humans. This review provides a status report for this promising area of research, (1) to summarize recent findings in the literature with respect to the validity of the original hypothesis proffered by the Tilly group, and, (2) to gauge the potential utility of ovarian stem cells as a treatment for certain forms of human infertility.
    Beschreibung: Support and the funding provided from the Hall Family Foundation.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 210336 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 21
    facet.materialart.
    Unbekannt
    The coastal environment and human health : microbial indicators, pathogens, sentinels and reservoirs (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S3, doi:10.1186/1476-069X-7-S2-S3.
    Beschreibung: Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans.
    Beschreibung: The Oceans and Human Health Initiative research described within this paper is supported by the National Science Foundation, The National Institute for Environmental Health Sciences and the National Oceanic and Atmospheric Administration. Grant numbers are: NIEHS P50 ES012742 and NSF OCE- 043072 (RJG, LAA-Z, MFP), NSF OCE04-32479 and NIEHS P50 ES012740 (RSF), NSF OCE-0432368 and NIEHS P50 ES12736 (HMS-G), NIEHS P50 ES012762 and NSF OCE-0434087 (JSM).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 22
    facet.materialart.
    Unbekannt
    Linking the oceans to public health : current efforts and future directions (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License The definitive version was published in Environmental Health 7 (2008): S6, doi:10.1186/1476-069X-7-S2-S6.
    Beschreibung: We review the major linkages between the oceans and public health, focusing on exposures and potential health effects due to anthropogenic and natural factors including: harmful algal blooms, microbes, and chemical pollutants in the oceans; consumption of seafood; and flooding events. We summarize briefly the current state of knowledge about public health effects and their economic consequences; and we discuss priorities for future research. We find that: • There are numerous connections between the oceans, human activities, and human health that result in both positive and negative exposures and health effects (risks and benefits); and the study of these connections comprises a new interdisciplinary area, "oceans and human health." • The state of present knowledge about the linkages between oceans and public health varies. Some risks, such as the acute health effects caused by toxins associated with shellfish poisoning and red tide, are relatively well understood. Other risks, such as those posed by chronic exposure to many anthropogenic chemicals, pathogens, and naturally occurring toxins in coastal waters, are less well quantified. Even where there is a good understanding of the mechanism for health effects, good epidemiological data are often lacking. Solid data on economic and social consequences of these linkages are also lacking in most cases. • The design of management measures to address these risks must take into account the complexities of human response to warnings and other guidance, and the economic tradeoffs among different risks and benefits. Future research in oceans and human health to address public health risks associated with marine pathogens and toxins, and with marine dimensions of global change, should include epidemiological, behavioral, and economic components to ensure that resulting management measures incorporate effective economic and risk/benefit tradeoffs.
    Beschreibung: Funding was provided in part by the NSF-NIEHS Oceans Centers at Woods Hole, University of Hawaii, University of Miami, and University of Washington, and the NOAA Oceans and Human Health Initiative Centers of Excellent in Charleston, Seattle and Milwaukee, the National Center for Environmental Health (NCEH) of the Centers for Disease Control and Prevention (CDC), and the WHOI Marine Policy Center. Grant numbers are: NIEHS P50 ES012742 and NSF OCE-043072 (HLKP, RJG, PH); NSF OCE 0432368 and NIEHS P50 ES12736 (LEF); NIEHS P50 ES012762 and NSF OCE-0434087 (EMF, AT, LRY); NSF OCE04-32479 and NIEHS P50 ES012740 (BAW)
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 23
    facet.materialart.
    Unbekannt
    A simple novel device for air sampling by electrokinetic capture (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 79, doi:10.1186/s40168-015-0141-2.
    Beschreibung: A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable. An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.
    Beschreibung: This work was partly supported by Breakout Labs, a program of the Thiel Foundation, and partly from personal funds from Julian Gordon and Prasanthi Gandhi. This work was supported in part by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Schlagwort(e): Atomic force microscopy ; Reverse transcriptase PCR ; Air sampling ; Field study ; Aerosol ; Nanoparticles ; Aerobiome ; Amplicon sequencing ; Bacteria ; Molds
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 24
    facet.materialart.
    Unbekannt
    The obese gut microbiome across the epidemiologic transition (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Emerging Themes in Epidemiology 13 (2016): 2, doi:10.1186/s12982-015-0044-5.
    Beschreibung: The obesity epidemic has emerged over the past few decades and is thought to be a result of both genetic and environmental factors. A newly identified factor, the gut microbiota, which is a bacterial ecosystem residing within the gastrointestinal tract of humans, has now been implicated in the obesity epidemic. Importantly, this bacterial community is impacted by external environmental factors through a variety of undefined mechanisms. We focus this review on how the external environment may impact the gut microbiota by considering, the host’s geographic location ‘human geography’, and behavioral factors (diet and physical activity). Moreover, we explore the relationship between the gut microbiota and obesity with these external factors. And finally, we highlight here how an epidemiologic model can be utilized to elucidate causal relationships between the gut microbiota and external environment independently and collectively, and how this will help further define this important new factor in the obesity epidemic.
    Beschreibung: BTL is supported by the Department of Veterans Affairs, Veterans Health Administration, Office of Research and Development, Career Development (Grant no. 1IK2BX001587-01).
    Schlagwort(e): Obesity ; Gut microbiome ; Geographical differences
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 25
    facet.materialart.
    Unbekannt
    Merging scleractinian genera : the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 108, doi:10.1186/s12862-016-0654-8.
    Beschreibung: In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals.
    Beschreibung: This research was supported by the Spanish Ministry of Science and Innovation (CGL2011-23306 and CTM2014-57949R) and EU CoCoNET—“Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential”—from the VII FP of the European Commission under grant agreement n° 287844. This paper also benefited from the ESF COCARDE network activities and commits to the Italian Flag Project ‘Ritmare’. Fund within the Innovation Economy Operational Programme POIG.02.02.00-00-025/09
    Schlagwort(e): Mitochondrial genome ; Microsatellites ; Genetic divergence ; Skeletal plasticity ; Desmophyllum dianthus ; Lophelia pertusa
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 26
    facet.materialart.
    Unbekannt
    Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 11 (2016): 46, doi:10.1186/s40793-016-0168-4.
    Beschreibung: Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
    Beschreibung: The work was supported by the U.S. Department of Energy, Office of Science JGI under Contract No. DE-AC02-05CH11231 for CSP 2010 project 1012224; USDA NIFA Award 2011-67019-30178, and the Utah Agricultural Experiment Station, Utah State University project UTA00371.
    Schlagwort(e): Nitrosospira ; Ammonia-oxidizing bacteria ; Nitrification ; Agricultural soil ; Ammonia monooxygenase ; Nitrous oxide ; Chemolithotroph
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 27
    facet.materialart.
    Unbekannt
    Interpreting comprehensive two-dimensional gas chromatography using peak topography maps with application to petroleum forensics (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chemistry Central Journal 10 (2016): 75, doi:10.1186/s13065-016-0211-y.
    Beschreibung: Comprehensive two-dimensional gas chromatography (GC×GC) provides high-resolution separations across hundreds of compounds in a complex mixture, thus unlocking unprecedented information for intricate quantitative interpretation. We exploit this compound diversity across the (GC×GC) topography to provide quantitative compound-cognizant interpretation beyond target compound analysis with petroleum forensics as a practical application. We focus on the (GC×GC) topography of biomarker hydrocarbons, hopanes and steranes, as they are generally recalcitrant to weathering. We introduce peak topography maps (PTM) and topography partitioning techniques that consider a notably broader and more diverse range of target and non-target biomarker compounds compared to traditional approaches that consider approximately 20 biomarker ratios. Specifically, we consider a range of 33–154 target and non-target biomarkers with highest-to-lowest peak ratio within an injection ranging from 4.86 to 19.6 (precise numbers depend on biomarker diversity of individual injections). We also provide a robust quantitative measure for directly determining “match” between samples, without necessitating training data sets. We validate our methods across 34 (GC×GC) injections from a diverse portfolio of petroleum sources, and provide quantitative comparison of performance against established statistical methods such as principal components analysis (PCA). Our data set includes a wide range of samples collected following the 2010 Deepwater Horizon disaster that released approximately 160 million gallons of crude oil from the Macondo well (MW). Samples that were clearly collected following this disaster exhibit statistically significant match (99.23±1.66)% using PTM-based interpretation against other closely related sources. PTM-based interpretation also provides higher differentiation between closely correlated but distinct sources than obtained using PCA-based statistical comparisons. In addition to results based on this experimental field data, we also provide extentive perturbation analysis of the PTM method over numerical simulations that introduce random variability of peak locations over the (GC×GC) biomarker ROI image of the MW pre-spill sample (sample #1 in Additional file 4: Table S1). We compare the robustness of the cross-PTM score against peak location variability in both dimensions and compare the results against PCA analysis over the same set of simulated images. Detailed description of the simulation experiment and discussion of results are provided in Additional file 1: Section S8. We provide a peak-cognizant informational framework for quantitative interpretation of (GC×GC) topography. Proposed topographic analysis enables (GC×GC) forensic interpretation across target petroleum biomarkers, while including the nuances of lesser-known non-target biomarkers clustered around the target peaks. This allows potential discovery of hitherto unknown connections between target and non-target biomarkers.
    Beschreibung: This research was made possible in part by a grant from the Gulf of Mexico Research Initiative (GoMRI-015), and the DEEP-C consortium, and in part by NSF Grants OCE-0969841 and RAPID OCE-1043976 as well as a WHOI interdisciplinary study award.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 28
    facet.materialart.
    Unbekannt
    Upside-down swimming behaviour of free-ranging narwhals (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2007 Dietz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Ecology 7 (2007): 14, doi:10.1186/1472-6785-7-14.
    Beschreibung: Free-ranging narwhals (Monodon monoceros) were instrumented in Admiralty Inlet, Canada with both satellite tags to study migration and stock separation and short-term, high-resolution digital archival tags to explore diving and feeding behaviour. Three narwhals were equipped with an underwater camera pod (Crittercam), another individual was equipped with a digital archival tag (DTAG), and a fifth with both units during August 2003 and 2004. Crittercam footage indicated that of the combined 286 minutes of recordings, 12% of the time was spent along the bottom. When the bottom was visible in the camera footage, the narwhals were oriented upside-down 80% of the time (range: 61 100%). The DTAG data (14.6 hours of recordings) revealed that during time spent below the surface, the two tagged narwhals were supine an average of 13% (range: 9–18%) of the time. Roughly 70% of this time spent in a supine posture occurred during the descent. Possible reasons for this upside-down swimming behaviour are discussed. No preference for a clockwise or counter-clockwise direction of roll was observed, discounting the possibility that rolling movements contribute to the asymmetric left-handed helical turns of the tusk.
    Beschreibung: This study was funded by the National Environmental Research Institute, the Greenland Institute of Natural Resources (organized by Mads Peter Heide-Jørgensen), the Department of Fisheries and Oceans, the Nunavut Wildlife Research Trust Fund and the Danish Cooperation for the Environment in the Arctic (DANCEA). Ari D. Shapiro received financial support from the WHOI Academic Programs Office, the National Science Foundation Research Fellowship and the National Defense Science & Engineering Graduate Fellowship.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/zip
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 29
    facet.materialart.
    Unbekannt
    Centers for Oceans and Human Health : contributions to an emerging discipline (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S1, doi:10.1186/1476-069X-7-S2-S1.
    Beschreibung: The oceans are the dominant feature of the planet and are fundamentally linked to human history and to human health. Concerns about the impact of the oceans on human health can be traced to ancient times. Jewish law prohibited the consumption of shellfish, probably reflecting the fact that filter-feeding bivalves can accumulate pathogens and toxins. The Portuguese explorer Pedro Fernandes de Queirós described symptoms associated with ciguatera fish poisoning after eating Caribbean sea bream in 1606, and several of British explorer James Cook's crew experienced similar symptoms after eating fish off the coast of Vanuatu in 1774 [1]. Roughly 1,200 people died from the consumption of fish and shellfish contaminated with methyl mercury in Minamata (Japan) during the 20th century; an even larger number were affected by chronic long-term neurotoxicological impacts [2]. A tsunami caused by an undersea earthquake on December 26, 2004 killed more than 225,000 people in eleven countries bordering the Indian Ocean; and more than 1,400 people died within a single day when the storm surge generated by Hurricane Katrina overwhelmed the New Orleans levee system on August 29, 2005 [3]. Looking ahead, the International Panel on Climate Change has projected a sea level rise of as much as 88 cm during the 21st century as a result of global warming [4], with major implications for the welfare and sustainability of coastal communities.
    Beschreibung: The support of the National Science Foundation (US) and the National Institute of Environmental Health Sciences (US) is gratefully acknowledged: Grant numbers NSF OCE04- 32479 and NIEHS P50 ES012740 (EAL), NSF OCE-0432368 and NIEHS P50 ES12736 (LEB), and NIEHS P50 ES012742 and NSF OCE-043072 (JJS).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 30
    facet.materialart.
    Unbekannt
    Centers for Oceans and Human Health : a unified approach to the challenge of harmful algal blooms (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License The definitive version was published in Environmental Health 7 (2008): S2, doi:10.1186/1476-069X-7-S2-S2.
    Beschreibung: Harmful algal blooms (HABs) are one focus of the national research initiatives on Oceans and Human Health (OHH) at NIEHS, NOAA and NSF. All of the OHH Centers, from the east coast to Hawaii, include one or more research projects devoted to studying HAB problems and their relationship to human health. The research shares common goals for understanding, monitoring and predicting HAB events to protect and improve human health: understanding the basic biology of the organisms; identifying how chemistry, hydrography and genetic diversity influence blooms; developing analytical methods and sensors for cells and toxins; understanding health effects of toxin exposure; and developing conceptual, empirical and numerical models of bloom dynamics. In the past several years, there has been significant progress toward all of the common goals. Several studies have elucidated the effects of environmental conditions and genetic heterogeneity on bloom dynamics. New methods have been developed or implemented for the detection of HAB cells and toxins, including genetic assays for Pseudo-nitzschia and Microcystis, and a biosensor for domoic acid. There have been advances in predictive models of blooms, most notably for the toxic dinoflagellates Alexandrium and Karenia. Other work is focused on the future, studying the ways in which climate change may affect HAB incidence, and assessing the threat from emerging HABs and toxins, such as the cyanobacterial neurotoxin β-N-methylamino-L-alanine. Along the way, many challenges have been encountered that are common to the OHH Centers and also echo those of the wider HAB community. Long-term field data and basic biological information are needed to develop accurate models. Sensor development is hindered by the lack of simple and rapid assays for algal cells and especially toxins. It is also critical to adequately understand the human health effects of HAB toxins. Currently, we understand best the effects of acute toxicity, but almost nothing is known about the effects of chronic, subacute toxin exposure. The OHH initiatives have brought scientists together to work collectively on HAB issues, within and across regions. The successes that have been achieved highlight the value of collaboration and cooperation across disciplines, if we are to continue to advance our understanding of HABs and their relationship to human health.
    Beschreibung: This work was funded through grants from the NSF/NIEHS Centers for Oceans and Human Health, NIEHS P50 ES012742 and NSF OCE-043072 (DLE and DMA), NSF OCE04-32479 and NIEHS P50 ES012740 (PB and RRB), NSF OCE-0432368 and NIEHS P50 ES12736 (LEB), NIEHS P50 ES012762 and NSF OCE-0434087 (RCS, KAL, MSP, MLW, and KAH). Additional support was provided by the ECOHAB Grant program NSF Grant OCE-9808173 and NOAA Grant NA96OP0099 (DMA), NOAA OHHI NA04OAR4600206 (RRB) and Washington State Sea Grant NA16RG1044 (RCS). KAL and VLT were supported in part by the West Coast Center for Oceans and Human Health (WCCOHH) as part of the NOAA Oceans and Human Health Initiative.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 31
    facet.materialart.
    Unbekannt
    Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: connecting sources to human exposure (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S5, doi:10.1186/1476-069X-7-S2-S5.
    Beschreibung: Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges.
    Beschreibung: The authors acknowledge the financial support for the NSF/NIEHS and NOAA Centers for Oceans and Human Health
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 32
    facet.materialart.
    Unbekannt
    Evolution by leaps : gene duplication in bacteria (2009)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Direct 4 (2009): 46, doi:10.1186/1745-6150-4-46.
    Beschreibung: Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today’s microbes. Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.
    Beschreibung: This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-08ER64511.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 33
    facet.materialart.
    Unbekannt
    Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum (2015)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 805, doi:10.1186/s12864-015-2052-9.
    Beschreibung: Organelle retention is a form of mixotrophy that allows organisms to reap metabolic benefits similar to those of photoautotrophs through capture of algal prey and sequestration of their plastids. Mesodinium rubrum is an abundant and broadly distributed photosynthetic marine ciliate that steals organelles from cryptophyte algae, such as Geminigera cryophila. M. rubrum is unique from most other acquired phototrophs because it also steals a functional nucleus that facilitates genetic control of sequestered plastids and other organelles. We analyzed changes in G. cryophila nuclear gene expression and transcript abundance after its incorporation into the cellular architecture of M. rubrum as an initial step towards understanding this complex system. We compared Illumina-generated transcriptomes of the cryptophyte Geminigera cryophila as a free-living cell and as a sequestered nucleus in M. rubrum to identify changes in protein abundance and gene expression. After KEGG annotation, proteins were clustered by functional categories, which were evaluated for over- or under-representation in the sequestered nucleus. Similarly, coding sequences were grouped by KEGG categories/pathways, which were then evaluated for over- or under-expression via read count strategies. At the time of sampling, the global transcriptome of M. rubrum was dominated (~58–62 %) by transcription from its stolen nucleus. A comparison of transcriptomes from free-living G. cryophila cells to those of the sequestered nucleus revealed a decrease in gene expression and transcript abundance for most functional protein categories within the ciliate. However, genes coding for proteins involved in photosynthesis, oxidative stress reduction, and several other metabolic pathways revealed striking exceptions to this general decline. Major changes in G. cryophila transcript expression after sequestration by M. rubrum and the ciliate’s success as a photoautotroph imply some level of control or gene regulation by the ciliate and at the very least reflect a degree of coordination between host and foreign organelles. Intriguingly, cryptophyte genes involved in protein transport are significantly under-expressed in M. rubrum, implicating a role for the ciliate’s endomembrane system in targeting cryptophyte proteins to plastid complexes. Collectively, this initial portrait of an acquired transcriptome within a dynamic and ecologically successful ciliate highlights the remarkable cellular and metabolic chimerism of this system.
    Beschreibung: The authors wish to acknowledge the support of NSF award 1354773.
    Schlagwort(e): Mesodinium rubrum ; Geminigera cryophila ; Karyoklepty ; Acquired phototrophy ; Transcriptome ; Differential gene expression ; Chimeric metabolism ; Organelle retention ; Mixotrophy
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/vnd.ms-excel
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 34
    facet.materialart.
    Unbekannt
    ITAG : an eco-sensor for fine-scale behavioral measurements of soft-bodied marine invertebrates (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Animal Biotelemetry 3 (2015): 31, doi:10.1186/s40317-015-0076-1.
    Beschreibung: Soft-bodied marine invertebrates comprise a keystone component of ocean ecosystems; however, we know little of their behaviors and physiological responses within their natural habitat. Quantifying ocean conditions and measuring organismal responses to the physical environment is vital to understanding the species or ecosystem-level influences of a changing ocean. Here we describe a novel, soft-bodied invertebrate eco-sensor tag (the ITAG), its trial attachments to squid and jellyfish, and the fine-scale behavioral measurements recorded on captive animals. Tags were deployed on five jellyfish (Aurelia aurita) and eight squid (Loligo forbesi) in laboratory conditions for up to 24 h. Using concurrent video and tag data, movement signatures for specific behaviors were identified. These behaviors included straight swimming (for jellyfish), and finning, jetting, direction reversal and turning (for squid). Overall activity levels were quantified using the root-mean-squared magnitude of acceleration, and finning was found to be the dominant squid swimming gait during captive squid experiments. External light sensors on the ITAG were used to compare squid swimming activity relative to ambient light across a ca. 20-h trial. The deployments revealed that while swimming was continuous for captive squid, energetically costly swimming behaviors (i.e., jetting and rapid direction reversals) occurred infrequently. These data reflect the usefulness of the ITAG to study trade-offs between behavior and energy expenditure in captive and wild animals. These data demonstrate that eco-sensors with sufficiently high sampling rates can be applied to quantify behavior of soft-bodied taxa and changes in behavior due to interactions with the surrounding environment. The methods and tool described here open the door for substantial lab and field-based measurements of fine-scale behavior, physiology, and concurrent environmental parameters that will inform fisheries management, and elucidate the ecology of these important keystone taxa.
    Beschreibung: This work was supported by WHOI’s Ocean Life Institute and the Innovative Technology Program, Hopkins Marine Station’s Marine Life Observatory (to KK), as well as the National Science Foundation’s Ocean Acidification Program (to TAM) and NSF’s Program for Innovative Development of Biological Research (to TAM, KK and KAS).
    Schlagwort(e): Jellyfish ; Cephalopod ; Activity pattern ; Activity pattern ; Climate ; High-temporal resolution ; Sensory
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 35
    facet.materialart.
    Unbekannt
    Meeting report of Ctenopalooza : the first international meeting of ctenophorologists (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in EvoDevo 7 (2016): 19, doi:10.1186/s13227-016-0057-3
    Beschreibung: Here we present a report on Ctenopalooza: A meeting of ctenophorologists held at the Whitney Laboratory for Marine Bioscience in St. Augustine, FL, USA, on March 14–15, 2016. In this report, we provide a summary of each of the sessions that occurred during this two-day meeting, which touched on most of the relevant areas of ctenophore biology. The report includes some major themes regarding the future of ctenophore research that emerged during Ctenopalooza. More information can be found at the meeting Web site: http://ctenopalooza.whitney.ufl.edu.
    Beschreibung: Ctenopalooza was sponsored by a grant from the National Science Foundation’s Division of Integrative Organismal Systems to Joseph Ryan (#1619712). We also acknowledge funding was provided by a grant from the University of Florida’s Office of Research to Joseph Ryan (Project #00075235). Additional funding was provided by The Whitney Laboratory for Marine Bioscience.
    Schlagwort(e): Ctenophora ; Ctenophore ; Ctenophore
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 36
    facet.materialart.
    Unbekannt
    Gene fusions and gene duplications : relevance to genomic annotation and functional analysis (2005)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2005 Serres and Riley. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 6 (2005): 33, doi:10.1186/1471-2164-6-33.
    Beschreibung: Background: Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. Results: Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused) proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. Conclusion: The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes it possible to generate protein groups related by both sequence and function, avoiding mixing of unrelated sequences. Organisms differ in sizes of groups of sequence-related proteins. A sample comparison of orthologs to selected E. coli paralogous groups correlates with known physiological and taxonomic relationships between the organisms.
    Beschreibung: The research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-01ER63202 and by National Aeronautics and Space Administration Astrobiology grant NCC2-1054.
    Schlagwort(e): Escherichia coli ; Multimodular proteins
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 382815 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 37
    facet.materialart.
    Unbekannt
    Design and function of superfast muscles : new insights into the physiology of skeletal muscle (2005)
    Annual Reviews
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Beschreibung: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Beschreibung: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Beschreibung: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Schlagwort(e): Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 567086 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 38
    facet.materialart.
    Unbekannt
    Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? (2007)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2007 Huang and Gogarten. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R99, doi:10.1186/gb-2007-8-6-r99.
    Beschreibung: Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria. We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont. Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.
    Beschreibung: This work was performed while JH held a National Research Council Associateship Award at the NASA Astrobiology Institute at the Marine Biological Laboratory in Woods Hole, Massachusetts (NCC2-1054). Additional support was provided through NSF (MCB-0237197) and NASA AISR (NNG04GP90G) grants to JPG.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 39
    facet.materialart.
    Unbekannt
    Athletic equipment microbiota are shaped by interactions with human skin (2015)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 25, doi:10.1186/s40168-015-0088-3.
    Beschreibung: Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
    Beschreibung: MW was supported by a Weinberg College of Arts and Sciences Summer Grant from Northwestern University. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. This work was also supported by the Alfred P Sloan Foundation’s Microbiology of the Built Environment research program. SMG was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5 T-32 EB-009412.
    Schlagwort(e): Gym microbiome ; Athletic equipment ; Microbiology ; Niche communities ; Next-generation sequencing
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: image/png
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 40
    facet.materialart.
    Unbekannt
    Continuous movement behavior of humpback whales during the breeding season in the southwest Indian Ocean : on the road again! (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Movement Ecology 5 (2017): 11, doi:10.1186/s40462-017-0101-5.
    Beschreibung: Humpback whales are known to undertake long-distance migration between feeding and breeding sites, but their movement behavior within their breeding range is still poorly known. Satellite telemetry was used to investigate movement of humpback whales during the breeding season and provide further understanding of the breeding ecology and sub-population connectivity within the southwest Indian Ocean (SWIO). Implantable Argos satellite tags were deployed on 15 whales (7 males and 6 females) during the peak of the breeding season in Reunion Island. A switching-state-space model was applied to the telemetry data, in order to discriminate between “transiting” and “localized” movements, the latter of which relates to meandering behavior within putative breeding habitats, and a kernel density analysis was used to assess the spatial scale of the main putative breeding sites. Whales were tracked for up to 71 days from 31/07/2013 to 16/10/2013. The mean transmission duration was 25.7 days and the mean distance travelled was 2125.8 km. The tracks showed consistent movement of whales from Reunion to Madagascar, demonstrating a high level of connectivity between the two sub-regions, and the use of yet unknown breeding sites such as underwater seamounts (La Perouse) and banks (Mascarene Plateau). A localized movement pattern occurred in distinct bouts along the tracks, suggesting that whales were involved in breeding activity for 4.3 consecutive days on average, after which they resume transiting for an average of 6.6 days. Males visited several breeding sites within the SWIO, suggesting for the first time a movement strategy at a basin scale to maximize mating. Unexpectedly, females with calf also showed extensive transiting movement, while they engaged in localized behavior mainly off Reunion and Sainte-Marie (East Madagascar). The results indicated that whales from Reunion do not represent a discrete population. Discrete breeding sites were identified, thereby highlighting priority areas for conservation. The study is a first attempt to quantify movement of humpback whales within the southwestern Indian Ocean breeding range. We demonstrate a wandering behavior with stopovers at areas that likely represent key breeding habitat, a strategy which may enhance likelihood of individual reproductive success.
    Beschreibung: The project was funded by the European Commission, under the Biodiversity and Ecosystem Services in territories of European overseas (BEST) program (Award number: 07.032700/2012/63511/SUB/B2).
    Schlagwort(e): Humpback whales ; Satellite tracking ; Reunion ; Indian Ocean ; Breeding behavior ; Movement pattern
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 41
    facet.materialart.
    Unbekannt
    Broadly sampled multigene trees of eukaryotes (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Evolutionary Biology 8 (2008): 14, doi:10.1186/1471-2148-8-14.
    Beschreibung: Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches.
    Beschreibung: This project was made possible by a collaborative grant from the National Science Foundation Assembling the Tree of Life program (EF 04-31117) that was awarded to L.A.K., D.B., J.L., D.J.P., and to the ATCC
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 42
    facet.materialart.
    Unbekannt
    Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities (2009)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Biology 7 (2009): 72, doi:10.1186/1741-7007-7-72.
    Beschreibung: Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses. Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.
    Beschreibung: The International Census of Marine Microbes and the W.M. Keck Foundation award to the Marine Biological Laboratory at Woods Hole (MA) supported the pyrosequencing part of this study. Further financial support came from a grant from the Deutsche Forschungsgemeinschaft to TS (STO414/3-1). Support for the unpublished work on Cariaco Basin protists came from NSF MCB-0348407 to VE (collaborative project with S Epstein at Northeastern University, Boston, MA, USA). Financial support to AC was provided by NSF MCB-0348045. Financial support to RC was provided by the ANR-Biodiversité project Aquaparadox.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 43
    facet.materialart.
    Unbekannt
    Ultrastructure and molecular phylogeny of Calkinsia aureus : cellular identity of a novel clade of deep-sea euglenozoans with epibiotic bacteria (2009)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Microbiology 9 (2009): 16, doi:10.1186/1471-2180-9-16.
    Beschreibung: The Euglenozoa is a large group of eukaryotic flagellates with diverse modes of nutrition. The group consists of three main subclades – euglenids, kinetoplastids and diplonemids – that have been confirmed with both molecular phylogenetic analyses and a combination of shared ultrastructural characteristics. Several poorly understood lineages of putative euglenozoans live in anoxic environments, such as Calkinsia aureus, and have yet to be characterized at the molecular and ultrastructural levels. Improved understanding of these lineages is expected to shed considerable light onto the ultrastructure of prokaryote-eukaryote symbioses and the associated cellular innovations found within the Euglenozoa and beyond. We collected Calkinsia aureus from core samples taken from the low-oxygen seafloor of the Santa Barbara Basin (580 – 592 m depth), California. These biflagellates were distinctively orange in color and covered with a dense array of elongated epibiotic bacteria. Serial TEM sections through individually prepared cells demonstrated that C. aureus shares derived ultrastructural features with other members of the Euglenozoa (e.g. the same paraxonemal rods, microtubular root system and extrusomes). However, C. aureus also possessed several novel ultrastructural systems, such as modified mitochondria (i.e. hydrogenosome-like), an "extrusomal pocket", a highly organized extracellular matrix beneath epibiotic bacteria and a complex flagellar transition zone. Molecular phylogenies inferred from SSU rDNA sequences demonstrated that C. aureus grouped strongly within the Euglenozoa and with several environmental sequences taken from low-oxygen sediments in various locations around the world. Calkinsia aureus possesses all of the synapomorphies for the Euglenozoa, but lacks traits that are specific to any of the three previously recognized euglenozoan subgroups. Molecular phylogenetic analyses of C. aureus demonstrate that this lineage is a member of a novel euglenozoan subclade consisting of uncharacterized cells living in low-oxygen environments. Our ultrastructural description of C. aureus establishes the cellular identity of a fourth group of euglenozoans, referred to as the "Symbiontida".
    Beschreibung: This work was supported by grants to BSL from the Tula Foundation (Centre for Microbial Diversity and Evolution), the National Science and Engineering Research Council of Canada (NSERC 283091-04) and the Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity. Funding for the collection of sediments and participation of VPE and JMB in this research was provided by the US National Science Foundation grant MCB-060484.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 44
    facet.materialart.
    Unbekannt
    Forensic analysis of the microbiome of phones and shoes (2015)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 21, doi:10.1186/s40168-015-0082-9.
    Beschreibung: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
    Beschreibung: This work was enabled by the generous support of the Alfred P Sloan foundation. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. S.M.G. was supported by an EPA STAR Graduate Fellowship and by a National Institutes of Health Training Grant 5 T-32 EB-009412.
    Schlagwort(e): Forensic microbiology ; Source-sink dynamics ; Shoe microbiome ; Phone microbiome ; Microbial time series
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Format: application/vnd.ms-excel
    Format: image/png
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 45
    facet.materialart.
    Unbekannt
    The ocean sampling day consortium (2015)
    BioMed Central
    Details
    Publikationsdatum: 2022-10-18
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Beschreibung: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Beschreibung: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Schlagwort(e): Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 46
    facet.materialart.
    Unbekannt
    Envelope structure of Synechococcus sp. WH8113, a nonflagellated swimming cyanobacterium (2005)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © 2001 Samuel et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. The definitive version was published in BMC Microbiology 1 (2001): 4, doi:10.1186/1471-2180-1-4.
    Beschreibung: Many bacteria swim by rotating helical flagellar filaments. Waterbury et al. discovered an exception, strains of the cyanobacterium Synechococcus that swim without flagella or visible changes in shape. Other species of cyanobacteria glide on surfaces. The hypothesis that Synechococcus might swim using traveling surface waves prompted this investigation. Results Using quick-freeze electron microscopy, we have identified a crystalline surface layer that encloses the outer membrane of the motile strain Synechococcus sp. WH8113, the components of which are arranged in a rhomboid lattice. Spicules emerge in profusion from the layer and extend up to 150 nm into the surrounding fluid. These spicules also send extensions inwards to the inner cell membrane where motility is powered by an ion-motive force. Conclusion The envelope structure of Synechococcus sp. WH8113 provides new constraints on its motile mechanism. The spicules are well positioned to transduce energy at the cell membrane into mechanical work at the cell surface. One model is that an unidentified motor embedded in the cell membrane utilizes the spicules as oars to generate a traveling wave external to the surface layer in the manner of ciliated eukaryotes.
    Beschreibung: ADTS was supported by the Rowland Institute for Science and is an Amgen Fellow of the Life Sciences Research Foundation.
    Schlagwort(e): Synechococcus sp. ; Motile mechanism
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: 6106667 bytes
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 47
    facet.materialart.
    Unbekannt
    Exploring historical trends using taxonomic name metadata (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 8 (2008): 144, doi:10.1186/1471-2148-8-144.
    Beschreibung: Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. From the over 10.7 million taxonomic names that are part of the uBio system, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs) and societal importance (e.g., world wars). The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.
    Beschreibung: The work presented here was funded in part by the MBLWHOI Library and the DAB Lindberg Research Fellowship from the Medical Library Association to INS.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Format: text/plain
    Format: application/vnd.ms-excel
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 48
    facet.materialart.
    Unbekannt
    Transcriptional profiling of reproductive development, lipid storage and molting throughout the last juvenile stage of the marine copepod Calanus finmarchicus (2015)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Zoology 11 (2014): 91, doi:10.1186/s12983-014-0091-8.
    Beschreibung: Calanus finmarchicus, a highly abundant copepod that is an important primary consumer in North Atlantic ecosystems, has a flexible life history in which copepods in the last juvenile developmental stage (fifth copepodid, C5) may either delay maturation and enter diapause or molt directly into adults. The factors that regulate this developmental plasticity are poorly understood, and few tools have been developed to assess the physiological condition of individual copepods. We sampled a cultured population of C. finmarchicus copepods daily throughout the C5 stage and assessed molt stage progression, gonad development and lipid storage. We used high-throughput sequencing to identify genes that were differentially expressed during progression through the molt stage and then used qPCR to profile daily expression of individual genes. Based on expression profiles of twelve genes, samples were statistically clustered into three groups: (1) an early period occurring prior to separation of the cuticle from the epidermis (apolysis) when expression of genes associated with lipid synthesis and transport (FABP and ELOV) and two nuclear receptors (ERR and HR78) was highest, (2) a middle period of rapid change in both gene expression and physiological condition, including local minima and maxima in several nuclear receptors (FTZ-F1, HR38b, and EcR), and (3) a late period when gonads were differentiated and expression of genes associated with molting (Torso-like, HR38a) peaked. The ratio of Torso-like to HR38b strongly differentiated the early and late groups. This study provides the first dynamic profiles of gene expression anchored with morphological markers of lipid accumulation, development and gonad maturation throughout a copepod molt cycle. Transcriptomic profiling revealed significant changes over the molt cycle in genes with presumed roles in lipid synthesis, molt regulation and gonad development, suggestive of a coupling of these processes in Calanus finmarchicus. Finally, we identified gene expression profiles that strongly differentiate between early and late development within the C5 copepodid stage. We anticipate that these findings and continued development of robust gene expression biomarkers that distinguish between diapause preparation and continuous development will ultimately enable novel studies of the intrinsic and extrinsic factors that govern diapause initiation in Calanus finmarchicus.
    Beschreibung: This work was supported by grant number OCE-1132567 from the National Science Foundation to MFB and AMT. Additional supported was provided by WHOI Early Career Scientist Awards provided to MFB and AMT.
    Schlagwort(e): Arthropod ; Crustacean ; Gene expression ; Molt cycle ; Transcriptomics
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/vnd.ms-excel
    Format: text/plain
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 49
    facet.materialart.
    Unbekannt
    Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 16, doi:10.1186/s40168-016-0161-6.
    Beschreibung: The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female partners during intercourse; however, the microbiota of sexual partners has not been well-studied. Pyrosequencing analysis of PCR-amplified 16S rDNA was used to examine BV-associated bacteria in monogamous couples with and without BV using vaginal, male urethral, and penile skin specimens. The penile skin and urethral microbiota of male partners of women with BV was significantly more similar to the vaginal microbiota of their female partner compared to the vaginal microbiota of non-partner women with BV. This was not the case for male partners of women with normal vaginal microbiota. Specific BV-associated species were concordant in women with BV and their male partners. In monogamous heterosexual couples in which the woman has BV, the significantly higher similarity between the vaginal microbiota and the penile skin and urethral microbiota of the male partner, supports the hypothesis that sexual exchange of BV-associated bacterial taxa is common.
    Beschreibung: This work was supported by National Institute of Health Grant R01 AI079071-01A1.
    Schlagwort(e): Bacterial vaginosis ; Microbiome ; Sexual transmission ; Penile skin ; Urethra ; Vagina
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 50
    facet.materialart.
    Unbekannt
    Erratum to: Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 149, doi:10.1186/s12862-016-0703-3.
    Beschreibung: As a result of vendor errors being introduced during processing, the original version of this article was published with some duplication errors in Table 1.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 51
    facet.materialart.
    Unbekannt
    Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 33, doi:10.1186/s13742-016-0138-1.
    Beschreibung: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (〉10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
    Beschreibung: Bioinformatic analysis was performed in part on computing resources at the University of Puerto Rico (UPR) Puerto Rico Center for Environmental Neuroscience (PRCEN)’s High Performance Computing Facility, which is supported by: Institutional Development Award Networks of Biomedical Research Excellent (INBRE) grant P20GM103475 from the National Institute of General Medical Sciences, National Institutes of Health; the Institute for Functional Nanomaterials (IFN) award from the Experimental Program to Stimulate Competitive Research (EPSCoR) Track 1 program of the National Science Foundation (NSF); and EPSCoR Track 2 awards for computational nanoscience (EPS 1002410, EPS 1010094). Funding and support of the research was provided by PRCEN thanks to an NSF Centers of Research Excellent in Science and Technology (CREST) award, number HRD-1137725.
    Schlagwort(e): Porites astreoides ; Calcification ; Biomineralization ; Coral ; Symbiodinium ; Dinoflagellate ; Zooxanthellae ; Symbiosis ; Swimming larvae ; Larval settlement
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 52
    facet.materialart.
    Unbekannt
    Automated simultaneous analysis phylogenetics (ASAP) : an enabling tool for phlyogenomics (2008)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Bioinformatics 9 (2008): 103, doi:10.1186/1471-2105-9-103.
    Beschreibung: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.
    Beschreibung: This work is funded in part by NSF DBI-0421604 to GC and RD. INS is supported in part by the Ellison Medical Foundation.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 53
    facet.materialart.
    Unbekannt
    Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus) (2015)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 243, doi:10.1186/s12864-015-1288-8.
    Beschreibung: With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ electric organ, main electric organ, and Hunter’s electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.
    Beschreibung: This project has been funded in part by NSF Grant MCB No. 1144012 (MRS), NSF Grant DEB No. 0741450 (JSA), NSF Grant CNS No. 1248109 (GAU), W.M. Keck Foundation Distinguished Young Scholars in Medical Research (CDN), NIH R01 GM084879 (HZ), NIH grant R01 GM088670 (RA), NIH grant 1SC1GM092297-01A1 (GAU), the Morgridge Graduate Fellowship (JDV and LLT), University of Wisconsin Genetics NIH Graduate Training Grant (LLT); and the Cornell University Center for Vertebrate Genomics (JRG).
    Schlagwort(e): Electric eel ; Genome ; Transcriptome ; miRNA ; Gene ontology
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/vnd.ms-excel
    Format: text/plain
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 54
    facet.materialart.
    Unbekannt
    Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Beschreibung: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Beschreibung: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Schlagwort(e): Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 55
    facet.materialart.
    Unbekannt
    Recovering complete and draft population genomes from metagenome datasets (2016)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 8, doi:10.1186/s40168-016-0154-5.
    Beschreibung: Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
    Beschreibung: This work was supported by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Schlagwort(e): Metagenomics ; Genotype ; Assembly ; Binning ; Curation
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 56
    facet.materialart.
    Unbekannt
    Fine-scale foraging movements by fish-eating killer whales (Orcinus orca) relate to the vertical distributions and escape responses of salmonid prey (Oncorhynchus spp.) (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Movement Ecology 5 (2017): 3, doi:10.1186/s40462-017-0094-0.
    Beschreibung: We sought to quantitatively describe the fine-scale foraging behavior of northern resident killer whales (Orcinus orca), a population of fish-eating killer whales that feeds almost exclusively on Pacific salmon (Oncorhynchus spp.). To reconstruct the underwater movements of these specialist predators, we deployed 34 biologging Dtags on 32 individuals and collected high-resolution, three-dimensional accelerometry and acoustic data. We used the resulting dive paths to compare killer whale foraging behavior to the distributions of different salmonid prey species. Understanding the foraging movements of these threatened predators is important from a conservation standpoint, since prey availability has been identified as a limiting factor in their population dynamics and recovery. Three-dimensional dive tracks indicated that foraging (N = 701) and non-foraging dives (N = 10,618) were kinematically distinct (Wilks’ lambda: λ 16 = 0.321, P 〈 0.001). While foraging, killer whales dove deeper, remained submerged longer, swam faster, increased their dive path tortuosity, and rolled their bodies to a greater extent than during other activities. Maximum foraging dive depths reflected the deeper vertical distribution of Chinook (compared to other salmonids) and the tendency of Pacific salmon to evade predators by diving steeply. Kinematic characteristics of prey pursuit by resident killer whales also revealed several other escape strategies employed by salmon attempting to avoid predation, including increased swimming speeds and evasive maneuvering. High-resolution dive tracks reconstructed using data collected by multi-sensor accelerometer tags found that movements by resident killer whales relate significantly to the vertical distributions and escape responses of their primary prey, Pacific salmon.
    Beschreibung: This work was supported by the Species at Risk Program, Fisheries and Oceans Canada; the University of Cumbria’s Research and Scholarship Development Fund; a Marie Curie Intra-European Fellowship (IEF) to VD; a University of British Columbia Zoology Graduate Fellowship to BW; and a Natural Sciences and Engineering Research Council (NSERC) Alexander Graham Bell Canada Graduate Scholarship to BW.
    Schlagwort(e): Foraging ; Movement ; Diving behavior ; Biologging ; Dtag ; Accelerometry ; Killer whale ; Orcinus orca ; Pacific salmon
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 57
    facet.materialart.
    Unbekannt
    Optimization of DNA extraction for advancing coral microbiota investigations (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 5 (2017): 18, doi:10.1186/s40168-017-0229-y.
    Beschreibung: We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition. During phase I, total DNA was extracted from seven coral species in a replicated experimental design using four different MO BIO Laboratories, Inc., DNA Isolation kits: PowerSoil®, PowerPlant® Pro, PowerBiofilm®, and UltraClean® Tissue & Cells (with three homogenization permutations). Technical performance of the treatments was evaluated using DNA yield and amplification efficiency of small subunit ribosomal RNA (SSU ribosomal RNA (rRNA)) genes. During phase II, potential extraction biases were examined via microbial community analysis of SSU rRNA gene sequences amplified from the most successful DNA extraction treatments. In phase I of the study, the PowerSoil® and PowerPlant® Pro extracts contained low DNA concentrations, amplified poorly, and were not investigated further. Extracts from PowerBiofilm® and UltraClean® Tissue and Cells permutations were further investigated in phase II, and analysis of sequences demonstrated that overall microbial community composition was dictated by coral species and not extraction treatment. Finer pairwise comparisons of sequences obtained from Orbicella faveolata, Orbicella annularis, and Acropora humilis corals revealed subtle differences in community composition between the treatments; PowerBiofilm®-associated sequences generally had higher microbial richness and the highest coverage of dominant microbial groups in comparison to the UltraClean® Tissue and Cells treatments, a result likely arising from using a combination of different beads during homogenization. Both the PowerBiofilm® and UltraClean® Tissue and Cells treatments are appropriate for large-scale analyses of coral microbiota. However, studies interested in detecting cryptic microbial members may benefit from using the PowerBiofilm® DNA treatment because of the likely enhanced lysis efficiency of microbial cells attributed to using a variety of beads during homogenization. Consideration of the methodology involved with microbial DNA extraction is particularly important for studies investigating complex host-associated microbiota.
    Beschreibung: This project was supported by NSF award OCE-1233612 to AA and NSF GRFP award to LW.
    Schlagwort(e): Coral microbiota ; DNA extraction ; Optimization ; SSU ribosomal RNA gene ; Amplicon sequencing
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 58
    facet.materialart.
    Unbekannt
    Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 12 (2017): 50, doi:10.1186/s40793-017-0266-y.
    Beschreibung: Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the B. thermophilus symbiosis.
    Beschreibung: This study was supported by the EU-funded Marie Curie Initial Training Network “Symbiomics” (project no. 264774). RP was supported by a fellowship of the Institute of Marine Biotechnology, Greifswald. MK was supported by a NSERC Banting Postdoctoral Fellowship. LS was supported by a DAAD scholarship. SMS was supported by US National Science Foundation grant OCE-1136727.
    Schlagwort(e): Uncultured endosymbiont ; Hydrothermal vents ; Marine invertebrate symbiosis ; Thiotrophy ; Autotrophy ; Atlantis (Ship : 1996-) Cruise AT26-10
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 59
    facet.materialart.
    Unbekannt
    DESMAN : a new tool for de novo extraction of strains from metagenomes (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology 18 (2017): 181, doi:10.1186/s13059-017-1309-9.
    Beschreibung: We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.
    Beschreibung: CQ is funded through a Medical Research Council fellowship (MR/M50161X/1) as part of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) consortium (MR/L015080/1). GC was supported by a European Research Council Starting Grant (3C-BIOTECH 261330). AME was supported by a Frank R. Lillie Research Innovation Award.
    Schlagwort(e): Metagenomes ; Strain ; Niche
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 60
    facet.materialart.
    Unbekannt
    Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mobile DNA 8 (2017): 19, doi:10.1186/s13100-017-0103-2.
    Beschreibung: In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes. A tripartite TE classification scheme is proposed to account for their replicative, integrative, and structural components, and the need to expand in vitro and in vivo studies of their structural and biological properties is emphasized. Bioinformatic studies have now become front and center of novel TE discovery, and experimental pursuits of these discoveries hold great promise for both basic and applied science.
    Beschreibung: The work in the author’s laboratory is supported by the US National Institutes of Health (GM111917) and by the US National Science Foundation (MCB-1121334).
    Schlagwort(e): Mobile genetic elements ; Classification ; Phylogeny ; Reverse transcriptase ; Transposase
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 61
    facet.materialart.
    Unbekannt
    Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system (2017)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 18 (2017): 217, doi:10.1186/s12864-017-3540-x.
    Beschreibung: Understanding gene expression changes over lifespan in diverse animal species will lead to insights to conserved processes in the biology of aging and allow development of interventions to improve health. Rotifers are small aquatic invertebrates that have been used in aging studies for nearly 100 years and are now re-emerging as a modern model system. To provide a baseline to evaluate genetic responses to interventions that change health throughout lifespan and a framework for new hypotheses about the molecular genetic mechanisms of aging, we examined the transcriptome of an asexual female lineage of the rotifer Brachionus manjavacas at five life stages: eggs, neonates, and early-, late-, and post-reproductive adults. There are widespread shifts in gene expression over the lifespan of B. manjavacas; the largest change occurs between neonates and early reproductive adults and is characterized by down-regulation of developmental genes and up-regulation of genes involved in reproduction. The expression profile of post-reproductive adults was distinct from that of other life stages. While few genes were significantly differentially expressed in the late- to post-reproductive transition, gene set enrichment analysis revealed multiple down-regulated pathways in metabolism, maintenance and repair, and proteostasis, united by genes involved in mitochondrial function and oxidative phosphorylation. This study provides the first examination of changes in gene expression over lifespan in rotifers. We detected differential expression of many genes with human orthologs that are absent in Drosophila and C. elegans, highlighting the potential of the rotifer model in aging studies. Our findings suggest that small but coordinated changes in expression of many genes in pathways that integrate diverse functions drive the aging process. The observation of simultaneous declines in expression of genes in multiple pathways may have consequences for health and longevity not detected by single- or multi-gene knockdown in otherwise healthy animals. Investigation of subtle but genome-wide change in these pathways during aging is an important area for future study.
    Beschreibung: Funding for this project was provided by R01 AG037960-01, the American Federation for Aging Research, and the Bay and Paul Foundations.
    Schlagwort(e): Aging ; Rotifer ; Monogonont ; RNA-Seq ; Transcriptome
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 62
    facet.materialart.
    Unbekannt
    Fukushima Daiichi–derived radionuclides in the ocean : transport, fate, and impacts (2017)
    Annual Reviews
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Beschreibung: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Beschreibung: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Schlagwort(e): Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 63
    facet.materialart.
    Unbekannt
    Eutrophication governs predator-prey interactions and temperature effects in Aedes aegypti populations. (2019)
    BioMed Central
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Krol, L., Gorsich, E. E., Hunting, E. R., Govender, D., van Bodegom, P. M., & Schrama, M. Eutrophication governs predator-prey interactions and temperature effects in Aedes aegypti populations. Parasites & Vectors, 12(1), (2019):179, doi:10.1186/s13071-019-3431-x.
    Beschreibung: Background Mosquito population dynamics are driven by large-scale (e.g. climatological) and small-scale (e.g. ecological) factors. While these factors are known to independently influence mosquito populations, it remains uncertain how drivers that simultaneously operate under natural conditions interact to influence mosquito populations. We, therefore, developed a well-controlled outdoor experiment to assess the interactive effects of two ecological drivers, predation and nutrient availability, on mosquito life history traits under multiple temperature regimes. Methods We conducted a temperature-controlled mesocosm experiment in Kruger National Park, South Africa, with the yellow fever mosquito, Aedes aegypti. We investigated how larval survival, emergence and development rates were impacted by the presence of a locally-common invertebrate predator (backswimmers Anisops varia Fieber (Notonectidae: Hemiptera), nutrient availability (oligotrophic vs eutrophic, reflecting field conditions), water temperature, and interactions between each driver. Results We observed that the effects of predation and temperature both depended on eutrophication. Predation caused lower adult emergence in oligotrophic conditions but higher emergence under eutrophic conditions. Higher temperatures caused faster larval development rates in eutrophic but not oligotrophic conditions. Conclusions Our study shows that ecological bottom-up and top-down drivers strongly and interactively govern mosquito life history traits for Ae. aegypti populations. Specifically, we show that eutrophication can inversely affect predator–prey interactions and mediate the effect of temperature on mosquito survival and development rates. Hence, our results suggest that nutrient pollution can overrule biological constraints on natural mosquito populations and highlights the importance of studying multiple factors.
    Beschreibung: This study was supported by the Gratama Fund, Grant Number 2016.08, which was awarded to MS, supported by the Uyttenboogaart-Eliasen foundation for comparative entomology, Grant No. SUB.2016.12.08 and the RCN-IDEAS grant which was awarded to EEG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Schlagwort(e): Ecological drivers ; Vector-borne ; Anthropogenic pressures ; Interaction effects ; Temperature ; Biodiversity decline
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    ARTIKEL (OA)
  • 64
    Digitale Medien
    Digitale Medien
    TOROIDAL DNA CONDENSATES: Unraveling the Fine Structure and the Role of Nucleation in Determining Size (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 295-318 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144500
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 65
    Digitale Medien
    Digitale Medien
    STRUCTURAL AND SEQUENCE MOTIFS OF PROTEIN (HISTONE) METHYLATION ENZYMES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 267-294 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144452
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 66
    Digitale Medien
    Digitale Medien
    ION CONDUCTION AND SELECTIVITY IN K+ CHANNELS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 153-171 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144655
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 67
    Digitale Medien
    Digitale Medien
    CHEMICAL SYNTHESIS OF PROTEINS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 91-118 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144700
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 68
    Digitale Medien
    Digitale Medien
    THE STRUCTURE-FUNCTION DILEMMA OF THE HAMMERHEAD RIBOZYME (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 415-440 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.122004.184428
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 69
    Digitale Medien
    Digitale Medien
    SINGLE-MOLECULE RNA SCIENCE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 399-414 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144641
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 70
    Digitale Medien
    Digitale Medien
    MODELING WATER, THE HYDROPHOBIC EFFECT, AND ION SOLVATION (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 173-199 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144517
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 71
    Digitale Medien
    Digitale Medien
    PROTEIN-DNA RECOGNITION PATTERNS AND PREDICTIONS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 379-398 
    Details
    ISSN: 1056-8700
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Physik
    Notizen: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144537
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 72
    Digitale Medien
    Digitale Medien
    THE LYMPHATIC VASCULATURE: Recent Progress and Paradigms (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 21 (2005), S. 457-483 
    Details
    ISSN: 1081-0706
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie , Medizin
    Notizen: The field of lymphatic research has been recently invigorated by the identification of genes and mechanisms that control various aspects of lymphatic development. We are beginning to understand how, starting from a subgroup of embryonic venous endothelial cells, the whole lymphatic system forms in a stepwise manner. The generation of genetically engineered mice with defects in different steps of the lymphangiogenic program has provided models that are increasing our understanding of the lymphatic system in health and disease. This knowledge, in turn, should lead to the development of better diagnostic methods and treatments of lymphatic disorders and tumor metastasis.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.cellbio.21.012704.132338
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 73
    Digitale Medien
    Digitale Medien
    THE PREPARATION OF SKELETAL CATALYSTS * (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 127-142 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: The preparation of skeletal catalysts is considered, with particular reference to the preparation of skeletal nickel and skeletal copper. Skeletal catalysts have physical properties that are highly desired for some industrial processes, and the means of controlling these properties to optimize performance is reviewed. The preparation can be affected by the initial alloy composition, the quenching process, the leaching procedure, aging and by the addition of promoters. These processes may affect either or both the chemical and physical characteristics of the catalysts. Preparation procedures need to be adjusted for individual reactions if optimal performance is required. The effect of the preparation conditions on the structure and catalytic performance of these systems is reviewed.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102303.140758
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 74
    Digitale Medien
    Digitale Medien
    THE OXIDATION OF NIAL: What Can We Learn from Ab Initio Calculations? (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 167-207 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: We review here the theory of the early stages of oxidation of the (110) surface of Ni1x Alx, based on ab initio calculations using a plane-wave pseudopotential method. The clean surface and several oxidized surfaces have been investigated, with oxygen coverages up to 2ML of oxygen (1ML = 3 O atoms per 2 surface Al atoms). The theory to date is a description in terms of equilibrium thermodynamics, with a comparison of the free energies of several surfaces of different composition, implemented at the atomic scale. Three environmental parameters are singled out as control variables in this treatment, namely the alloy composition x (assumed to be near 0.5), the temperature T and the partial pressure of oxygen pO2. With certain reasonable approximations an analytic formula for the surface energy ?? is derived in terms of these variables and some constants that are calculated ab initio together with others that are derived from experimental thermodynamic tables. At oxygen pressures just above the threshold for bulk oxidation of NiAl, the calculations explain the observed formation of a thin film of alumina in place of NiAl surface layers, with the consequent dissolution of Ni into the bulk. Ab initio calculations illustrate how the energetics of supplying Al to the surface depends on bulk stoichiometry, which alters the relative stability of different surface oxidation states so as to favour oxidation more if the alloy is Al-rich than if it is Ni-rich.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.101503.091652
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 75
    Digitale Medien
    Digitale Medien
    DESIGNING CATALYSTS FOR CLEAN TECHNOLOGY, GREEN CHEMISTRY, AND SUSTAINABLE DEVELOPMENT (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 315-350 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: There is a pressing need for cleaner fuels (free or aromatics and of minimal sulfur content) or ones that convert chemical energy directly to electricity, silently and without production of noxious oxides and particulates; chemical, petrochemical and pharmaceutical processes that may be conducted in a one-step, solvent-free manner and that use air as the preferred oxidant; and industrial processes that minimize consumption of energy, production of waste, or the use of corrosive, explosive, volatile, and nonbiodegradable materials. All these needs and other desiderata, such as the in situ production and containment of aggressive and hazardous reagents, and the avoidance of use of ecologically harmful elements, may be achieved by designing the appropriate heterogeneous inorganic catalyst, which ideally should be cheap, readily preparable and fully characterizable, preferably under in situ reaction conditions. A range of nanoporous and nanoparticle catalysts that meet most of the stringent demands of sustainable development and responsible (clean) technology is described. Specific examples that are highlighted include the production of adipic acid (precursor of polyamides and urethanes) without the use of concentrated nitric acid nor the production of greenhouse gases such as nitrous oxide; the production of caprolactam (precursor of nylon) without the use of oleum and hydroxylamine sulfate; and the terminal oxyfunctionalization of linear alkanes in air. The topic of biocatalysis and sustainable development is also briefly discussed for the epoxidation of terpenes and fatty acid methyl esters; for the generation of polymers, polylactides, and polyesters; and for the production of 1,3-propanediol from corn.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102003.140852
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 76
    Digitale Medien
    Digitale Medien
    POROUS ALUMINOPHOSPHATES :From Molecular Sieves to Designed Acid Catalysts (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 351-395 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: This review covers the synthesis, characterization, and physico-chemical properties of microporous and mesoporous aluminophosphates and silicoaluminophosphates molecular sieves. Particular emphasis is given to the materials that have found applications as acid catalysts. We consider the evolution of the synthesis procedures from the first discoveries to the current methodologies and give perspectives for new possible synthesis strategies. Emphasis is given to the use of specially prepared precursors/reactants designed for the use as molecular sieves. Experimental (especially MAS-NMR and FTIR spectroscopy) and theoretical approaches to the description of the Si insertion into the ALPO framework and to the acidic properties of SAPOs and MeAPSOs materials are discussed.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.103103.120732
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 77
    Digitale Medien
    Digitale Medien
    THE DIFFUSION-MULTIPLE APPROACH TO DESIGNING ALLOYS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 51-73 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: The diffusion-multiple approachĐ??the creation of composition gradients and intermetallic phases by long-term annealing of junctions of three or more phases/alloysĐ??enables the generation of a large number of phases and compositions for efficient mapping of phase diagrams, phase properties, and kinetics. With an efficiency much higher than that of a conventional approach, many critical materials data, which otherwise would be too time-consuming and expensive to acquire, can be obtained and employed to accelerate alloy design. The critical data for structural materials design include phase diagrams, diffusion coefficients, precipitation kinetics, solution-strengthening effects, and precipitation-strengthening effects. All these data can be obtained from diffusion multiples. The combination of the diffusion-multiple approach with the CALPHAD approach can impact computational design of structural materials. The diffusion-multiple approach can also be applied to combinatorial screening of functional materials having unique physical, chemical, or other properties when micro-scale measurement techniques are available for these properties. Examples are shown to illustrate the progress made to date on applying the diffusion-multiple approach to accelerated design/discovery of materials.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.100303.111314
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 78
    Digitale Medien
    Digitale Medien
    COMPOSITE MATERIALS FOR WIND POWER TURBINE BLADES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 505-538 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: Renewable energy resources, of which wind energy is prominent, are part of the solution to the global energy problem. Wind turbine and the rotorblade concepts are reviewed, and loadings by wind and gravity as important factors for the fatigue performance of the materials are considered. Wood and composites are discussed as candidates for rotorblades. The fibers and matrices for composites are described, and their high stiffness, low density, and good fatigue performance are emphasized. Manufacturing technologies for composites are presented and evaluated with respect to advantages, problems, and industrial potential. The important technologies of today are prepreg (pre-impregnated) technology and resin infusion technology. The mechanical properties of fiber composite materials are discussed, with a focus on fatigue performance. Damage and materials degradation during fatigue are described. Testing procedures for documentation of properties are reviewed, and fatigue loading histories are discussed, together with methods for data handling and statistical analysis of (large) amounts of test data. Future challenges for materials in the field of wind turbines are presented, with a focus on thermoplastic composites, new structural materials concepts, new structural design aspects, structural health monitoring, and the coming trends and markets for wind energy.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.100303.110641
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 79
    Digitale Medien
    Digitale Medien
    CHEMICAL DESIGN AND IN SITU CHARACTERIZATION OF ACTIVE SURFACES FOR SELECTIVE CATALYSIS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 397-426 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: This review illustrates how catalytically active molecular structures are created on oxide surfaces by attachment of metal complexes with subsequent structural transformation and molecular imprinting on the surfaces. Also discussed is how the designed surfaces are characterized in situ by physical techniques including conventional and time-resolved X-ray absorption fine structure. The structural transformation and molecular imprinting for attached metal complexes can provide a new class of catalytic materials with a high complexity for selective catalysis including shape-selective and asymmetric catalysis.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102003.142526
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 80
    Digitale Medien
    Digitale Medien
    APPLICATION OF EXAFS TO MOLTEN SALTS AND IONIC LIQUID TECHNOLOGY (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 29-49 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: This paper describes the use of extended X-ray absorption fine structure spectroscopy (EXAFS) to examine the structure of molten salts and ionic liquids and species dissolved in them. The EXAFS theory is briefly described as are the methods by which EXAFS of these systems can be studied. A range of applications have used EXAFS to investigate the structure of metallic species in ionic liquids from extraction studies to catalysts. The area of structural investigations of ionic liquids is still being developed, although growing rapidly, whereas the structure of molten salts has been studied using EXAFS in more detail.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.100303.121832
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 81
    Digitale Medien
    Digitale Medien
    MATERIALS CHARACTERIZATION IN THE ABERRATION-CORRECTED SCANNING TRANSMISSION ELECTRON MICROSCOPE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 539-569 
    Details
    ISSN: 1531-7331
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Maschinenbau
    Notizen: In the nanoscience era, the properties of many exciting new materials and devices will depend on the details of their composition down to the level of single atoms. Thus the characterization of the structure and electronic properties of matter at the atomic scale is becoming ever more vital for economic and technological as well as for scientific reasons. The combination of atomic-resolution Z-contrast scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) represents a powerful method to link the atomic and electronic structure to macroscopic properties, allowing materials, nanoscale systems, and interfaces to be probed in unprecedented detail. Z-contrast STEM uses electrons that have been scattered to large angles for imaging. The relative intensity of each atomic column is roughly proportional to Z2, where Z is the atomic number. Recent developments in correcting the aberrations of the lenses in the electron microscope have pushed the achievable spatial resolution and the sensitivity for imaging and spectroscopy in the STEM into the sub-A??ngstrom (sub-A??) regime, providing a new level of insight into the structure/property relations of complex materials. Images acquired with an aberration-corrected instrument show greatly improved contrast. The signal-to-noise ratio is sufficiently high to allow sensitivity even to single atoms in both imaging and spectroscopy. This is a key achievement because the detection and measurement of the response of individual atoms has become a challenging issue to provide new insight into many fields, such as catalysis, ceramic materials, complex oxide interfaces, or grain boundaries. In this article, the state-of-the-art for the characterization of all of these different types of materials by means of aberration-corrected STEM and EELS are reviewed.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102103.090513
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 82
    Digitale Medien
    Digitale Medien
    THE EVOLUTIONARY ENIGMA OF MIXED MATING SYSTEMS IN PLANTS: Occurrence, Theoretical Explanations, and Empirical Evidence (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 47-79 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175539
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 83
    Digitale Medien
    Digitale Medien
    BIODIVERSITY AND LITTER DECOMPOSITION IN TERRESTRIAL ECOSYSTEMS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 191-218 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: We explore empirical and theoretical evidence for the functional significance of plant-litter diversity and the extraordinary high diversity of decomposer organisms in the process of litter decomposition and the consequences for biogeochemical cycles. Potential mechanisms for the frequently observed litter-diversity effects on mass loss and nitrogen dynamics include fungi-driven nutrient transfer among litter species, inhibition or stimulation of microorganisms by specific litter compounds, and positive feedback of soil fauna due to greater habitat and food diversity. Theory predicts positive effects of microbial diversity that result from functional niche complementarity, but the few existing experiments provide conflicting results. Microbial succession with shifting enzymatic capabilities enhances decomposition, whereas antagonistic interactions among fungi that compete for similar resources slow litter decay. Soil-fauna diversity manipulations indicate that the number of trophic levels, species identity, and the presence of keystone species have a strong impact on decomposition, whereas the importance of diversity within functional groups is not clear at present. In conclusion, litter species and decomposer diversity can significantly influence carbon and nutrient turnover rates; however, no general or predictable pattern has emerged. Proposed mechanisms for diversity effects need confirmation and a link to functional traits for a comprehensive understanding of how biodiversity interacts with decomposition processes and the consequences of ongoing biodiversity loss for ecosystem functioning.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.112904.151932
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 84
    Digitale Medien
    Digitale Medien
    MODEL SELECTION IN PHYLOGENETICS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 445-466 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152633
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 85
    Digitale Medien
    Digitale Medien
    CONSEQUENCES OF THE CRETACEOUS/PALEOGENE MASS EXTINCTION FOR MARINE ECOSYSTEMS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 295-317 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: One of the greatest mass extinctions in Earth's history occurred at the end of the Cretaceous era, sixty-five million years (Myr) ago. Considerable evidence indicates that the impact of a large asteroid or comet was the ultimate cause of this extraordinary event. At the time of mass extinction, the organic flux to the deep sea collapsed, and production of calcium carbonate by marine plankton radically declined. These biogeochemical processes did not fully recover for a few million years. The drastic decline and long lag in final recovery of these processes are most simply explained as consequences of open-ocean ecosystem alteration by the mass extinction. If this explanation is correct, the extent and timing of marine biogeochemical recovery from the end-Cretaceous event was ultimately contingent on the extent and timing of open-ocean ecosystem recovery. The biogeochemical recovery may in turn have created new evolutionary opportunities for a diverse array of marine organisms.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.35.021103.105715
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 86
    Digitale Medien
    Digitale Medien
    THE GENETICS AND EVOLUTION OF FLUCTUATING ASYMMETRY (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 1-21 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: Variation in the subtle differences between right and left sides of bilateral characters, or fluctuating asymmetry (FA), has long been considered to be primarily environmental in origin, and this has promoted its use as a measure of developmental instability (DI) in populations. There is little evidence for specific genes that govern FA per se. Numerous studies show that FA levels in various characters are influenced by dominance and especially epistatic interactions among genes. An epistatic genetic basis for FA may complicate its primary use in comparisons of DI levels in outbred or wild populations subjected or not subjected to various environmental stressors. Although the heritability of FA typically is very low or zero, epistasis can generate additive genetic variation for FA that may allow it to evolve especially in populations subjected to bottlenecks, hybridizations, or periods of rapid environmental changes caused by various stresses.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152640
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 87
    Digitale Medien
    Digitale Medien
    MEASUREMENT OF INTERACTION STRENGTH IN NATURE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 419-444 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: Understanding and predicting the dynamics of multispecies systems generally require estimates of interaction strength among species. Measuring interaction strength is difficult because of the large number of interactions in any natural system, long-term feedback, multiple pathways of effects between species pairs, and possible nonlinearities in interaction-strength functions. Presently, the few studies that extensively estimate interaction strength suggest that distributions of interaction strength tend to be skewed toward few strong and many weak interactions. Modeling studies indicate that such skewed patterns tend to promote system stability and arise during assembly of persistent communities. Methods for estimating interaction strength efficiently from traits of organisms, such as allometric relationships, show some promise. Methods for estimating community response to environmental perturbations without an estimate of interaction strength may also be of use. Spatial and temporal scale may affect patterns of interaction strength, but these effects require further investigation and new multispecies modeling frameworks. Future progress will be aided by development of long-term multispecies time series of natural communities, by experimental tests of different methods for estimating interaction strength, and by increased understanding of nonlinear functional forms.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175535
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 88
    Digitale Medien
    Digitale Medien
    INTRODUCTION OF NON-NATIVE OYSTERS: Ecosystem Effects and Restoration Implications (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 643-689 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152638
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 89
    Digitale Medien
    Digitale Medien
    THE FUNCTIONAL SIGNIFICANCE OF RIBOSOMAL (r)DNA VARIATION: Impacts on the Evolutionary Ecology of Organisms (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 219-242 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152620
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 90
    Digitale Medien
    Digitale Medien
    LIFE-HISTORY EVOLUTION IN REPTILES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 23-46 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: Two consequences of terrestrial ectothermy (low energy needs and behavioral control of body temperatures) have had major consequences for the evolution of reptile life-history traits. For example, reproducing females can manipulate incubation temperatures and thus phenotypic traits of their offspring by retaining developing eggs in utero. This ability has resulted in multiple evolutionary transitions from oviparity to viviparity in cool-climate reptile populations. The spatial and temporal heterogeneity of operative temperatures in terrestrial habitats also has favored careful nest-site selection and a matching of embryonic reaction norms to thermal regimes during incubation (e.g., via temperature-dependent sex determination). Many of the life-history features in which reptiles differ from endothermic vertebratesĐ??such as their small offspring sizes, large litter sizes, and infrequent reproductionĐ??are direct consequences of ectothermy, reflecting freedom from heat-conserving constraints on body size and energy storage. Ectothermy confers immense flexibility, enabling a dynamic matching of life-history traits to local circumstances. This flexibility has generated massive spatial and temporal variation in life-history traits via phenotypic plasticity as well as adaptation. The diversity of life histories in reptiles can best be interpreted within a conceptual framework that views reptiles as low-energy, variable-temperature systems.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152631
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 91
    Digitale Medien
    Digitale Medien
    PHYLOGENOMICS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 541-562 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.35.112202.130205
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 92
    Digitale Medien
    Digitale Medien
    BIODIVERSITY-ECOSYSTEM FUNCTION RESEARCH: Is It Relevant to Conservation? (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 267-294 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: It has often been argued that conserving biodiversity is necessary for maintaining ecosystem functioning. We critically evaluate the current evidence for this argument. Although there is substantial evidence that diversity is able to affect function, particularly for plant communities, it is unclear if these patterns will hold for realistic scenarios of extinctions, multitrophic communities, or larger spatial scales. Experiments are conducted at small spatial scales, the very scales at which diversity tends to increase owing to exotics. Stressors may affect function by many pathways, and diversity-mediated effects on function may be a minor pathway, except in the case of multiple-stressor insurance effects. In general, the conservation case is stronger for stability measures of function than stock and flux measures, in part because it is easier to attribute value unambiguously to stability and in part because stock and flux measures of functions are anticipated to be more affected by multitrophic dynamics. Nor is biodiversity-ecosystem function theory likely to help conservation managers in practical decisions, except in the particular case of restoration. We give recommendations for increasing the relevance of this area of research for conservation.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152636
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 93
    Digitale Medien
    Digitale Medien
    INSECTS ON PLANTS: Diversity of Herbivore Assemblages Revisited (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 597-620 
    Details
    ISSN: 1543-592X
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Biologie
    Notizen: The diversity and composition of herbivore assemblages was a favored theme for community ecology in the 1970s and culminated in 1984 with Insects on Plants by Strong, Lawton and Southwood. We scrutinize findings since then, considering analyses of country-wide insect-host catalogs, field studies of local herbivore communities, and comparative studies at different spatial scales. Studies in tropical forests have advanced significantly and offer new insights into stratification and host specialization of herbivores. Comparative and long-term data sets are still scarce, which limits assessment of general patterns in herbivore richness and assemblage structure. Methods of community phylogenetic analysis, complex networks, spatial and among-host diversity partitioning, and metacommunity models represent promising approaches for future work.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175520
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 94
    Digitale Medien
    Digitale Medien
    Infrared Spectroscopic Observations of the Outer Planets, their Satellites, and the Asteroids (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 43-75 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.000355
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 95
    Digitale Medien
    Digitale Medien
    Formation of the Terrestrial Planets (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 77-113 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.000453
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 96
    Digitale Medien
    Digitale Medien
    Stellar Masses (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 115-164 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.000555
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 97
    Digitale Medien
    Digitale Medien
    Stellar Chromospheres (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 439-488 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.002255
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 98
    Digitale Medien
    Digitale Medien
    The Structure of Extended Extragalactic Radio Sources (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 165-218 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.001121
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 99
    Digitale Medien
    Digitale Medien
    Microwave Background Radiation as a Probe of the Contemporary Structure and History of the Universe (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 537-560 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.002541
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
  • 100
    Digitale Medien
    Digitale Medien
    Abundances in Stellar Populations and the Interstellar Medium in Galaxies (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 19 (1981), S. 77-113 
    Details
    ISSN: 0066-4146
    Quelle: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Thema: Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1146/annurev.aa.19.090181.000453
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    Artikel (Nationallizenzen)
    Volltext
Schließen ⊗
Diese Webseite nutzt Cookies und das Analyse-Tool Matomo. Weitere Informationen finden Sie hier...