bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective
Authors: Chehida Yacine Ben , Thumloup Julie , Schumacher Cassie , Harkins Timothy , Aguilar Alex , Borrell Asunción , Ferreira Marisa , Rojas-Bracho Lorenzo , Roberston Kelly M. , Taylor Barbara L. , Víkingsson Gísli A. , Weyna Arthur , Romiguier Jonathan , Morin Phillip A. , Fontaine Michael C. 
Published: November 2019

AbstractHistorical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastalversusoceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dall’s, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.
Different principles govern different scales of brain folding
Authors: Mallela Arka N. , Deng Hansen , Bush Alan , Goldschmidt Ezequiel 
Published: November 2019

ABSTRACTThe signature folds of the human brain are formed through a complex and developmentally regulated process. In vitro and in silico models of this process demonstrate a random pattern of sulci and gyri, unlike the highly ordered and conserved structure seen in the human cortex. Here, we account for the large-scale pattern of cortical folding by combining advanced fetal MRI with nonlinear diffeomorphic registration and volumetric analysis. Our analysis demonstrates that in utero brain growth follows a logistic curve, in the absence of an external volume constraint. The Sylvian fissure forms from interlobar folding, where separate lobes overgrow and close an existing subarachnoid space. In contrast, other large sulci, which are the ones represented in existing models, fold through an invagination of a flat surface, a mechanistically different process. Cortical folding is driven by multiple spatially and temporally different mechanisms, therefore regionally distinct biological process may be responsible for the global geometry of the adult brain.
Global analysis of non-animal peroxidases provides insights into the evolutionary basis of this gene family in green lineage
Authors: Mbadinga Duchesse Lacour Mbadinga , Li Qiang , Ranocha Philippe , Martinez Yves , Cooper Endymion D. , Dunand Christophe 
Published: November 2019

AbstractThe non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolutionary history of this family of proteins. Here, we report for the first time an exhaustive evolutionary analysis of non-animal peroxidases using integratedin silicoand biochemical strategies. Thanks to the availability of numerous genomic sequences from many species belonging to different kingdoms together with expert and exhaustive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organismsin silico. First, we show that the presence or absence of non-animal peroxidases can be correlated with the presence or absence of certain organelles or with specific biological processes. Examining a wide range of organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class III peroxidases (CIII Prx) were only detected in plants and Class II peroxidases (CII Prx) in fungi related to wood decay and plant degradation.Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed in protein extracts obtained from 30 different eukaryotic organisms strongly support the distribution of the sequences resulting from ourin silicoanalysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.
Sympathetic innervation directs Ankyrin G, voltage-gated Navand KCNQ1 channels to the neuro-cardiac junctions
Authors: Shcherbakova Olga G. 
Published: November 2019

AbstractThe sympathetic nervous system plays a central role in the cardiovascular response to acute stress by increasing heart rate and contractility. Despite the importance of functional connections between sympathetic nerves and cardiac myocytes, very little is known about the structural and functional organization of the neuro-cardiac synapses. Earlier, we demonstrated that specialized signaling domains are organized in cardiac myocytes at sites of contact with sympathetic neurons2. In the present study, we addressed the question if sympathetic innervation may affect localization of the cardiac ion channels. We have found that ankyrin G, scaffold protein involved in targeting ion channels and transporters, is localized at the postsynaptic sites in the cardiac myocytes innervated by sympathetic neurons. Consistent with the roles of ankyrin G in targeting Navchannels to specific domains in neurons and cardiac myocytes, we have observed an increased density of Navchannels at the neuro-cardiac junctions in co-cultures of cardiac myocytes and sympathetic neurons. We have also found that KCNQ1 channels are enriched at that sites. The increased density of Navand KCNQ1 channels at the sites of sympathetic innervation is likely to play a role in regulation of the cardiac excitability by sympathetic nervous system.
ThemicroRNA476a/RFL module regulates adventitious root formation through a mitochondria-dependent pathway inPopulus
Authors: Xu Changzheng , Tao Yuanxun , Fu Xiaokang , Guo Li , Xing Haitao , Li Chaofeng , Su HuiLi , Wang Xianqiang , Hu Jian , Fan Di , Chiang Vincent L. , Luo Keming 
Published: November 2019

AbstractAdventitious root (AR) formation at the base of stem cuttings determines the efficiency of clonal propagation for woody plants. Many endogenous and environmental factors influence AR formation. However, our knowledge about the regulation of AR development by mitochondrial metabolism in plants is very limited. Here we identifiedPopulus-specificmiR476aas a novel regulator of wound-induced adventitious rooting via orchestrating mitochondrial homeostasis in poplar.MiR476aexhibited inducible expression during AR formation and directly targets severalRestorer of Fertility like(RFL) genes encoding mitochondrion-localized pentatricopeptide repeat proteins. Genetic modification ofmiR476-RFLexpression revealed themiR476/RFL-mediated dynamic regulation of mitochondrial homeostasis on AR formation in transgenic poplar. Furthermore, mitochondrial perturbation via exogenous chemical inhibitor validated that themiR476a/RFL-directed AR formation depended on mitochondrial regulation though modulating the auxin pathway. Our results established a miRNA-directed mitochondrion-auxin signaling cascade required for AR development, providing novel insights into the understanding of mitochondrial regulation on plant developmental plasticity.
Statistical power: implications for planning MEG studies
Authors: Chaumon Maximilien , Puce Aina , George Nathalie 
Published: November 2019

AbstractStatistical power is key for robust, replicable science. Here, we systematically explored how numbers of trials and subjects affect statistical power in MEG sensor-level data. More specifically, we simulated “experiments” using the MEG resting-state dataset of the Human Connectome Project (HCP). We divided the data in two conditions, injected a dipolar source at a known anatomical location in the “signal condition”, but not in the “noise condition”, and detected significant differences at sensor level with classical paired t-tests across subjects, using amplitude, squared amplitude, and global field power (GFP) measures. Group-level detectability of these simulated effects varied drastically with anatomical origin. We thus examined in detail which spatial properties of the sources affected detectability, looking specifically at the distance from closest sensor and orientation of the source, and at the variability of these parameters across subjects. In line with previous single-subject studies, we found that the most detectable effects originate from source locations that are closest to the sensors and oriented tangentially with respect to the head surface. In addition, cross-subject variability in orientation also affected group-level detectability, boosting detection in regions where this variability was small and hindering detection in regions where it was large. Incidentally, we observed a considerable covariation of source position, orientation, and their cross-subject variability in individual brain anatomical space, making it difficult to assess the impact of each of these variables independently of one another. We thus also performed simulations where we controlled spatial properties independently of individual anatomy. These additional simulations confirmed the strong impact of distance and orientation and further showed that orientation variability across subjects affects detectability, whereas position variability does not. Importantly, our study indicates that strict unequivocal recommendations as to the ideal number of trials and subjects for any experiment cannot be realistically provided for neurophysiological studies and should be adapted according to the brain regions under study.
Manual dexterity of mice during food-handling involves the thumb and a set of fast basic movements
Authors: Barrett John M. , Tapies Martinna G. Raineri , Shepherd Gordon M. G. 
Published: November 2019

AbstractThe small first digit (D1) of the mouse’s hand resembles a volar pad, but its thumb-like anatomy suggests ethological importance for manipulating small objects. To explore this possibility, we recorded high-speed close-up video of mice eating seeds and other food items. Analyses of ethograms and automated tracking with DeepLabCut revealed multiple distinct microstructural features of food-handling. First, we found that mice indeed made extensive use of D1 for dexterous manipulations. In particular, mice used D1 to hold food with either of two grip types: a pincer-type grasp, or a “thumb-hold” grip, pressing with D1 from the side. Thumb-holding was preferentially used for handling smaller items, with the smallest items held between the two D1s alone. Second, we observed that mice cycled rapidly between two postural modes while feeding, with the hands positioned either at the mouth (oromanual phase) or resting below (holding phase). Third, we identified two highly stereotyped D1-related movements during feeding, including an extraordinarily fast (∼20 ms) “regrip” maneuver, and a fast (∼100 ms) “sniff” maneuver. Lastly, in addition to these characteristic simpler movements and postures, we also observed highly complex movements, including rapid D1-assisted rotations of food items and dexterous simultaneous double-gripping of two food fragments. Manipulation behaviors were generally conserved for different food types, and for head-fixed mice. Wild squirrels displayed a similar repertoire of D1-related movements. Our results define, for the mouse, a set of kinematic building-blocks of manual dexterity, and reveal an outsized role for D1 in these actions.
Estimating mutual information under measurement error
Authors: Ma Cong , Kingsford Carl 
Published: November 2019

AbstractMutual information is widely used to characterize dependence between biological signals, such as co-expression between genes or co-evolution between amino acids. However, measurement error of the biological signals is rarely considered in estimating mutual information. Measurement error is widespread and non-negligible in some cases. As a result, the distribution of the signals is blurred, and the mutual information may be biased when estimated using the blurred measurements. We derive a corrected estimator for mutual information that accounts for the distribution of measurement error. Our corrected estimator is based on the correction of the probability mass function (PMF) or probability density function (PDF, based on kernel density estimation). We prove that the corrected estimator is asymptotically unbiased in the (semi-) discrete case when the distribution of measurement error is known. We show that it reduces the estimation bias in the continuous case under certain assumptions. On simulated data, our corrected estimator leads to a more accurate estimation for mutual information when the sample size is not the limiting factor for estimating PMF or PDF accurately. We compare the uncorrected and corrected estimator on the gene expression data of TCGA breast cancer samples and show a difference in both the value and the ranking of estimated mutual information between the two estimators.
The Landscape of Mutations in Human Fumarate Hydratase
Authors: Shorthouse David , Hall Michael W J , Hall Benjamin A 
Published: November 2019

ABSTRACTFumarate Hydratase (FH) is an enzyme of the citric acid (TCA) cycle that is responsible for reversibly catalysing the conversion between fumarate and malate. FH loss and subsequent buildup of the oncometabolite fumarate causes hereditary leiomyomatosis and renal cell carcinoma. We explore the mutational landscape of FH in silico, predict the functional effects of many already detected mutations, and categorise detected but un-characterised mutations in human populations. Using mutational energy predicting tools such as Rosetta and FoldX we accurately predict mutations and mutational hotspots with high disruptive capability. Furthermore, through performing molecular dynamics simulations we show that hinge regions of the protein can be stabilized or destabilized by mutations, with new mechanistic implications of the consequences on the binding affinity of the enzyme for its substrates. Finally, we categorise all potential mutations in FH into functional groups, and predict which known mutations in the human population are loss-of-function, and therefore predispose patients to papillary renal carcinoma – we validate our findings through analysis of metabolomics data of characterized cell lines.
Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes
Authors: Moi David , Kilchoer Laurent , Aguilar Pablo S. , Dessimoz Christophe 
Published: November 2019

AbstractPhylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be jointly lost or retained across the tree of life. Phylogenetic profiling has customarily been more widely used with prokaryotes than eukaryotes, because the method is thought to require many diverse genomes. There are now many eukaryotic genomes available, but these are considerably larger, and typical phylogenetic profiling methods require quadratic time or worse in the number of genes. We introduce a fast, scalable phylogenetic profiling approach entitled HogProf, which leverages hierarchical orthologous groups for the construction of large profiles and locality-sensitive hashing for efficient retrieval of similar profiles. We show that the approach outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the tool to reconstruct networks and query for interactors of the kinetochore complex as well as conserved proteins involved in sexual reproduction: Hap2, Spo11 and Gex1. HogProf enables large-scale phylogenetic profiling across the three domains of life, and will be useful to predict biological pathways among the hundreds of thousands of eukaryotic species that will become available in the coming few years. HogProf is available athttps://github.com/DessimozLab/HogProf.
Exposure to PM2.5 during pregnancy or lactation increases methylation while reducing the expression of Pdx1 and NEUROG3 in mouse pancreatic islets
Authors: Ataíde Lima Raquel Patricia , Boico Vitor Ferreira , Peruca Guilherme Francisco , Cruz Rodrigues Kellen Cristina da , Yariwake Victor Yuji , Neto Daisuke Hayashi , de Carvalho Costa Maria José , Rebelo Santos-Silva Junia Carolina , Anhê Gabriel Forato , Nascimento Saldiva Paulo Hilário , Veras Mariana Matera , de Oliveira Prada Patrícia 
Published: November 2019

ABSTRACTAir pollution is comprised of several substances, including particulate matter (PM). Exposure to air pollution may trigger alterations in DNA methylation thus modifying gene expression patterns. This phenomenon is likely to mediate the relationship between exposure to air pollution and adverse health effects. The purpose of this study was analyzing the effects of exposure to PM2.5 during pregnancy or lactation and whether it would cause multigenerational epigenetic alterations in the promoter region of the genes Pdx1 and NEUROG3 within mouse pancreatic islets. Our results show that maternal exposure to PM2.5 led to an elevation in blood glucose levels within the two following generations (F1 and F2). There was also an increase in DNA methylation in the aforementioned promoter regions accompanied by reduced gene expression in generations F1 and F2 upon F0 exposure to PM2.5 during pregnancy. These data suggest that maternal exposure to PM2.5 from air pollution, particularly during pregnancy, may lead to a multigenerational and lifelong negative impact on glucose homeostasis mediated by an increase in DNA methylation within the promoter region of the genes Pdx1 and NEUROG3 in pancreatic islets.
Marine deforestation leads to widespread loss of ecosystem function
Authors: Edwards Matthew S , Konar Brenda , Kim Ju-Hyoung , Gabara Scott , Sullaway Genoa , McHugh Tristin A , Spector Michael , Small Sadie L 
Published: November 2019

AbstractTrophic interactions can result in changes to the abundance and distribution of habitat-forming species that dramatically reduce ecosystem health and functioning. Nowhere may this be as dramatic as in the coastal zone of the Aleutian Archipelago, where overgrazing by herbivorous sea urchins that began in the 1980s resulted in widespread deforestation of the region’s kelp forests. Here we show that this deforestation resulted in decreased macroalgal and invertebrate abundance and diversity, increased benthic irradiances, and reduced rates of gross primary production and respiration by the ecosystem. These opposing metabolic processes remain in balance, however, which resulted in little-to-no changes to net ecosystem production. These patterns were consistent across nine islands spanning more than 1000 kilometers of the archipelago. In light of the worldwide declines in kelp forests observed in recent decades, our findings suggest that marine deforestation profoundly affects the health of coastal ecosystems and how they function.Significance statementWidespread marine deforestation results in reduced biodiversity and primary productivity throughout more than 1000 km of the Aleutian Archipelago.
Polyploidy in the adultDrosophilabrain
Authors: Nandakumar Shyama , Grushko Olga , Buttitta Laura A. 
Published: November 2019

AbstractLong-lived cells such as terminally differentiated postmitotic neurons and glia must cope with the accumulation of damage over the course of an animal’s lifespan. How long-lived cells deal with ageing-related damage is poorly understood. Here we show that polyploid cells accumulate in the ageing adult fly brain and that polyploidy protects against DNA damage-induced cell death. Multiple types of neurons and glia that are diploid at eclosion, become polyploid with age in the adultDrosophilabrain. The optic lobes exhibit the highest levels of polyploidy, associated with an elevated DNA damage response in this brain region with age. Inducing oxidative stress or exogenous DNA damage leads to an earlier onset of polyploidy, and polyploid cells in the adult brain are more resistant to DNA damage-induced cell death than diploid cells. Our results suggest polyploidy may serve a protective role for neurons and glia in ageingDrosophila melanogasterbrains.
The role of organizational climate in setting project goals
Authors: Zwikael Ofer , Meredith Jack R. 
Published: November 2019

PurposeProject goal setting, led by a project proposal development team, is an important operations process because effective goal setting aligned with the operations strategy can enhance project investment decision making, project success and thereby operations performance. The purpose of this paper is to argue that because of the strategic nature of this task, the organizational climate (OC) that the proposal development team works in is critical for the effectiveness of their goal setting.Design/methodology/approachThe authors raise hypotheses regarding the role OC plays in enhancing the effectiveness of the support senior executives provide to project proposal teams. The authors test the hypotheses in a longitudinal survey of 200 managers in the USA.FindingsResults show that a formal organizational process used by proposal development teams for setting project goals is highly effective and that an appropriate OC further intensifies the positive effect of such a process. However, a formal organizational process has no positive effect on effective goal setting if implemented in an environment with a poor OC.Originality/valueThe paper contributes to the literature by finding that a positive OC intensifies the already positive effect of organizational support. In practice, the creation of such a climate can enhance project goal setting, project success, and as a result, operations performance.