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  • American Institute of Physics (AIP)
  • Annual Reviews
  • BioMed Central
  • 2015-2019  (69,865)
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  • 1
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    Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms (2018)
    BioMed Central
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    Publication Date: 2021-03-29
    Keywords: 551
    Language: English
    Type: article , publishedVersion
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  • 2
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    Spatial compartmentalization of free radical formation and mitochondrial heterogeneity in bivalve gills revealed by live-imaging techniques (2016)
    BioMed Central
    In:  EPIC3Frontiers in Zoology, BioMed Central, 13(4)
    Details
    Publication Date: 2016-02-05
    Description: Background: Reactive oxygen (ROS) and nitrogen (RNS) species are produced during normal unstressed metabolic activity in aerobic tissues. Most analytical work uses tissue homogenates, and lacks spatial information on the tissue specific sites of actual ROS formation. Live-imaging techniques (LIT) utilize target-specific fluorescent dyes to visualize biochemical processes at cellular level. Results: Together with oxidative stress measurements, here we report application of LIT to bivalve gills for ex-vivo analysis of gill physiology and mapping of ROS and RNS formation in the living tissue. Our results indicate that a) mitochondria located in the basal parts of the epithelial cells close to the blood vessels are hyperpolarized with high Δψm, whereas b) the peripheral mitochondria close to the cilia have low (depolarized) Δψm. These mitochondria are densely packed (mitotracker Deep Red 633 staining), have acidic pH (Ageladine-A) and collocate with high formation of nitric oxide (DAF-2DA staining). NO formation is also observed in the endothelial cells surrounding the filament blood sinus. ROS (namely H2O2, HOO• and ONOO− radicals, assessed through C-H2DFFDA staining) are mainly formed within the blood sinus of the filaments and are likely to be produced by hemocytes as defense against invading pathogens. On the ventral bend of the gills, subepithelial mucus glands contain large mucous vacuoles showing higher fluorescence intensities for O2 •- than the rest of the tissue. Whether this O2 •- production is instrumental to mucus formation or serves antimicrobial protection of the gill surface is unknown. Cells of the ventral bends contain the superoxide forming mucocytes and show significantly higher protein carbonyl formation than the rest of the gill tissue. Conclusions: In summary, ROS and RNS formation is highly compartmentalized in bivalve gills under unstressed conditions. The main mechanisms are the differentiation of mitochondria membrane potential and basal ROS formation in inner and outer filament layers, as well as potentially antimicrobial ROS formation in the central blood vessel. Our results provide new insight into this subject and highlight the fact that studying ROS formation in tissue homogenates may not be adequate to understand the underlying mechanism in complex tissues. Keywords: Bivalve, Gill, Live-imaging, Fluorescence, Mitochondria, ROS, RNS * Correspondence:
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Biology 13 (2015): 105, doi:10.1186/s12915-015-0213-6
    Description: The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth ~3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines. We report observations from sediments of three DHAB (Urania, Discovery, L’Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTrackerTM Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L’Atalante normoxic control sediments were fit, while specimens from L’Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L’Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions. We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time.
    Description: Supported by NSF grants OCE-0849578 to VPE and JMB, OCE-1061391 to JMB and VPE, and The Investment in Science Fund at WHOI.
    Keywords: Athalassohaline ; Bryozoa ; CellTrackerTM Green ; Discovery ; L’Atalante ; Loricifera ; Meiofauna ; Nematoda ; Ultrastructure ; Urania
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics (2017)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 5 (2017): 50, doi:10.1186/s40168-017-0270-x.
    Description: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. We used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients. Our analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8 weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems. The analytical strategy adopted in our study can provide genomic insights into bacterial populations that may be critical to the efficacy of FMT due to their success in gut colonization and metabolic properties, and guide cultivation efforts to investigate mechanistic underpinnings of this procedure beyond associations.
    Description: AME was supported by the Frank R. Lillie Research Innovation Award and startup funds from the University of Chicago. This project was supported by the Mutchnik Family Charitable Fund and the University of Chicago Gastro-Intestinal Research Foundation.
    Keywords: Fecal microbiota transplantation ; Colonization ; Metagenomics ; Metagenome-assembled genomes
    Repository Name: Woods Hole Open Access Server
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  • 5
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    The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae (2018)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbial Cell Factories 17 (2018): 170, doi:10.1186/s12934-018-1018-4.
    Description: Ammonium assimilation is linked to fundamental cellular processes that include the synthesis of non-essential amino acids like glutamate and glutamine. In Saccharomyces cerevisiae glutamate can be synthesized from α-ketoglutarate and ammonium through the action of NADP-dependent glutamate dehydrogenases Gdh1 and Gdh3. Gdh1 and Gdh3 are evolutionarily adapted isoforms and cover the anabolic role of the GDH-pathway. Here, we review the role and function of the GDH pathway in glutamate metabolism and we discuss the additional contributions of the pathway in chromatin regulation, nitrogen catabolite repression, ROS-mediated apoptosis, iron deficiency and sphingolipid-dependent actin cytoskeleton modulation in S.cerevisiae. The pleiotropic effects of GDH pathway in yeast biology highlight the importance of glutamate homeostasis in vital cellular processes and reveal new features for conserved enzymes that were primarily characterized for their metabolic capacity. These newly described features constitute insights that can be utilized for challenges regarding genetic engineering of glutamate homeostasis and maintenance of redox balances, biosynthesis of important metabolites and production of organic substrates. We also conclude that the discussed pleiotropic features intersect with basic metabolism and set a new background for further glutamate-dependent applied research of biotechnological interest.
    Description: The writing of the manuscript was supported by the European Union (European Social Fund – ESF) and by the Greek National Strategic Reference Framework (NSRF) THALIS: – UOC “Mitochondrial dysfunction in neurodegenerative diseases” (Grant Code 377226).
    Keywords: Glutamate dehydrogenase ; GDH1 ; GDH2 ; GDH3 ; Ammonium assimilation ; GABA shunt ; ROS-mediated apoptosis ; Chromatin regulation ; Nitrogen catabolite repression ; S. cerevisiae
    Repository Name: Woods Hole Open Access Server
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  • 6
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    A simple novel device for air sampling by electrokinetic capture (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 79, doi:10.1186/s40168-015-0141-2.
    Description: A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable. An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.
    Description: This work was partly supported by Breakout Labs, a program of the Thiel Foundation, and partly from personal funds from Julian Gordon and Prasanthi Gandhi. This work was supported in part by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Keywords: Atomic force microscopy ; Reverse transcriptase PCR ; Air sampling ; Field study ; Aerosol ; Nanoparticles ; Aerobiome ; Amplicon sequencing ; Bacteria ; Molds
    Repository Name: Woods Hole Open Access Server
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  • 7
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    The obese gut microbiome across the epidemiologic transition (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Emerging Themes in Epidemiology 13 (2016): 2, doi:10.1186/s12982-015-0044-5.
    Description: The obesity epidemic has emerged over the past few decades and is thought to be a result of both genetic and environmental factors. A newly identified factor, the gut microbiota, which is a bacterial ecosystem residing within the gastrointestinal tract of humans, has now been implicated in the obesity epidemic. Importantly, this bacterial community is impacted by external environmental factors through a variety of undefined mechanisms. We focus this review on how the external environment may impact the gut microbiota by considering, the host’s geographic location ‘human geography’, and behavioral factors (diet and physical activity). Moreover, we explore the relationship between the gut microbiota and obesity with these external factors. And finally, we highlight here how an epidemiologic model can be utilized to elucidate causal relationships between the gut microbiota and external environment independently and collectively, and how this will help further define this important new factor in the obesity epidemic.
    Description: BTL is supported by the Department of Veterans Affairs, Veterans Health Administration, Office of Research and Development, Career Development (Grant no. 1IK2BX001587-01).
    Keywords: Obesity ; Gut microbiome ; Geographical differences
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Merging scleractinian genera : the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 108, doi:10.1186/s12862-016-0654-8.
    Description: In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals.
    Description: This research was supported by the Spanish Ministry of Science and Innovation (CGL2011-23306 and CTM2014-57949R) and EU CoCoNET—“Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential”—from the VII FP of the European Commission under grant agreement n° 287844. This paper also benefited from the ESF COCARDE network activities and commits to the Italian Flag Project ‘Ritmare’. Fund within the Innovation Economy Operational Programme POIG.02.02.00-00-025/09
    Keywords: Mitochondrial genome ; Microsatellites ; Genetic divergence ; Skeletal plasticity ; Desmophyllum dianthus ; Lophelia pertusa
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 11 (2016): 46, doi:10.1186/s40793-016-0168-4.
    Description: Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
    Description: The work was supported by the U.S. Department of Energy, Office of Science JGI under Contract No. DE-AC02-05CH11231 for CSP 2010 project 1012224; USDA NIFA Award 2011-67019-30178, and the Utah Agricultural Experiment Station, Utah State University project UTA00371.
    Keywords: Nitrosospira ; Ammonia-oxidizing bacteria ; Nitrification ; Agricultural soil ; Ammonia monooxygenase ; Nitrous oxide ; Chemolithotroph
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  • 10
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    Interpreting comprehensive two-dimensional gas chromatography using peak topography maps with application to petroleum forensics (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chemistry Central Journal 10 (2016): 75, doi:10.1186/s13065-016-0211-y.
    Description: Comprehensive two-dimensional gas chromatography (GC×GC) provides high-resolution separations across hundreds of compounds in a complex mixture, thus unlocking unprecedented information for intricate quantitative interpretation. We exploit this compound diversity across the (GC×GC) topography to provide quantitative compound-cognizant interpretation beyond target compound analysis with petroleum forensics as a practical application. We focus on the (GC×GC) topography of biomarker hydrocarbons, hopanes and steranes, as they are generally recalcitrant to weathering. We introduce peak topography maps (PTM) and topography partitioning techniques that consider a notably broader and more diverse range of target and non-target biomarker compounds compared to traditional approaches that consider approximately 20 biomarker ratios. Specifically, we consider a range of 33–154 target and non-target biomarkers with highest-to-lowest peak ratio within an injection ranging from 4.86 to 19.6 (precise numbers depend on biomarker diversity of individual injections). We also provide a robust quantitative measure for directly determining “match” between samples, without necessitating training data sets. We validate our methods across 34 (GC×GC) injections from a diverse portfolio of petroleum sources, and provide quantitative comparison of performance against established statistical methods such as principal components analysis (PCA). Our data set includes a wide range of samples collected following the 2010 Deepwater Horizon disaster that released approximately 160 million gallons of crude oil from the Macondo well (MW). Samples that were clearly collected following this disaster exhibit statistically significant match (99.23±1.66)% using PTM-based interpretation against other closely related sources. PTM-based interpretation also provides higher differentiation between closely correlated but distinct sources than obtained using PCA-based statistical comparisons. In addition to results based on this experimental field data, we also provide extentive perturbation analysis of the PTM method over numerical simulations that introduce random variability of peak locations over the (GC×GC) biomarker ROI image of the MW pre-spill sample (sample #1 in Additional file 4: Table S1). We compare the robustness of the cross-PTM score against peak location variability in both dimensions and compare the results against PCA analysis over the same set of simulated images. Detailed description of the simulation experiment and discussion of results are provided in Additional file 1: Section S8. We provide a peak-cognizant informational framework for quantitative interpretation of (GC×GC) topography. Proposed topographic analysis enables (GC×GC) forensic interpretation across target petroleum biomarkers, while including the nuances of lesser-known non-target biomarkers clustered around the target peaks. This allows potential discovery of hitherto unknown connections between target and non-target biomarkers.
    Description: This research was made possible in part by a grant from the Gulf of Mexico Research Initiative (GoMRI-015), and the DEEP-C consortium, and in part by NSF Grants OCE-0969841 and RAPID OCE-1043976 as well as a WHOI interdisciplinary study award.
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  • 11
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    Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum (2015)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 805, doi:10.1186/s12864-015-2052-9.
    Description: Organelle retention is a form of mixotrophy that allows organisms to reap metabolic benefits similar to those of photoautotrophs through capture of algal prey and sequestration of their plastids. Mesodinium rubrum is an abundant and broadly distributed photosynthetic marine ciliate that steals organelles from cryptophyte algae, such as Geminigera cryophila. M. rubrum is unique from most other acquired phototrophs because it also steals a functional nucleus that facilitates genetic control of sequestered plastids and other organelles. We analyzed changes in G. cryophila nuclear gene expression and transcript abundance after its incorporation into the cellular architecture of M. rubrum as an initial step towards understanding this complex system. We compared Illumina-generated transcriptomes of the cryptophyte Geminigera cryophila as a free-living cell and as a sequestered nucleus in M. rubrum to identify changes in protein abundance and gene expression. After KEGG annotation, proteins were clustered by functional categories, which were evaluated for over- or under-representation in the sequestered nucleus. Similarly, coding sequences were grouped by KEGG categories/pathways, which were then evaluated for over- or under-expression via read count strategies. At the time of sampling, the global transcriptome of M. rubrum was dominated (~58–62 %) by transcription from its stolen nucleus. A comparison of transcriptomes from free-living G. cryophila cells to those of the sequestered nucleus revealed a decrease in gene expression and transcript abundance for most functional protein categories within the ciliate. However, genes coding for proteins involved in photosynthesis, oxidative stress reduction, and several other metabolic pathways revealed striking exceptions to this general decline. Major changes in G. cryophila transcript expression after sequestration by M. rubrum and the ciliate’s success as a photoautotroph imply some level of control or gene regulation by the ciliate and at the very least reflect a degree of coordination between host and foreign organelles. Intriguingly, cryptophyte genes involved in protein transport are significantly under-expressed in M. rubrum, implicating a role for the ciliate’s endomembrane system in targeting cryptophyte proteins to plastid complexes. Collectively, this initial portrait of an acquired transcriptome within a dynamic and ecologically successful ciliate highlights the remarkable cellular and metabolic chimerism of this system.
    Description: The authors wish to acknowledge the support of NSF award 1354773.
    Keywords: Mesodinium rubrum ; Geminigera cryophila ; Karyoklepty ; Acquired phototrophy ; Transcriptome ; Differential gene expression ; Chimeric metabolism ; Organelle retention ; Mixotrophy
    Repository Name: Woods Hole Open Access Server
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  • 12
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    ITAG : an eco-sensor for fine-scale behavioral measurements of soft-bodied marine invertebrates (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Animal Biotelemetry 3 (2015): 31, doi:10.1186/s40317-015-0076-1.
    Description: Soft-bodied marine invertebrates comprise a keystone component of ocean ecosystems; however, we know little of their behaviors and physiological responses within their natural habitat. Quantifying ocean conditions and measuring organismal responses to the physical environment is vital to understanding the species or ecosystem-level influences of a changing ocean. Here we describe a novel, soft-bodied invertebrate eco-sensor tag (the ITAG), its trial attachments to squid and jellyfish, and the fine-scale behavioral measurements recorded on captive animals. Tags were deployed on five jellyfish (Aurelia aurita) and eight squid (Loligo forbesi) in laboratory conditions for up to 24 h. Using concurrent video and tag data, movement signatures for specific behaviors were identified. These behaviors included straight swimming (for jellyfish), and finning, jetting, direction reversal and turning (for squid). Overall activity levels were quantified using the root-mean-squared magnitude of acceleration, and finning was found to be the dominant squid swimming gait during captive squid experiments. External light sensors on the ITAG were used to compare squid swimming activity relative to ambient light across a ca. 20-h trial. The deployments revealed that while swimming was continuous for captive squid, energetically costly swimming behaviors (i.e., jetting and rapid direction reversals) occurred infrequently. These data reflect the usefulness of the ITAG to study trade-offs between behavior and energy expenditure in captive and wild animals. These data demonstrate that eco-sensors with sufficiently high sampling rates can be applied to quantify behavior of soft-bodied taxa and changes in behavior due to interactions with the surrounding environment. The methods and tool described here open the door for substantial lab and field-based measurements of fine-scale behavior, physiology, and concurrent environmental parameters that will inform fisheries management, and elucidate the ecology of these important keystone taxa.
    Description: This work was supported by WHOI’s Ocean Life Institute and the Innovative Technology Program, Hopkins Marine Station’s Marine Life Observatory (to KK), as well as the National Science Foundation’s Ocean Acidification Program (to TAM) and NSF’s Program for Innovative Development of Biological Research (to TAM, KK and KAS).
    Keywords: Jellyfish ; Cephalopod ; Activity pattern ; Activity pattern ; Climate ; High-temporal resolution ; Sensory
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  • 13
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    Meeting report of Ctenopalooza : the first international meeting of ctenophorologists (2016)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in EvoDevo 7 (2016): 19, doi:10.1186/s13227-016-0057-3
    Description: Here we present a report on Ctenopalooza: A meeting of ctenophorologists held at the Whitney Laboratory for Marine Bioscience in St. Augustine, FL, USA, on March 14–15, 2016. In this report, we provide a summary of each of the sessions that occurred during this two-day meeting, which touched on most of the relevant areas of ctenophore biology. The report includes some major themes regarding the future of ctenophore research that emerged during Ctenopalooza. More information can be found at the meeting Web site: http://ctenopalooza.whitney.ufl.edu.
    Description: Ctenopalooza was sponsored by a grant from the National Science Foundation’s Division of Integrative Organismal Systems to Joseph Ryan (#1619712). We also acknowledge funding was provided by a grant from the University of Florida’s Office of Research to Joseph Ryan (Project #00075235). Additional funding was provided by The Whitney Laboratory for Marine Bioscience.
    Keywords: Ctenophora ; Ctenophore ; Ctenophore
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  • 14
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    Athletic equipment microbiota are shaped by interactions with human skin (2015)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 25, doi:10.1186/s40168-015-0088-3.
    Description: Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
    Description: MW was supported by a Weinberg College of Arts and Sciences Summer Grant from Northwestern University. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. This work was also supported by the Alfred P Sloan Foundation’s Microbiology of the Built Environment research program. SMG was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Gym microbiome ; Athletic equipment ; Microbiology ; Niche communities ; Next-generation sequencing
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    Continuous movement behavior of humpback whales during the breeding season in the southwest Indian Ocean : on the road again! (2017)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Movement Ecology 5 (2017): 11, doi:10.1186/s40462-017-0101-5.
    Description: Humpback whales are known to undertake long-distance migration between feeding and breeding sites, but their movement behavior within their breeding range is still poorly known. Satellite telemetry was used to investigate movement of humpback whales during the breeding season and provide further understanding of the breeding ecology and sub-population connectivity within the southwest Indian Ocean (SWIO). Implantable Argos satellite tags were deployed on 15 whales (7 males and 6 females) during the peak of the breeding season in Reunion Island. A switching-state-space model was applied to the telemetry data, in order to discriminate between “transiting” and “localized” movements, the latter of which relates to meandering behavior within putative breeding habitats, and a kernel density analysis was used to assess the spatial scale of the main putative breeding sites. Whales were tracked for up to 71 days from 31/07/2013 to 16/10/2013. The mean transmission duration was 25.7 days and the mean distance travelled was 2125.8 km. The tracks showed consistent movement of whales from Reunion to Madagascar, demonstrating a high level of connectivity between the two sub-regions, and the use of yet unknown breeding sites such as underwater seamounts (La Perouse) and banks (Mascarene Plateau). A localized movement pattern occurred in distinct bouts along the tracks, suggesting that whales were involved in breeding activity for 4.3 consecutive days on average, after which they resume transiting for an average of 6.6 days. Males visited several breeding sites within the SWIO, suggesting for the first time a movement strategy at a basin scale to maximize mating. Unexpectedly, females with calf also showed extensive transiting movement, while they engaged in localized behavior mainly off Reunion and Sainte-Marie (East Madagascar). The results indicated that whales from Reunion do not represent a discrete population. Discrete breeding sites were identified, thereby highlighting priority areas for conservation. The study is a first attempt to quantify movement of humpback whales within the southwestern Indian Ocean breeding range. We demonstrate a wandering behavior with stopovers at areas that likely represent key breeding habitat, a strategy which may enhance likelihood of individual reproductive success.
    Description: The project was funded by the European Commission, under the Biodiversity and Ecosystem Services in territories of European overseas (BEST) program (Award number: 07.032700/2012/63511/SUB/B2).
    Keywords: Humpback whales ; Satellite tracking ; Reunion ; Indian Ocean ; Breeding behavior ; Movement pattern
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    Forensic analysis of the microbiome of phones and shoes (2015)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 21, doi:10.1186/s40168-015-0082-9.
    Description: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
    Description: This work was enabled by the generous support of the Alfred P Sloan foundation. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. S.M.G. was supported by an EPA STAR Graduate Fellowship and by a National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Forensic microbiology ; Source-sink dynamics ; Shoe microbiome ; Phone microbiome ; Microbial time series
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    The ocean sampling day consortium (2015)
    BioMed Central
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    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
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    Transcriptional profiling of reproductive development, lipid storage and molting throughout the last juvenile stage of the marine copepod Calanus finmarchicus (2015)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Zoology 11 (2014): 91, doi:10.1186/s12983-014-0091-8.
    Description: Calanus finmarchicus, a highly abundant copepod that is an important primary consumer in North Atlantic ecosystems, has a flexible life history in which copepods in the last juvenile developmental stage (fifth copepodid, C5) may either delay maturation and enter diapause or molt directly into adults. The factors that regulate this developmental plasticity are poorly understood, and few tools have been developed to assess the physiological condition of individual copepods. We sampled a cultured population of C. finmarchicus copepods daily throughout the C5 stage and assessed molt stage progression, gonad development and lipid storage. We used high-throughput sequencing to identify genes that were differentially expressed during progression through the molt stage and then used qPCR to profile daily expression of individual genes. Based on expression profiles of twelve genes, samples were statistically clustered into three groups: (1) an early period occurring prior to separation of the cuticle from the epidermis (apolysis) when expression of genes associated with lipid synthesis and transport (FABP and ELOV) and two nuclear receptors (ERR and HR78) was highest, (2) a middle period of rapid change in both gene expression and physiological condition, including local minima and maxima in several nuclear receptors (FTZ-F1, HR38b, and EcR), and (3) a late period when gonads were differentiated and expression of genes associated with molting (Torso-like, HR38a) peaked. The ratio of Torso-like to HR38b strongly differentiated the early and late groups. This study provides the first dynamic profiles of gene expression anchored with morphological markers of lipid accumulation, development and gonad maturation throughout a copepod molt cycle. Transcriptomic profiling revealed significant changes over the molt cycle in genes with presumed roles in lipid synthesis, molt regulation and gonad development, suggestive of a coupling of these processes in Calanus finmarchicus. Finally, we identified gene expression profiles that strongly differentiate between early and late development within the C5 copepodid stage. We anticipate that these findings and continued development of robust gene expression biomarkers that distinguish between diapause preparation and continuous development will ultimately enable novel studies of the intrinsic and extrinsic factors that govern diapause initiation in Calanus finmarchicus.
    Description: This work was supported by grant number OCE-1132567 from the National Science Foundation to MFB and AMT. Additional supported was provided by WHOI Early Career Scientist Awards provided to MFB and AMT.
    Keywords: Arthropod ; Crustacean ; Gene expression ; Molt cycle ; Transcriptomics
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    Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis (2016)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 16, doi:10.1186/s40168-016-0161-6.
    Description: The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female partners during intercourse; however, the microbiota of sexual partners has not been well-studied. Pyrosequencing analysis of PCR-amplified 16S rDNA was used to examine BV-associated bacteria in monogamous couples with and without BV using vaginal, male urethral, and penile skin specimens. The penile skin and urethral microbiota of male partners of women with BV was significantly more similar to the vaginal microbiota of their female partner compared to the vaginal microbiota of non-partner women with BV. This was not the case for male partners of women with normal vaginal microbiota. Specific BV-associated species were concordant in women with BV and their male partners. In monogamous heterosexual couples in which the woman has BV, the significantly higher similarity between the vaginal microbiota and the penile skin and urethral microbiota of the male partner, supports the hypothesis that sexual exchange of BV-associated bacterial taxa is common.
    Description: This work was supported by National Institute of Health Grant R01 AI079071-01A1.
    Keywords: Bacterial vaginosis ; Microbiome ; Sexual transmission ; Penile skin ; Urethra ; Vagina
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    Erratum to: Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 149, doi:10.1186/s12862-016-0703-3.
    Description: As a result of vendor errors being introduced during processing, the original version of this article was published with some duplication errors in Table 1.
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    Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 33, doi:10.1186/s13742-016-0138-1.
    Description: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (〉10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
    Description: Bioinformatic analysis was performed in part on computing resources at the University of Puerto Rico (UPR) Puerto Rico Center for Environmental Neuroscience (PRCEN)’s High Performance Computing Facility, which is supported by: Institutional Development Award Networks of Biomedical Research Excellent (INBRE) grant P20GM103475 from the National Institute of General Medical Sciences, National Institutes of Health; the Institute for Functional Nanomaterials (IFN) award from the Experimental Program to Stimulate Competitive Research (EPSCoR) Track 1 program of the National Science Foundation (NSF); and EPSCoR Track 2 awards for computational nanoscience (EPS 1002410, EPS 1010094). Funding and support of the research was provided by PRCEN thanks to an NSF Centers of Research Excellent in Science and Technology (CREST) award, number HRD-1137725.
    Keywords: Porites astreoides ; Calcification ; Biomineralization ; Coral ; Symbiodinium ; Dinoflagellate ; Zooxanthellae ; Symbiosis ; Swimming larvae ; Larval settlement
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    Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus) (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 243, doi:10.1186/s12864-015-1288-8.
    Description: With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ electric organ, main electric organ, and Hunter’s electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.
    Description: This project has been funded in part by NSF Grant MCB No. 1144012 (MRS), NSF Grant DEB No. 0741450 (JSA), NSF Grant CNS No. 1248109 (GAU), W.M. Keck Foundation Distinguished Young Scholars in Medical Research (CDN), NIH R01 GM084879 (HZ), NIH grant R01 GM088670 (RA), NIH grant 1SC1GM092297-01A1 (GAU), the Morgridge Graduate Fellowship (JDV and LLT), University of Wisconsin Genetics NIH Graduate Training Grant (LLT); and the Cornell University Center for Vertebrate Genomics (JRG).
    Keywords: Electric eel ; Genome ; Transcriptome ; miRNA ; Gene ontology
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    Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium (2016)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Description: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Description: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Keywords: Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
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    Recovering complete and draft population genomes from metagenome datasets (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 8, doi:10.1186/s40168-016-0154-5.
    Description: Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
    Description: This work was supported by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Keywords: Metagenomics ; Genotype ; Assembly ; Binning ; Curation
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    Fine-scale foraging movements by fish-eating killer whales (Orcinus orca) relate to the vertical distributions and escape responses of salmonid prey (Oncorhynchus spp.) (2017)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Movement Ecology 5 (2017): 3, doi:10.1186/s40462-017-0094-0.
    Description: We sought to quantitatively describe the fine-scale foraging behavior of northern resident killer whales (Orcinus orca), a population of fish-eating killer whales that feeds almost exclusively on Pacific salmon (Oncorhynchus spp.). To reconstruct the underwater movements of these specialist predators, we deployed 34 biologging Dtags on 32 individuals and collected high-resolution, three-dimensional accelerometry and acoustic data. We used the resulting dive paths to compare killer whale foraging behavior to the distributions of different salmonid prey species. Understanding the foraging movements of these threatened predators is important from a conservation standpoint, since prey availability has been identified as a limiting factor in their population dynamics and recovery. Three-dimensional dive tracks indicated that foraging (N = 701) and non-foraging dives (N = 10,618) were kinematically distinct (Wilks’ lambda: λ 16 = 0.321, P 〈 0.001). While foraging, killer whales dove deeper, remained submerged longer, swam faster, increased their dive path tortuosity, and rolled their bodies to a greater extent than during other activities. Maximum foraging dive depths reflected the deeper vertical distribution of Chinook (compared to other salmonids) and the tendency of Pacific salmon to evade predators by diving steeply. Kinematic characteristics of prey pursuit by resident killer whales also revealed several other escape strategies employed by salmon attempting to avoid predation, including increased swimming speeds and evasive maneuvering. High-resolution dive tracks reconstructed using data collected by multi-sensor accelerometer tags found that movements by resident killer whales relate significantly to the vertical distributions and escape responses of their primary prey, Pacific salmon.
    Description: This work was supported by the Species at Risk Program, Fisheries and Oceans Canada; the University of Cumbria’s Research and Scholarship Development Fund; a Marie Curie Intra-European Fellowship (IEF) to VD; a University of British Columbia Zoology Graduate Fellowship to BW; and a Natural Sciences and Engineering Research Council (NSERC) Alexander Graham Bell Canada Graduate Scholarship to BW.
    Keywords: Foraging ; Movement ; Diving behavior ; Biologging ; Dtag ; Accelerometry ; Killer whale ; Orcinus orca ; Pacific salmon
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    Optimization of DNA extraction for advancing coral microbiota investigations (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 5 (2017): 18, doi:10.1186/s40168-017-0229-y.
    Description: We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition. During phase I, total DNA was extracted from seven coral species in a replicated experimental design using four different MO BIO Laboratories, Inc., DNA Isolation kits: PowerSoil®, PowerPlant® Pro, PowerBiofilm®, and UltraClean® Tissue & Cells (with three homogenization permutations). Technical performance of the treatments was evaluated using DNA yield and amplification efficiency of small subunit ribosomal RNA (SSU ribosomal RNA (rRNA)) genes. During phase II, potential extraction biases were examined via microbial community analysis of SSU rRNA gene sequences amplified from the most successful DNA extraction treatments. In phase I of the study, the PowerSoil® and PowerPlant® Pro extracts contained low DNA concentrations, amplified poorly, and were not investigated further. Extracts from PowerBiofilm® and UltraClean® Tissue and Cells permutations were further investigated in phase II, and analysis of sequences demonstrated that overall microbial community composition was dictated by coral species and not extraction treatment. Finer pairwise comparisons of sequences obtained from Orbicella faveolata, Orbicella annularis, and Acropora humilis corals revealed subtle differences in community composition between the treatments; PowerBiofilm®-associated sequences generally had higher microbial richness and the highest coverage of dominant microbial groups in comparison to the UltraClean® Tissue and Cells treatments, a result likely arising from using a combination of different beads during homogenization. Both the PowerBiofilm® and UltraClean® Tissue and Cells treatments are appropriate for large-scale analyses of coral microbiota. However, studies interested in detecting cryptic microbial members may benefit from using the PowerBiofilm® DNA treatment because of the likely enhanced lysis efficiency of microbial cells attributed to using a variety of beads during homogenization. Consideration of the methodology involved with microbial DNA extraction is particularly important for studies investigating complex host-associated microbiota.
    Description: This project was supported by NSF award OCE-1233612 to AA and NSF GRFP award to LW.
    Keywords: Coral microbiota ; DNA extraction ; Optimization ; SSU ribosomal RNA gene ; Amplicon sequencing
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    Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 12 (2017): 50, doi:10.1186/s40793-017-0266-y.
    Description: Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the B. thermophilus symbiosis.
    Description: This study was supported by the EU-funded Marie Curie Initial Training Network “Symbiomics” (project no. 264774). RP was supported by a fellowship of the Institute of Marine Biotechnology, Greifswald. MK was supported by a NSERC Banting Postdoctoral Fellowship. LS was supported by a DAAD scholarship. SMS was supported by US National Science Foundation grant OCE-1136727.
    Keywords: Uncultured endosymbiont ; Hydrothermal vents ; Marine invertebrate symbiosis ; Thiotrophy ; Autotrophy ; Atlantis (Ship : 1996-) Cruise AT26-10
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    DESMAN : a new tool for de novo extraction of strains from metagenomes (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology 18 (2017): 181, doi:10.1186/s13059-017-1309-9.
    Description: We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.
    Description: CQ is funded through a Medical Research Council fellowship (MR/M50161X/1) as part of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) consortium (MR/L015080/1). GC was supported by a European Research Council Starting Grant (3C-BIOTECH 261330). AME was supported by a Frank R. Lillie Research Innovation Award.
    Keywords: Metagenomes ; Strain ; Niche
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    Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories (2017)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mobile DNA 8 (2017): 19, doi:10.1186/s13100-017-0103-2.
    Description: In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes. A tripartite TE classification scheme is proposed to account for their replicative, integrative, and structural components, and the need to expand in vitro and in vivo studies of their structural and biological properties is emphasized. Bioinformatic studies have now become front and center of novel TE discovery, and experimental pursuits of these discoveries hold great promise for both basic and applied science.
    Description: The work in the author’s laboratory is supported by the US National Institutes of Health (GM111917) and by the US National Science Foundation (MCB-1121334).
    Keywords: Mobile genetic elements ; Classification ; Phylogeny ; Reverse transcriptase ; Transposase
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    Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system (2017)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 18 (2017): 217, doi:10.1186/s12864-017-3540-x.
    Description: Understanding gene expression changes over lifespan in diverse animal species will lead to insights to conserved processes in the biology of aging and allow development of interventions to improve health. Rotifers are small aquatic invertebrates that have been used in aging studies for nearly 100 years and are now re-emerging as a modern model system. To provide a baseline to evaluate genetic responses to interventions that change health throughout lifespan and a framework for new hypotheses about the molecular genetic mechanisms of aging, we examined the transcriptome of an asexual female lineage of the rotifer Brachionus manjavacas at five life stages: eggs, neonates, and early-, late-, and post-reproductive adults. There are widespread shifts in gene expression over the lifespan of B. manjavacas; the largest change occurs between neonates and early reproductive adults and is characterized by down-regulation of developmental genes and up-regulation of genes involved in reproduction. The expression profile of post-reproductive adults was distinct from that of other life stages. While few genes were significantly differentially expressed in the late- to post-reproductive transition, gene set enrichment analysis revealed multiple down-regulated pathways in metabolism, maintenance and repair, and proteostasis, united by genes involved in mitochondrial function and oxidative phosphorylation. This study provides the first examination of changes in gene expression over lifespan in rotifers. We detected differential expression of many genes with human orthologs that are absent in Drosophila and C. elegans, highlighting the potential of the rotifer model in aging studies. Our findings suggest that small but coordinated changes in expression of many genes in pathways that integrate diverse functions drive the aging process. The observation of simultaneous declines in expression of genes in multiple pathways may have consequences for health and longevity not detected by single- or multi-gene knockdown in otherwise healthy animals. Investigation of subtle but genome-wide change in these pathways during aging is an important area for future study.
    Description: Funding for this project was provided by R01 AG037960-01, the American Federation for Aging Research, and the Bay and Paul Foundations.
    Keywords: Aging ; Rotifer ; Monogonont ; RNA-Seq ; Transcriptome
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    Fukushima Daiichi–derived radionuclides in the ocean : transport, fate, and impacts (2017)
    Annual Reviews
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Description: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Description: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Keywords: Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
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    Eutrophication governs predator-prey interactions and temperature effects in Aedes aegypti populations. (2019)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Krol, L., Gorsich, E. E., Hunting, E. R., Govender, D., van Bodegom, P. M., & Schrama, M. Eutrophication governs predator-prey interactions and temperature effects in Aedes aegypti populations. Parasites & Vectors, 12(1), (2019):179, doi:10.1186/s13071-019-3431-x.
    Description: Background Mosquito population dynamics are driven by large-scale (e.g. climatological) and small-scale (e.g. ecological) factors. While these factors are known to independently influence mosquito populations, it remains uncertain how drivers that simultaneously operate under natural conditions interact to influence mosquito populations. We, therefore, developed a well-controlled outdoor experiment to assess the interactive effects of two ecological drivers, predation and nutrient availability, on mosquito life history traits under multiple temperature regimes. Methods We conducted a temperature-controlled mesocosm experiment in Kruger National Park, South Africa, with the yellow fever mosquito, Aedes aegypti. We investigated how larval survival, emergence and development rates were impacted by the presence of a locally-common invertebrate predator (backswimmers Anisops varia Fieber (Notonectidae: Hemiptera), nutrient availability (oligotrophic vs eutrophic, reflecting field conditions), water temperature, and interactions between each driver. Results We observed that the effects of predation and temperature both depended on eutrophication. Predation caused lower adult emergence in oligotrophic conditions but higher emergence under eutrophic conditions. Higher temperatures caused faster larval development rates in eutrophic but not oligotrophic conditions. Conclusions Our study shows that ecological bottom-up and top-down drivers strongly and interactively govern mosquito life history traits for Ae. aegypti populations. Specifically, we show that eutrophication can inversely affect predator–prey interactions and mediate the effect of temperature on mosquito survival and development rates. Hence, our results suggest that nutrient pollution can overrule biological constraints on natural mosquito populations and highlights the importance of studying multiple factors.
    Description: This study was supported by the Gratama Fund, Grant Number 2016.08, which was awarded to MS, supported by the Uyttenboogaart-Eliasen foundation for comparative entomology, Grant No. SUB.2016.12.08 and the RCN-IDEAS grant which was awarded to EEG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Keywords: Ecological drivers ; Vector-borne ; Anthropogenic pressures ; Interaction effects ; Temperature ; Biodiversity decline
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    Infrared Spectroscopic Observations of the Outer Planets, their Satellites, and the Asteroids (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 43-75 
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    Topics: Physics
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    Formation of the Terrestrial Planets (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 77-113 
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    Stellar Masses (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 115-164 
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    Stellar Chromospheres (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 439-488 
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    The Structure of Extended Extragalactic Radio Sources (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 165-218 
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    Microwave Background Radiation as a Probe of the Contemporary Structure and History of the Universe (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 537-560 
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    Abundances in Stellar Populations and the Interstellar Medium in Galaxies (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 19 (1981), S. 77-113 
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    The Chemical Composition, Structure, and Dynamics of Globular Clusters (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 19 (1981), S. 319-356 
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    The Evolution of Galaxies in Clusters (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 185-222 
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    Sagittarius a and its Environment (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 223-265 
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    Coronal Mass Ejections (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 267-289 
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    Astronomical Fourier Transform Spectroscopy Revisited (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 291-317 
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    Extragalactic Radio Jets (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 319-358 
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    High-Energy Neutral Radiations from the Sun (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 359-387 
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    Origin and History of the Outer Planets: Theoretical Models and Observational Constraints (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 389-424 
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    The Origin of Ultra-High-Energy Cosmic Rays (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 425-444 
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    The Influence of Environment on the HI Content of Galaxies (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 445-470 
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    Black Hole Models for Active Galactic Nuclei (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 471-506 
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    Observations of SS 433 (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 507-536 
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    Neutron Stars in Interacting Binary Systems (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 537-592 
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    Helioseismology: Oscillations as a Diagnostic of the Solar Interior (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 593-619 
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    Model Atmospheres (1965)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 3 (1965), S. 135-216 
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    Chemical Evidence Bearing on the Origin of the Solar System (1965)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 3 (1965), S. 217-234 
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    Cosmic Magnetobremsstrahlung (Synchrotron Radiation) (1965)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 3 (1965), S. 297-350 
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    Radar Astronomy (1965)
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    Annual Review of Astronomy and Astrophysics 3 (1965), S. 377-411 
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    Gamma Radiation from Celestial Objects (1967)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 5 (1967), S. 481-524 
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    The Dynamics of Disk-Shaped Galaxies (1967)
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    Annual Review of Astronomy and Astrophysics 5 (1967), S. 453-464 
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    Thermonuclear Reaction Rates (1967)
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    Annual Review of Astronomy and Astrophysics 5 (1967), S. 525-570 
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    The Structure of Sunspots (1968)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 6 (1968), S. 135-164 
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    Variable Radio Sources (1968)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 6 (1968), S. 417-448 
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    Cosmic Rays in the Galaxy (1969)
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 1-38 
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    The Large-Scale Distribution of Hydrogen in the Galaxy (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 39-66 
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    X Rays from the Sun (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 121-148 
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    Radar Studies of Planetary Surfaces (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 201-248 
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    The Interiors of the Planets (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 177-200 
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    Motions of Planetary Atmospheres (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 303-352 
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    The Moon's Surface (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 473-526 
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    High-Resolution Observations of Radio Sources (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 7 (1969), S. 619-664 
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    Water Transport in Soils (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 77-102 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Transonic Flow Past Oscillating Airfoils (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 181-222 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Scientific Progress on Fire (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 223-236 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Toward a Statistical Theory of Suspension (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 237-269 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Coastal Circulation and Wind-Induced Currents (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 271-301 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Models of Wind-Driven Currents on the Continental Shelf (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 389-433 
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    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Stokeslets and Eddies in Creeping Flow (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 335-363 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Continuous Drawing of Liquids to Form Fibers (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 365-387 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Particle Motions in a Viscous Fluid (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 12 (1980), S. 435-476 
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    My Early Aerodynamic Research Thoughts and Memories (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 13 (1981), S. 1-8 
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    Existence Theorems for the Equations of Motion of a Compressible Viscous Fluid (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 13 (1981), S. 79-95 
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    Meniscus Stability (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 13 (1981), S. 189-216 
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    Field-Flow Fractionation (Polarization Chromatography) (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 13 (1981), S. 351-378 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Frazil Ice in Rivers and Oceans (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 13 (1981), S. 379-397 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Vilhelm Bjerknes and his Students (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 1-12 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Sediment Ripples and Dunes (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 13-37 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Topology of Three-Dimensional Separated Flows (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 61-85 
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    Dynamics of Lakes, Reservoirs, and Cooling Ponds (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 153-187 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Turbulent Jets and Plumes (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 189-212 
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    The Computation of Transonic Potential Flows (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 261-283 
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    The Fluid Dynamics of Heart Valves: Experimental, Theoretical, and Computational Methods (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 235-259 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Dynamics of Oil Ganglia During Immiscible Displacement in Water-Wet Porous Media (1982)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 14 (1982), S. 365-393 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    The Deformation of Small Viscous Drops and Bubbles in Shear Flows (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 16 (1984), S. 45-66 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Wave Action and Wave-Mean Flow Interaction, with Application to Stratified Shear Flows (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 16 (1984), S. 11-44 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Numerical Simulation of Turbulent Flows (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 16 (1984), S. 99-137 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Computer-Extended Series (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 16 (1984), S. 287-309 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Dynamic Parameters of Gaseous Detonations (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 16 (1984), S. 311-336 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Perturbed Free Shear Layers (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 16 (1984), S. 365-422 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Stratified Flows (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 1 (1969), S. 73-110 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Hydrodynamic Noise (1969)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 1 (1969), S. 197-222 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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