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  • BioMed Central  (79,508)
  • 2015-2019  (39,847)
  • 2010-2014  (39,661)
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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
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  • 2
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    Ecological comparison of cellular stress responses among populations – normalizing RT-qPCR values to investigate differential environmental adaptations (2013)
    BioMed Central
    In:  EPIC3BMC Ecology, BioMed Central, 13(1), pp. 21, ISSN: 1472-6785
    Details
    Publication Date: 2019-07-16
    Description: Background: Rising temperatures and other environmental factors influenced by global climate change can cause increased physiological stress for many species and lead to range shifts or regional population extinctions. To advance the understanding of species’ response to change and establish links between individual and ecosystem adaptations, physiological reactions have to be compared between populations living in different environments. Although changes in expression of stress genes are relatively easy to quantify, methods for reliable comparison of the data remain a contentious issue. Using normalization algorithms and further methodological considerations, we compare cellular stress response gene expression levels measured by RT-qPCR after air exposure experiments among different subpopulations of three species of the intertidal limpet Nacella. Results: Reference gene assessment algorithms reveal that stable reference genes can differ among investigated populations and / or treatment groups. Normalized expression values point to differential defense strategies to air exposure in the investigated populations, which either employ a pronounced cellular stress response in the inducible Hsp70 forms, or exhibit a comparatively high constitutive expression of Hsps (heat shock proteins) while showing only little response in terms of Hsp induction. Conclusions: This study serves as a case study to explore the methodological prerequisites of physiological stress response comparisons among ecologically and phylogenetically different organisms. To improve the reliability of gene expression data and compare the stress responses of subpopulations under potential genetic divergence, reference gene stability algorithms are valuable and necessary tools. As the Hsp70 isoforms have been shown to play different roles in the acute stress responses and increased constitutive defenses of populations in their different habitats, these comparative studies can yield insight into physiological strategies of adaptation to environmental stress and provide hints for the prudent use of the cellular stress response as a biomarker to study environmental stress and stress adaptation of populations under changing environmental conditions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 3
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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)
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    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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  • 4
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    Data hosting infrastructure for primary biodiversity data (2012)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 12 Suppl. 15 (2011): S5, doi:10.1186/1471-2105-12-S15-S5.
    Description: Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized.
    Repository Name: Woods Hole Open Access Server
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  • 5
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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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  • 6
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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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  • 7
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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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  • 8
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    Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection (2013)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Microbiology 13 (2013): 150, doi:10.1186/1471-2180-13-150.
    Description: Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group. Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins. Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The “isolated island character” of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).
    Description: This work was funded by NSF grants OCE-0849578 and OCE- 1061774 to VE and support from Carl Zeiss fellowship to AS and from the Deutsche Forschungsgemeinschaft (grants STO414/3-2 and STO414/7-1) to TS.
    Keywords: Ciliates ; Hypersaline ; Deep-sea anoxic basins ; DHABs ; Brine ; Species sorting ; Environmental filtering ; Niche separation
    Repository Name: Woods Hole Open Access Server
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  • 9
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    The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales (2013)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 13 (2013): 187, doi:10.1186/1471-2148-13-187.
    Description: We recently reported (Curr Biol 22:683–688, 2012) that the eyes of giant and colossal squid can grow to three times the diameter of the eyes of any other animal, including large fishes and whales. As an explanation to this extreme absolute eye size, we developed a theory for visual performance in aquatic habitats, leading to the conclusion that the huge eyes of giant and colossal squid are uniquely suited for detection of sperm whales, which are important squid-predators in the depths where these squid live. A paper in this journal by Schmitz et al. (BMC Evol Biol 13:45, 2013) refutes our conclusions on the basis of two claims: (1) using allometric data they argue that the eyes of giant and colossal squid are not unexpectedly large for the size of the squid, and (2) a revision of the values used for modelling indicates that large eyes are not better for detection of approaching sperm whales than they are for any other task. We agree with Schmitz et al. that their revised values for intensity and abundance of planktonic bioluminescence may be more realistic, or at least more appropriately conservative, but argue that their conclusions are incorrect because they have not considered some of the main arguments put forward in our paper. We also present new modelling to demonstrate that our conclusions remain robust, even with the revised input values suggested by Schmitz et al.
    Keywords: Vision ; Eyes ; Giant squid ; Sperm whale ; Bioluminescence ; Mesopelagic
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families (2013)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mobile DNA 4 (2013): 19, doi:10.1186/1759-8753-4-19.
    Description: Penelope-like elements (PLEs) are an enigmatic group of retroelements sharing a common ancestor with telomerase reverse transcriptases. In our previous studies, we identified endonuclease-deficient PLEs that are associated with telomeres in bdelloid rotifers, small freshwater invertebrates best known for their long-term asexuality and high foreign DNA content. Completion of the high-quality draft genome sequence of the bdelloid rotifer Adineta vaga provides us with the opportunity to examine its genomic transposable element (TE) content, as well as TE impact on genome function and evolution. We performed an exhaustive search of the A. vaga genome assembly, aimed at identification of canonical PLEs combining both the reverse transcriptase (RT) and the GIY-YIG endonuclease (EN) domains. We find that the RT/EN-containing Penelope families co-exist in the A. vaga genome with the EN-deficient RT-containing Athena retroelements. Canonical PLEs are present at very low copy numbers, often as a single-copy, and there is no evidence that they might preferentially co-mobilize EN-deficient PLEs. We also find that Penelope elements can participate in expansion of A. vaga multigene families via trans-action of their enzymatic machinery, as evidenced by identification of intron-containing host genes framed by the Penelope terminal repeats and characteristic target-site duplications generated upon insertion. In addition, we find that Penelope open reading frames (ORFs) in several families have incorporated long stretches of coding sequence several hundred amino acids (aa) in length that are highly enriched in asparagine residues, a phenomenon not observed in other retrotransposons. Our results show that, despite their low abundance and low transcriptional activity in the A. vaga genome, endonuclease-containing Penelope elements can participate in expansion of host multigene families. We conclude that the terminal repeats represent the cis-acting sequences required for mobilization of the intervening region in trans by the Penelope-encoded enzymatic activities. We also hypothesize that the unusual capture of long N-rich segments by the Penelope ORF occurs as a consequence of peculiarities of its replication mechanism. These findings emphasize the unconventional nature of Penelope retrotransposons, which, in contrast to all other retrotransposon types, are capable of dispersing intron-containing genes, thereby questioning the validity of traditional estimates of gene retrocopies in PLE-containing eukaryotic genomes.
    Description: This research was supported by grants MCB-0821956 and MCB-1121334 from the U.S. National Science Foundation to I.A.
    Keywords: Retrotransposon ; Reverse transcriptase ; GIY-YIG endonuclease
    Repository Name: Woods Hole Open Access Server
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  • 11
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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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  • 12
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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
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  • 13
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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
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  • 14
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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
    Repository Name: Woods Hole Open Access Server
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  • 15
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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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  • 16
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    The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex (2012)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 12 (2012): 134, doi:10.1186/1471-2148-12-134.
    Description: Chemically mediated prezygotic barriers to reproduction likely play an important role in speciation. In facultatively sexual monogonont rotifers from the Brachionus plicatilis cryptic species complex, mate recognition of females by males is mediated by the Mate Recognition Protein (MRP), a globular glycoprotein on the surface of females, encoded by the mmr-b gene family. In this study, we sequenced mmr-b copies from 27 isolates representing 11 phylotypes of the B. plicatilis species complex, examined the mode of evolution and selection of mmr-b, and determined the relationship between mmr-b genetic distance and mate recognition among isolates. Isolates of the B. plicatilis species complex have 1–4 copies of mmr-b, each composed of 2–9 nearly identical tandem repeats. The repeats within a gene copy are generally more similar than are gene copies among phylotypes, suggesting concerted evolution. Compared to housekeeping genes from the same isolates, mmr-b has accumulated only half as many synonymous differences but twice as many non-synonymous differences. Most of the amino acid differences between repeats appear to occur on the outer face of the protein, and these often result in changes in predicted patterns of phosphorylation. However, we found no evidence of positive selection driving these differences. Isolates with the most divergent copies were unable to mate with other isolates and rarely self-crossed. Overall the degree of mate recognition was significantly correlated with the genetic distance of mmr-b. Discrimination of compatible mates in the B. plicatilis species complex is determined by proteins encoded by closely related copies of a single gene, mmr-b. While concerted evolution of the tandem repeats in mmr-b may function to maintain identity, it can also lead to the rapid spread of a mutation through all copies in the genome and thus to reproductive isolation. The mmr-b gene is evolving rapidly, and novel alleles may be maintained and increase in frequency via asexual reproduction. Our analyses indicate that mate recognition, controlled by MMR-B, may drive reproductive isolation and allow saltational sympatric speciation within the B. plicatilis cryptic species complex, and that this process may be largely neutral.
    Description: This work was supported by the National Science Foundation grant BE/GenEn MCG- 0412647.
    Keywords: Mate recognition ; Reproductive isolation ; Speciation ; Concerted evolution ; Gene family
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  • 17
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    Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology (2013)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 12 (2012): 209, doi:10.1186/1471-2148-12-209.
    Description: Marine phytoplankton drift passively with currents, have high dispersal potentials and can be comprised of morphologically cryptic species. To examine molecular subdivision in the marine diatom Thalassiosira rotula, variations in rDNA sequence, genome size, and growth rate were examined among isolates collected from the Atlantic and Pacific Ocean basins. Analyses of rDNA included T. gravida because morphological studies have argued that T. rotula and T. gravida are conspecific. Culture collection isolates of T. gravida and T. rotula diverged by 7.0 ± 0.3% at the ITS1 and by 0.8 ± 0.03% at the 28S. Within T. rotula, field and culture collection isolates were subdivided into three lineages that diverged by 0.6 ± 0.3% at the ITS1 and 0% at the 28S. The predicted ITS1 secondary structure revealed no compensatory base pair changes among lineages. Differences in genome size were observed among isolates, but were not correlated with ITS1 lineages. Maximum acclimated growth rates of isolates revealed genotype by environment effects, but these were also not correlated with ITS1 lineages. In contrast, intra-individual variation in the multi-copy ITS1 revealed no evidence of recombination amongst lineages, and molecular clock estimates indicated that lineages diverged 0.68 Mya. The three lineages exhibited different geographic distributions and, with one exception, each field sample was dominated by a single lineage. The degree of inter- and intra-specific divergence between T. gravida and T. rotula suggests they should continue to be treated as separate species. The phylogenetic distinction of the three closely-related T. rotula lineages was unclear. On the one hand, the lineages showed no physiological differences, no consistent genome size differences and no significant changes in the ITS1 secondary structure, suggesting there are no barriers to interbreeding among lineages. In contrast, analysis of intra-individual variation in the multicopy ITS1 as well as molecular clock estimates of divergence suggest these lineages have not interbred for significant periods of time. Given the current data, these lineages should be considered a single species. Furthermore, these T. rotula lineages may be ecologically relevant, given their differential abundance over large spatial scales.
    Description: This research was supported by National Science Foundation grants, NSF 0727227 (to TAR) and NSF SBE0245039 (to URI, TAR). Part of the research was conducted using instrumentation supported by NSF-EPSCoR grants 0554548 and 1004057.
    Keywords: Phytoplankton ; Phylogeography ; Dispersal ; Physiology ; Intraspecific diversity
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  • 18
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    The taxonomic name resolution service : an online tool for automated standardization of plant names (2013)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.
    Description: The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.
    Description: BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191).
    Keywords: Biodiversity informatics ; Database integration ; Taxonomy ; Plants
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    Genomic impact of eukaryotic transposable elements (2013)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mobile DNA 3 (2012): 19, doi:10.1186/1759-8753-3-19.
    Description: The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.
    Description: The conference was supported in part by the National Institutes of Health grant 5 P41 LM006252.
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  • 20
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    Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum (2015)
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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
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    ITAG : an eco-sensor for fine-scale behavioral measurements of soft-bodied marine invertebrates (2016)
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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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    Meeting report of Ctenopalooza : the first international meeting of ctenophorologists (2016)
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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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    High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus (2010)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 559, doi:10.1186/1471-2164-11-559.
    Description: Bathymodiolus azoricus is a deep-sea hydrothermal vent mussel found in association with large faunal communities living in chemosynthetic environments at the bottom of the sea floor near the Azores Islands. Investigation of the exceptional physiological reactions that vent mussels have adopted in their habitat, including responses to environmental microbes, remains a difficult challenge for deep-sea biologists. In an attempt to reveal genes potentially involved in the deep-sea mussel innate immunity we carried out a high-throughput sequence analysis of freshly collected B. azoricus transcriptome using gills tissues as the primary source of immune transcripts given its strategic role in filtering the surrounding waterborne potentially infectious microorganisms. Additionally, a substantial EST data set was produced and from which a comprehensive collection of genes coding for putative proteins was organized in a dedicated database, "DeepSeaVent" the first deep-sea vent animal transcriptome database based on the 454 pyrosequencing technology. A normalized cDNA library from gills tissue was sequenced in a full 454 GS-FLX run, producing 778,996 sequencing reads. Assembly of the high quality reads resulted in 75,407 contigs of which 3,071 were singletons. A total of 39,425 transcripts were conceptually translated into amino-sequences of which 22,023 matched known proteins in the NCBI non-redundant protein database, 15,839 revealed conserved protein domains through InterPro functional classification and 9,584 were assigned with Gene Ontology terms. Queries conducted within the database enabled the identification of genes putatively involved in immune and inflammatory reactions which had not been previously evidenced in the vent mussel. Their physical counterpart was confirmed by semi-quantitative quantitative Reverse-Transcription-Polymerase Chain Reactions (RT-PCR) and their RNA transcription level by quantitative PCR (qPCR) experiments. We have established the first tissue transcriptional analysis of a deep-sea hydrothermal vent animal and generated a searchable catalog of genes that provides a direct method of identifying and retrieving vast numbers of novel coding sequences which can be applied in gene expression profiling experiments from a non-conventional model organism. This provides the most comprehensive sequence resource for identifying novel genes currently available for a deep-sea vent organism, in particular, genes putatively involved in immune and inflammatory reactions in vent mussels. The characterization of the B. azoricus transcriptome will facilitate research into biological processes underlying physiological adaptations to hydrothermal vent environments and will provide a basis for expanding our understanding of genes putatively involved in adaptations processes during post-capture long term acclimatization experiments, at "sea-level" conditions, using B. azoricus as a model organism.
    Description: We acknowledge the Portuguese Foundation for Science and Technology, FCT-Lisbon and the Regional Azorean Directorate for Science and Technology, DRCT-Azores, for pluri-annual and programmatic PIDDAC and FEDER funding to IMAR/DOP Research Unit #531 and the Associated Laboratory #9 (ISR-Lisboa); the Luso-American Foundation FLAD (Project L-V- 173/2006); the Biotechnology and Biomedicine Institute of the Azores (IBBA), project M.2.1.2/I/029/2008-BIODEEPSEA and the project n° FCOMP-01-0124- FEDER-007376 (ref: FCT PTDC/MAR/65991/2006-IMUNOVENT; coordinated by RB) under the auspices of the COMPETE program.
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    Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates (2012)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Systems Biology 5 Suppl 2 (2011): S15, doi:10.1186/1752-0509-5-S2-S15.
    Description: The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa
    Description: This research is partially supported by the National Science Foundation (NSF) DMS-1043075 and OCE 1136818.
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    A quantitative reference transcriptome for Nematostella vectensis early embryonic development : a pipeline for de novo assembly in emerging model systems (2013)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in EvoDevo 4 (2013): 16, doi:10.1186/2041-9139-4-16.
    Description: The de novo assembly of transcriptomes from short shotgun sequences raises challenges due to random and non-random sequencing biases and inherent transcript complexity. We sought to define a pipeline for de novo transcriptome assembly to aid researchers working with emerging model systems where well annotated genome assemblies are not available as a reference. To detail this experimental and computational method, we used early embryos of the sea anemone, Nematostella vectensis, an emerging model system for studies of animal body plan evolution. We performed RNA-seq on embryos up to 24 h of development using Illumina HiSeq technology and evaluated independent de novo assembly methods. The resulting reads were assembled using either the Trinity assembler on all quality controlled reads or both the Velvet and Oases assemblers on reads passing a stringent digital normalization filter. A control set of mRNA standards from the National Institute of Standards and Technology (NIST) was included in our experimental pipeline to invest our transcriptome with quantitative information on absolute transcript levels and to provide additional quality control. We generated 〉200 million paired-end reads from directional cDNA libraries representing well over 20 Gb of sequence. The Trinity assembler pipeline, including preliminary quality control steps, resulted in more than 86% of reads aligning with the reference transcriptome thus generated. Nevertheless, digital normalization combined with assembly by Velvet and Oases required far less computing power and decreased processing time while still mapping 82% of reads. We have made the raw sequencing reads and assembled transcriptome publically available. Nematostella vectensis was chosen for its strategic position in the tree of life for studies into the origins of the animal body plan, however, the challenge of reference-free transcriptome assembly is relevant to all systems for which well annotated gene models and independently verified genome assembly may not be available. To navigate this new territory, we have constructed a pipeline for library preparation and computational analysis for de novo transcriptome assembly. The gene models defined by this reference transcriptome define the set of genes transcribed in early Nematostella development and will provide a valuable dataset for further gene regulatory network investigations.
    Keywords: Transcriptome ; Gene regulatory network ; Nematostella embryonic development ; Body plan evolution ; Next-generation sequencing ; Illumina HiSeq ; Trinity ; Oases ; RNA-seq
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    Athletic equipment microbiota are shaped by interactions with human skin (2015)
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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)
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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
    Repository Name: Woods Hole Open Access Server
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    Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis (2014)
    BioMed Central
    In:  EPIC3BMC Genomics, BioMed Central, 15(1), pp. 1051
    Details
    Publication Date: 2015-01-05
    Description: BACKGROUND: Global change will affect patterns of nutrient upwelling in marine environments, potentially becoming even stricter regulators of phytoplankton primary productivity. To better understand phytoplankton nutrient utilization on the subcellular basis, we assessed the transcriptomic responses of the life-cycle stages of the biogeochemically important microalgae Emiliania huxleyi to nitrogen limitation. Cells grown in batch cultures were harvested at 'early' and 'full' nitrogen limitation and were compared with non-limited cells. We applied microarray-based transcriptome profilings, covering ~10.000 known E. huxleyi gene models, and screened for expression patterns that indicate the subcellular responses. RESULTS: The diploid life-cycle stage scavenges nitrogen from external organic sources and -like diatoms- uses the ornithine-urea cycle to rapidly turn over cellular nitrogen. The haploid stage reacts similarly, although nitrogen scavenging is less pronounced and lipid oxidation is more prominent. Generally, polyamines and proline appear to constitute major organic pools that back up cellular nitrogen. Both stages induce a malate:quinone-oxidoreductase that efficiently feeds electrons into the respiratory chain and drives ATP generation with reduced respiratory carbon throughput. CONCLUSIONS: The use of the ornithine-urea cycle to budget the cellular nitrogen in situations of limitation resembles the responses observed earlier in diatoms. This suggests that underlying biochemical mechanisms are conserved among distant clades of marine phototrophic protists. The ornithine-urea cycle and proline oxidation appear to constitute a sensory-regulatory system that monitors and controls cellular nitrogen budgets under limitation. The similarity between the responses of the life-cycle stages, despite the usage of different genes, also indicates a strong functional consistency in the responses to nitrogen-limitation that appears to be owed to biochemical requirements. The malate:quinone-oxidoreductase is a genomic feature that appears to be absent from diatom genomes, and it is likely to strongly contribute to the uniquely high endurance of E. huxleyi under nutrient limitation.
    Repository Name: EPIC Alfred Wegener Institut
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    Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish (2011)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 643, doi:10.1186/1471-2164-11-643.
    Description: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.
    Description: This work was supported by NIH grants R01ES015912 and P42ES007381 (Superfund Basic Research Program at Boston University) (to JJS). MEJ was a Guest Investigator at the Woods Hole Oceanographic Institution (WHOI) and was supported by grants from the Swedish research council Formas and Carl Trygger's foundation. AK was a Post-doctoral Fellow at WHOI, and was supported by a fellowship from the Japanese Society for Promotion of Science (JSPS). JZ and TP were Guest Students at the WHOI and were supported by a CAPES Ph.D. Fellowship and CNPq Ph.D. Sandwich Fellowship (JZ), and by a CNPq Ph.D. Fellowship (TP), from Brazil.
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    Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production (2013)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 14 (2013): 412, doi:10.1186/1471-2164-14-412.
    Description: Sexual reproduction is a widely studied biological process because it is critically important to the genetics, evolution, and ecology of eukaryotes. Despite decades of study on this topic, no comprehensive explanation has been accepted that explains the evolutionary forces underlying its prevalence and persistence in nature. Monogonont rotifers offer a useful system for experimental studies relating to the evolution of sexual reproduction due to their rapid reproductive rate and close relationship to the putatively ancient asexual bdelloid rotifers. However, little is known about the molecular underpinnings of sex in any rotifer species. We generated mRNA-seq libraries for obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of the monogonont rotifer, Brachionus calyciflorus, to identify genes specific to both modes of reproduction. Our differential expression analysis identified receptors with putative roles in signaling pathways responsible for the transition from asexual to sexual reproduction. Differential expression of a specific copy of the duplicated cell cycle regulatory gene CDC20 and specific copies of histone H2A suggest that such duplications may underlie the phenotypic plasticity required for reproductive mode switch in monogononts. We further identified differential expression of genes involved in the formation of resting eggs, a process linked exclusively to sex in this species. Finally, we identified transcripts from the bdelloid rotifer Adineta ricciae that have significant sequence similarity to genes with higher expression in CP strains of B. calyciflorus. Our analysis of global gene expression differences between facultatively sexual and exclusively asexual populations of B. calyciflorus provides insights into the molecular nature of sexual reproduction in rotifers. Furthermore, our results offer insight into the evolution of obligate asexuality in bdelloid rotifers and provide indicators important for the use of monogononts as a model system for investigating the evolution of sexual reproduction.
    Description: This work was funded by National Institutes of Health Institute of General Medical Sciences (grant number 5R01GM079484, to JML and DMW).
    Keywords: Evolution of sexual reproduction ; Differential expression analysis ; Gene ontology analysis ; Meiosis ; Gametogenesis ; Resting eggs ; Mixis induction
    Repository Name: Woods Hole Open Access Server
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    VAMPS : a website for visualization and analysis of microbial population structures (2014)
    BioMed Central
    Details
    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 BMC Bioinformatics 15 (2014): 41, doi:10.1186/1471-2105-15-41.
    Description: The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
    Description: Funding provided by the National Science Foundation [grant NSF/BDI 0960626 to SMH] and the Sloan Foundation through a collaborative project with the Microbiology of the Built Environment program.
    Keywords: Microbiome ; Microbial ecology ; Microbial diversity ; Data visualization ; Website ; Bacteria ; SSU rRNA ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
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    Scientific names of organisms : attribution, rights, and licensing (2014)
    BioMed Central
    Details
    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 BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.
    Description: As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.
    Keywords: Scientific names ; Taxonomy ; Copyright ; Intellectual property rights ; Name-based infrastructure ; Big data
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    Forensic analysis of the microbiome of phones and shoes (2015)
    BioMed Central
    Details
    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
    Repository Name: Woods Hole Open Access Server
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    The ocean sampling day consortium (2015)
    BioMed Central
    Details
    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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    Characterization of differential transcript abundance through time during Nematostella vectensis development (2013)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 14 (2013): 266, doi:10.1186/1471-2164-14-266.
    Description: Nematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vectensis development with in situ mRNA hybridization. This has provided detailed spatial resolution and a qualitative perspective on changes in expression. However, little is known about broad transcriptome-level patterns of gene expression through time. Here we examine the expression of N. vectensis genes through the course of development with quantitative RNA-seq. We provide an overview of changes in the transcriptome through development, and examine the maternal to zygotic transition, which has been difficult to investigate with other tools. We measured transcript abundance in N. vectensis with RNA-seq at six time points in development: zygote (2 hours post fertilization (HPF)), early blastula (7 HPF), mid-blastula (12 HPF), gastrula (24 HPF), planula (5 days post fertilization (DPF)) and young polyp (10 DPF). The major wave of zygotic expression appears between 7–12 HPF, though some changes occur between 2–7 HPF. The most dynamic changes in transcript abundance occur between the late blastula and early gastrula stages. More transcripts are upregulated between the gastrula and planula than downregulated, and a comparatively lower number of transcripts significantly change between planula and polyp. Within the maternal to zygotic transition, we identified a subset of maternal factors that decrease early in development, and likely play a role in suppressing zygotic gene expression. Among the first genes to be expressed zygotically are genes whose proteins may be involved in the degradation of maternal RNA. The approach presented here is highly complementary to prior studies on spatial patterns of gene expression, as it provides a quantitative perspective on a broad set of genes through time but lacks spatial resolution. In addition to addressing the problems identified above, our work provides an annotated matrix that other investigators can use to examine genes and developmental events that we do not examine in detail here.
    Description: This work was supported by seed funds from the Brown-MBL Partnership and the National Science Foundation Graduate Student Research Fellowship. Infrastructure for data transfer from the sequencer was supported by the National Science Foundation EPSCoR Program under Grant No. 1004057 (Infrastructure to Advance Life Sciences in the Ocean State).
    Keywords: Nematostella vectensis ; Transcriptome ; Gene expression ; Maternal to zygotic transition ; Development
    Repository Name: Woods Hole Open Access Server
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    Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats (2014)
    BioMed Central
    Details
    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 BMC Evolutionary Biology 14 (2014): 6, doi:10.1186/1471-2148-14-6.
    Description: The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other “dioxin-like compounds” (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.
    Description: This work was supported in part by the Hudson River Foundation (grant 004/02A; final report available at http://www.hudsonriver.org/ls/), by National Institute of Environmental Health Sciences (NIEHS) grant P42ES007381 (Superfund Basic Research Program at Boston University), by grant F32HD062178 from the Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHHD), and by the National Science Foundation (DEB-1120263). Data interpretation was aided by reference to a preliminary draft of the F. heteroclitus genome sequence, which was supported by funding from the National Science Foundation (collaborative research grants DEB-1120512, DEB-1265282, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398).
    Keywords: Local adaptation ; Pollution ; Molecular mechanism ; Resistance ; Tolerance ; Convergent evolution ; Population genetics
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    Comparisons of Shewanella strains based on genome annotations, modeling, and experiments (2014)
    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 BMC Systems Biology 8 (2014): 31, doi:10.1186/1752-0509-8-31.
    Description: Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains. In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels – for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models. We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.
    Description: This work was funded by a grant from the NSF (NSF 1053712) and was also supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), U.S. Department of Energy, and is a contribution of the PNNL Biofuels Scientific Focus Area (BSFA) and the PNNL Foundational Scientific Focus Area (FSFA).
    Keywords: Constraint-based model ; Electron acceptors ; Phenotype ; FBA
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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)
    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 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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    One nutritional symbiosis begat another : Phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects (2010)
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    Publication Date: 2022-05-26
    Description: © 2009 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 9 (2009): 292, doi:10.1186/1471-2148-9-292.
    Description: Bacterial endosymbiosis has a recurring significance in the evolution of insects. An estimated 10-20% of insect species depend on bacterial associates for their nutrition and reproductive viability. Members of the ant tribe Camponotini, the focus of this study, possess a stable, intracellular bacterial mutualist. The bacterium, Blochmannia, was first discovered in Camponotus and has since been documented in a distinct subgenus of Camponotus, Colobopsis, and in the related genus Polyrhachis. However, the distribution of Blochmannia throughout the Camponotini remains in question. Documenting the true host range of this bacterial mutualist is an important first step toward understanding the various ecological contexts in which it has evolved, and toward identifying its closest bacterial relatives. In this study, we performed a molecular screen, based on PCR amplification of 16S rDNA, to identify bacterial associates of diverse Camponotini species. Phylogenetic analyses of 16S rDNA gave four important insights: (i) Blochmannia occurs in a broad range of Camponotini genera including Calomyrmex, Echinopla, and Opisthopsis, and did not occur in outgroups related to this tribe (e.g., Notostigma). This suggests that the mutualism originated in the ancestor of the tribe Camponotini. (ii) The known bacteriocyte-associated symbionts of ants, in Formica, Plagiolepis, and the Camponotini, arose independently. (iii) Blochmannia is nestled within a diverse clade of endosymbionts of sap-feeding hemipteran insects, such as mealybugs, aphids, and psyllids. In our analyses, a group of secondary symbionts of mealybugs are the closest relatives of Blochmannia. (iv) Blochmannia has cospeciated with its known hosts, although deep divergences at the genus level remain uncertain. The Blochmannia mutualism occurs in Calomyrmex, Echinopla, and Opisthopsis, in addition to Camponotus, and probably originated in the ancestral lineage leading to the Camponotini. This significant expansion of its known host range implies that the mutualism is more ancient and ecologically diverse than previously documented. Blochmannia is most closely related to endosymbionts of sap-feeding hemipterans, which ants tend for their carbohydrate-rich honeydew. Based on phylogenetic results, we propose Camponotini might have originally acquired this bacterial mutualist through a nutritional symbiosis with other insects.
    Description: Funding for this research was provided by grants from the NSF (MCB-0604177) and NIH (R01GM062626) to JJW, and from the NSF-supported Ant AToL project (EF-0431330) to PSW and SGB.
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    Cytochrome P450 diversity and induction by gorgonian allelochemicals in the marine gastropod Cyphoma gibbosum (2011)
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    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Ecology 10 (2010): 24, doi:10.1186/1472-6785-10-24.
    Description: Intense consumer pressure strongly affects the structural organization and function of marine ecosystems, while also having a profound effect on the phenotype of both predator and prey. Allelochemicals produced by prey often render their tissues unpalatable or toxic to a majority of potential consumers, yet some marine consumers have evolved resistance to host chemical defenses. A key challenge facing marine ecologists seeking to explain the vast differences in consumer tolerance of dietary allelochemicals is understanding the biochemical and molecular mechanisms underlying diet choice. The ability of marine consumers to tolerate toxin-laden prey may involve the cooperative action of biotransformation enzymes, including the inducible cytochrome P450s (CYPs), which have received little attention in marine invertebrates despite the importance of allelochemicals in their evolution. Here, we investigated the diversity, transcriptional response, and enzymatic activity of CYPs possibly involved in allelochemical detoxification in the generalist gastropod Cyphoma gibbosum, which feeds exclusively on chemically defended gorgonians. Twelve new genes in CYP family 4 were identified from the digestive gland of C. gibbosum. Laboratory-based feeding studies demonstrated a 2.7- to 5.1-fold induction of Cyphoma CYP4BK and CYP4BL transcripts following dietary exposure to the gorgonian Plexaura homomalla, which contains high concentrations of anti-predatory prostaglandins. Phylogenetic analysis revealed that C. gibbosum CYP4BK and CYP4BL were most closely related to vertebrate CYP4A and CYP4F, which metabolize pathophysiologically important fatty acids, including prostaglandins. Experiments involving heterologous expression of selected allelochemically-responsive C. gibbosum CYP4s indicated a possible role of one or more CYP4BL forms in eicosanoid metabolism. Sequence analysis further demonstrated that Cyphoma CYP4BK/4BL and vertebrate CYP4A/4F forms share identical amino acid residues at key positions within fatty acid substrate recognition sites. These results demonstrate differential regulation of CYP transcripts in a marine consumer feeding on an allelochemical-rich diet, and significantly advance our understanding of both the adaptive molecular mechanisms that marine consumers use to cope with environmental chemical pressures and the evolutionary history of allelochemical-metabolizing enzymes in the CYP superfamily.
    Description: Financial support for this work was provided by the Ocean Life Institute Tropical Research Initiative Grant (WHOI) to KEW and MEH; the Robert H. Cole Endowed Ocean Ventures Fund (WHOI) to KEW; the National Undersea Research Center - Program Development Proposal (CMRC-03PRMN0103A) to KEW and a National Science Foundation Graduate Research Fellowship to KEW.
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    Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site (2011)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 12 (2011): 263, doi:10.1186/1471-2164-12-263.
    Description: Populations of Atlantic killifish (Fundulus heteroclitus) have evolved resistance to the embryotoxic effects of polychlorinated biphenyls (PCBs) and other halogenated and nonhalogenated aromatic hydrocarbons that act through an aryl hydrocarbon receptor (AHR)-dependent signaling pathway. The resistance is accompanied by reduced sensitivity to induction of cytochrome P450 1A (CYP1A), a widely used biomarker of aromatic hydrocarbon exposure and effect, but whether the reduced sensitivity is specific to CYP1A or reflects a genome-wide reduction in responsiveness to all AHR-mediated changes in gene expression is unknown. We compared gene expression profiles and the response to 3,3',4,4',5-pentachlorobiphenyl (PCB-126) exposure in embryos (5 and 10 dpf) and larvae (15 dpf) from F. heteroclitus populations inhabiting the New Bedford Harbor, Massachusetts (NBH) Superfund site (PCB-resistant) and a reference site, Scorton Creek, Massachusetts (SC; PCB-sensitive). Analysis using a 7,000-gene cDNA array revealed striking differences in responsiveness to PCB-126 between the populations; the differences occur at all three stages examined. There was a sizeable set of PCB-responsive genes in the sensitive SC population, a much smaller set of PCB-responsive genes in NBH fish, and few similarities in PCB-responsive genes between the two populations. Most of the array results were confirmed, and additional PCB-regulated genes identified, by RNA-Seq (deep pyrosequencing). The results suggest that NBH fish possess a gene regulatory defect that is not specific to one target gene such as CYP1A but rather lies in a regulatory pathway that controls the transcriptional response of multiple genes to PCB exposure. The results are consistent with genome-wide disruption of AHR-dependent signaling in NBH fish.
    Description: This work was supported in part by National Institutes of Health grants P42ES007381 (Superfund Basic Research Program at Boston University) and by a grant from the WHOI Ocean Life Institute.
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    NetiNeti : discovery of scientific names from text using machine learning methods (2013)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 13 (2012): 211, doi:10.1186/1471-2105-13-211.
    Description: A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and biodiversity text sources. A scientific name acts as an important metadata element to link biological information. We present NetiNeti (Name Extraction from Textual Information-Name Extraction for Taxonomic Indexing), a machine learning based approach for recognition of scientific names including the discovery of new species names from text that will also handle misspellings, OCR errors and other variations in names. The system generates candidate names using rules for scientific names and applies probabilistic machine learning methods to classify names based on structural features of candidate names and features derived from their contexts. NetiNeti can also disambiguate scientific names from other names using the contextual information. We evaluated NetiNeti on legacy biodiversity texts and biomedical literature (MEDLINE). NetiNeti performs better (precision = 98.9% and recall = 70.5%) compared to a popular dictionary based approach (precision = 97.5% and recall = 54.3%) on a 600-page biodiversity book that was manually marked by an annotator. On a small set of PubMed Central’s full text articles annotated with scientific names, the precision and recall values are 98.5% and 96.2% respectively. NetiNeti found more than 190,000 unique binomial and trinomial names in more than 1,880,000 PubMed records when used on the full MEDLINE database. NetiNeti also successfully identifies almost all of the new species names mentioned within web pages. We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org.
    Description: This project was funded by the Ellison Medical Foundation and a grant from the National Library of Medicine (R01 LM009725).
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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)
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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)
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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)
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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 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)
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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 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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    Eutrophication governs predator-prey interactions and temperature effects in Aedes aegypti populations. (2019)
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    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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    The microbiome in pediatric cystic fibrosis patients : the role of shared environment suggests a window of intervention (2014)
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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 Microbiome 2 (2014): 14, doi:10.1186/2049-2618-2-14.
    Description: Cystic fibrosis (CF) is caused by mutations in the CFTR gene that predispose the airway to infection. Chronic infection by pathogens such as Pseudomonas aeruginosa leads to inflammation that gradually degrades lung function, resulting in morbidity and early mortality. In a previous study of CF monozygotic twins, we demonstrate that genetic modifiers significantly affect the establishment of persistent P. aeruginosa colonization in CF. Recognizing that bacteria other than P. aeruginosa contribute to the CF microbiome and associated pathology, we used deep sequencing of sputum from pediatric monozygotic twins and nontwin siblings with CF to characterize pediatric bacterial communities and the role that genetics plays in their evolution. We found that the microbial communities in sputum from pediatric patients living together were much more alike than those from pediatric individuals living apart, regardless of whether samples were taken from monozygous twins or from nontwin CF siblings living together, which we used as a proxy for dizygous twins. In contrast, adult communities were comparatively monolithic and much less diverse than the microbiome of pediatric patients. Taken together, these data and other recent studies suggest that as patients age, the CF microbiome becomes less diverse, more refractory to treatment and dominated by mucoid P. aeruginosa, as well as being associated with accelerated pulmonary decline. Our studies show that the microbiome of pediatric patients is susceptible to environmental influences, suggesting that interventions to preserve the community structure found in young CF patients might be possible, perhaps slowing disease progression.
    Description: This work was supported by the Flatley Foundation of Boston (to GAO, BAS and AHG), National Institutes of Health (NIH) grants P20 GM103413-10 and R01 HL074175-09 (to BAS), a Cystic Fibrosis Foundation Research Development Program grant (STANTO07R0), Cystic Fibrosis Foundation Research Development Program grant R025-CR07 (to DMG), NIH grants R01 HL068927-09 and R01 DK44003 (to GRC), Cystic Fibrosis Foundation grant CUTTIN06P0 (to GRC), NIH grant R01 AI091699 (to GAO) and NIH grant 4UH3DK083993 (to MLS).
    Keywords: Cystic fibrosis ; Microbiome ; Pseudomonas aeruginosa ; Sputum
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    Genetic, morphological, and chemical patterns of plant hybridization (2014)
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    Evolution of hematophagous habit in Triatominae (Heteroptera: Reduviidae) (2015)
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    Publication Date: 2015-02-19
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    Expression pattern of heat shock proteins during acute thermal stress in the Antarctic sea urchin, Sterechinus neumayeri (2016)
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    Publication Date: 2016-03-10
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    Agricultural landscapes as habitat for birds in central Chile (2017)
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    Publication Date: 2017-05-31
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    Comparison of organic matter in intermittent and perennial rivers of Mediterranean Chile with the support of citizen science (2019)
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    Publication Date: 2019-07-05
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    Frugivory and seed dispersal in the endemic cactus Eulychnia acida: extending the anachronism hypothesis to the Chilean Mediterranean ecosystem (2018)
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    Publication Date: 2018-09-25
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    A new population of Darwin's fox (Lycalopex fulvipes) in the Valdivian Coastal Range (2014)
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    Publication Date: 2014-03-26
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    Successional patterns along soil development gradients formed by glacier retreat in the Maritime Antarctic, King George Island (2016)
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    Publication Date: 2016-04-06
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    Conservation of biodiversity in private lands: are Chilean landowners willing to keep threatened species in their lands? (2014)
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    Publication Date: 2014-03-26
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    Temporal and spatial variation of the pollinator assemblages in Alstroemeria ligtu (Alstroemeriaceae) (2014)
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    Breeding strategies of open-cup-nesting birds in sub-Antarctic forests of Navarino Island, Chile (2019)
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    Publication Date: 2019-05-30
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    Protected areas in Chile: are we managing them? (2018)
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    Persistence of Dromiciops gliroides in landscapes dominated by Pinus radiata plantations (2017)
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    Publication Date: 2017-03-21
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    Nestmate recognition in defense against nest invasion by conspecifics during swarming in a one-piece nesting termite (2016)
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    Prosopis tamarugo Phil.: a native tree from the Atacama Desert groundwater table depth thresholds for conservation (2015)
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    Publication Date: 2015-12-01
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    The ecological value of long-term studies of birds and mammals in Central America, South America and Antarctica (2017)
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    Publication Date: 2017-09-06
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    Reproductive output of mosses under experimental warming on Fildes Peninsula, King George Island, maritime Antarctica (2016)
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    Publication Date: 2016-09-13
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    Plant composition and structure of two post-livestock areas of Tamaulipan thornscrub, Mexico (2018)
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    Publication Date: 2018-04-14
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    Reptiles in Monterey pine plantations of the Coastal Range of Central Chile (2014)
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    Publication Date: 2014-11-06
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    Photosynthetic UV stress tolerance of the Antarctic snow alga Chlorella sp. modified by enhanced temperature? (2016)
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    Effect of Didymosphenia geminata coverage on the phytobenthic community in an Andean basin of Chile (2018)
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    Ultrastructure of sensilla on antennae and maxillary palps in three Mesembrinellidae species (2018)
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    Differentiation and characterization of burrows of two species of armadillos in the Brazilian Cerrado (2015)
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    The presence of the marsupial Dromiciops gliroides in Parque Nacional Los Alerces, Chubut, Southern Argentina, after the synchronous maturation and flowering of native bamboo and subsequent rodent irruption (2015)
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    Publication Date: 2015-10-15
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    Oak canopy arthropod communities: which factors shape its structure? (2015)
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    Publication Date: 2015-08-18
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    Morphological variation of Cosmos bipinnatus (Asteraceae) and its relation to abiotic variables in central Mexico (2015)
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    Rapid changes in tree composition and biodiversity: consequences of dams on dry seasonal forests (2015)
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    Effect of host-plant genetic diversity on oak canopy arthropod community structure in central Mexico (2015)
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    Fragmentation of Chilean Andean rivers: expected effects of hydropower development (2019)
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    Winter diet of the long-eared owl Asio otus (Strigiformes: Strigidae) in the grasslands of Janos, Chihuahua, Mexico (2017)
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    Spatial distribution pattern of Mytilus chilensis beds in the Reloncaví fjord: hypothesis on associated processes (2015)
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    Assessment of the efficiency in trapping North American mink (Neovison vison) for population control in Patagonia (2015)
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    Rolling Pampas agroecosystem: which landscape attributes are relevant for determining bird distributions? (2014)
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    Influence of forest type and host plant genetic relatedness on the canopy arthropod community structure of Quercus crassifolia (2015)
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    Evidence that the house finch (Carpodacus mexicanus) uses scent to avoid omnivore mammals (2015)
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    Movement behavior of the Monito del monte (Dromiciops gliroides): new insights into the ecology of a unique marsupial (2019)
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    Suaeda foliosa Moq. (Caryophyllales: Amaranthaceae) first record of the genus and species for Valparaíso Region, Chile (2015)
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    Robles in Lagunas de Epulauquen, Argentina: previous and recent evidence of their distinctive character (2014)
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    Invasion of North American beaver (Castor canadensis) in the province of Magallanes, Southern Chile: comparison between dating sites through interviews with the local community and dendrochronology (2015)
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    Anuran larvae as prey and hosts of invertebrates in Neotropical aquatic habitats (2014)
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    Tail autotomy effects on the escape behavior of the lizard Gonatodes albogularis (Squamata: Sphaerodactylidae), from Córdoba, Colombia (2015)
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    Publication Date: 2015-01-07
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