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  • 1
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    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing (2014)
    Public Library of Science (PLoS)
    In:  PLoS Biology, 12 (6). e1001889.
    Details
    Publication Date: 2019-03-05
    Type: Article , PeerReviewed
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  • 2
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    The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2 (2007)
    Public Library of Science (PLoS)
    Details
    Publication Date: 2022-05-25
    Description: This is an open-access article distributed under the terms of the Creative Commons Public Domain dedication. The definitive version was published in PLoS Biology 4 (2006): e383, doi:10.1371/journal.pbio.0040383.
    Description: Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
    Description: This work was performed under the auspices of the United States Department of Energy by Lawrence Livermore National Laboratory, University of California, under contract W-7405-ENG-48. Genome closure was funded in part by a University of South Florida Innovative Teaching Grant (to KMS). KMS, SKF, and CAK gratefully acknowledge support from the United States Department of Agriculture Higher Education Challenge Grants Program (Award # 20053841115876). SMS kindly acknowledges support through a fellowship received from the Hanse Wissenschaftskolleg in Delmenhorst, Germany (http://www.h-w-k.de). MH was supported by a Woods Hole Oceanographic Institution postdoctoral scholarship.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: 4436005 bytes
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  • 3
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    Towards a Neuronal Gauge Theory (2016)
    Public Library of Science (PLoS)
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    Publication Date: 2016-03-09
    Description: Given the amount of knowledge and data accruing in the neurosciences, is it time to formulate a general principle for neuronal dynamics that holds at evolutionary, developmental, and perceptual timescales? In this paper, we propose that the brain (and other self-organised biological systems) can be characterised via the mathematical apparatus of a gauge theory. The picture that emerges from this approach suggests that any biological system (from a neuron to an organism) can be cast as resolving uncertainty about its external milieu, either by changing its internal states or its relationship to the environment. Using formal arguments, we show that a gauge theory for neuronal dynamics—based on approximate Bayesian inference—has the potential to shed new light on phenomena that have thus far eluded a formal description, such as attention and the link between action and perception.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
    Published by Public Library of Science (PLoS)
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  • 4
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    Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities (2016)
    Public Library of Science (PLoS)
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    Publication Date: 2016-04-16
    Description: The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5’-TCCRAC-3’; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5’-TCCRAC-3’). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5’-TCCRAC-3’). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 5
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    Molecular phylogeny of the Orthalicoidea land snails: Further support and surprises (2023)
    Public Library of Science (PLoS)
    In:  PLOS ONE vol. 18 no. 7, pp. e0288533-e0288533
    Details
    Publication Date: 2024-02-28
    Description: The superfamily Orthalicoidea comprises approximately 2,000 species of terrestrial gastropods, mostly concentrated in the Neotropics but also present in southern Africa and Oceania. We provide a multi-marker molecular phylogeny of this superfamily, reassessing its \nfamily- and genus-level classification. We exclude two families from the group, Odontostomidae and Vidaliellidae, transferring them to Rhytidoidea based on their phylogenetic relationships as recovered herein. Two new families are recognized herein as members of \nOrthalicoidea, Tomogeridae and Cyclodontinidae fam. nov. The family Megaspiridae and \nthe subfamily Prestonellinae are paraphyletic but are retained herein for taxonomic stability. \nThe subfamily Placostylinae is synonymized with Bothriembryontinae. The new genera \nAlterorhinus gen. nov. and Sanniostracus gen. nov. containing some Brazilian species are \ndescribed here to better reflect the phylogeny. The fossil record and paleobiogeographic \nhistory of the group is explored under the new phylogenetic framework.
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 6
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    A multi-taxon analysis of European Red Lists reveals major threats to biodiversity (2023)
    Public Library of Science (PLoS)
    In:  PLOS ONE vol. 18 no. 11, pp. e0293083-e0293083
    Details
    Publication Date: 2024-04-09
    Description: Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    Ionotropic Chemosensory Receptors Mediate the Taste and Smell of Polyamines (2016)
    Public Library of Science (PLoS)
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    Publication Date: 2016-05-05
    Description: The ability to find and consume nutrient-rich diets for successful reproduction and survival is fundamental to animal life. Among the nutrients important for all animals are polyamines, a class of pungent smelling compounds required in numerous cellular and organismic processes. Polyamine deficiency or excess has detrimental effects on health, cognitive function, reproduction, and lifespan. Here, we show that a diet high in polyamine is beneficial and increases reproductive success of flies, and we unravel the sensory mechanisms that attract Drosophila to polyamine-rich food and egg-laying substrates. Using a combination of behavioral genetics and in vivo calcium imaging, we demonstrate that Drosophila uses multisensory detection to find and evaluate polyamines present in overripe and fermenting fruit, their favored feeding and egg-laying substrate. In the olfactory system, two coexpressed ionotropic receptors (IRs), IR76b and IR41a, mediate the long-range attraction to the odor. In the gustatory system, multimodal taste sensation by IR76b receptor and GR66a bitter receptor neurons is used to evaluate quality and valence of the polyamine providing a mechanism for the fly’s high attraction to polyamine-rich and sweet decaying fruit. Given their universal and highly conserved biological roles, we propose that the ability to evaluate food for polyamine content may impact health and reproductive success also of other animals including humans.
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    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 8
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    The Effects of Context and Attention on Spiking Activity in Human Early Visual Cortex (2016)
    Public Library of Science (PLoS)
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    Publication Date: 2016-03-26
    Description: Here we report the first quantitative analysis of spiking activity in human early visual cortex. We recorded multi-unit activity from two electrodes in area V2/V3 of a human patient implanted with depth electrodes as part of her treatment for epilepsy. We observed well-localized multi-unit receptive fields with tunings for contrast, orientation, spatial frequency, and size, similar to those reported in the macaque. We also observed pronounced gamma oscillations in the local-field potential that could be used to estimate the underlying spiking response properties. Spiking responses were modulated by visual context and attention. We observed orientation-tuned surround suppression: responses were suppressed by image regions with a uniform orientation and enhanced by orientation contrast. Additionally, responses were enhanced on regions that perceptually segregated from the background, indicating that neurons in the human visual cortex are sensitive to figure-ground structure. Spiking responses were also modulated by object-based attention. When the patient mentally traced a curve through the neurons’ receptive fields, the accompanying shift of attention enhanced neuronal activity. These results demonstrate that the tuning properties of cells in the human early visual cortex are similar to those in the macaque and that responses can be modulated by both contextual factors and behavioral relevance. Our results, therefore, imply that the macaque visual system is an excellent model for the human visual cortex.
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    Topics: Biology
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  • 9
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    Growth-Blocking Peptides As Nutrition-Sensitive Signals for Insulin Secretion and Body Size Regulation (2016)
    Public Library of Science (PLoS)
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    Publication Date: 2016-03-09
    Description: In Drosophila , the fat body, functionally equivalent to the mammalian liver and adipocytes, plays a central role in regulating systemic growth in response to nutrition. The fat body senses intracellular amino acids through Target of Rapamycin (TOR) signaling, and produces an unidentified humoral factor(s) to regulate insulin-like peptide (ILP) synthesis and/or secretion in the insulin-producing cells. Here, we find that two peptides, Growth-Blocking Peptide (GBP1) and CG11395 (GBP2), are produced in the fat body in response to amino acids and TOR signaling. Reducing the expression of GBP1 and GBP2 (GBPs) specifically in the fat body results in smaller body size due to reduced growth rate. In addition, we found that GBPs stimulate ILP secretion from the insulin-producing cells, either directly or indirectly, thereby increasing insulin and insulin-like growth factor signaling activity throughout the body. Our findings fill an important gap in our understanding of how the fat body transmits nutritional information to the insulin producing cells to control body size.
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    Topics: Biology
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  • 10
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    Neuropeptides Modulate Female Chemosensory Processing upon Mating in Drosophila (2016)
    Public Library of Science (PLoS)
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    Publication Date: 2016-05-05
    Description: A female’s reproductive state influences her perception of odors and tastes along with her changed behavioral state and physiological needs. The mechanism that modulates chemosensory processing, however, remains largely elusive. Using Drosophila , we have identified a behavioral, neuronal, and genetic mechanism that adapts the senses of smell and taste, the major modalities for food quality perception, to the physiological needs of a gravid female. Pungent smelling polyamines, such as putrescine and spermidine, are essential for cell proliferation, reproduction, and embryonic development in all animals. A polyamine-rich diet increases reproductive success in many species, including flies. Using a combination of behavioral analysis and in vivo physiology, we show that polyamine attraction is modulated in gravid females through a G-protein coupled receptor, the sex peptide receptor (SPR), and its neuropeptide ligands, MIPs (myoinhibitory peptides), which act directly in the polyamine-detecting olfactory and taste neurons. This modulation is triggered by an increase of SPR expression in chemosensory neurons, which is sufficient to convert virgin to mated female olfactory choice behavior. Together, our data show that neuropeptide-mediated modulation of peripheral chemosensory neurons increases a gravid female’s preference for important nutrients, thereby ensuring optimal conditions for her growing progeny.
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    Topics: Biology
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