ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

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
  • American Chemical Society  (175.232)
  • Cell Press  (29.378)
  • BioMed Central  (14.039)
  • ELSEVIER SCIENCE BV
  • 2020-2023  (34)
  • 2020-2020
  • 2005-2009  (218.631)
Sammlung
Verlag/Herausgeber
Erscheinungszeitraum
Jahr
  • 1
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Ecological Modelling, ELSEVIER SCIENCE BV, 220(18), pp. 2173-2186, ISSN: 0304-3800
    Publikationsdatum: 2018-02-16
    Beschreibung: We present a five-year (1997-2001) numerical simulation of daily mean chlorophyll a concentrations at station Geesthacht Weir on the lower Elbe River (Germany) using an extremely simple Lagrangian model driven by (a) water discharge, global radiation, water temperature, and (b) silica observations at station Schmilka in the upper reach of the Elbe River. Notwithstanding the lack of many mechanistic details, the model is able to reproduce observed chlorophyll a variability surprisingly well, including a number of sharp valleys and ascents/descents in the observed time series. The model's success is based on the assumption of three key effects: prevailing light conditions, sporadic limitation of algal growth due to lack of silica and algae loss rates that increase above an empirically specified temperature threshold of 20 degrees C. Trimmed-down model versions are studied to analyse the model's success in terms of these mechanisms. In each of the five years the model consistently fails, however, to properly simulate characteristic steep increases of chlorophyll a concentrations after pronounced spring minima. Curing this model deficiency by global model re-calibration was found to be impossible. However, suspension of silica consumption by algae for up to 10 days in spring is shown to serve as a successful placeholder for processes that are disregarded in the model but apparently play an important role in the distinctly marked period of model failure. For the remainder of the year the very simple model was found to be adequate
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 2
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Ecological Modelling, ELSEVIER SCIENCE BV, 213(2), pp. 229-244, ISSN: 0304-3800
    Publikationsdatum: 2018-02-16
    Beschreibung: A simple Lagrangian water quality model was designed to investigate the hypothesis of sporadic silica limitations of diatom growth in the lower Elbe River in Germany. For each fluid parcel a limited reservoir of silica was specified to be consumed by diatoms. The model's simplicity notwithstanding, a set of six selected model parameters could not be fully identified from existing observations at one station. After the introduction of prior knowledge of the ranges of meaningful parameter values, calibration of the over-parameterised model manifested itself primarily in the generation of posterior parameter covariances. Estimations of the covariance matrix based on (a) second order partial derivatives of a quadratic cost function at its optimum and (b) Monte Carlo simulations exploring the whole space of parameter values gave consistent results. Diagonalisation of the covariance matrix yielded two linear parameter combinations that were most effectively controlled by data from periods with and without lack of silica, respectively. The two parameter combinations were identified as the essential inputs that govern the successful simulation of intermittently decreasing chlorophyll a concentrations in summer. A satisfactory simulation of the pronounced chlorophyll a minimum in spring, by contrast, was found to be beyond the means of the simple model.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 3
    Publikationsdatum: 2017-04-04
    Beschreibung: Red Pompeian paintings, very famous for their deep intensity, are currently suffering from darkening. The origins of this darkening degradation are not clearly identified yet and remain a major issue for curators. In the specific case of cinnabar (HgS)-based red pigment, a photoinduced conversion into black metacinnabar is usually suspected. This work is focused on the blackening of red cinnabar paintings coated on a sparry calcite mortar. Different samples exhibiting different levels of degradation were selected upon visual observations and analyzed by synchrotron-based microanalytical techniques. Atomic and molecular compositions of the different debased regions revealed two possible degradation mechanisms. On one hand, micro X-ray fluorescence elemental maps show peculiar distributions of chlorine and sulfur. On the other hand, X-ray absorption spectroscopy performed at both Cl and S K-edges confirms the presence of characteristic degradation products: (i) Hg- Cl compounds (e.g., corderoite, calomel, and terlinguaite), which may result from the reaction with exogenous NaCl, in gray areas; (ii) gypsum, produced by the calcite sulfation, in black coatings. Metacinnabar is never detected. Finally, a cross section was analyzed to map the in-depth alteration gradient. Reduced and oxidized sulfur distributions reveal that the sulfated black coating consists of a 5-ím-thick layer covering intact cinnabar.
    Beschreibung: Published
    Beschreibung: 7484-7492
    Beschreibung: reserved
    Schlagwort(e): Microspectroscopy Analysis ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 4
    Publikationsdatum: 2019-08-23
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 5
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Marine Geology, ELSEVIER SCIENCE BV, 254(3-4), pp. 197-215, ISSN: 0025-3227
    Publikationsdatum: 2019-07-17
    Beschreibung: We studied the impact of the last glacial (late Weichselian) sea level cycle on sediment architecture in theinner Kara Sea using high-resolution acoustic sub-bottom profiling. The acoustic lines were ground-truthedwith dated sediment cores. Furthermore we refined the location of the eastern LGM ice margin, by new subbottom profiles. New model results of post-Last Glacial Maximum (LGM) isostatic rebound for this area allowa well-constrained interpretation of acoustic units in terms of sequence stratigraphy. The lowstand (orregressive) system tract sediments are absent but are represented by an unconformity atop of Pleistocenesediments on the shelf and by a major incised dendritic paleo-river network. The subsequent transgressiveand highstand system tracts are best preserved in the incised channels and the recent estuaries while onlyminor sediment accumulation on the adjacent shelf areas is documented. The Kara Sea can be subdividedinto three areas: estuaries (A), the shelf (B) and (C) deeper lying areas that accumulated a total of 114 x1010 t of Holocene sediments.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 6
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Earth-Science Reviews, ELSEVIER SCIENCE BV, 228, pp. 103987, ISSN: 0012-8252
    Publikationsdatum: 2022-03-30
    Beschreibung: The seabed plays a key role in the marine carbon cycle as a) the terminal location of aerobic oxidation of organic matter, b) the greatest anaerobic bioreactor, and c) the greatest repository for reactive organic carbon on Earth. We compiled data on the oxygen uptake of marine sediments with the objective to understand the constraints on mineralization rates of deposited organic matter and their relation to key environmental parameters. The compiled database includes nearly 4000 O 2 uptake data and is available as supplementary material. It includes also information on bottom water O 2 concentration, O 2 penetration depth, geographic position, water depth, and full information on the data sources. We present the different in situ and ex situ approaches to measure the total oxygen uptake (TOU) and the diffusive oxygen uptake (DOU) of sediments and discuss their robustness towards methodological errors and statistical uncertainty. We discuss O 2 transport through the benthic and diffusive boundary layers, the diffusion- and fauna-mediated O 2 uptake, and the coupling of aerobic respiration to anaerobic processes. Five regional examples are presented to illustrate the diversity of the seabed: Eutrophic seas, oxygen minimum zones, abyssal plains, mid-oceanic gyres, and hadal trenches. A multiple correlation analysis shows that seabed O 2 uptake is primarily controlled by ocean depth and sea surface primary productivity. The O2 penetration depth scales with the DOU according to a power law that breaks down under the abyssal ocean gyres. The developed multiple correlation model was used to draw a global map of seabed O2 uptake rates. Respiratory coefficients, differentiated for depth regions of the ocean, were used to convert the global O 2 uptake to organic carbon oxidation. The resulting global budget shows an oxidation of 212 Tmol C yr − 1 in marine sediments with a 5-95% confidence interval of 175-260 Tmol C yr − 1 . A comparison with the global flux of particulate organic carbon (POC) from photic surface waters to the deep sea, determined from multiple sediment trap studies, suggests a deficit in the sedimentation flux at 2000 m water depth of about 70% relative to the carbon turnover in the underlying seabed. At the ocean margins, the flux of organic carbon from rivers and from vegetated coastal ecosystems contributes greatly to the budget and may even exceed the phytoplankton production on the inner continental shelf.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 7
    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 ...
  • 8
    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 ...
  • 9
    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 ...
  • 10
    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 ...
  • 11
    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 ...
  • 12
    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 ...
  • 13
    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 ...
  • 14
    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 ...
  • 15
    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 ...
  • 16
    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 ...
  • 17
    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 ...
  • 18
    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 ...
  • 19
    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 ...
  • 20
    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 ...
  • 21
    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 ...
  • 22
    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 ...
  • 23
    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 ...
  • 24
    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 ...
  • 25
    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 ...
  • 26
    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 ...
  • 27
    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 ...
  • 28
    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 ...
  • 29
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Aquaculture, ELSEVIER SCIENCE BV, 254(1-4), pp. 714-729, ISSN: 0044-8486
    Publikationsdatum: 2015-06-25
    Beschreibung: For most fish species raised in marine aquaculture, the use of live feeds cannot be replaced by formulated diets. Artemia nauplii and rotifers are still the most commonly used live feeds. A good alternative lies in the use of copepods which could lead to the cultivation of new fish species. Cold stored subitaneous eggs from the continuously cultured calanoid copepod Acartia tonsa were used to investigate the effect of storage upon the viability of the eggs, the development of the copepod community originating from the cold stored eggs. Finally a 3 days snapshot of the egg production of the first generation of females was followed. This was done in order to develop a database usable within copepod dependent hatcheries. The viability of cold stored A. tonsa eggs remained high (〉 70% hatching rate) for 11 months of storage. Generally, the period of storage was observed to decrease the viability (hatching rate) of the eggs and no hatching was observed after twenty months of cold storage. Hatched populations of copepods experienced increased mortality rate with longer storage of the eggs from which they originated. This mortality ranged from 0.035 to 0.13 d− 1 for non-stored (fresh) and 12 months stored eggs, respectively. However, all copepod communities originating from fresh to 12 months stored eggs reached adulthood. Additionally, the egg production from the stored generation was apparently normal and the viability of their eggs was not statistically different when compared to productions from non-stored communities. Contents of total fatty acids decreased during the storage period. Contents of free amino acids were not statistically different for eggs cold stored up to 12 months, but had decreased severely by 20 months. In conclusion, we consider it safe to store the eggs for up to one year at 2–3 °C during which the eggs retain their viability and biochemical composition. Cold storage of calanoid copepod eggs is relevant for aquaculture as inoculum for culturing live food.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , peerRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 30
    Publikationsdatum: 2022-02-26
    Beschreibung: ARTICLE INFO Keywords: Amazonia GDGT Amazon River Biomarkers Compound-specific isotopes N-Alkanes Paleoclimate proxies Plant waxes ABSTRACT Lipid biomarker proxies from terrigenous sediments have been extensively used to understand variations in paleoenvironmental conditions, but many of the mechanisms affecting these proxies during riverine transport are still poorly understood. Here, we analyze glycerol dialkyl glycerol tetraether (GDGT) distributions and n-alkane isotopic compositions of soils and sediments from the Amazon River Basin. Our dataset includes suspended sediments of the Amazon River and its main tributaries, as well as soils and sediments of the Xingu River, a large clearwater tributary draining the easternmost part of the Amazon River Basin. Our sampling design aimed at understanding the processes behind spatially distinct GDGT distributions and n-alkane isotopic signatures across lowland Amazonia. Gradual changes in the fractional abundances of isoprenoid GDGTs and in 5- and 6- methyl branched GDGT ratios in suspended sediments of the Amazon River towards its mouth suggest that riverine production is an increasingly important control on the distribution of GDGTs in the lower parts of the system, while values from the western parts are more in line with a dominant soil sourcing. In the Xingu River, indices based on the fractional abundances of branched GDGTs and long-chain n-alkanes demonstrate a strong contri- bution of terrestrial organic material during the high-water season and an important aquatic component during low-water season. Meanwhile, average stable carbon (δ13C) and hydrogen (δD) isotopic signatures of long-chain n-alkanes in soils, riverbed and suspended sediments of the Xingu River are similar and reinforce the relatively conservative behaviour of these proxies within large river systems. The average compound-specific δ13C signa- tures of sediments in the Xingu River are within the expected range for C3 vegetation and do not seem to capture the signals from the nearby deforested areas. n-Alkanes δD signals in the Xingu Basin are similar to values ob- tained in the Amazon River mouth and indicate that n-alkanes sourced from easternmost Amazonian lowlands may predominate over signals from western areas.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 31
    Publikationsdatum: 2022-01-07
    Beschreibung: Microplastic (MP) pollution has been found in the Southern Ocean surrounding Antarctica, but many local regions within this vast area remain uninvestigated. The remote Weddell Sea contributes to the global thermohaline circulation, and one of the two Antarctic gyres is located in that region. In the present study, we evaluate MP (〉300 μm) concentration and composition in surface (n = 34) and subsurface water samples (n = 79, ∼11.2 m depth) of the Weddell Sea. All putative MP were analyzed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. MP was found in 65% of surface and 11.4% of subsurface samples, with mean (±standard deviation (SD)) concentrations of 0.01 (±0.01 SD) MP m–3 and 0.04 (±0.1 SD) MP m–3, respectively, being within the range of previously reported values for regions south of the Polar Front. Additionally, we aimed to determine whether identified paint fragments (n = 394) derive from the research vessel. Environmentally sampled fragments (n = 101) with similar ATR-FTIR spectra to reference paints from the research vessel and fresh paint references generated in the laboratory were further subjected to micro-X-ray fluorescence spectroscopy (μXRF) to compare their elemental composition. This revealed that 45.5% of all recovered MP derived from vessel-induced contamination. However, 11% of the measured fragments could be distinguished from the reference paints via their elemental composition. This study demonstrates that differentiation based purely on visual characteristics and FTIR spectroscopy might not be sufficient for accurately determining sample contamination sources.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , peerRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 32
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Dynamics of Atmospheres and Oceans, ELSEVIER SCIENCE BV, 93, pp. 101206, ISSN: 0377-0265
    Publikationsdatum: 2022-02-15
    Beschreibung: This study evaluates the dependence of simulated surface air temperatures on model resolution and orography for the mid-Holocene. Sensitivity experiments with the atmospheric general circulation model ECHAM5 are performed with low (∼3.75°, 19 vertical levels) and high (∼1.1°, 31 vertical levels) resolution. Results are compared to the respective preindustrial runs. It is found that the large-scale temperature anomalies for the mid-Holocene (compared to preindustrial) are significantly different in the low- and high-resolution versions. For boreal winter, differences are mainly related to circulation changes caused by the response to thermal forcing in conjunction with orographic resolution. For summer, shortwave cloud radiative forcing emerges as an important factor. The anomaly differences (low minus high resolution version) in the Northern Hemisphere are regionally as large as the anomalous mid-Holocene temperature signals. Furthermore, they depend on the applied surface boundary conditions. We conclude that the resolution matters for the Northern Hemisphere response in mid-Holocene simulations, which should be taken into account in model-model and data-model comparisons.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 33
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Global and Planetary Change, ELSEVIER SCIENCE BV, 204, pp. 103558, ISSN: 0921-8181
    Publikationsdatum: 2022-02-15
    Beschreibung: Previous studies on surface temperature reconstructions for the last 2000 years (2 k) revealed a long-term cooling trend for the last millennium in comparison to the previous millennium. However, knowledge on the decadal- to centennial-scale variability in sea surface temperature and the underlying governing mechanisms throughout the period is limited. We reconstructed high-resolution continuous sea surface temperature changes over the last 2 k in the northwest Pacific margin based on the alkenone unsaturation index. Our alkenone temperature record revealed enhanced and more rapidly changing climate variability during the last millennium (approximately 1200–1850 Common Era) than during the previous millennium. Cold and hot extremes also occurred more frequently during the last millennium. The enhanced and rapidly changing climate variability appears to be associated with frequent volcanic eruptions and grand solar minima. The reconstructed surface temperature variability tends to be associated with variations in the East Asia summer monsoon and the Pacific Decadal Oscillation, implying that these variations are also enhanced in the last millennium than in the previous millennium.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 34
    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 ...
  • 35
    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 ...
  • 36
    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 ...
  • 37
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Geomorphology, ELSEVIER SCIENCE BV, 413(108328), pp. 1-10, ISSN: 0169-555X
    Publikationsdatum: 2022-07-13
    Beschreibung: Here we present dense acoustic and swath bathymetry data sets as well as geological age constraints that allow a new view on past glacial processes at the Siberian termination of Lomonosov Ridge in the Arctic Ocean between 81° and 84° 20′ N. Here, the seabed is marked by three sets of streamlined glacial lineations observed at present water depths of ~760 m to 1250 m. The shallower streamlined glacial lineations were likely formed during MIS 6 and the deeper ones during MIS 12. Other observations include recessional moraines and pockmarks on a flattened ridge crest. In the subsurface, an acoustically transparent unit above well stratified strata is interpreted as subglacial diamicton overlying pre-glacial sediments at an erosional contact. Furthermore, the diamicton is interpreted to have been deposited as lenses in glacially-eroded proximal settings. In contrast, some parts of the seafloor and subsurface show no glacial overprint in water depths as shallow as 819 m. To explain these findings, we propose that the Siberian termination of Lomonosov Ridge was covered by an ice mass of spatial and temporal variable thickness between ~780 to ~1250 m, that was likely composed of sea ice and thick icebergs calved from ice shelves.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , NonPeerReviewed
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 38
    Publikationsdatum: 2022-10-27
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Meaders, J. L., de Matos, S. N., & Burgess, D. R. A pushing mechanism for microtubule aster positioning in a large cell type. Cell Reports, 33(1), (2020): 108213, doi:10.1016/j.celrep.2020.108213.
    Beschreibung: After fertilization, microtubule (MT) sperm asters undergo long-range migration to accurately position pronuclei. Due to the large sizes of zygotes, the forces driving aster migration are considered to be from pulling on the astral MTs by dynein, with no significant contribution from pushing forces. Here, we re-investigate the forces responsible for sperm aster centration in sea urchin zygotes. Our quantifications of aster geometry and MT density preclude a pulling mechanism. Manipulation of aster radial lengths and growth rates, combined with quantitative tracking of aster migration dynamics, indicates that aster migration is equal to the length of rear aster radii, supporting a pushing model for centration. We find that dynein inhibition causes an increase in aster migration rates. Finally, ablation of rear astral MTs halts migration, whereas front and side ablations do not. Collectively, our data indicate that a pushing mechanism can drive the migration of asters in a large cell type.
    Beschreibung: We would like to thank Dr. Jesse Gatlin for sending us the Tau-mCherry fusion protein for imaging live MTs. We would also like to thank Dr. Timothy Mitchison, Dr. Christine Field, and Dr. James Pelletier for supplying us with CA4, p150-CC1, and EB1-GFP peptides, as well as for fruitful discussions. Finally, we would like to thank Dr. Charles Shuster and Leslie Toledo-Jacobo for constructive feedback when preparing the manuscript. We thank Bret Judson and the Boston College Imaging Core for infrastructure and support. This material is based upon work supported by NSF grant no. 124425 to D.R.B.
    Schlagwort(e): Dynein ; Aster ; Microtubule ; Centrosome ; Pronucleus ; Fertilization ; Aster position
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 39
    Publikationsdatum: 2022-10-27
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stolp, Z. D., Kulkarni, M., Liu, Y., Zhu, C., Jalisi, A., Lin, S., Casadevall, A., Cunningham, K. W., Pineda, F. J., Teng, X., & Hardwick, J. M. Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Reports, 39(2), (2022): 110647, https://doi.org/10.1016/j.celrep.2022.110647.
    Beschreibung: Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans.
    Beschreibung: Funding sources: National Institutes of Health, United States grants AI144373 and NS127076 (J.M.H.), AI115016 and AI153414 (K.W.C.), and AI052733, AI152078, and HL059842 (A.C.); National Natural Science Foundation of China 31970550; and the Priority Academic Program Development of the Jiangsu Higher Education Institutes (X.T.).
    Schlagwort(e): Yeast ; Programmed cell death ; Vesicle trafficking ; AP-3 ; Vacuole ; Cryptococcus ; Yck3 ; Regulated cell death ; Lysosome ; Vacuolar membrane permeabilization
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 40
    Publikationsdatum: 2022-10-26
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walsh, A. N., Reddy, C. M., Niles, S. F., McKenna, A. M., Hansel, C. M., & Ward, C. P. Plastic formulation is an emerging control of its photochemical fate in the ocean. Environmental Science & Technology, 55(18), (2021): 12383–12392, https://doi.org/10.1021/acs.est.1c02272.
    Beschreibung: Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15–36% inorganic additives, primarily calcium carbonate (13–34%) and titanium dioxide (TiO2; 1–2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68–94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
    Beschreibung: Funding was provided by the Seaver Institute, the Gerstner Family Foundation, Woods Hole Oceanographic Institution, and the National Science Foundation Graduate Research Fellowship Program (A.N.W.). The Ion Cyclotron Resonance user facility at the National High Magnetic Field Laboratory is supported by the National Science Foundation Division of Chemistry and Division of Materials Research through DMR-1644779 and the State of Florida.
    Schlagwort(e): Plastic pollution ; Marine debris ; Additives ; Dissolved organic carbon ; Photochemical oxidation ; FT-ICR-MS ; Titanium dioxide
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 41
    Publikationsdatum: 2022-10-14
    Beschreibung: With a growing concern over rapid Antarctic ice loss in recent years, the Amundsen Sea, one of the fastest-melting areas in Antarctica, currently becomes a hotspot for the Earth sciences in the context of its linkage to global climate. As a center of strong physical and biological coupling processes, polynyas of the Amundsen Sea could act as sentinels of changes in atmosphere–ice–ocean interactions, offering a unique perspective into its sensitivity to climate variability. Here, we present a new, multiproxy-based high-resolution sedimentary record from the Amundsen Sea polynya, which provides new insights into environmental conditions of the region over the last 350 years and their linkages to climatic factors. Our results show that the polynya witnessed step-wise environmental shifts in parallel with the phases and strength of large-scale climate patterns, i.e., the Southern Annular Mode (SAM) and El Niño–Southern Oscillation (ENSO). Notably, intersite correlation of on-shelf Circumpolar Deep Water (CDW) intrusion signals at different locals suggests that the CDW may have gained increased access to the shelves at the time of a strong coupling of positive SAM and El Niño states. We tentatively speculate that anomalous large-scale atmospheric and oceanic circulation patterns over the Southern Hemisphere, forced by increasing greenhouse gas levels, were strongly involved in the mid-20th century CDW invigoration, which may be greater in scale that goes well beyond the Amundsen Sea region. This result is relevant to the current debate on spatial heterogeneity in the timing and phasing of major climatic events in Antarctica, underscoring an unambiguous connection of the Antarctic climate state to the large-scale ocean–atmosphere reorganizations. Our study also extends a growing evidence that today's global warming trend is expected to have a severe effect on future configuration of Antarctic continental ice-shelf environment.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 42
    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Beschreibung: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Beschreibung: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Schlagwort(e): Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 43
    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mazzotta, M. G., Reddy, C. M., & Ward, C. P. Rapid degradation of cellulose diacetate by marine microbes. Environmental Science & Technology Letters, 9(1), (2022): 37-41. https://doi.org/10.1021/acs.estlett.1c00843.
    Beschreibung: The persistence of cellulose diacetate (CDA), a biobased plastic used in textiles and single-use consumer products, in the ocean is currently unknown. Here, we probe the disintegration and degradation of CDA-based materials (25 μm films, 510 μm foam, and 97 g/m2 fabric) by marine microbes in a continuous flow seawater mesocosm. Photographic evidence and mass loss measurements demonstrate that CDA-based materials disintegrate in months. Disintegration is marked by the increasing esterase and cellulase activity of the biofilm community, suggesting that marine microbes degrade CDA. The natural abundance stable (13C) and radiocarbon (14C) isotopic signature of carbon dioxide respired during short-term bottle incubations confirms the rapid degradation of both acetyl and cellulosic components of CDA by seawater microbial communities. These findings challenge the paradigm set by governmental agencies and advocacy groups that CDA-based materials persist in the ocean for decades, and represent a positive step toward identifying high-utility, biobased plastics with low environmental persistence.
    Beschreibung: M.G.M., C.M.R., and C.P.W. thank Eastman Chemical Co. and Woods Hole Oceanographic Institution (WHOI) for scientific and financial support.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 44
    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xie, L., Liu, X., Caratenuto, A., Tian, Y., Chen, F., DeGiorgis, J. A., Wan, Y., & Zheng, Y. Environmentally friendly and efficient hornet nest envelope-based photothermal absorbers. Acs Omega, 6(50), (2021): 34555–34562, https://doi.org/10.1021/acsomega.1c04851.
    Beschreibung: Water shortage is a critical global issue that threatens human health, environmental sustainability, and the preservation of Earth’s climate. Desalination from seawater and sewage is a promising avenue for alleviating this stress. In this work, we use the hornet nest envelope material to fabricate a biomass-based photothermal absorber as part of a desalination isolation system. This system realizes an evaporation rate of 3.98 kg m–2 h–1 under one-sun illumination, with prolonged evaporation rates all above 4 kg m–2 h–1. This system demonstrates a strong performance of 3.86 kg m–2 h–1 in 3.5 wt % saltwater, illustrating its effectiveness in evaporation seawater. Thus, with its excellent evaporation rate, great salt rejection ability, and easy fabrication approach, the hornet nest envelope constitutes a promising natural material for solar water treatment applications.
    Beschreibung: The authors acknowledge the support from the National Science Foundation, USA, through grant number CBET-1941743 and the National Science Foundation under EPSCoR Cooperation Agreement OIA-1655221.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 45
    Publikationsdatum: 2022-08-30
    Beschreibung: Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O2) may lead to excess O2 in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O2 and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O2-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O2 in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O2 in the DBL and Chla in the underlying tissue, with patches of high O2 in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O2 concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O2 is related to ciliary-induced flows, causing a lateral redistribution of O2 in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O2 transport allocates parts of the O2 surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , NonPeerReviewed
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 46
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Earth-Science Reviews, ELSEVIER SCIENCE BV, 221(103803), ISSN: 0012-8252
    Publikationsdatum: 2022-08-21
    Beschreibung: Benthic organisms and their bioturbation activities have a profound effect on a multitude of sediment properties. While many studies have already explored benthic impacts at small temporal and spatial scales, little is known on how the small-scale effects accumulate and interactively guide large-scale (km-scale) morphological evolution. Here we firstly summarize the most important processes of benthos affecting sediment stability and then explore existing biomorphodynamic modeling studies both at small- and large-scales. In general, microbenthos (body size 〈0.1 mm) mainly stabilizes sediments while meio- (0.1–1 mm) and macrobenthos (〉1 mm) may stabilize or destabilize sediments. Among all types of sediment, fine-grained fraction (silt and clay) is most sensitive to the impact of benthos. Benthic organisms have the capability to mediate sediment transport and sedimentation patterns beyond their habitats on the long-term and over a large-scale. However, so far, numerical models evaluating benthic impact are limited to explorative studies and have not reached a stage where they can be used for predictive modeling. The barriers hindering a further development of biomorphodynamic models include not only limited understanding of fundamental biological/bio-physical processes affecting morphological development and dynamic feedback loops among them but also a shortage of data for model calibration and confirmation of simulation results. On the other hand, thriving for higher model complexity does not necessarily lead to better performance. Before conducting biomorphodynamic modeling, researchers must figure out which questions can be answered in a meaningful sense with simulation results that can be compared with observations and which level of modeling complexity is sufficient for that purpose.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , NonPeerReviewed
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 47
    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 ...
  • 48
    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 ...
  • 49
    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 ...
  • 50
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Global and Planetary Change, ELSEVIER SCIENCE BV, 186, ISSN: 0921-8181
    Publikationsdatum: 2022-06-14
    Beschreibung: The 318-m long sediment record from Lake El'gygytgyn, NE Russia situated in the present-day herb tundra zone, provides a unique archive of high Arctic environmental changes since ca 3.6 million years ago (Ma). This paper focuses on pollen-derived vegetation change during the mid-Pliocene Warm Period (mPWP) and in particular during Marine Isotope Stage (MIS) M2, which is known torepresent the coldest interval ofthe Pliocene. Building on initial pollen studies, we provide a more complete record and a more detailed discussion of climaticallydriven vegetation and environmental changes in the northeastern Russian Arctic, spanning the 203-thousandyear interval between 3.383 and 3.180 Ma ago. Pine-spruce-fir-larch-Douglas fir forests dominated the area around Lake El'gygytgyn between 3.383 and 3.330 Ma (MIS MG4 - MIS MG2). Colder and drier climate caused a decrease of coniferous forests and widespread Sphagnum habitats around the lake between 3.370 and 3.357 Ma. After 3.3 Ma, the presence of spruce, fir and Douglas fir decreased again. A very pronounced cooling took place at the first half of MIS M2 (3.312–3.283 Ma), when treeless tundra- and steppe-like habitats became common in the regional vegetation. Climate conditions were similar or only slightly warmer and wetter to those of the Holocene. Numerous coprophilous fungi spores identified in the MIS M2 pollen samples suggest the presence of grazing mammals around the lake. Larch-pine forests with some spruce started to dominate the area again after ca. 3.282 Ma, thus pointing to a significant climate amelioration during the mPWP. However, the forested area decreased, while herb- and shrub-dominated vegetation spread again during MIS KM6 (especially 3.235–3.223 Ma), suggesting a noticeable climatic deterioration and relatively cold and dry conditions.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 51
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McLean, C., & Kujawinski, E. B. AutoTuner: high fidelity and robust parameter selection for metabolomics data processing. Analytical Chemistry, 92(8), (2020): 5724-5732, doi:10.1021/acs.analchem.9b04804.
    Beschreibung: Untargeted metabolomics experiments provide a snapshot of cellular metabolism but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run-time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly used parameter selection tool, and compared the resulting parameters’ influence on the properties of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100–1000× speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.
    Beschreibung: We thank Titus Brown and Ben Temperton for advice on the algorithm validation, Arthur Eschenlauer for constructive feedback on the software design, Krista Longnecker for continuous support and discussions, Gabriel Leventhal for mathematics advice, the users of AutoTuner for debugging help through Github, and David Angeles-Albores and two anonymous reviewers for critical feedback on the manuscript. Funding support included the National GEM Consortium and NSF graduate research program fellowships (C.M.) and grants from the MIT Microbiome Center (Award 6936800, E.B.K.) and the Simons Foundation (Award ID #509034, E.B.K.).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 52
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reusch, S., Biswas, A., Hirst, W. G., & Reber, S. Affinity purification of label-free tubulins from xenopus egg extracts. STAR Protocols, 1(3), (2020): 100151, doi:10.1016/j.xpro.2020.100151.
    Beschreibung: Cytoplasmic extracts from unfertilized Xenopus eggs have made important contributions to our understanding of microtubule dynamics, spindle assembly, and scaling. Until recently, these in vitro studies relied on the use of heterologous tubulin. This protocol allows for the purification of physiologically relevant Xenopus tubulins in milligram yield, which are a complex mixture of isoforms with various post-translational modifications. The protocol is applicable to any cell or tissue of interest. For complete details on the use and execution of this protocol, please refer to Hirst et al. (2020).
    Beschreibung: This article was prompted by our stay at the Marine Biological Laboratory (MBL), Woods Hole, MA, in the summer of 2016 funded by the Princeton-Humboldt Strategic Partnership Grant together with the lab of Sabine Petry (Princeton University). We are grateful to the National Xenopus Resource (NXR) for supplying frogs. For mass spectrometry, we would like to acknowledge the assistance of Benno Kuropka and Chris Weise from the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). We thank the Protein Expression Purification and Characterization (PEPC) facility at the MPI-CBG; in particular, we thank Aliona Bogdanova and Barbara Borgonovo. We thank all former and current members of the Reber lab for discussions and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding from the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 53
    Publikationsdatum: 2022-05-26
    Beschreibung: Author Posting. © American Chemical Society, 2020. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Chemical Research in Toxicology, 33(4), (2020): 860-879, doi:10.1021/acs.chemrestox.9b00476.
    Beschreibung: The Ah receptor (AHR) has been studied for almost five decades. Yet, we still have many important questions about its role in normal physiology and development. Moreover, we still do not fully understand how this protein mediates the adverse effects of a variety of environmental pollutants, such as the polycyclic aromatic hydrocarbons (PAHs), the chlorinated dibenzo-p-dioxins (“dioxins”), and many polyhalogenated biphenyls. To provide a platform for future research, we provide the historical underpinnings of our current state of knowledge about AHR signal transduction, identify a few areas of needed research, and then develop concepts such as adaptive metabolism, ligand structural diversity, and the importance of proligands in receptor activation. We finish with a discussion of the cognate physiological role of the AHR, our perspective on why this receptor is so highly conserved, and how we might think about its cognate ligands in the future.
    Beschreibung: This review is dedicated in memory of the career of Alan Poland, one of the truly great minds in pharmacology and toxicology. This work was supported by the National Institutes of Health Grants R35-ES028377, T32-ES007015, P30-CA014520, P42-ES007381, and U01-ES1026127, The UW SciMed GRS Program, and The Morgridge Foundation. The authors would like to thank Catherine Stanley of UW Media Solutions for her artwork.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 54
    Publikationsdatum: 2022-12-07
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in James, B., de Vos, A., Aluwihare, L., Youngs, S., Ward, C., Nelson, R., Michel, A., Hahn, M., & Reddy, C. Divergent forms of pyroplastic: lessons learned from the M/V X-Press Pearl ship fire. ACS Environmental Au, 2(5), (2022): 467–479, https://doi.org/10.1021/acsenvironau.2c00020.
    Beschreibung: In late May 2021, the M/V X-Press Pearl container ship caught fire while anchored 18 km off the coast of Colombo, Sri Lanka and spilled upward of 70 billion pieces of plastic or “nurdles” (∼1680 tons), littering the country’s coastline. Exposure to combustion, heat, chemicals, and petroleum products led to an apparent continuum of changes from no obvious effects to pieces consistent with previous reports of melted and burned plastic (pyroplastic) found on beaches. At the middle of this continuum, nurdles were discolored but appeared to retain their prefire morphology, resembling nurdles that had been weathered in the environment. We performed a detailed investigation of the physical and surface properties of discolored nurdles collected on a beach 5 days after the ship caught fire and within 24 h of their arrival onshore. The color was the most striking trait of the plastic: white for nurdles with minimal alteration from the accident, orange for nurdles containing antioxidant degradation products formed by exposure to heat, and gray for partially combusted nurdles. Our color analyses indicate that this fraction of the plastic released from the ship was not a continuum but instead diverged into distinct groups. Fire left the gray nurdles scorched, with entrained particles and pools of melted plastic, and covered in soot, representing partial pyroplastics, a new subtype of pyroplastic. Cross sections showed that the heat- and fire-induced changes were superficial, leaving the surfaces more hydrophilic but the interior relatively untouched. These results provide timely and actionable information to responders to reevaluate cleanup end points, monitor the recurrence of these spilled nurdles, gauge short- and long-term effects of the spilled nurdles to the local ecosystem, and manage the recovery of the spill. These findings underscore partially combusted plastic (pyroplastic) as a type of plastic pollution that has yet to be fully explored despite the frequency at which plastic is burned globally.
    Beschreibung: This work was supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. Additional support was provided by the WHOI Marine Microplastics Catalyst Program, the WHOI Marine Microplastics Innovation Accelerator Program, the WHOI Investment in Science Fund, the March Marine Initiative (a program of March Limited, Bermuda), The Seaver Institute, Gerstner Philanthropies, the Wallace Research Foundation, the Richard Saltonstall Charitable Foundation, the Harrison Foundation, Hollis and Ermine Lovell Charitable Foundation, and the Richard Grand Foundation. AdV was supported by funding from the Schmidt Foundation.
    Schlagwort(e): Microplastic ; Resin pellets ; Pollution ; Additives ; Open burning ; Weathering ; Maritime accident
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 55
    Publikationsdatum: 2022-11-03
    Beschreibung: This is the first study presenting temporal changes of the macrofauna biodiversity along the bathymetric gradient from the shelf to abyssal depths in the eastern Fram Striat. In this region, between 2004 and 2008, a significant increase in surface water temperature was observed due to the transport of Atlantic water from lower latitudes and was defined as a Warm Water Anomaly (WWA). Effects of the WWA in the eastern Fram Strait were observed across the entire food web, from the pelagic to the deep seafloor. The material for our study was collected before (in 2000) and after the WWA (in 2010 and 2017) at station depths ranging from 203 m to 5561 m. Samples of macrofauna and surface sediments were collected with use of a box corer to analyze species composition and functional traits, and environmental characteristics in sediments. We explore the influence of environmental changes on the structure (species composition and diversity) and functioning (functional trait composition and diversity) of macrofauna communities. An increase of primary production in surface waters during and after the WWA was reflected in a higher food availability at the seafloor from shelf to abyssal depths. Warming induced environmental changes led to an increase of macrofauna density and taxonomic diversity at all water depths. Macrofauna species composition significantly changed after the WWA. At all study sites, macrofauna functional diversity increased after the warm period. Functional trait composition changed significantly along the bathymetric transect. Despite changes in the taxonomic composition, macrofauna communities at the shallowest stations showed high functional redundancy, i.e., trait composition remained unchanged after the WWA. At water depths below 1500 m, where functional redundancy was significantly lower, functional trait composition changed significantly after the WWA. Our results suggest that macrofauna communities on the shelves are more resistant to environmental changes compared to deep-sea assemblages in the eastern Fram Strait.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 56
    Publikationsdatum: 2022-11-07
    Beschreibung: Microplastics (MP) have been recorded in various environments around the globe. For a better understanding of distribution patterns and for providing a basis for risk assessments, detailed data on MP concentrations and polymer compositions are required. This study investigated the effluents of two German wastewater treatment plants (WWTP) monthly over one year, in order to better understand their temporal input of MP into the receiving river systems. MP item data down to 11 μm were obtained by means of Fourier Transform Infrared (FTIR) spectroscopy under the application of an improved polymer database. Complementary mass data were obtained by pyrolysis gas chromatography–mass spectrometry (Py-GC/MS) (for one WWTP). Both FTIR and Py-GC/MS analysis revealed a homogeneous polymer composition over the year, with a general dominance of polyolefins. Elevated MP item and mass concentrations (maximum: 3 × 104 items m−3 and 3.8 × 103 μg m−3) were observed during winter months and were accompanied by either heavy rainfall (increased discharge and total organic carbon) or elevated turbidity values. These observations emphasize the need for the assessment of background parameters in future MP monitoring studies. By providing monthly data over one year on MP items and masses in WWTP effluents, this study helps enhancing the understanding of temporal MP dynamics and can act as a valuable reference point for future assessments.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , peerRev
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 57
    Publikationsdatum: 2022-12-22
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Venkataraman, Y. R., White, S. J., & Roberts, S. B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics, 23(1), (2022): 556, https://doi.org/10.1186/s12864-022-08781-5.
    Beschreibung: Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- 〉 T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation.
    Beschreibung: This work was funded by National Science Foundation award 1634167 to SBR. The Hall Conservation Genetics Research Fund (YRV) supported sequencing for this project.
    Schlagwort(e): Pacific oyster ; Bivalve ; Ocean acidification ; DNA methylation ; Gonad development
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 58
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Widner, B., Kido Soule, M. C., Ferrer-González, F. X., Moran, M. A., & Kujawinski, E. B. Quantification of amine- and alcohol-containing metabolites in saline samples using pre-extraction benzoyl chloride derivatization and ultrahigh performance liquid chromatography tandem mass spectrometry (UHPLC MS/MS). Analytical Chemistry, 93(11), (2021): 4809-4817, https://doi.org/10.1021/acs.analchem.0c03769.
    Beschreibung: Dissolved metabolites serve as nutrition, energy, and chemical signals for microbial systems. However, the full scope and magnitude of these processes in marine systems are unknown, largely due to insufficient methods, including poor extraction of small, polar compounds using common solid-phase extraction resins. Here, we utilized pre-extraction derivatization and ultrahigh performance liquid chromatography electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) to detect and quantify targeted dissolved metabolites in seawater and saline culture media. Metabolites were derivatized with benzoyl chloride by their primary and secondary amine and alcohol functionalities and quantified using stable isotope-labeled internal standards (SIL-ISs) produced from 13C6-labeled benzoyl chloride. We optimized derivatization, extraction, and sample preparation for field and culture samples and evaluated matrix-derived biases. We have optimized this quantitative method for 73 common metabolites, of which 50 cannot be quantified without derivatization due to low extraction efficiencies. Of the 73 metabolites, 66 were identified in either culture media or seawater and 45 of those were quantified. This derivatization method is sensitive (detection limits = pM to nM), rapid (∼5 min per sample), and high throughput.
    Beschreibung: Funding included the Gordon and Betty Moore Foundation (Award GBMF5503 to M.A.M. and E.B.K.), Simons Foundation International (Award 409923 to E.B.K.), and the National Science Foundation (Award 1656311 to M.A.M.).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 59
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirst, W. G., Kiefer, C., Abdosamadi, M. K., Schäffer, E., & Reber, S. In Vitro reconstitution and imaging of microtubule dynamics by fluorescence and label-free microscopy. STAR Protocols, 1(3), (2020): 100177, doi:10.1016/j.xpro.2020.100177.
    Beschreibung: Dynamic microtubules are essential for many processes in the lives of eukaryotic cells. To study and understand the mechanisms of microtubule dynamics and regulation, in vitro reconstitution with purified components has proven a vital approach. Imaging microtubule dynamics can be instructive for a given species, isoform composition, or biochemical modification. Here, we describe two methods that visualize microtubule dynamics at high speed and high contrast: (1) total internal reflection fluorescence microscopy and (2) label-free interference reflection microscopy.
    Beschreibung: We thank the AMBIO imaging facility (Charité, Berlin) and Nikon at MBL for imaging support. We thank all former and current members of the Reber lab for discussion and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding by the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University. C.K. thanks the Deutsche Forschungsgesellschaft (DFG, JA 2589/1-1). C.K. and M.A. thank Steve Simmert and Tobias Jachowski former and current members of the Schäffer lab.
    Schlagwort(e): Biophysics ; Cell Biology ; Microscopy
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 60
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geisterfer, Z. M., Oakey, J., & Gatlin, J. C. . Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography. STAR Protocols, 1(3), (2020): 100221, doi:10.1016/j.xpro.2020.100221.
    Beschreibung: Cell-free extract derived from the eggs of the African clawed frog Xenopus laevis is a well-established model system that has been used historically in bulk aliquots. Here, we describe a microfluidic approach for isolating discrete, biologically relevant volumes of cell-free extract, with more expansive and precise control of extract shape compared with extract-oil emulsions. This approach is useful for investigating the mechanics of intracellular processes affected by cell geometry or cytoplasmic volume, including organelle scaling and positioning mechanisms. For complete details on the use and execution of this protocol, please refer to Geisterfer et al. (2020).
    Beschreibung: This work was made possible by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant no. 2P20GM103432. It was also supported by additional funding provided by the NIGMS under grant no. R01GM113028, the NSF Faculty CAREER Program under award no. BBBE 1254608, Whitman Center fellowships at the Marine Biological Laboratory, and the Biomedical Scholars program of the Pew Charitable Trusts. We thank Drs. Aaron Groen and Tim Mitchison for their intellectual contributions and involvement in some of the pioneering experiments that set the foundation for this approach.
    Schlagwort(e): Biophysics ; Cell Biology ; Cell isolation ; Microscopy ; Model Organisms
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 61
    Publikationsdatum: 2022-11-18
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tian, Y., Liu, X., Li, J., Deng, Y., DeGiorgis, J. A., Zhou, S., Caratenuto, A., Minus, M. L., Wan, Y., Xiao, G., & Zheng, Y. Farm-waste-derived recyclable photothermal evaporator. Cell Reports Physical Science, 2(9), (2021): 100549, https://doi.org/10.1016./j.xcrp.2021.100549
    Beschreibung: Interfacial solar steam generation is emerging as a promising technique for efficient desalination. Although increasing efforts have been made, challenges exist for achieving a balance among a plethora of performance indicators—for example, rapid evaporation, durability, low-cost deployment, and salt rejection. Here, we demonstrate that carbonized manure can convert 98% of sunlight into heat, and the strong capillarity of porous carbon fibers networks pumps sufficient water to evaporation interfaces. Salt diffusion within microchannels enables quick salt drainage to the bulk seawater to prevent salt accumulation. With these advantages, this biomass-derived evaporator is demonstrated to feature a high evaporation rate of 2.81 kg m−2 h−1 under 1 sun with broad robustness to acidity and alkalinity. These advantages, together with facial deployment, offer an approach for converting farm waste to energy with high efficiency and easy implementation, which is particularly well suited for developing regions.
    Beschreibung: This project is supported by the National Science Foundation through grant no. CBET-1941743. This project is based upon work supported in part by the National Science Foundation under EPSCoR Cooperative Agreement no. OIA-1655221.
    Schlagwort(e): Biomass ; Recyclable ; Manure ; Farm waste ; Photothermal evaporation ; Desalination
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 62
    facet.materialart.
    Unbekannt
    ELSEVIER SCIENCE BV
    In:  EPIC3Science of The Total Environment, ELSEVIER SCIENCE BV, pp. 154886-154886, ISSN: 0048-9697
    Publikationsdatum: 2022-11-28
    Beschreibung: Some of the highest microplastic concentrations in marine environments have been reported from the Fram Strait in the Arctic. This region supports a diverse ecosystem dependent on high concentrations of zooplankton at the base of the food web. Zooplankton samples were collected during research cruises using Bongo and MOCNESS nets in the boreal summers of 2018 and 2019. Using FTIR scanning spectroscopy in combination with an automated polymer identification approach, we show that all five species of Arctic zooplankton investigated had ingested microplastics. Amphipod species, found in surface waters or closely associated with sea ice, had ingested significantly more microplastic per individual (Themisto libellula: 1.8, Themisto abyssorrum: 1, Apherusa glacialis: 1) than copepod species (Calanus hyperboreus: 0.21, Calanus glacialis/finmarchicus: 0.01). The majority of microplastics ingested were below 50 μm in size, all were fragments and several different polymer types were present. We quantified microplastics in water samples collected at six of the same stations as the Calanus using an underway sampling system (inlet at 6.5 m water depth). Fragments of several polymer types and anthropogenic cellulosic fibres were present, with an average concentration of 7 microplastic particles (MP) L−1 (0–18.5 MP L−1). In comparison to the water samples, those microplastics found ingested by zooplankton were significantly smaller, highlighting that the smaller-sized microplastics were being selected for by the zooplankton. High levels of microplastic ingestion in zooplankton have been associated with negative effects on growth, development, and fecundity. As Arctic zooplankton only have a short window of biological productivity, any negative effect could have broad consequences. As global plastic consumption continues to increase and climate change continues to reduce sea ice cover, releasing ice-bound microplastics and leaving ice free areas open to exploitation, the Arctic could be exposed to further plastic pollution which could place additional strain on this fragile ecosystem.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Format: application/pdf
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 63
    Publikationsdatum: 2022-10-21
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Colson, B. C., & Michel, A. P. M. Flow-through quantification of microplastics using impedance spectroscopy. ACS Sensors, 6(1), (2021): 238–244, doi:10.1021/acssensors.0c02223.
    Beschreibung: Understanding the sources, impacts, and fate of microplastics in the environment is critical for assessing the potential risks of these anthropogenic particles. However, our ability to quantify and identify microplastics in aquatic ecosystems is limited by the lack of rapid techniques that do not require visual sorting or preprocessing. Here, we demonstrate the use of impedance spectroscopy for high-throughput flow-through microplastic quantification, with the goal of rapid measurement of microplastic concentration and size. Impedance spectroscopy characterizes the electrical properties of individual particles directly in the flow of water, allowing for simultaneous sizing and material identification. To demonstrate the technique, spike and recovery experiments were conducted in tap water with 212–1000 μm polyethylene beads in six size ranges and a variety of similarly sized biological materials. Microplastics were reliably detected, sized, and differentiated from biological materials via their electrical properties at an average flow rate of 103 ± 8 mL/min. The recovery rate was ≥90% for microplastics in the 300–1000 μm size range, and the false positive rate for the misidentification of the biological material as plastic was 1%. Impedance spectroscopy allowed for the identification of microplastics directly in water without visual sorting or filtration, demonstrating its use for flow-through sensing.
    Beschreibung: The authors thank the Richard Saltonstall Charitable Foundation and the National Academies Keck Futures Initiative (NAKFI DBS13) for their funding support.
    Schlagwort(e): Microplastics ; Plastics ; Impedance spectroscopy ; Dielectric properties ; Instrumentation ; Particle detection ; Flow-through ; Environmental sensing
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 64
  • 65
    Publikationsdatum: 2007-07-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 66
    Publikationsdatum: 2007-08-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 67
    Publikationsdatum: 2006-03-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 68
    Publikationsdatum: 2005-01-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 69
    Publikationsdatum: 2009-04-27
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 70
    Publikationsdatum: 2007-05-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 71
    Publikationsdatum: 2005-10-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 72
    Publikationsdatum: 2009-12-14
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 73
    Publikationsdatum: 2009-01-12
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 74
  • 75
    Publikationsdatum: 2008-03-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 76
    Publikationsdatum: 2006-04-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 77
  • 78
    Publikationsdatum: 2008-11-10
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 79
    Publikationsdatum: 2008-08-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 80
    Publikationsdatum: 2007-07-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 81
    Publikationsdatum: 2007-07-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 82
    Publikationsdatum: 2008-02-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 83
    Publikationsdatum: 2009-09-14
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 84
    Publikationsdatum: 2006-10-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 85
    Publikationsdatum: 2008-06-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 86
    Publikationsdatum: 2006-05-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 87
    Publikationsdatum: 2005-03-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 88
    Publikationsdatum: 2008-02-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 89
  • 90
    Publikationsdatum: 2008-03-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 91
    Publikationsdatum: 2007-12-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 92
    Publikationsdatum: 2007-06-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 93
    Publikationsdatum: 2009-03-23
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 94
    Publikationsdatum: 2006-10-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 95
    Publikationsdatum: 2005-08-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 96
    Publikationsdatum: 2008-09-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 97
    Publikationsdatum: 2005-03-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 98
  • 99
    Publikationsdatum: 2005-09-01
    Print ISSN: 0276-7333
    Digitale ISSN: 1520-6041
    Thema: Chemie und Pharmazie
    Publiziert von American Chemical Society
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 100
Schließen ⊗
Diese Webseite nutzt Cookies und das Analyse-Tool Matomo. Weitere Informationen finden Sie hier...