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10.1101/498378 | Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting | AO_SCPLOWBSTRACTC_SCPLOWMany recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number of loci available for analysis. The question we seek to answer in this study is: What happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two large biological data sets, we show that running such methods on data with paralogs can still provide accurate results. We use multiple different methods, some of which are based directly on the multispecies coalescent (MSC) model, and some of which have been proven to be statistically consistent under it. We also treat the paralogous loci in multiple ways: from explicitly denoting them as paralogs, to randomly selecting one copy per species. In all cases the inferred species trees are as accurate as equivalent analyses using single-copy orthologs. Our results have significant implications for the use of ILS-aware phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci. This will greatly increase the amount of data that can be used for phylogenetic inference. | evolutionary biology |
10.1101/501221 | Neurocomputational underpinnings of expected surprise | Predictive coding accounts of brain functions profoundly influence current approaches to perceptual synthesis. However, a fundamental paradox has emerged, that may be very relevant for understanding hallucinations, psychosis or cognitive inflexibility. This paradox is that in some situations surprise or prediction error related responses can decrease when predicted and yet, they can increase when we know they are predictable. This paradox is resolved by recognizing that brain responses reflect precision weighted prediction error. This then presses us to disambiguate the contributions of precision and prediction error in electrophysiology. We report, for the first time, an experimental paradigm that may be able to meet this challenge. We examined brain responses to unexpected and expected surprising sounds, assuming that the latter yield a smaller prediction error but much more amplified by a larger precision weight. Importantly, addressing this modulation requires the modelling of trial-by-trial variations of brain responses, that we reconstructed within a fronto-temporal network by combining EEG and MEG. Our results reveal an adaptive learning of surprise with larger integration of past (relevant) information in the context of expected surprises. Within the auditory hierarchy, this adaptation was found tied down to specific connections and reveals in particular and crucially precision encoding through neuronal excitability. Strikingly, these fine processes are automated as sound sequences were unattended. These findings directly speak to applications in psychiatry, where it has been suggested that a specifically impaired precision weighting is at the heart of several conditions such as schizophrenia and autism. | neuroscience |
10.1101/502328 | Visual exposure enhances stimulus encoding and persistence in primary cortex | The brain adapts to the sensory environment. For example, simple sensory exposure can modify the response properties of early sensory neurons. How these changes affect the overall encoding and maintenance of stimulus information across neuronal populations remains unclear. We perform parallel recordings in the primary visual cortex of anesthetized cats and find that brief, repetitive exposure to structured visual stimuli enhances stimulus encoding by decreasing the selectivity and increasing the range of the neuronal responses that persist after stimulus presentation. Low-dimensional projection methods and simple classifiers demonstrate that visual exposure increases the segregation of persistent neuronal population responses into stimulus-specific clusters. These observed refinements preserve the representational details required for stimulus reconstruction and are detectable in post-exposure spontaneous activity. Assuming response facilitation and recurrent network interactions as the core mechanisms underlying stimulus persistence, we show that the exposure-driven segregation of stimulus responses can arise through strictly local plasticity mechanisms, also in the absence of firing rate changes. Our findings provide evidence for the existence of an automatic, unguided optimization process that enhances the encoding power of neuronal populations in early visual cortex, thus potentially benefiting simple readouts at higher stages of visual processing. | neuroscience |
10.1101/501627 | Sensory coding and causal impact of mouse cortex in a visual decision | Correlates of sensory stimuli and motor actions are found in multiple cortical areas, but such correlates do not indicate whether these areas are causally relevant to task performance. We trained mice to discriminate visual contrast and report their decision by turning a wheel. Widefield calcium imaging and Neuropixels recordings in cortex revealed stimulus-related activity in visual (VIS) and frontal (MOs) areas, and widespread movement-related activity across the whole dorsal cortex. Optogenetic inactivation biased choices only when targeted at VIS and MOs, at times corresponding to peak stimulus decoding. A neurometric model based on summing and subtracting activity in VIS and MOs successfully described behavioral performance and predicted the effect of optogenetic inactivation. Thus, local sensory signals in visual and frontal cortex play a causal role in task performance, while widespread dorsal cortical signals correlating with movement reflect processes that do not play a causal role. | neuroscience |
10.1101/501627 | Sensory coding and causal impact of mouse cortex in a visual decision | Correlates of sensory stimuli and motor actions are found in multiple cortical areas, but such correlates do not indicate whether these areas are causally relevant to task performance. We trained mice to discriminate visual contrast and report their decision by turning a wheel. Widefield calcium imaging and Neuropixels recordings in cortex revealed stimulus-related activity in visual (VIS) and frontal (MOs) areas, and widespread movement-related activity across the whole dorsal cortex. Optogenetic inactivation biased choices only when targeted at VIS and MOs, at times corresponding to peak stimulus decoding. A neurometric model based on summing and subtracting activity in VIS and MOs successfully described behavioral performance and predicted the effect of optogenetic inactivation. Thus, local sensory signals in visual and frontal cortex play a causal role in task performance, while widespread dorsal cortical signals correlating with movement reflect processes that do not play a causal role. | neuroscience |
10.1101/500108 | Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics | Cancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with i the ability to eradicate cancer at its source. In acute myeloid leukemia (AML), leukemic stem cells (LSCs) underlie mortality but are difficult to isolate due to their low abundance and high similarity to healthy hematopoietic stem cells (HSCs). Here, we demonstrate that LSCs, HSCs, and pre-leukemic stem cells can be identified and molecularly profiled by combining single-cell transcriptomics with lineage tracing using both nuclear and mitochondrial somatic variants. While mutational status discriminates between healthy and cancerous cells, gene expression distinguishes stem cells and progenitor cell populations. Our approach enables the identification of LSC-specific gene expression programs and the characterization of differentiation blocks induced by leukemic mutations. Taken together, we demonstrate the power of single-cell multi-omic approaches in characterizing cancer stem cells. | genomics |
10.1101/504332 | Differential dominance of an allele of the Drosophila tbetah gene challenges standard genetic techniques | The biogenic amine octopamine (OA) and its precursor tyramine (TA) are involved in controlling a plethora of different physiological and behavioral processes. The tyramine-{beta}-hydroxylase (t{beta}h) gene encodes the enzyme catalyzing the last synthesis step from TA to OA. Here, we report differential dominance (from recessive to overdominant) of the putative null t{beta}hnM18 allele in two behavioral measures in Buridans paradigm (walking speed and stripe deviation) and a proboscis extension assay in the fruit fly Drosophila melanogaster. The behavioral analysis of transgenic t{beta}h expression experiments in mutant and wild type flies as well as of OA- and TA-receptor mutants revealed a complex interaction of both aminergic systems. Our analysis suggests that the different neuronal networks responsible for the three phenotypes show differential sensitivity to t{beta}h gene expression levels. The evidence suggests that this sensitivity is brought about by a TA/OA opponent system modulating the involved neuronal circuits. This conclusion entails important implications for standard transgenic techniques, commonly used in functional genetics. | genetics |
10.1101/506261 | Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. | Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying mechanisms are not well understood. C. elegans undergo four molts at regular 8-10 h intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns, accelerated in let-7(-) mutants, and similar to wild type animals in let-7(-) nhr-23(-) double mutants. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7 binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also co-regulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network possibly by functioning as a cycle counter. | developmental biology |
10.1101/508572 | Cyclic Nucleotide-Gated Ion Channel 2 modulates auxin homeostasis and signaling | Cyclic Nucleotide Gated Ion Channels (CNGCs) have been firmly established as Ca2+-conducting ion channels that regulate a wide variety of physiological responses in plants. CNGC2 has been implicated in plant immunity and Ca2+ signaling due to the autoimmune phenotypes exhibited by null mutants of CNGC2. However, cngc2 mutants display additional phenotypes that are unique among autoimmune mutants, suggesting that CNGC2 has functions beyond defense and generates distinct Ca2+ signals in response to different triggers. In this study we found that cngc2 mutants showed reduced gravitropism, consistent with a defect in auxin signaling. This was mirrored in the diminished auxin response detected by the auxin reporters DR5::GUS and DII-VENUS and in a strongly impaired auxin-induced Ca2+ response. Moreover, the cngc2 mutant exhibits higher levels of the endogenous auxin indole-3-acetic acid (IAA), indicating that excess auxin in cngc2 causes its pleiotropic phenotypes. These auxin signaling defects and the autoimmunity syndrome of cngc2 could be suppressed by loss-of-function mutations in the auxin biosynthesis gene YUCCA6 (YUC6), as determined by identification of the cngc2 suppressor mutant repressor of cngc2 (rdd1) as an allele of YUC6. A loss-of-function mutation in the upstream auxin biosynthesis gene TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA1, WEAK ETHYLENE INSENSITIVE8) also suppressed the cngc2 phenotypes, further supporting the tight relationship between CNGC2 and the TAA-YUC-dependent auxin biosynthesis pathway. Taking these results together, we propose that the Ca2+ signal generated by CNGC2 is a part of the negative feedback regulation of auxin homeostasis in which CNGC2 balances cellular auxin perception by influencing auxin biosynthesis. | plant biology |
10.1101/508242 | Identifying complex sequence patterns with a variable-convolutional layer effectively and efficiently | Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named Variable Convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length from data adaptively. Empirical evaluations on DNA-protein binding and DNase footprinting cases well demonstrated that vConv-based networks have superior performance to their convolutional counterparts regardless of model complexity. Meanwhile, vConv could be readily integrated into multi-layer neural networks as an "in-place replacement" of canonical convolutional layer. All source codes are freely available on GitHub for academic usage. | bioinformatics |
10.1101/508242 | Identifying complex sequence patterns in massive omics data with a variable-convolutional layer in deep neural network | Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named Variable Convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length from data adaptively. Empirical evaluations on DNA-protein binding and DNase footprinting cases well demonstrated that vConv-based networks have superior performance to their convolutional counterparts regardless of model complexity. Meanwhile, vConv could be readily integrated into multi-layer neural networks as an "in-place replacement" of canonical convolutional layer. All source codes are freely available on GitHub for academic usage. | bioinformatics |
10.1101/508242 | Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network | Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named Variable Convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length from data adaptively. Empirical evaluations on DNA-protein binding and DNase footprinting cases well demonstrated that vConv-based networks have superior performance to their convolutional counterparts regardless of model complexity. Meanwhile, vConv could be readily integrated into multi-layer neural networks as an "in-place replacement" of canonical convolutional layer. All source codes are freely available on GitHub for academic usage. | bioinformatics |
10.1101/512780 | Rigorous equations for isothermal titration calorimetry: theoretical and practical consequences | The author has withdrawn his manuscript because:
The withdrawn preprint was about methodological aspects in Isothermal Titration Calorimetry (ITC) used to obtain thermodynamic information about reactions like A + B {rightleftarrows} C where A is initially in the cell and B injected from a syringe. The preprint considered the two possible methods in ITC:
1/ the Multiple Injection Method (MIM) making use of short-time injections separated by sufficient time to allow the reaction to reach equilibrium before a new injection.
2/ the Single Injection Method (SIM) making use of a slow continuous injection.
The first result mentioned is about a new equation linking the rate of heat evolution with the injected volume (equations 9 and 10). With this equation and with the hypothesis that there is always perfect mixing of the cell content it was concluded that an ideal titration curve (i.e. not affected by any external influence) for a simple reaction like A + B {rightleftarrows} C cannot change sign (section 3.2). This conclusion turns out to be incorrect when taking in consideration real conditions with imperfect mixing, particularly with MIM using injections often of very short duration, which prevents from reaching perfect mixing. The major problem is that this erroneous conclusion was accompanied with comparisons of the results from well-established programs, which led to the conclusion that these were in error on this point (section 3.6).
I therefore felt necessary to withdraw this preprint to avoid casting doubts unduly on these programs used extensively.
Note that many other aspects in this preprint remain correct (section 3.8). A new version of this work, limited to SIM and considering imperfect mixing, will be submitted for publication under the title: "Isothermal titration calorimetry in the single-injection mode with imperfect mixing".
If you have any questions, please contact me at dumasp@igbmc.fr or at p.dumas@unistra.fr
Sorry for the inconvenience.
Philippe Dumas
November 6, 2021 | biophysics |
10.1101/513572 | Discovering footprints of evolutionary chromatin response to transposons activity: merging biophysics with bioinformatics | Transposons are genome components that account for the majority of genome size in many organisms, behaving as parasitic entities and interfering with the translation mechanism. Chromatin structure influences the activity of transposons, by coordinating genome accessibility for the expression and insertion of these sequences. As a case study, we show evidences of an evolutionary response of the chromatin structure to a variation in the activity of Long Interspersed Elements (LINEs) during mammals evolution, with focus on the murine radiation and primate evolution. LINEs activity was measured using a biophysical approach for modeling LINEs as an ecosystem, where different strains of transposons might reproduce, die and compete for access to the translational machinery of the host. The model, based on the discrete stochastic processes of amplification and deactivation of LINEs copies, has been adapted to the data using Bayesian statistics to estimate its main parameters: rate of growth of transposons copy number and rate of past competition between transposons variants. This approach allows to estimate the activity of ancient LINE strains still present in the genome as deactivated components, and the possible competition among different strains. We leverage these results to highlight how the change in the chromatin structure of the murine species seems to be following an increase of LINEs activity during the appearance of the murine specific strain Lx. On the contrary, a similar response is absent in primates evolution, which follows a decrease of LINEs activity during the amplication of primate specific LIMA/LPB strains. | biophysics |
10.1101/516443 | Chloroplasts alter their morphology and accumulate at the pathogen interface during infection by Phytophthora infestans | Upon immune activation, chloroplasts switch off photosynthesis, produce anti-microbial compounds, and associate with the nucleus through tubular extensions called stromules. Although it is well-established that chloroplasts alter their position in response to light, little is known about the dynamics of chloroplasts movement in response to pathogen attack. Here, we report that chloroplasts accumulate at the pathogen interface during infection by the Irish potato famine pathogen Phytophthora infestans, associating with the specialized membrane that engulfs the pathogen haustorium. Chemical inhibition of actin polymerization reduces the accumulation of chloroplasts at the pathogen haustoria, suggesting this process is partially dependent on the actin cytoskeleton. However, chloroplast accumulation at haustoria does not necessarily rely on movement of the nucleus to this interface and is not affected by light conditions. Stromules are typically induced during infection, embracing haustoria and interconnecting chloroplasts, to form dynamic organelle clusters. We found that infection-triggered stromule formation relies on BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) mediated surface immune signaling, whereas chloroplast repositioning towards haustoria does not. Consistent with the defense-related induction of stromules, effector mediated suppression of BAK1 mediated immune signaling reduced stromule formation during infection. On the other hand, immune recognition of the same effector stimulated stromules, presumably via a different pathway. These findings implicate chloroplasts in a polarized response upon pathogen attack and point to more complex functions of these organelles in plant-pathogen interactions. | plant biology |
10.1101/516831 | Sequestration of RBM10 in Nuclear Bodies: Targeting Sequences and Biological Significance | RBM10 is an RNA-binding protein that regulates alternative splicing (AS). It localizes to the extra-nucleolar nucleoplasm and S1-1 nuclear bodies (NBs) in the nucleus. We investigated the biological significance of this localization in relation to its molecular function. Our analyses, employing deletion mutants, revealed that RBM10 possesses two S1-1 NB-targeting sequences (NBTSs), one in the KEKE motif region and another in the C2H2 Zn finger (ZnF). These NBTSs act synergistically to localize RBM10 to S1-1 NBs. The C2H2 ZnF not only acts as an NBTS, but is also essential for AS regulation by RBM10. Moreover, RBM10 does not participate in S1-1 NB formation, and without alterations of RBM10 protein levels, its NB-localization changes, increasing as cellular transcriptional activity declines, and vice versa. These results indicate that RBM10 is a transient component of S1-1 NBs and is sequestered in NBs via its NBTSs when cellular transcription decreases. We propose that the C2H2 ZnF exerts its NB-targeting activity when RBM10 is unbound by pre-mRNAs, and that NB-localization of RBM10 is a mechanism to control its AS activity in the nucleus.
Note that the previous title of this manuscript was Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance. | molecular biology |
10.1101/518936 | Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex | Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses indicated that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodelers known to be important for heterochromatin silencing. Deletion of Rbm10 results in significant reduction of Clr6 in heterochromatin. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation. | molecular biology |
10.1101/519629 | A Data-Driven Transcriptional Taxonomy of Adipogenic Chemicals to Identify White and Brite Adipogens | BackgroundChemicals in disparate structural classes activate specific subsets of PPAR{gamma}s transcriptional programs to generate adipocytes with distinct phenotypes.
ObjectivesOur objectives were to 1) establish a novel classification method to predict PPAR{gamma} ligands and modifying chemicals, and 2) create a taxonomy to group chemicals based on their effects on PPAR{gamma}s transcriptome and downstream metabolic functions. We tested the hypothesis that environmental adipogens highly ranked by the taxonomy, but segregated from therapeutic PPAR{gamma} ligands, would induce white but not brite adipogenesis.
Methods3T3-L1 cells were differentiated in the presence of 76 chemicals (negative controls, nuclear receptor ligands known to influence adipocyte biology, potential environmental PPAR{gamma} ligands). Differentiation was assessed by measuring lipid accumulation. mRNA expression was determined by RNA-Seq and validated by RT-qPCR. A novel classification model was developed using an amended random forest procedure. A subset of environmental contaminants identified as strong PPAR{gamma} agonists were analyzed by their effects on lipid handling, mitochondrial biogenesis and cellular respiration in 3T3-L1 cells and human preadipocytes.
ResultsWe used lipid accumulation and RNA sequencing data to develop a classification system that 1) identified PPAR{gamma} agonists, and 2) sorted chemicals into likely white or brite adipogens. Expression of Cidec was the most efficacious indicator of strong PPAR{gamma} activation. Two known environmental PPAR{gamma} ligands, tetrabromobisphenol A and triphenyl phosphate, which sorted distinctly from therapeutic ligands, induced white adipocyte genes but failed to induce Pgc1a and Ucp1, and induced fatty acid uptake but not mitochondrial biogenesis in 3T3-L1 cells. Moreover, two chemicals identified as highly ranked PPAR{gamma} agonists, tonalide and quinoxyfen, induced white adipogenesis without the concomitant health-promoting characteristics of brite adipocytes in mouse and human preadipocytes.
DiscussionA novel classification procedure accurately identified environmental chemicals as PPAR{gamma} ligands distinct from known PPAR{gamma}-activating therapeutics. The computational and experimental framework has general applicability to the classification of as-yet uncharacterized chemicals. | pharmacology and toxicology |
10.1101/521369 | Stimulation of phospholipase Cβ1 by Gαq promotes the assembly of stress granule proteins | During adverse conditions, mammalian cells regulate protein production by sequestering the translational machinery in membrane-less organelles known as stress granules. Here, we found that activation of the G protein subunit Gq promoted the formation of particles that contained stress granule proteins through a mechanism linked to the presence of phospholipase C{beta}1 (PLC{beta}1) in the cytosol. In experiments with PC12 and A10 cells, we showed that under basal conditions, cytosolic PLC{beta}1 bound to stress granule associated proteins, including PABPC1, eIF5A, and Ago2. Knockdown of cytosolic PLC{beta}1 with siRNA or promoting its relocalization to the plasma membrane by activating Gq resulted in the formation of particles containing the stress granule markers, PABPC1, G3BP1, and Ago2. Our studies showed that the composition of these particles resemble those formed under osmotic stress and are distinct from those formed by other stresses. Our results fit a simple thermodynamic model in which cytosolic PLC{beta}1 solubilizes stress granule proteins such that its movement to activated Gq releases these particles to enable the formation of stress granules. Together, our data are suggestive of a link between Gq-coupled signals and protein translation through stress granule formation. | biochemistry |
10.1101/522441 | A neuroendocrine pathway modulating osmotic stress in Drosophila | Environmental factors challenge the physiological homeostasis in animals, thereby evoking stress responses. Various mechanisms have evolved to counter stress at the organism level, including regulation by neuropeptides. In recent years, much progress has been made on the mechanisms and neuropeptides that regulate responses to metabolic/nutritional stress, as well as those involved in countering osmotic and ionic stresses. Here, we identified a peptidergic pathway that links these types of regulatory functions. We uncover the neuropeptide Corazonin (Crz), previously implicated in responses to metabolic stress, as a neuroendocrine factor that inhibits the release of a diuretic hormone, CAPA, and thereby modulates the tolerance to osmotic and ionic stress. Both knockdown of Crz and acute injections of Crz peptide impact desiccation tolerance and recovery from chill-coma. Mapping of the Crz receptor (CrzR) expression identified three pairs of Capa-expressing neurons (Va neurons) in the ventral nerve cord that mediate these effects of Crz. We show that Crz acts to restore water/ion homeostasis by inhibiting release of CAPA neuropeptides via inhibition of cAMP production in Va neurons. Knockdown of CrzR in Va neurons affects CAPA signaling, and consequently increases tolerance for desiccation, ionic stress and starvation, but delays chill-coma recovery. Optogenetic activation of Va neurons stimulates excretion and simultaneous activation of Crz and CAPA-expressing neurons reduces this response, supporting the inhibitory action of Crz. Thus, Crz inhibits Va neurons to maintain osmotic and ionic homeostasis, which in turn affects stress tolerance. Earlier work demonstrated that systemic Crz signaling restores nutrient levels by promoting food search and feeding. Here we additionally propose that Crz signaling also ensures osmotic homeostasis by inhibiting release of CAPA neuropeptides and suppressing diuresis. Thus, Crz ameliorates stress-associated physiology through systemic modulation of both peptidergic neurosecretory cells and the fat body in Drosophila.
Author summaryInsects are among the largest groups of animals and have adapted to inhabit almost all environments on Earth. Their success in surviving extreme conditions stems largely from their ability to withstand environmental stress, such as desiccation and cold. However, the neural mechanisms that are responsible for coordinating responses to counter these stresses are largely unknown. To address this, we delineate a neuroendocrine axis utilizing the neuropeptides Corazonin (Crz) and CAPA, that coordinate responses to metabolic and osmotic stress. We show that Crz inhibits the release of a diuretic peptide, CAPA from a set of neurosecretory cells. CAPA in turn influences osmotic and ionic balance via actions on the Malpighian tubules (the insect analogs of the kidney) and the intestine. Taken together with earlier work, our data suggest that Crz acts to restore metabolic homeostasis at starvation and osmotic homeostasis during desiccation by inhibiting release of the diuretic hormone CAPA. Hence, this work provides a mechanistic understanding of the neuroendocrine mitigation of metabolic and osmotic stress by two peptide systems. | neuroscience |
10.1101/522904 | Development and maintenance of synaptic structure is mediated by the alpha-tubulin acetyltransferase MEC-17/αTAT1 | The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author | cell biology |
10.1101/520536 | The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth | In all eutherian mammals, growth of the fetus is dependent upon a functional placenta, but whether and how the latter adapts to putative fetal signals is currently unknown. Here we demonstrate, through fetal, endothelial, hematopoietic and trophoblast-specific genetic manipulations in the mouse, that endothelial and fetus-derived IGF2 is required for the continuous expansion of the feto-placental microvasculature in late pregnancy. The effects of IGF2 on placental microvasculature expansion are mediated, in part, through IGF2R and angiopoietin-Tie2/TEK signalling. Additionally, IGF2 exerts IGF2R-ERK1/2-dependent pro-proliferative and angiogenic effects on primary feto-placental endothelial cells ex vivo. Endothelial and fetus-derived IGF2 also plays an important role in trophoblast morphogenesis, acting through Gcm1 and Synb. Thus, our study reveals a direct role for the imprinted Igf2-Igf2r axis on matching placental development to fetal growth and establishes the principle that hormone-like signals from the fetus play important roles in controlling placental microvasculature and trophoblast morphogenesis. | developmental biology |
10.1101/520536 | The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth | In all eutherian mammals, growth of the fetus is dependent upon a functional placenta, but whether and how the latter adapts to putative fetal signals is currently unknown. Here we demonstrate, through fetal, endothelial, hematopoietic and trophoblast-specific genetic manipulations in the mouse, that endothelial and fetus-derived IGF2 is required for the continuous expansion of the feto-placental microvasculature in late pregnancy. The effects of IGF2 on placental microvasculature expansion are mediated, in part, through IGF2R and angiopoietin-Tie2/TEK signalling. Additionally, IGF2 exerts IGF2R-ERK1/2-dependent pro-proliferative and angiogenic effects on primary feto-placental endothelial cells ex vivo. Endothelial and fetus-derived IGF2 also plays an important role in trophoblast morphogenesis, acting through Gcm1 and Synb. Thus, our study reveals a direct role for the imprinted Igf2-Igf2r axis on matching placental development to fetal growth and establishes the principle that hormone-like signals from the fetus play important roles in controlling placental microvasculature and trophoblast morphogenesis. | developmental biology |
10.1101/521401 | Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes | Chromatin undergoes drastic structural organization and epigenetic reprogramming during embryonic development. We present here a consistent view of the chromatin structural change, epigenetic reprogramming and the corresponding sequence dependence in both mouse and human embryo development. The two types of domains, identified earlier as forests and prairies, become spatially segregated during embryonic development, with the exception of zygotic genome activation (ZGA) and implantation, at which notable domain mixing occurs. Structural segregation largely coincides with DNA methylation and gene expression changes. Genes located in mixed prairie domains show proliferation and ectoderm differentiation-related function in ZGA and implantation, respectively. Chromatin of ectoderm shows the weakest and endoderm the strongest domain segregation in germ layers. This chromatin structure difference between different germ layers generally enlarges in further differentiation. The systematic chromatin structure establishment and its sequence-based segregation strongly suggest DNA sequence as a possible driving force for the establishment of chromatin 3D structures which affect profoundly the expression profile. Other possible factors correlated with/influencing chromatin structures, including temperature, germ layers, and cell cycle, were discussed for an understanding of concerted chromatin structure and epigenetic changes in development. | developmental biology |
10.1101/527002 | Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing | The Kruppel-like factor (Klf) gene family encodes for transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation, and development in bilaterians. While Klf genes have been shown to functionally specify various cell types in non-bilaterian animals, their role in early diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis results in abnormal development of several organs including the pharynx, tentacle bulbs, and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.
Summary StatementUsing CRISPR/Cas9 genome editing and morpholino oligonucleotide knockdown, this study shows that tissues derived from the endoderm are dependent upon Klf5 ortholog expression for proper development and patterning in the ctenophore Mnemiopsis leidyi. | developmental biology |
10.1101/525600 | Cellular transformation by combined lineage conversion and oncogene expression | Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senescence in human fibroblasts and primary hepatocytes. However, reprogramming fibroblasts to a liver progenitor fate, induced hepatocytes (iHeps), makes them sensitive to transformation by the same oncogenes. The transformed iHeps are highly proliferative, tumorigenic in nude mice, and bear gene expression signatures of liver cancer. These results show that tumorigenesis is triggered by a combination of three elements: the set of driver mutations, the cellular lineage, and the state of differentiation of the cells along the lineage. Our results provide direct support for the role of cell identity as a key determinant in transformation, and establish a paradigm for studying the dynamic role of oncogenic drivers in human tumorigenesis. | cancer biology |
10.1101/525600 | Cellular transformation by combined lineage conversion and oncogene expression | Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senescence in human fibroblasts and primary hepatocytes. However, reprogramming fibroblasts to a liver progenitor fate, induced hepatocytes (iHeps), makes them sensitive to transformation by the same oncogenes. The transformed iHeps are highly proliferative, tumorigenic in nude mice, and bear gene expression signatures of liver cancer. These results show that tumorigenesis is triggered by a combination of three elements: the set of driver mutations, the cellular lineage, and the state of differentiation of the cells along the lineage. Our results provide direct support for the role of cell identity as a key determinant in transformation, and establish a paradigm for studying the dynamic role of oncogenic drivers in human tumorigenesis. | cancer biology |
10.1101/527754 | Phosphorylation-dependent routing of RLP44 towards brassinosteroid or phytosulfokine signalling | Plants rely on a complex network of cell surface receptors to integrate developmental and environmental cues into behaviour adapted to the conditions. The largest group of these receptors, leucine-rich repeat receptor-like kinases, form a complex interaction network that is modulated and extended by receptor-like proteins. This raises the question of how specific outputs can be generated when receptor proteins are engaged in a plethora of promiscuous interactions. RECEPTOR-LIKE PROTEIN 44 (RLP44) acts to promote both brassinosteroid and phytosulfokine signalling, which orchestrate a wide variety of cellular responses. However, it is unclear how these activities are coordinated. Here, we show that RLP44 is phosphorylated in its highly conserved C-terminal cytosolic tail and that this post-translational modification governs its subcellular localization. RLP44 variants in which phosphorylation is blocked enter endocytosis prematurely, leading to an almost entirely intracellular localization, whereas phospho-mimicking or ectopic phosphorylation results in preferential RLP44 localization at the plasma membrane. Phosphorylation of the C-terminus is essential for brassinosteroid-associated functions of RLP44. In contrast, RLP44s role in phytosulfokine signalling is not affected by its phospho-status. Detailed mutational analysis suggests that phospho-charge, rather than modification of individual amino acids determines routing of RLP44 to its target receptor complexes, providing a framework to understand how a common component of different receptor complexes can get specifically engaged in a particular signalling pathway. | plant biology |
10.1101/529040 | Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice | In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads from fecal DNA, used to characterize the gut microbial communities present in these mice. These sequence reads included sufficient reads derived from the host mouse to identify the individual. A number of microbiome samples appeared to contain a mixture of DNA from two mice. We describe a method for identifying sample mix-ups in such microbiome data, as well as a method for evaluating sample mixtures in this context. | genetics |
10.1101/529040 | Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice | In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads from fecal DNA, used to characterize the gut microbial communities present in these mice. These sequence reads included sufficient reads derived from the host mouse to identify the individual. A number of microbiome samples appeared to contain a mixture of DNA from two mice. We describe a method for identifying sample mix-ups in such microbiome data, as well as a method for evaluating sample mixtures in this context. | genetics |
10.1101/529560 | Widespread latitudinal asymmetry in marginal population performance | AimRange shifts are expected to occur when populations at one range margin perform better than those at the other margin, yet no global trend in population performances at range margins has been demonstrated empirically across a wide range of taxa and biomes. Here we test the prediction that, if impacts of ongoing climate change on population performance are widespread, then populations from the high-latitude margin (HLM) should perform as well as or better than central populations, whereas populations at low-latitude margins (LLM) populations should perform worse.
LocationGlobal
Time period1898-2020
Major taxa studiedPlants and animals
MethodsTo test our prediction, we used a meta-analysis quantifying the empirical support for asymmetry in the performance of high- and low-latitude margin populations compared to central populations. Performance estimates were derived from 51 papers involving 113 margin-centre comparisons from 54 species and 705 populations. We then related these performance differences to climatic differences among populations. We also tested whether patterns are consistent across taxonomic kingdoms (plants vs. animals) and across habitats (marine vs. terrestrial).
ResultsPopulations at margins performed significantly worse than central populations and this trend was primarily driven by the low-latitude margin. Although the difference was of small magnitude, it was largely consistent across biological kingdoms and habitats. The differences in performance were positively related to the difference in average temperatures between populations during the period 1985-2016.
Major conclusionsThe observed asymmetry in marginal population performance confirms predictions about the effects of global climate change. It indicates that changes in demographic rates in marginal populations, despite extensive short-term variation, can serve as early-warning signals of impending range shifts. | ecology |
10.1101/529719 | Chemogenetic inhibition of a monosynaptic projection from the basolateral amygdala to the ventral hippocampus reduces appetitive and consummatory alcohol drinking behaviors | Alcohol use disorder (AUD) and anxiety/stressor disorders frequently co-occur and this dual diagnosis represents a major health and economic problem worldwide. The basolateral amygdala (BLA) is a key brain region that is known to contribute to the etiology of both disorders. Although many studies have implicated BLA hyperexcitability in the pathogenesis of AUD and comorbid conditions, relatively little is known about the specific efferent projections from this brain region that contribute to these disorders. Recent optogenetic studies have shown that the BLA sends a strong monosynaptic excitatory projection to the ventral hippocampus (vHC) and that this circuit modulates anxiety- and fear-related behaviors. However, it is not known if this pathway influences alcohol drinking-related behaviors. Here, we employed a rodent operant drinking regimen that procedurally separates appetitive (e.g. seeking) and consummatory (e.g. intake) behaviors, chemogenetics, and brain region-specific microinjections, to determine if BLA-vHC circuitry influences alcohol drinking-related measures. We first confirmed prior optogenetic findings that silencing this circuit reduced anxiety-like behaviors on the elevated plus-maze. We then demonstrated that inhibiting the BLA-vHC pathway significantly reduced appetitive alcohol drinking-related behaviors while having no effect on consummatory measures. Sucrose seeking measures were also reduced following chemogenetic inhibition of this circuit. Taken together, these findings provide the first indication that the BLA-vHC circuit may regulate appetitive alcohol drinking-related behaviors and add to a growing body of evidence suggesting that dysregulation of this pathway may contribute to the pathophysiology of AUD and anxiety/stressor-related disorders.
HIGHLIGHTSO_LIThe basolateral amygdala sends a monosynaptic glutamatergic projection to the ventral hippocampus
C_LIO_LIInhibiting this circuit reduces anxiety-like behaviors in male Long Evans rats
C_LIO_LIInhibition of this pathway also decreases operant alcohol seeking-related behaviors
C_LI | neuroscience |
10.1101/530329 | Thunor: Visualization and Analysis of High-Throughput Dose-response Datasets | High-throughput cell proliferation assays to quantify drug-response are becoming increasingly common and powerful with the emergence of improved automation and multi-time point analysis methods. However, pipelines for analysis of these datasets that provide reproducible, efficient, and interactive visualization and interpretation are sorely lacking. To address this need, we introduce Thunor, an open-source software platform to manage, analyze, and visualize large, dose-dependent cell proliferation datasets. Thunor supports both end-point and time-based proliferation assays as input. It provides a simple, user-friendly interface with interactive plots and publication-quality images of cell proliferation time courses, dose-response curves, and derived dose-response metrics, e.g. IC50, including across datasets or grouped by tags. Tags are categorical labels for cell lines and drugs, used for aggregation, visualization, and statistical analysis, e.g. cell line mutation or drug class/target pathway. A graphical plate map tool is included to facilitate plate annotation with cell lines, drugs, and concentrations upon data upload. Datasets can be shared with other users via point-and-click access control. We demonstrate the utility of Thunor to examine and gain insight from two large drug response datasets: a large, publicly available cell viability database and an in-house, high-throughput proliferation rate dataset. Thunor is available from www.thunor.net. | pharmacology and toxicology |
10.1101/530220 | High-pass filtering artifacts in multivariate classification of neural time series data | 0.BackgroundTraditionally, EEG/MEG data are high-pass filtered and baseline-corrected to remove slow drifts. Minor deleterious effects of high-pass filtering in traditional time-series analysis have been well-documented, including temporal displacements. However, its effects on time-resolved multivariate pattern classification analyses (MVPA) are largely unknown.
New MethodTo prevent potential displacement effects, we extend an alternative method of removing slow drift noise - robust detrending - with a procedure in which we mask out all cortical events from each trial. We refer to this method as trial-masked robust detrending.
ResultsIn both real and simulated EEG data of a working memory experiment, we show that both high-pass filtering and standard robust detrending create artifacts that result in the displacement of multivariate patterns into activity silent periods, particularly apparent in temporal generalization analyses, and especially in combination with baseline correction. We show that trial-masked robust detrending is free from such displacements.
Comparison with Existing Method(s)Temporal displacement may emerge even with modest filter cut-off settings such as 0.05 Hz, and even in regular robust detrending. However, trial-masked robust detrending results in artifact-free decoding without displacements. Baseline correction may unwittingly obfuscate spurious decoding effects and displace them to the rest of the trial.
ConclusionsDecoding analyses benefits from trial-masked robust detrending, without the unwanted side effects introduced by filtering or regular robust detrending. However, for sufficiently clean data sets and sufficiently strong signals, no filtering or detrending at all may work adequately. Implications for other types of data are discussed, followed by a number of recommendations. | neuroscience |
10.1101/528638 | The HIV-1 ribonucleoprotein dynamically regulates its condensate behavior and drives acceleration of protease activity through membraneless granular phase separation | A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase separated molecular sponges, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ~2400 Gag and ~120 GagPol by viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak-strong-moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules. | molecular biology |
10.1101/531822 | Long-term potentiation in neurogliaform cells modulates excitation-inhibition balance in the temporoammonic pathway | Apical dendrites of pyramidal neurons integrate information from higher-order cortex and thalamus, and gate signaling and plasticity at proximal synapses. In the hippocampus, neurogliaform cells and other interneurons located within stratum lacunosum-moleculare mediate powerful inhibition of CA1 pyramidal neuron distal dendrites. Is the recruitment of such inhibition itself subject to use-dependent plasticity, and if so, what induction rules apply? Here we show that interneurons in mouse stratum lacunosum-moleculare exhibit Hebbian NMDA receptor-dependent long-term potentiation (LTP). Such plasticity can be induced by selective optogenetic stimulation of afferent fibers in the temporoammonic pathway from the entorhinal cortex, but not by equivalent stimulation of afferents from the thalamic nucleus reuniens. We further show that theta-burst patterns of afferent firing induces LTP in neurogliaform interneurons identified using neuron-derived neurotrophic factor (Ndnf)-Cre mice. Theta-burst activity of entorhinal cortex afferents led to an increase in disynaptic feed-forward inhibition, but not monosynaptic excitation, of CA1 pyramidal neurons. Activity-dependent synaptic plasticity of neurogliaform cells in stratum lacunosum-moleculare thus alters the excitation-inhibition balance at entorhinal cortex inputs to the apical dendrites of pyramidal neurons, implying a dynamic role for these interneurons in gating CA1 dendritic computations.
Significance statementElectrogenic phenomena in distal dendrites of principal neurons in the hippocampus have a major role in gating synaptic plasticity at afferent synapses on proximal dendrites. Apical dendrites also receive powerful feed-forward inhibition mediated in large part by neurogliaform neurons. Here we show that theta-burst activity in afferents from the entorhinal cortex induces Hebbian long-term potentiation at excitatory synapses recruiting these GABAergic cells. Such LTP increases disynaptic inhibition of principal neurons, thus shifting the excitation-inhibition balance in the temporoammonic pathway in favor of inhibition, with implications for computations and learning rules in proximal dendrites. | neuroscience |
10.1101/532952 | Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks | Remote sensing can transform the speed, scale, and cost of biodiversity and forestry surveys. Data acquisition currently outpaces the ability to identify individual organisms in high resolution imagery. We outline an approach for identifying tree-crowns in RGB imagery while using a semi-supervised deep learning detection network. Individual crown delineation has been a long-standing challenge in remote sensing and available algorithms produce mixed results. We show that deep learning models can leverage existing Light Detection and Ranging (LIDAR)-based unsupervised delineation to generate trees that are used for training an initial RGB crown detection model. Despite limitations in the original unsupervised detection approach, this noisy training data may contain information from which the neural network can learn initial tree features. We then refine the initial model using a small number of higher-quality hand-annotated RGB images. We validate our proposed approach while using an open-canopy site in the National Ecological Observation Network. Our results show that a model using 434,551 self-generated trees with the addition of 2848 hand-annotated trees yields accurate predictions in natural landscapes. Using an intersection-over-union threshold of 0.5, the full model had an average tree crown recall of 0.69, with a precision of 0.61 for the visually-annotated data. The model had an average tree detection rate of 0.82 for the field collected stems. The addition of a small number of hand-annotated trees improved the performance over the initial self-supervised model. This semi-supervised deep learning approach demonstrates that remote sensing can overcome a lack of labeled training data by generating noisy data for initial training using unsupervised methods and retraining the resulting models with high quality labeled data. | ecology |
10.1101/532952 | Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks | Remote sensing can transform the speed, scale, and cost of biodiversity and forestry surveys. Data acquisition currently outpaces the ability to identify individual organisms in high resolution imagery. We outline an approach for identifying tree-crowns in RGB imagery while using a semi-supervised deep learning detection network. Individual crown delineation has been a long-standing challenge in remote sensing and available algorithms produce mixed results. We show that deep learning models can leverage existing Light Detection and Ranging (LIDAR)-based unsupervised delineation to generate trees that are used for training an initial RGB crown detection model. Despite limitations in the original unsupervised detection approach, this noisy training data may contain information from which the neural network can learn initial tree features. We then refine the initial model using a small number of higher-quality hand-annotated RGB images. We validate our proposed approach while using an open-canopy site in the National Ecological Observation Network. Our results show that a model using 434,551 self-generated trees with the addition of 2848 hand-annotated trees yields accurate predictions in natural landscapes. Using an intersection-over-union threshold of 0.5, the full model had an average tree crown recall of 0.69, with a precision of 0.61 for the visually-annotated data. The model had an average tree detection rate of 0.82 for the field collected stems. The addition of a small number of hand-annotated trees improved the performance over the initial self-supervised model. This semi-supervised deep learning approach demonstrates that remote sensing can overcome a lack of labeled training data by generating noisy data for initial training using unsupervised methods and retraining the resulting models with high quality labeled data. | ecology |
10.1101/533323 | Multi-omic analyses reveal a role for mammalian CIC in cell cycle regulation and mitotic fidelity | CIC encodes a transcriptional repressor that is inactivated by loss-of-function mutations in several cancer types, indicating that it may function as a tumor suppressor. Recent studies have indicated that CIC may regulate cell cycle genes in humans; however, a systematic investigation of this proposed role has not yet been reported. Here, we used single-cell RNA sequencing to show that inactivation of CIC in human cell lines correlated with transcriptional dysregulation of genes involved in cell cycle control. We also mapped CICs protein-protein and genetic interaction networks, identifying interactions between CIC and members of the Switch/Sucrose Non-Fermenting (SWI/SNF) complex as well as revealing novel candidate interactions between CIC and cell cycle regulators. We further showed that CIC loss was associated with an increased frequency of mitotic defects in human cell lines and in a mouse model. Our study thus positions CIC as a cell cycle regulator and indicates that CIC loss can lead to mitotic errors, consistent with CICs emerging role as a tumor suppressor of relevance in several cancer contexts. | cancer biology |
10.1101/534834 | Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data | Advances in single-cell transcriptomics enable measuring the gene expression of individual cells, allowing cells to be ordered by their state in a dynamic biological process. Many algorithms assign pseudotimes to each cell, representing the progress along the biological process. Ordering the expression data according to such pseudotimes can be valuable for understanding the underlying regulator-gene interactions in a biological process, such as differentiation. However, the distribution of cells sampled along a transitional process, and hence that of the pseudotimes assigned to them, is not uniform. This prevents using many standard mathematical methods for analyzing the ordered gene expression states. We present Single-cell Inference of Networks using Granger Ensembles (SINGE), an algorithm for gene regulatory network inference from single-cell gene expression data. Given ordered single-cell data, SINGE uses kernel-based Granger Causality regression, which smooths the irregular pseudotimes and missing expression values. It then aggregates the predictions from an ensemble of regression analyses with a modified Borda count to compile a ranked list of candidate interactions between transcriptional regulators and their target genes. In two mouse embryonic stem cell differentiation case studies, SINGE outperforms other contemporary algorithms for gene network reconstruction. However, a more detailed examination reveals caveats about transcriptional network reconstruction with single-cell RNA-seq data. Network inference methods, including SINGE, may have near random performance for predicting the targets of many individual regulators even if the overall performance is good. In addition, including uninformative pseudotime values can hurt the performance of network reconstruction methods. A MATLAB implementation of SINGE is available at https://github.com/gitter-lab/SINGE. | bioinformatics |
10.1101/534750 | Multiple sources of Shh are critical for the generation and scaling of ventral spinal cord oligodendrocyte precursor populations. | Graded Sonic Hedgehog (Shh) signaling emanating from notochord and floorplate patterns the early neural tube. Soon thereafter, Shh signaling strength within the ventricular zone becomes dis-contiguous and discontinuous along the ventral to dorsal axis suggesting a distribution of Shh that cannot be achieved by diffusion alone. Here we discover that sequential activation of Shh expression by ventricular zone derivatives is critical for counteracting a precocious exhaustion of the Olig2 precursor cell population of the pMN domain at the end of motor neuron genesis and during the subsequent phase of ventral oligodendrocyte precursor production. Selective expression of Shh by motor neurons of the lateral motor column at the beginning of oligodendrogenesis ensures a more yielding pMN domain at limb levels compared to thoracic levels. Thus, patterned expression of Shh by ventricular zone derivatives including earlier born neurons contributes to the scaling of the spinal cord along the anterior - posterior axis by regulating the activity of a select ventricular zone precursor domain at later stages of development. | developmental biology |
10.1101/536078 | Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments | Gas hydrates harbor gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate-methane transition zone, metal (iron/manganese) reduction zone, and gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na+/H+ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent (TRAP) transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g., high salt brines, high pressure, and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K+-stimulated pyrophosphatase and capsule proteins.
Originality-Significance StatementThis work provides insights into the metabolism and adaptations of microbes that are ubiquitous and abundant in methane-rich ecosystems. Our findings suggest that bacterial fermentation is a source of acetate for aceticlastic methanogenesis and a driver of iron reduction in the metal reduction zone. Atribacteria, the most abundant phylum in gas hydrate-bearing sediments, possess multiple strategies to cope with environmental stress. | microbiology |
10.1101/538165 | A Stomata Classification and Detection System in Microscope Images of Maize Cultivars | Research on stomata, i.e., morphological structures of plants, has increased in popularity in the last years. These structures (pores) are in charge of the interaction between the internal plant system and the environment, working on different processes such as photosynthesis and transpiration stream. Besides, a better understanding of the pore mechanism plays a significant role when exploring the evolution process, as well as the behavior of plants. Although the study of stomata in dicots species of plants has advanced considerably in the past years, there is little information about stomata of cereal grasses. Also, automated detection of these structures have been considered in the literature, but some gaps are still uncovered. This fact is motivated by high morphological variation of stomata and the presence of noise from the image acquisition step. In this work, we propose a new methodology for automatic stomata classification and a new detection system in microscope images for maize cultivars. We have achieved an approximated accuracy of 97.1% in the identification of stomata regions using classifiers based on deep learning features, which figures out as a nearly perfect classification system. | plant biology |
10.1101/540971 | A scalar Poincare map for struggling in Xenopus tadpoles | Short-term synaptic plasticity is widely found in many areas of the central nervous system. In particular, it is believed that synaptic depression can act as a mechanism to allow simple networks to generate a range of different firing patterns. The locomotor circuit of hatchling Xenopus tadpoles produces two types of behaviours: swimming and the slower, stronger struggling movement that is associated with rhythmic bends of the whole body. Struggling is accompanied by anti-phase bursts in neurons on each side of the spinal cord and is believed to be governed by a short-term synaptic depression of commissural inhibition. To better understand burst generation in struggling, we study a minimal network of two neurons coupled through depressing inhibitory synapses. Depending on the strength of the synaptic conductance between the two neurons, such a network can produce symmetric n - n anti-phase bursts, where neurons fire n spikes in alternation, with the period of such solutions increasing with the strength of the synaptic conductance. Relying on the timescale disparity in the model, we reduce the eight-dimensional network equations to a fully explicit scalar Poincare burst map. This map tracks the state of synaptic depression from one burst to the next, and captures the complex bursting dynamics of the network. Fixed points of this map are associated with stable burst solutions of the full network model, and are created through fold bifurcations of maps. We derive conditions that describe period increment bifurcations between stable n - n and (n + 1) - (n + 1) bursts, producing a full bifurcation diagram of the burst cycle period. Predictions of the Poincare map fit excellently with numerical simulations of the full network model, and allow the study of parameter sensitivity for rhythm generation. | neuroscience |
10.1101/542340 | Protein appetite drives macronutrient-related differences in ventral tegmental area neural activity | Control of protein intake is essential for numerous biological processes as several amino acids cannot be synthesized de novo, however, its neurobiological substrates are still poorly understood. In the present study, we combined in vivo fiber photometry with nutrient-conditioned flavor in a rat model of protein appetite to record neuronal activity in the ventral tegmental area (VTA), a central brain region for the control of food-related processes. In adult male rats, protein restriction increased preference for casein (protein) over maltodextrin (carbohydrate). Moreover, protein consumption was associated with a greater VTA response relative to carbohydrate. After initial nutrient preference, a switch from a normal balanced diet to protein restriction induced rapid development of protein preference but required extensive exposure to macronutrient solutions to induce greater VTA responses to casein. Furthermore, prior protein restriction induced long-lasting food preference and VTA responses. This study reveals that VTA circuits are involved in protein appetite in times of need, a crucial process for all animals to acquire an adequate amount of protein in their diet.
Significance StatementAcquiring insufficient protein in ones diet has severe consequences for health and ultimately will lead to death. In addition, a low level of dietary protein has been proposed as a driver of obesity as it can leverage up intake of fat and carbohydrate. However, much remains unknown about the role of the brain in ensuring adequate intake of protein. Here, we show that in a state of protein restriction a key node in brain reward circuitry, the ventral tegmental area, is activated more strongly during consumption of protein than carbohydrate. Moreover, although rats behavior changed to reflect new protein status, patterns of neural activity were more persistent and only loosely linked to protein status. | neuroscience |
10.1101/544981 | Dot1L-dependent H3K79 methylation facilitates histone variant H2A.Z exchange at DNA double strand breaks and is required for high fidelity, homology-directed DNA repair | In eukaryotic cells, the homology-directed repair (HDR) and non-homologous end joining (NHEJ) pathways are required for the repair of DNA double strand breaks (DSB). The high-fidelity HDR pathway is particularly important for maintenance of genomic stability. In mammals, histone post-translational modifications and histone variant exchange into nucleosomes at sites of DSB generate an open chromatin state necessary for repair to take place. However, the specific contributions of histone modifications to histone variant exchange at DSB sites and the influence of these changes on the DNA repair process and genome stability are incompletely understood. Here we show that Dot1L-catalyzed methylation of H3 histone on lysine 79 (H3K79) is required for efficient HDR of DSB. In cells with DNA DSB either lacking Dot1L or expressing a methylation-dead Dot1L, there is altered kinetics of DNA repair factor recruitment, markedly decreased H2A.Z incorporation at DSB sites, and a specific and profound reduction in HDR, which results in significant genomic instability. These findings demonstrate a new role for Dot1L, identifying it as a critical regulator of the DNA repair process and a steward of genomic integrity. | molecular biology |
10.1101/541805 | Optical measurement of voltage sensing by endogenous ion channel | A primary goal of molecular physiology is to understand how conformational changes of proteins affect the function of cells, tissues, and organisms. Here, we describe an imaging method for measuring the conformational changes of the voltage sensors of endogenous ion channel proteins within live tissue, without genetic modification. We synthesized GxTX-594, a variant of the peptidyl tarantula toxin guangxitoxin-1E, conjugated to a fluorophore optimal for two-photon excitation imaging through light-scattering tissue. GxTX-594 targets the voltage sensors of Kv2 proteins, which form potassium channels and plasma membrane-endoplasmic reticulum junctions. GxTX-594 dynamically labels Kv2 proteins on cell surfaces in response to voltage stimulation. To interpret dynamic changes in labeling intensity, we developed a statistical thermodynamic model that relates the conformational changes of Kv2 voltage sensors to labeling intensity. We used two-photon excitation imaging of rat brain slices to image Kv2 proteins in neurons. This imaging method enabled identification of conformational changes of endogenous Kv2 voltage sensors in tissue. | biophysics |
10.1101/546309 | BLight: Efficient exact associative structure for k-mers | MotivationA plethora of methods and applications share the fundamental need to associate information to words for high throughput sequence analysis. Doing so for billions of k-mers is commonly a scalability problem, as exact associative indexes can be memory expensive. Recent works take advantage of overlaps between k-mers to leverage this challenge. Yet existing data structures are either unable to associate information to k-mers or are not lightweight enough.
ResultsWe present BLight, a static and exact data structure able to associate unique identifiers to k-mers and determine their membership in a set without false positive, that scales to huge k-mer sets with a low memory cost. This index combines an extremely compact representation along with very fast queries. Besides, its construction is efficient and needs no additional memory. Our implementation achieves to index the k-mers from the human genome using 8GB of RAM (23 bits per k-mer) within 10 minutes and the k-mers from the large axolotl genome using 63 GB of memory (27 bits per k-mer) within 76 minutes. Furthermore, while being memory efficient, the index provides a very high throughput: 1.4 million queries per second on a single CPU or 16.1 million using 12 cores. Finally, we also present how BLight can practically represent metagenomic and transcriptomic sequencing data to highlight its wide applicative range.
AvailabilityWe wrote the BLight index as an open source C++ library under the AGPL3 license available at github.com/Malfoy/BLight. It is designed as a user-friendly library and comes along with code usage samples. | bioinformatics |
10.1101/548412 | Work Flows for Cellular Epidemiology, From Conception to Translation | The authors have withdrawn their manuscript after issues with the cell viability validation (Fig. 8) were found. In the interest of furthering science and ensuring that clinical decisions are based on best practices and evidence, the issue is described in more detail in the peer-reviewed, published paper: https://www.frontiersin.org/articles/10.3389/fphys.2021.647603/full
Knothe Tate ML, Srikantha A, Wojek C, Zeidler D (2021) Connectomics of Bone to Brain-- Probing Physical Renderings of Cellular Experience, Frontiers in Physiology 12: 1018, doi: 10.3389/fphys.2021.647603
As noted in that published work: "Osteocyte coordinates can be extracted from the YOLO classified image set, enabling high throughput analyses of massive datasets, which in the future could include other cellular inhabitants of tissues including blood cells, immune cells, chondrocytes, etc. While the method shows great promise for automated detection of cells, the greatest limitation of the method is the definition of appropriate and unbiased classifiers. The definition of osteocytes as pyknotic and viable based on the number of cell processes was shown to be flawed in a parallel study testing the assumption using biochemical based viability measures (Anastopolous and Knothe Tate, 2021)."
Therefore, the authors do not wish this work to be cited as reference for the project.
If you have any questions, please contact the corresponding author. | physiology |
10.1101/547794 | Maize brace root mechanics vary by whorl, genotype, and reproductive stage | Root lodging is responsible for significant crop losses world-wide. During root lodging, roots fail by breaking, buckling, or pulling out of the ground. In maize, above-ground roots, called brace roots, have been shown to reduce root lodging susceptibility. However, the underlying structural-functional properties of brace roots that prevent root lodging are poorly defined. In this study, we quantified structural mechanical properties, geometry, and bending moduli for brace roots from different whorls, genotypes, and reproductive stages. Using 3-point bend tests, we show that brace root mechanics are variable by whorl, genotype, and reproductive stage. Generally, we find that within each genotype and reproductive stage, the brace roots from the whorl closest to the ground had higher structural mechanical properties and a lower bending modulus than brace roots from the second whorl. There was additional variation between genotypes and reproductive stages. Specifically, genotypes with higher structural mechanical properties also had a higher bending modulus, and senesced brace roots had lower structural mechanical properties than hydrated brace roots. Collectively these results highlight the importance of considering whorl-of-origin, genotype, and reproductive stage for quantification of brace root mechanics, which is important for mitigating crop loss due to root mechanical failure. | plant biology |
10.1101/549386 | Urinary glucocorticoids in harbour seal (Phoca vitulina) pups during rehabilitation | The glucocorticoid (GC) hormone cortisol is often measured in animals to indicate their welfare and stress levels. However, the levels of other naturally occurring GCs are usually overlooked. We aimed to investigate whether aspects of the care and conditions of harbour seal (Phoca vitulina) pups in rehabilitation centres are reflected in urinary concentrations of four endogenous GCs. Urine samples were collected non-invasively from pups taken in as "orphans" at five different rehabilitation centres: three on the Irish Sea and two in the southern North Sea. Concentrations of urinary cortisol, cortisone, prednisolone and prednisone were analysed by mass spectrometry. Urinary concentrations of endogenous prednisolone and prednisone occurred in similar magnitude to cortisol, for the first time in any mammal species. The levels of all GC concentrations decreased as pups gained mass, but the most significant effect was for prednisone. Pups with mass less than 11kg, i.e. healthy average birth mass, had significantly higher levels of prednisone (but not of the other GCs) than pups of 11kg or more. Cortisol, cortisone and prednisolone concentrations were slightly higher for pups without access to water than those with water; however, we found no significant effect of social group on GC levels. Based on these findings, we tentatively suggest that the GCs may be elevated in harbour seal pups during rehabilitation in response to some physiological factors deviating from the norm of free-living pups. Our findings highlight the importance of measuring other GCs, in addition to cortisol, for understanding stressors affecting the welfare of seal pup in rehabilitation. | zoology |
10.1101/550368 | The pharmacodynamic inoculum effect from the perspective of bacterial population modeling | SynopsisO_ST_ABSBackgroundC_ST_ABSThe quantitative determination of the effects of antimicrobials is essential for our understanding of pharmacodynamics and for their rational clinical application. However, common pharmacodynamic measures of antimicrobial efficacy, such as the MIC and the pharmacodynamic function, fail to capture the observed dependence of efficacy on the bacterial population size -- a phenomenon called inoculum effect.
ObjectivesWe aimed to assess the relationship between bacterial inoculum size and pharmacodynamic parameters, and to determine the consequences of the inoculum effect on bacterial population dynamics under treatment with antimicrobials.
MethodsWe used the mathematical multi-hit model to quantify the effect of the inoculum on the pharmacodynamic parameters. The model describes antimicrobial action mechanistically, which allowed us to test various hypotheses concerning the mechanistic basis of the inoculum effect.
ResultsOur model showed that the inoculum effect can arise from the binding dynamics of antimicrobial molecules to bacterial targets alone and does not require enzymatic degradation of antimicrobials. With enzymatic degradation, however, the inoculum effect is more pronounced. We propose to include the inoculum effect when measuring antimicrobial efficacy, i. e. to extend the pharmacodynamic function with the inoculum effect. This extended pharmacodynamic function mimiced simple long-term population dynamics well. More complex scenarios were only captured with the mechanism-based multi-hit model. In simulations with competing antimicrobial-sensitive and -resistant bacteria, neglecting the inoculum effect lead to an overestimation of the competitive ability of the resistant strain.
ConclusionsOur work emphasizes that the pharmacodynamic function -- and in general any efficacy measure, e.g. the MIC -- should include information about the inoculum size on which it is based, and ideally account for the inoculum effect. | pharmacology and toxicology |
10.1101/551580 | Opposing steroid signals modulate protein homeostasis through deep changes in fat metabolism in Caenorhabditis elegans | Protein homeostasis is crucial for viability of all organisms, and mutations that enhance protein aggregation cause different human pathologies, including polyglutamine (polyQ) diseases, such as some spinocerebellar ataxias or Huntington disease. Here, we report that neuronal Stomatin-like protein UNC-1 protects against aggregation of prone-to-aggregate proteins, like polyQs, -synuclein and {beta}-amyloid, in C. elegans. UNC-1, in IL2 neurons, antagonizes the function of the cytosolic sulfotransferase SSU-1 in neurohormonal signalling from ASJ neurons. The target of this hormone is the nuclear hormone receptor NHR-1, which acts cell-autonomously to protect from aggregation in muscles. A second nuclear hormone receptor, DAF-12, functions oppositely to NHR-1 to maintain protein homeostasis. Transcriptomics analyses reveal deep changes in the expression of genes involved in fat metabolism, in unc-1 mutants, which are regulated by NHR-1. This suggest that fat metabolism changes, controlled by neurohormonal signalling, contributes to modulate protein homeostasis. | genetics |
10.1101/547877 | Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks. | AO_SCPLOWBSTRACTC_SCPLOWTransposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called "dark matter of the genome", the part of the genome in which nothing is immediately recognizable as biologically functional.
We developed a new method, based on k-mers, to identify degenerate TE sequences. With this new algorithm, we detect up to 10% of the A. thaliana genome as derived from as yet unidentified TEs, bringing the proportion of the genome known to be derived from TEs up to 50%. A significant proportion of these sequences overlapped conserved non-coding sequences identified in crucifers and rosids, and transcription factor binding sites. They are overrepresented in some gene regulation networks, such as the flowering gene network, suggesting a functional role for these sequences that have been conserved for more than 100 million years, since the spread of flowering plants in the Cretaceous. | genomics |
10.1101/547877 | Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks. | AO_SCPLOWBSTRACTC_SCPLOWTransposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called "dark matter of the genome", the part of the genome in which nothing is immediately recognizable as biologically functional.
We developed a new method, based on k-mers, to identify degenerate TE sequences. With this new algorithm, we detect up to 10% of the A. thaliana genome as derived from as yet unidentified TEs, bringing the proportion of the genome known to be derived from TEs up to 50%. A significant proportion of these sequences overlapped conserved non-coding sequences identified in crucifers and rosids, and transcription factor binding sites. They are overrepresented in some gene regulation networks, such as the flowering gene network, suggesting a functional role for these sequences that have been conserved for more than 100 million years, since the spread of flowering plants in the Cretaceous. | genomics |
10.1101/550640 | Rabies virus with a destabilization domain added to its nucleoprotein spreads between neurons only if the domain is removed | Monosynaptic tracing using rabies virus is an important technique in neuroscience, allowing brain-wide labeling of neurons directly presynaptic to a targeted neuronal population. A 2017 article reported development of a noncytotoxic version - a major advance - based on attenuating the rabies virus by addition of a destabilization domain to the C-terminus of a viral protein. However, this modification did not appear to hinder the ability of the virus to spread between neurons. We analyzed two viruses provided by the authors and show here that both were mutants that had lost the intended modification, explaining the papers paradoxical results. We then made a virus that actually did have the intended modification and found that it did not spread under the conditions described in the original paper - namely, without an exogenous protease being expressed in order to remove the destabilization domain - but that it did spread, albeit with relatively low efficiency, if the protease was supplied. We conclude that the new approach is not robust but that it may become a viable technique given further optimization and validation.
SIGNIFICANCE STATEMENTRabies virus, which spreads between synaptically connected neurons, has been one of the primary tools used by neuroscientists to reveal the organization of the brain. A new modification to rabies virus was recently reported to allow the mapping of connected neurons without adverse effects on the cells health, unlike earlier versions. Here we show that the conclusions of that study were probably incorrect and based on having used viruses that had lost the intended modification because of mutations. We also show that a rabies virus that does retain the intended modification does not spread between neurons under the conditions reported previously; however, it does spread between neurons under different conditions, suggesting that the approach may be successful if refined further. | neuroscience |
10.1101/550640 | Rabies virus with a destabilization domain added to its nucleoprotein spreads between neurons only if the domain is removed | Monosynaptic tracing using rabies virus is an important technique in neuroscience, allowing brain-wide labeling of neurons directly presynaptic to a targeted neuronal population. A 2017 article reported development of a noncytotoxic version - a major advance - based on attenuating the rabies virus by addition of a destabilization domain to the C-terminus of a viral protein. However, this modification did not appear to hinder the ability of the virus to spread between neurons. We analyzed two viruses provided by the authors and show here that both were mutants that had lost the intended modification, explaining the papers paradoxical results. We then made a virus that actually did have the intended modification and found that it did not spread under the conditions described in the original paper - namely, without an exogenous protease being expressed in order to remove the destabilization domain - but that it did spread, albeit with relatively low efficiency, if the protease was supplied. We conclude that the new approach is not robust but that it may become a viable technique given further optimization and validation.
SIGNIFICANCE STATEMENTRabies virus, which spreads between synaptically connected neurons, has been one of the primary tools used by neuroscientists to reveal the organization of the brain. A new modification to rabies virus was recently reported to allow the mapping of connected neurons without adverse effects on the cells health, unlike earlier versions. Here we show that the conclusions of that study were probably incorrect and based on having used viruses that had lost the intended modification because of mutations. We also show that a rabies virus that does retain the intended modification does not spread between neurons under the conditions reported previously; however, it does spread between neurons under different conditions, suggesting that the approach may be successful if refined further. | neuroscience |
10.1101/555276 | Dynamically Linking Influenza Virus Infection Kinetics, Lung Injury, Inflammation, and Disease Severity | Influenza viruses cause a significant amount of morbidity and mortality. Understanding host immune control efficacy and how different factors influence lung injury and disease severity are critical. Here, we established dynamical connections between viral loads, infected cells, CD8+ T cell-mediated clearance, lung injury, inflammation, and disease severity using an integrative model-experiment exchange. The model was validated through CD8 depletion and whole lung histomorphometry, which showed that the infected area matched the model-predicted infected cell dynamics and that the resolved area paralleled the relative CD8 dynamics. Inflammation could further be predicted by the infected cell dynamics, and additional analyses revealed nonlinear relations between lung injury, inflammation, and disease severity. These links between important pathogen kinetics and host pathology enhance our ability to forecast disease progression, potential complications, and therapeutic efficacy. | systems biology |
10.1101/556571 | Transcriptomic analysis of human and mouse muscle during hyperinsulinemia demonstrates insulin receptor downregulation as a mechanism for insulin resistance | Hyperinsulinemia is commonly viewed as a compensatory response to insulin resistance, yet studies have suggested that chronically elevated insulin may also drive insulin resistance. The molecular mechanisms underpinning this potentially cyclic process remain poorly defined, especially on a transcriptome-wide level. To study the direct effects of prolonged exposure to excess insulin in muscle cells, we incubated C2C12 myotubes with elevated insulin for 16 hours, followed by 6 hours of serum starvation, and established that acute AKT and ERK signaling were attenuated in this model of in vitro hyperinsulinemia. Global RNA-sequencing of cells both before and after nutrient withdrawal highlighted genes in the insulin signaling, FOXO signaling, and glucose metabolism pathways indicative of hyperinsulinemia and starvation programs. We observed that hyperinsulinemia led to a substantial reduction in insulin receptor (Insr) gene expression, and subsequently a reduced surface INSR and total INSR protein, both in vitro and in vivo. Transcriptomic meta-analysis in >450 human samples demonstrated that fasting insulin reliably and negatively correlated with insulin receptor (INSR) mRNA in skeletal muscle. Bioinformatic modeling combined with RNAi, identified SIN3A as a negative regulator of Insr mRNA (and JUND, MAX, and MXI as positive regulators of Irs2 mRNA). Together, our analysis identifies novel mechanisms which may explain the cyclic processes underlying hyperinsulinemia-induced insulin resistance in muscle, a process directly relevant to the etiology and disease progression of type 2 diabetes. | physiology |
10.1101/558890 | Endocytosis against high turgor pressure is made easier by partial protein coating and a freely rotating base | During clathrin-mediated endocytosis, a patch of flat plasma membrane is deformed into a vesicle. In walled cells, such as plants and fungi, the turgor pressure is high and pushes the membrane against the cell wall, thus hindering membrane internalization. In this paper, we study how a patch of membrane is deformed against turgor pressure by force and by curvature-generating proteins. We show that a large amount of force is needed to merely start deforming the membrane and an even larger force is needed to pull a membrane tube. The magnitude of these forces strongly depends on how the base of the membrane is constrained and how the membrane is coated with curvature-generating proteins. In particular, these forces can be reduced by partially but not fully coating the membrane patch with curvature-generating proteins. Our theoretical results show excellent agreement with experimental data.
SIGNIFICANCEYeast cells have been widely used as a model system to study clathrin-mediated endocytosis. The mechanics of membrane during endocytosis has been extensively studied mostly in low turgor pressure condition, which is relevant for mammalian cells but not for yeast cells. It has been suggested that as a result of high turgor pressure in yeast cells, a large amount of force is needed to drive the progress of the membrane invagination. In this paper, we investigated biologically relevant mechanisms to reduce the force requirement. We highlight the role of boundary conditions at the membrane base, which is a factor that has been largely ignored in previous studies. We also investigate the role of curvature-generating proteins and show that a large protein coat does not necessarily reduce the force barrier for endocytosis. | biophysics |
10.1101/560011 | Negative Affect Induces Rapid Learning of Counterfactual Representations: A Model-based Facial Expression Analysis Approach | Whether we are making life-or-death decisions or thinking about the best way to phrase an email, counterfactual emotions including regret and disappointment play an ever-present role in how we make decisions. Functional theories of counterfactual thinking suggest that the experience and future expectation of counterfactual emotions should promote goal-oriented behavioral change. Although many studies find empirical support for such functional theories, the generative cognitive mechanisms through which counterfactual thinking facilitates changes in behavior are underexplored. Here, we develop generative models of risky decision-making that extend regret and disappointment theory to experience-based tasks, which we use to examine how people incorporate counterfactual information into their decisions across time. Further, we use computer-vision to detect positive and negative affect (valence) intensity from participants faces in response to feedback, which we use to explore how experienced emotion may correspond to cognitive mechanisms of learning, outcome valuation, or exploration/exploitation--any of which could result in functional changes in behavior. Using hierarchical Bayesian modeling and Bayesian model comparison methods, we found that a model assuming: (1) people learn to explicitly represent and subjectively weight counterfactual outcomes with increasing experience, and (2) people update their counterfactual expectations more rapidly as they experience increasingly intense negative affect best characterized empirical data. Our findings support functional accounts of regret and disappointment and demonstrate the potential for generative modeling and model-based facial expression analysis to enhance our understanding of cognition-emotion interactions. | neuroscience |
10.1101/559948 | Coding Triplets in the Transfer RNA acceptor Arm and Their Role in Present and Past tRNA Recognition | The mechanism and evolution of the recognition scheme between key components of the translation system, i.e., tRNAs, synthetases and elongation factors, are fundamental issues in understanding the translation of genetic information into proteins. Statistical analysis of bacterial tRNA sequences reveals that for six amino acids, i.e. for Ala, Asp, Gly, His, Pro and Ser, a string of 10 nucleotides preceding the tRNA 3end, carries cognate coding triplets to nearly full extent. The triplets conserved in positions 63-67 are implicated in the recognition by EF-Tu, and those conserved in positions 68-72, in the identification of cognate tRNAs and their derived minihelices, by class IIa synthetases. These coding triplets are suggested to have primordial origin, being engaged in aminoacylation of prebiotic tRNAs and in the establishment of the canonical codon set. | genetics |
10.1101/561548 | Internal noise measures in coarse and fine motion direction discrimination tasks, and the correlation with autism traits | Motion perception is essential for visual guidance of behaviour and is known to be limited by both internal additive noise (arising from random fluctuations in neural activity), and by motion pooling (global integration of local motion signals across space). People with autism spectrum disorder (ASD) display abnormalities in motion processing, which has been linked to both elevated noise and abnormal pooling. However, to date, the impact of a third limit - induced internal noise (internal noise that scales up with increases is external noise) - has not been investigated in motion perception of any group. Here, we describe a new double-pass motion direction discrimination paradigm that quantifies additive noise, induced noise, and motion pooling. We measure the impact of induced noise on direction discrimination, which we ascribe to fluctuations in decision-related variables. We report that internal noise is higher individuals with high ASD traits only on coarse but not fine motion direction discrimination tasks. However, we report no significant correlations between autism traits, and additive noise, induced noise or motion pooling, in either task. We conclude that internal noise may be higher in individuals with many ASD traits, and that the assessment of induced internal noise is a useful way of exploring decision-related limits on motion perception, irrespective of ASD traits. | neuroscience |
10.1101/565796 | Polymer brush bilayers under stationary shear motion at linear response regime: A theoretical approach | Statistical mechanics is employed to tackle the problem of polymer brush bilayers under stationary shear motion. The article addresses, solely, the linear response regime in which the polymer brush bilayers behave very much similar to the Newtonian fluids. My approach to this long-standing problem split drastically from the work already published Kreer, T, Soft Matter, 12, 3479 (2016). It has been thought for many decades that the interpenetration between the brushes is source of the friction between the brush covered surfaces sliding over each other. Whiles, the present article strongly rejects the idea of interpenetration length in that issue. Instead, here, I show that structure of the whole system is significant in friction between brush covered surfaces and the interpenetration is absolutely insignificant. The results of this research would blow ones mind about how the polymer brush bilayers respond at small shear rates. | biophysics |
10.1101/568626 | What the odor is not: Estimation by elimination | Olfactory systems use a small number of broadly sensitive receptors to combinatorially encode a vast number of odors. We propose a method of decoding such distributed representations by exploiting a statistical fact: receptors that do not respond to an odor carry more information than receptors that do because they signal the absence of all odorants that bind to them. Thus, it is easier to identify what the odor is not, rather than what the odor is. For realistic numbers of receptors, response functions, and odor complexity, this method of elimination turns an underconstrained decoding problem into a solvable one, allowing accurate determination of odorants in a mixture and their concentrations. We construct a neural network realization of our algorithm based on the structure of the olfactory pathway. | neuroscience |
10.1101/571083 | The Cdc14 phosphatase controls resolution of recombination intermediates and crossover formation during meiosis | Meiotic defects derived from incorrect DNA repair during gametogenesis can lead to mutations, aneuploidies and infertility. Coordinated resolution of meiotic recombination intermediates is required for crossover formation, ultimately necessary for accurate completion of both rounds of chromosome segregation. Numerous master kinases orchestrate the correct assembly and activity of the repair machinery. Although much less is known, reversal of phosphorylation events in meiosis must also be key to coordinate the timing and functionality of repair enzymes. Cdc14 is an evolutionarily conserved phosphatase required for the dephosphorylation of multiple CDK1 targets. Mutations that inactivate this phosphatase lead to meiotic failure, but until now it was unknown if Cdc14 plays a direct role in meiotic recombination. Here, we show that elimination of Cdc14 leads to severe defects in the processing and resolution of recombination intermediates, causing a drastic depletion of crossovers when other repair pathways are compromised. We also show that Cdc14 is required for correct activity and localization of the Holliday Junction resolvase Yen1/GEN1. We reveal that Cdc14 regulates Yen1 activity from meiosis I onwards, and this function is essential for crossover resolution in the absence of other repair pathways. We also demonstrate that Cdc14 and Yen1 are required to safeguard sister chromatid segregation during the second meiotic division, a late action that is independent of the earlier role in crossover formation. Thus, this work uncovers previously undescribed functions of Cdc14 in the regulation of meiotic recombination. | genetics |
10.1101/572156 | The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA regulation | Dead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1s tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is specifically recognized, reconciling seemingly contradictory sequence motifs discovered in recent genome-wide studies. RRM1 acts as a main binding platform, including atypical extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA using an unusual binding pocket, leading to an unprecedented mode of tandem RRM-RNA recognition. We show that the consensus motif is sufficient to mediate upregulation of a reporter gene in human cells and that this process depends not only on RNA binding by the RRMs, but also on DND1s double-stranded RNA binding domain (dsRBD), which is dispensable for target binding in cellulo. Our results point to a model where DND1 target selection is mediated by a non-canonical mode of AU-rich RNA recognition by the tandem RRMs and a role for the dsRBD in the recruitment of effector complexes responsible for target regulation. | molecular biology |
10.1101/570556 | Conserving unprotected important coastal habitats in the Yellow Sea: shorebird occurrence, distribution and food resources at Lianyungang | The authors have withdrawn their manuscript since this preprint contain errors which have been corrected in the version published in the journal Global Ecology and Conservation (doi: 10.1016/j.gecco.2019.e00724). Therefore, the authors do not wish this preprint to be cited as reference for the project. If you have any questions, please contact the corresponding author. | ecology |
10.1101/570580 | Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline | AO_SCPLOWBSTRACTC_SCPLOWWith current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment worsens. However, mutualism is often costly to maintain, and evolution might counter-select it when not profitable enough. We investigate how evolution of mutualism affects the coexistence of two mutualistic species, e.g. a plant-pollinator or plant-fungi system. Specifically, using eco-evolutionary dynamics, we study the evolution of the focal species investment in the mutualistic interaction of a focal species (e.g. plant attractiveness via flower or nectar production for pollinators or carbon exudate for mycorrhizal fungi), and how it is affected by the decline of the partner population with which it is interacting. We assume an allocation trade-off so that investment in the mutualistic interaction reduces the species intrinsic growth rate. First, we investigate how evolution changes species persistence, biomass production, and the intensity of the mutualistic interaction. We show that concave trade-offs allow evolutionary convergence to stable coexistence. We next assume an external disturbance that decreases the partner population by lowering its intrinsic growth rate. Such declines result in the evolution of lower investment of the focal species in the mutualistic interaction, which eventually leads to the extinction of the partner species. With asymmetric mutualism favouring the partner, the evolutionary disappearance of the mutualistic interaction is delayed. Our results suggest that evolution may account for the current collapse of some mutualistic system like plant-pollinator ones, and that restoration attempts should be enforced early enough to prevent potential negative effects driven by evolution. | ecology |
10.1101/570580 | Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline | AO_SCPLOWBSTRACTC_SCPLOWWith current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment worsens. However, mutualism is often costly to maintain, and evolution might counter-select it when not profitable enough. We investigate how evolution of mutualism affects the coexistence of two mutualistic species, e.g. a plant-pollinator or plant-fungi system. Specifically, using eco-evolutionary dynamics, we study the evolution of the focal species investment in the mutualistic interaction of a focal species (e.g. plant attractiveness via flower or nectar production for pollinators or carbon exudate for mycorrhizal fungi), and how it is affected by the decline of the partner population with which it is interacting. We assume an allocation trade-off so that investment in the mutualistic interaction reduces the species intrinsic growth rate. First, we investigate how evolution changes species persistence, biomass production, and the intensity of the mutualistic interaction. We show that concave trade-offs allow evolutionary convergence to stable coexistence. We next assume an external disturbance that decreases the partner population by lowering its intrinsic growth rate. Such declines result in the evolution of lower investment of the focal species in the mutualistic interaction, which eventually leads to the extinction of the partner species. With asymmetric mutualism favouring the partner, the evolutionary disappearance of the mutualistic interaction is delayed. Our results suggest that evolution may account for the current collapse of some mutualistic system like plant-pollinator ones, and that restoration attempts should be enforced early enough to prevent potential negative effects driven by evolution. | ecology |
10.1101/570580 | Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline | AO_SCPLOWBSTRACTC_SCPLOWWith current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment worsens. However, mutualism is often costly to maintain, and evolution might counter-select it when not profitable enough. We investigate how evolution of mutualism affects the coexistence of two mutualistic species, e.g. a plant-pollinator or plant-fungi system. Specifically, using eco-evolutionary dynamics, we study the evolution of the focal species investment in the mutualistic interaction of a focal species (e.g. plant attractiveness via flower or nectar production for pollinators or carbon exudate for mycorrhizal fungi), and how it is affected by the decline of the partner population with which it is interacting. We assume an allocation trade-off so that investment in the mutualistic interaction reduces the species intrinsic growth rate. First, we investigate how evolution changes species persistence, biomass production, and the intensity of the mutualistic interaction. We show that concave trade-offs allow evolutionary convergence to stable coexistence. We next assume an external disturbance that decreases the partner population by lowering its intrinsic growth rate. Such declines result in the evolution of lower investment of the focal species in the mutualistic interaction, which eventually leads to the extinction of the partner species. With asymmetric mutualism favouring the partner, the evolutionary disappearance of the mutualistic interaction is delayed. Our results suggest that evolution may account for the current collapse of some mutualistic system like plant-pollinator ones, and that restoration attempts should be enforced early enough to prevent potential negative effects driven by evolution. | ecology |
10.1101/571380 | Event segmentation reveals working memory forgetting rate | We encounter the world as a continuous flow and effortlessly segment sequences of events into episodes. This process of event segmentation engages working memory (WM) for tracking the flow of events and impacts subsequent memory accuracy. WM is limited in how much information is retained (i.e., WM capacity) and for how long the information is retained (i.e., forgetting rate). It is unclear which aspect of WM limitations affects event segmentation. In two separate experiments with multiple tasks, we estimated participants WM capacity and forgetting rate in a dynamic context and evaluated their relationship to event segmentation. The results across tasks show that individuals who reported more movie segments than others (fine-segmenters) have a faster decaying WM. A separate task assessing long-term memory retrieval reveals that the coarse-segmenters have better recognition of temporal order of events in contrast to the fine-segmenters who performed better at free recall. The findings show that event segmentation employs dissociable memory strategies and depends on how long information is retained in WM. | neuroscience |
10.1101/573907 | Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa | Pairing of homologous chromosomes represents a critical step of meiosis in nearly all sexually reproducing species. While in some organisms meiotic pairing requires programmed DNA breakage and recombination, in many others it engages homologous chromosomes that remain apparently intact. The mechanistic nature of such recombination-independent pairing represents a fundamental question in molecular genetics. Using meiotic silencing by unpaired DNA (MSUD) in Neurospora crassa as a model process, we demonstrate the existence of a cardinally different approach to DNA homology recognition in meiosis. The main advantage of MSUD over other experimental systems lies in its ability to identify any relatively short DNA fragment lacking a homologous allelic partner. Here we show that MSUD does not rely on the canonical mechanism of meiotic recombination, yet it is promoted by REC8, a conserved component of the meiotic cohesin complex. We also show that certain patterns of interspersed homology are recognized as pairable during MSUD. Such patterns need to be co-linear and must contain short tracts of sequence identity spaced apart with a periodicity of 21 or 22 base-pairs. By using these values as a guiding parameter in all-atom molecular modeling, we discover that homologous double-stranded DNA molecules can associate by forming quadruplex-based contacts with an interval of 2.5 helical turns, which requires right-handed plectonemic coiling and additional conformational changes in the intervening double-helical segments. These results (i) reconcile genetic and biophysical lines of evidence for the existence of direct homologous dsDNA-dsDNA pairing, (ii) identify a role for this process in initiating post-transcriptional silencing, and (iii) suggest that chromosomes are cross-matched in meiosis by a precise mechanism that operates on intact double-stranded DNA molecules. | molecular biology |
10.1101/576116 | Publicly available transcriptomes provide the opportunity for dual RNA-Seq meta analysis in Plasmodium infection | Dual RNA-Seq is the simultaneous transcriptomic analysis of interacting symbionts, for example, in malaria. Potential cross-species interactions identified by correlated gene expression might highlight interlinked signaling, metabolic or gene regulatory pathways in addition to physically interacting proteins. Often, malaria studies address one of the interacting organisms - host or parasite - rendering the other "contamination". Here we perform a meta-analysis using such studies for cross-species expression analysis.
We screened experiments for gene expression from host and Plasmodium. Out of 171 studies in Homo sapiens, Macaca mulatta and Mus musculus, we identified 63 potential studies containing host and parasite data. While 16 studies (1950 samples) explicitly performed dual RNA-Seq, 47 (1398 samples) originally focused on one organism. We found 915 experimental replicates from 20 blood studies to be suitable for co-expression analysis and used orthologs for meta-analysis across different host-parasite systems. Centrality metrics from the derived gene expression networks correlated with gene essentiality in the parasites. We found indications of host immune response to elements of the Plasmodium protein degradation system, an antimalarial drug target. We identified well-studied immune responses in the host with our co-expression networks as our approach recovers known broad processes interlinked between hosts and parasites in addition to individual host and parasite protein associations.
The set of core interactions represents commonalities between human malaria and its model systems for prioritization in laboratory experiments. Our approach might also allow insights into the transferability of model systems for different pathways in malaria studies.
ImportanceMalaria still causes about 400,000 deaths a year and is one the most studied infectious diseases. The disease is studied in mice and monkeys as lab models to derive potential therapeutic intervention in human malaria. Interactions between Plasmodium spp. and its hosts are either conserved across different host-parasite systems or idiosyncratic to those systems. Here we use correlation of gene expression from different RNA-Seq studies to infer common host-parasite interactions across human, mouse and monkey studies. We, firstly, find a set of very conserved interactors, worth further scrutiny in focussed laboratory experiments. Secondly, this work might help assess to which extent experiments and knowledge on different pathways can be transferred from models to humans for potential therapy. | bioinformatics |
10.1101/576793 | Common variants associated with OSMR expression contribute to carotid plaque vulnerability, but not to cardiovascular disease in humans | Background and aimsOncostatin M (OSM) signaling is implicated in atherosclerosis, however the mechanism remains unclear. We investigated the impact of common genetic variants in OSM and its receptors, OSMR and LIFR, on overall plaque vulnerability, plaque phenotype, intraplaque OSMR and LIFR expression, coronary artery calcification burden and cardiovascular disease susceptibility.
Methods and resultsWe queried Genotype-Tissue Expression data and found that rs13168867 (C allele) was associated with decreased OSMR expression and that rs10491509 (A allele) was associated with increased LIFR expression in arterial tissues. No variant was significantly associated with OSM expression.
We associated these two variants with plaque characteristics from 1,443 genotyped carotid endarterectomy patients in the Athero-Express Biobank Study. After correction for multiple testing, rs13168867 was significantly associated with an increased overall plaque vulnerability ({beta}=0.118 {+/-} s.e.=0.040, p=3.00x10-3, C allele). Looking at individual plaque characteristics, rs13168867 showed strongest associations with intraplaque fat ({beta}=0.248 {+/-} s.e.=0.088, p=4.66 x 10-3, C allele) and collagen content ({beta}=-0.259 {+/-} s.e.=0.095, p=6.22 x 10-3, C allele), but these associations were not significant after correction for multiple testing. rs13168867 was not associated with intraplaque OSMR expression. Neither was intraplaque OSMR expression associated with plaque vulnerability and no known OSMR eQTLs were associated with coronary artery calcification burden, or cardiovascular disease susceptibility. No associations were found for rs10491509 in the LIFR locus.
ConclusionsOur study suggests that rs1316887 in the OSMR locus is associated with increased plaque vulnerability, but not with coronary calcification or cardiovascular disease risk. It remains unclear through which precise biological mechanisms OSM signaling exerts its effects on plaque morphology. However, the OSM-OSMR/LIFR pathway is unlikely to be causally involved in lifetime cardiovascular disease susceptibility. | genetics |
10.1101/576793 | Common variants associated with OSMR expression contribute to carotid plaque vulnerability, but not to cardiovascular disease in humans | Background and aimsOncostatin M (OSM) signaling is implicated in atherosclerosis, however the mechanism remains unclear. We investigated the impact of common genetic variants in OSM and its receptors, OSMR and LIFR, on overall plaque vulnerability, plaque phenotype, intraplaque OSMR and LIFR expression, coronary artery calcification burden and cardiovascular disease susceptibility.
Methods and resultsWe queried Genotype-Tissue Expression data and found that rs13168867 (C allele) was associated with decreased OSMR expression and that rs10491509 (A allele) was associated with increased LIFR expression in arterial tissues. No variant was significantly associated with OSM expression.
We associated these two variants with plaque characteristics from 1,443 genotyped carotid endarterectomy patients in the Athero-Express Biobank Study. After correction for multiple testing, rs13168867 was significantly associated with an increased overall plaque vulnerability ({beta}=0.118 {+/-} s.e.=0.040, p=3.00x10-3, C allele). Looking at individual plaque characteristics, rs13168867 showed strongest associations with intraplaque fat ({beta}=0.248 {+/-} s.e.=0.088, p=4.66 x 10-3, C allele) and collagen content ({beta}=-0.259 {+/-} s.e.=0.095, p=6.22 x 10-3, C allele), but these associations were not significant after correction for multiple testing. rs13168867 was not associated with intraplaque OSMR expression. Neither was intraplaque OSMR expression associated with plaque vulnerability and no known OSMR eQTLs were associated with coronary artery calcification burden, or cardiovascular disease susceptibility. No associations were found for rs10491509 in the LIFR locus.
ConclusionsOur study suggests that rs1316887 in the OSMR locus is associated with increased plaque vulnerability, but not with coronary calcification or cardiovascular disease risk. It remains unclear through which precise biological mechanisms OSM signaling exerts its effects on plaque morphology. However, the OSM-OSMR/LIFR pathway is unlikely to be causally involved in lifetime cardiovascular disease susceptibility. | genetics |
10.1101/577833 | Liver X Receptor; Controls Hepatic Stellate Cell Activation via Hedgehog Signaling | Liver X receptors (LXR) and {beta} serve important roles in cholesterol homeostasis, anti-inflammatory processes and the activation of hepatic stellate cells (HSCs). However, the development of therapies for liver fibrosis based on LXR agonists have been hampered due to side-effects such as liver steatosis. In this study, we demonstrated that HSCs expressed high levels of LXR{beta}, but not LXR, and that overexpression of LXR{beta} suppressed fibrosis and HSC activation in a carbon tetrachloride (CCl4)-induced fibrosis mouse model, without resulting in liver steatosis. Furthermore, Hedgehog (Hh)-regulated proteins, markedly increased in the CCl4-affected liver and mainly expressed in activated HSCs, were repressed under conditions of LXR{beta} overexpression. In addition, LXR{beta} knockout led to activation of Hh signaling and triggering of HSC activation, while overexpression of LXR{beta} led to the inhibition of the Hh pathway and suppression of HSC activation. These results suggest that LXR{beta} suppresses the activation mechanism of HSCs by inhibiting Hh signaling. In conclusion, LXR{beta}, by restoring the differentiation of HSCs, may be a promising therapeutic target for liver fibrosis without the adverse side-effects of LXR activation. | cell biology |
10.1101/579151 | Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations | Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations. | genetics |
10.1101/579151 | Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations | Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations. | genetics |
10.1101/580258 | A candidate causal variant underlying both enhanced cognitive performance and increased risk of bipolar disorder | Bipolar disorder is a highly heritable mental illness, but the relevant genetic variants and molecular mechanisms are largely unknown. Recent GWASs have identified an intergenic region associated with both cognitive performance and bipolar disorder. This region contains dozens of putative fetal brain-specific enhancers and is located [~]0.7 Mb upstream of the neuronal transcription factor POU3F2. We identified a candidate causal variant, rs77910749, that falls within a highly conserved putative enhancer, LC1. This human-specific variant is a single-base deletion in a PAX6 binding site and is predicted to be functional. We hypothesized that rs77910749 alters LC1 activity and hence POU3F2 expression during neurodevelopment. Indeed, transgenic reporter mice demonstrated LC1 activity in the developing cerebral cortex and amygdala. Furthermore, ex vivo reporter assays in embryonic mouse brain and human iPSC-derived cerebral organoids revealed increased enhancer activity conferred by the variant. To probe the in vivo function of LC1, we deleted the orthologous mouse region, which resulted in amygdala-specific changes in Pou3f2 expression. Lastly, humanized rs77910749 knock-in mice displayed behavioral defects in sensory gating, an amygdala-dependent endophenotype seen in patients with bipolar disorder. Our study suggests a molecular mechanism underlying the long-speculated link between enhanced cognitive performance and neuropsychiatric disease. | genetics |
10.1101/581660 | PME-1 suppresses anoikis, and is associated with therapy relapse of PTEN-deficient prostate cancers | While organ-confined PCa is mostly therapeutically manageable, metastatic progression of PCa remains an unmet clinical challenge. Resistance to anoikis, a form of cell death initiated by cell detachment from the surrounding extracellular matrix, is one of the cellular processes critical for PCa progression towards aggressive disease. Therefore, further understanding of anoikis regulation in PCa might provide therapeutic opportunities. Here, we discover that PCa tumors with concomitantly compromised function of two tumor suppressor phosphatases, PP2A and PTEN, are particularly aggressive, having less than 50% 5-year secondary-therapy free patient survival. Functionally, overexpression of PME-1, a PP2A inhibitor protein, inhibits anoikis in PTEN-deficient PCa cells. In vivo, PME-1 inhibition increased apoptosis in in ovo PCa tumor xenografts, and attenuated PCa cell survival in zebrafish circulation. Molecularly, PME-1 deficient PCa cells display increased trimethylation at lysines 9 and 27 of histone H3 (H3K9me3 and H3K27me3), a phenotype corresponding to increased apoptosis sensitivity. In summary, we discover that PME-1 overexpression supports anoikis resistance in PTEN-deficient PCa cells. Clinically, the results identify PME-1 as a candidate biomarker for a subset of particularly aggressive PTEN-deficient PCa. | cancer biology |
10.1101/581827 | A stable pollination environment limits current but not potential evolution of floral traits | The vast variation in floral traits at a macroevolutionary level is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of long periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection on floral traits, or by low trait ability to respond even if selection is present. We studied Ulex parviflorus, a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of floral traits, using genome-wide molecular relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability observed in the wild is not heritable. A separate trait, floral weight, in turn presents high heritability, but is not currently under selection. We show how a stable environment can lead to a lack of evolutionary change, yet maintain heritable variation to respond to future selection pressures. | evolutionary biology |
10.1101/582056 | Protein structure without structure determination: direct coupling analysis based on in vitro evolution | Protein structure is tightly inter-twined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit the function for which a protein was evolutionary selected to gain information on protein structure and on the landscape explored during the early stages of molecular and natural evolution. To answer to this question, we developed a new methodology, which we named CAMELS (Coupling Analysis by Molecular Evolution Library Sequencing), that is able to obtain the in vitro evolution of a protein from an artificial selection based on function. We were able to observe with CAMELS many features of the TEM-1 beta lactamase local fold exclusively by generating and sequencing large libraries of mutational variants. We demonstrated that we can, whenever a functional phenotypic selection of a protein is available, sketch the structural and evolutionary landscape of a protein without utilizing purified proteins, collecting physical measurements or relying on the pool of natural protein variants. | evolutionary biology |
10.1101/581876 | Variations in Structural MRI Quality Significantly Impact Commonly-Used Measures of Brain Anatomy | Subject motion can introduce noise into neuroimaging data and result in biased estimations of brain structure. In-scanner motion can compromise data quality in a number of ways and varies widely across developmental and clinical populations. However, quantification of structural image quality is often limited to proxy or indirect measures gathered from functional scans; this may be missing true differences related to these potential artifacts. In this study, we take advantage of novel informatic tools, the CAT12 toolbox, to more directly measure image quality from T1-weighted images to understand if these measures of image quality: 1) relate to rigorous quality-control checks visually completed by human raters; 2) are associated with sociodemographic variables of interest; 3) influence regional estimates of cortical surface area, cortical thickness, and subcortical volumes from the commonly-used Freesurfer tool suite. We leverage public-access data that includes a community-based sample of children and adolescents, spanning a large age-range (N=388; ages 5-21). Interestingly, even after visually inspecting our data, we find image quality significantly impacts derived cortical surface area, cortical thickness, and subcortical volumes from multiple regions across the brain ([~]23.4% of all areas investigated). We believe these results are important for research groups completing structural MRI studies using Freesurfer or other morphometric tools. As such, future studies should consider using measures of image quality to minimize the influence of this potential confound in group comparisons or studies focused on individual differences. | neuroscience |
10.1101/585133 | Rapid neural representations of personally relevant faces | The faces of those most personally relevant to us are our primary source of social information, making their timely perception a priority. Recent research indicates that gender, age and identity of faces can be decoded from EEG/MEG data within 100ms. Yet the time course and neural circuitry involved in representing the personal relevance of faces remain unknown. We applied simultaneous EEG-fMRI to examine neural responses to emotional faces of female participants romantic partners, friends, and a stranger. Combining EEG and fMRI in cross-modal representational similarity analyses, we provide evidence that representations of personal relevance start prior to structural encoding at 100ms, with correlated representations in visual cortex, but also in prefrontal and midline regions involved in value representation, and monitoring and recall of self-relevant information. Our results add to an emerging body of research that suggests that models of face perception need to be updated to account for rapid detection of personal relevance in cortical circuitry beyond the core face processing network. | neuroscience |
10.1101/584409 | Single trial dynamics of attentional intensity in visual area V4 | Understanding how activity of visual neurons represents distinct components of attention and their dynamics that account for improved visual performance remains elusive because single-unit experiments have not isolated the intensive aspect of attention from attentional selectivity. We isolated attentional intensity and its single trial dynamics as determined by spatially non-selective attentional performance in an orientation discrimination task while recording from neurons in monkey visual area V4. We found that attentional intensity is a distinct cognitive signal that can be distinguished from spatial selectivity, reward expectations and motor actions. V4 spiking on single trials encodes a combination of sensory and cognitive signals on different time scales. Attentional intensity and the detection of behaviorally relevant sensory signals are well represented, but immediate reward expectation and behavioral choices are poorly represented in V4 spiking. These results provide a detailed representation of perceptual and cognitive signals in V4 that are crucial for attentional performance. | neuroscience |
10.1101/583880 | Quantifying Climatic and Socio-Economic Influences on Urban Malaria in Surat, India: A Modelling Study | BackgroundCities are becoming increasingly important habitats for mosquito-borne infections. The pronounced heterogeneity of urban landscapes challenges our understanding of the spatio-temporal dynamics of these diseases, and of the influence of climate and socio-economic factors at different spatial scales. Here, we quantify this joint influence on malaria risk by taking advantage of an extensive dataset in both space and time for reported Plasmodium falciparum cases in the city of Surat, Northwest India.
MethodsWe analyzed 10 years of monthly falciparum cases resolved at three nested spatial resolutions (for 7 zones, 32 units and 478 workers units subdivisions, respectively). With a Bayesian hierarchical mixed model that incorporates effects of population density, poverty, humidity and temperature, we investigate the main drivers of spatio-temporal malaria risk at the intermediate scale of districts. The significance of covariates and the model fit is then examined at lower and higher resolutions.
FindingsThe spatial variation of urban malaria cases is strongly stationary in time, whereby locations exhibiting high and low yearly cases remain largely consistent across years. Local socio-economic variation can be summarized with two main principal components, representing poverty and population density respectively. The model that incorporates these two factors together with local temperature and global relative humidity, best explains monthly malaria patterns at the intermediate resolution. The effects of local temperature and population density remain significant at the finest spatial scale. We further identify the specific areas where such increased resolution improves model fit.
InterpretationMalaria risk patterns within the city are largely driven by fixed spatial structures, highlighting the key role of local climate conditions and social inequality. As a result, malaria elimination efforts in the Indian subcontinent can benefit from identifying, predicting and targeting disease hotspots within cities. Spatio-temporal statistical models for the mesoscale of administrative units can inform control efforts, and be complemented with bespoke plans in the identified areas where finer scale data could be of value.
Research in contextO_ST_ABSEvidence before this studyC_ST_ABSUrban areas have become the new dominant ecosystem around the globe. Developing countries comprise the most urbanized regions of the world, with 80% of their population living in cities and an expected increase to 90% by 2050. The large and heterogeneous environments of today challenge the understanding and control of infectious disease dynamics, including of those transmitted by vectors. Malaria in the Indian subcontinent has an important urban component given the existence of a truly urban mosquito vector Anopheles stephensi. A literature search in Mendeley of "urban malaria" and "India" returned 161 publications, in their majority on diagnostics or brief reports on the disease, and on cross-sectional rather than longitudinal studies addressing the spatio-temporal variation of disease risk for a whole city, the subject of our work. A relevant exception is a study for the city of Ahmedabad; this not address multiple seasons across different spatial scales, and climatic conditions are not considered jointly with socio-economic drivers in the modeling. A second Mendeley search on A. stephensi returned 11 publications into two distinct groups: early entomological studies for India and recent reports of the mosquito in the Horn of Africa. This geographical expansion makes the specter of urban malaria a future possibility for the African continent where the disease remains so far rural and peri-urban.
Added value of this studyThis paper relies on an extensive surveillance data set of Plasmodium falciparum cases for Surat (India) to investigate the variation and drivers of malaria risk in an heterogenous urban environment. A statistical model for the spatio-temporal variability of cases is developed, which includes both climatic and socio-economic drivers, with the latter summarized into two major axes of variation. Model fits are compared across three spatial resolutions, ranging from a few zones to a few hundred units. Seasonal hotspots are shown to be largely stationary in time, which allows identification of dominant drivers, including population density and local temperatures, whereas humidity acts globally modulating year-to-year burden. More granular statistical models and datasets like the one analyzed here are needed to capture the effects of socioeconomic and climatic drivers, and to predict current and future malaria incidence patterns within cities.
Implications of all the available evidenceThe analysis identifies relevant resolution which can vary across the city for targeted intervention, including vector control, that would focus on reducing and eliminating transmission hotspots. The modeling framework, incorporating predictors representing climate at local vs. aggregate levels, and major axes of socio-economic variation, should apply to other vector-borne diseases and other cities for which surveillance records are available. The importance of spatially-explicit and sustained surveillance data for informing these models cannot be overstated. | ecology |
10.1101/585687 | Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species | Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allow to assess the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers - Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis - using a population genomics dataset of 23 562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes. | evolutionary biology |
10.1101/586545 | Effective clustering for single cell sequencing cancer data | Single cell sequencing (SCS) technologies provide a level of resolution that makes it indispensable for inferring from a sequenced tumor, evolutionary trees or phylogenies representing an accumulation of cancerous mutations. A drawback of SCS is elevated false negative and missing value rates, resulting in a large space of possible solutions, which in turn makes it difficult, sometimes infeasible using current approaches and tools. One possible solution is to reduce the size of an SCS instance -- usually represented as a matrix of presence, absence, and uncertainty of the mutations found in the different sequenced cells -- and to infer the tree from this reduced-size instance. In this work, we present a new clustering procedure aimed at clustering such categorical vector, or matrix data -- here representing SCS instances, called celluloid. We show that celluloid clusters mutations with high precision: never pairing too many mutations that are unrelated in the ground truth, but also obtains accurate results in terms of the phylogeny inferred downstream from the reduced instance produced by this method. We demonstrate the usefulness of a clustering step by applying the entire pipeline (clustering + inference method) to a real dataset, showing a significant reduction in the runtime, raising considerably the upper bound on the size of SCS instances which can be solved in practice. Our approach, celluloid: clustering single cell sequencing data around centroids is available at https://github.com/AlgoLab/celluloid/ under an MIT license, as well as on the Python Package Index (PyPI) at https://pypi.org/project/celluloid-clust/ | cancer biology |
10.1101/586313 | Global mammalian zooregions reveal a signal of past human impacts | Ecologists have long documented that the worlds biota is spatially organized in regions with boundaries shaped by processes acting on geological and evolutionary timescales. Although growing evidence suggests that human impact has been key in how biodiversity is currently assembled, its role as a driver of the geographical organization of biodiversity remains unclear. Here, we quantify the relative importance of human land use from [~]5000 years ago to predict the current assemblage of terrestrial mammals in biogeographical regions across the Earth. Results show that past anthropogenic land use has left an imprint on the taxonomic differentiation of some of the largest biogeographical realms, whereas land use at present stands out as a driver of the taxonomic differences between medium-sized subregions, i.e., within and among continents. Our findings highlight the far-reaching effect that past anthropogenic actions have had on the organization of biodiversity globally. | ecology |
10.1101/586313 | Global mammalian zooregions reveal a signal of past human impacts | Ecologists have long documented that the worlds biota is spatially organized in regions with boundaries shaped by processes acting on geological and evolutionary timescales. Although growing evidence suggests that human impact has been key in how biodiversity is currently assembled, its role as a driver of the geographical organization of biodiversity remains unclear. Here, we quantify the relative importance of human land use from [~]5000 years ago to predict the current assemblage of terrestrial mammals in biogeographical regions across the Earth. Results show that past anthropogenic land use has left an imprint on the taxonomic differentiation of some of the largest biogeographical realms, whereas land use at present stands out as a driver of the taxonomic differences between medium-sized subregions, i.e., within and among continents. Our findings highlight the far-reaching effect that past anthropogenic actions have had on the organization of biodiversity globally. | ecology |
10.1101/588020 | Recovery of trait heritability from whole genome sequence data | Heritability, the proportion of phenotypic variance explained by genetic factors, can be estimated from pedigree data 1, but such estimates are uninformative with respect to the underlying genetic architecture. Analyses of data from genome-wide association studies (GWAS) on unrelated individuals have shown that for human traits and disease, approximately one-third to two-thirds of heritability is captured by common SNPs 2-5. It is not known whether the remaining heritability is due to the imperfect tagging of causal variants by common SNPs, in particular if the causal variants are rare, or other reasons such as overestimation of heritability from pedigree data. Here we show that pedigree heritability for height and body mass index (BMI) appears to be largely recovered from whole-genome sequence (WGS) data on 25,465 unrelated individuals of European ancestry. We assigned 33.7 million genetic variants to groups based upon their minor allele frequencies (MAF) and linkage disequilibrium (LD) with variants nearby, and estimated and partitioned genetic variance accordingly. The estimated heritability was 0.68 (SE 0.10) for height and 0.30 (SE 0.10) for BMI, with a range of ~0.60 - 0.71 for height and ~0.25 - 0.35 for BMI, depending on quality control and analysis strategies. Low-MAF variants in low LD with neighbouring variants were enriched for heritability, to a greater extent for protein-altering variants, consistent with negative selection thereon. Cumulatively variants with 0.0001 < MAF < 0.1 explained 0.47 (SE 0.07) and 0.30 (SE 0.10) of heritability for height and BMI, respectively. Our results imply that rare variants, in particular those in regions of low LD, is a major source of the still missing heritability of complex traits and disease. | genetics |
10.1101/587030 | The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements | Transposable elements (TEs) are genomic parasites that can propagate by inserting copies of themselves into host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and their mobilization in the germline is a challenge to genome integrity. There are genomic defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with abundant and actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides an excellent opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. We sequenced RNA and small RNAs pools from the testes of juvenile and adult squirrels and compared results to TE and PIWI/piRNA dynamics in the European rabbit and house mouse. Interestingly in squirrels, despite a lack of young insertions, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three PIWI proteins were either not expressed, or only minimally expressed, prior to P8 in squirrel testis, but there was little TE expression change with the onset of PIWI expression. We found PIWIs largely did not reduce TE transcription, and the ping-pong cycle was significantly reduced among squirrel LINEs and SINEs compared to the mouse and rabbit. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins. | evolutionary biology |
10.1101/589168 | Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging. | Mutational spectrum of the mitochondrial genome (mtDNA) does not resemble signatures of any known mutagens and variation in mtDNA mutational spectra between different tissues and organisms is still incomprehensible. Since mitochondria is tightly involved in aerobic energy production, it is expected that mtDNA mutational spectra may be affected by the oxidative damage which is increasing with cellular and organismal aging. However, the well-documented mutational signature of the oxidative damage, G>T substitutions, is typical only for the nuclear genome while it is extremely rare and age-independent in mtDNA. Thus it is still unclear if there is a mitochondria - specific mutational signature of the oxidative damage. Here, reconstructing mtDNA mutational spectra for human cancers originated from 21 tissues with various cell turnover rate, human oocytes fertilized at different ages, and 424 mammalian species with variable generation length which is a proxy for oocyte age, we observed that the frequency of AH>GH substitutions (H - heavy chain notation) is positively correlated with cellular and organismal longevity. Moreover, this mutational bias from AH to GH affects nucleotide content at the fourfold degenerative synonymous positions leading to a deficit of AH and excess of GH, which is especially pronounced in long-lived mammals. Taking into account additionally, that AH>GH is sensitive to time being single stranded during mtDNA asynchronous replication and A>G is associated with oxidative damage of single-stranded DNA in recent bacterial experiments we propose that AH>GH is a mutational signature of oxidative damage in mtDNA. | genomics |
10.1101/589002 | Familiar neighbours, but not relatives, enhance fitness in a territorial mammal | SummaryOne of the outstanding questions in evolutionary biology is the extent to which mutually beneficial interactions and kin-selection can facilitate the evolution of cooperation by mitigating conflict between interacting organisms. The indirect fitness benefits gained from associating with kin are an important pathway to conflict resolution [1], but conflict can also be resolved if individuals gain direct benefits from cooperating with one another (e.g. mutualism or reciprocity) [2]. Owing to the kin-structured nature of many animal societies, it has been difficult for previous research to assess the relative importance of these mechanisms [3-5]. However, one area that might allow for the relative roles of kin-selection and mutualistic benefits to be disentangled is in the resolution of conflict over territorial space [6]. While much research has focused on group-living species, the question of how cooperation can first be favoured in solitary, territorial species remains a key question. Using 22 years of data from a population of North American red squirrels, we assessed how kinship and familiarity with neighbours affected fitness in a territorial mammal. While living near kin did not enhance fitness, familiarity with neighbours increased survival and annual reproductive success. These fitness benefits were strong enough to compensate for the effects of aging later in life, with potential consequences for the evolution of senescence. We suggest that such substantial fitness benefits provide the opportunity for the evolution of cooperation between adversarial neighbours, offering insight into the role that mutually beneficial behaviours might play in facilitating and stabilizing social systems.
Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY | evolutionary biology |
10.1101/590463 | The degree of polymerization and sulfation patterns in heparan sulfate are critical determinants of cytomegalovirus entry into host cells | Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been known to result in significant reduction in virus infectivity indicating that HS play important roles in initiating virus entry. In this study, we provide a series of evidence to prove that specific sulfations as well as the degree of polymerization (dp) of HS govern human cytomegalovirus (CMV) binding and infection. First, purified CMV extracellular virions preferentially bind to sulfated longer chain HS on a glycoarray compared to a variety of unsulfated glycosaminoglycans including unsulfated shorter chain HS. Second, the fraction of glycosaminoglycans (GAG) displaying higher dp and sulfation has a larger impact on CMV titers compared to other fractions. Third, cell lines deficient in specific glucosaminyl sulfotransferases produce significantly reduced CMV titers compared to wild-type cells and virus entry is compromised in these mutant cells. Finally, cells pretreated with a peptide that specifically binds sulfated-HS produce significantly reduced virus titers compared to the control peptide treated cells. Taken together, these results highlight the significance of HS chain length and sulfation patterns in CMV attachment and infectivity.
IMPORTANCEHeparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It binds to a variety of protein ligands, including cytokines, chemokines, growth factors and morphogens and regulates a wide range of biological activities, including developmental processes, angiogenesis, blood coagulation, and tumor metastasis. The molecular diversity in HS chains generates unique binding sites for specific ligands and can offer preferential binding for a specific virus over other viruses or cellular ligands. In the current study human cytomegalovirus (CMV) was found to bind preferentially to uniquely sulfated and polymerized HS. The HS mimics designed with these properties inhibited CMV infection. The results were corroborated by parallel studies in mutant mouse cells as well as using peptide inhibition. Combined together, the data suggests that CMV preferentially attaches to uniquely modified HS and thus this virus-host interaction is amenable to targeting by specifically designed HS mimics or peptides. | microbiology |
10.1101/592154 | Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes | Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a polymerase chain reaction (PCR) step (Nextera), and two were PCR-free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, we assessed two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at -80{degrees}C). All DNA isolations were performed in duplicate, totaling 80 samples excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generate comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously.
ImportancePrevious research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities. These findings suggest that library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure. Overall, we recommend that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions. Furthermore, if we are to obtain a more holistic insight from microbiome data generated around the world, we will need to provide more detailed sample metadata, including information about the different sample processing procedures, together with the DNA sequencing data at the public repositories. | microbiology |
10.1101/589572 | Phylogenetic inference of changes in amino acid propensities with single-position resolution | Fitness conferred by the same allele may differ between genotypes, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that confer different fitness in different groups of species from combined sequence and phylogenetic data. Using the fact that the probability of a substitution to an amino acid depends on its fitness, our method looks for amino acids such that substitutions to them occur more frequently in one group of lineages than in another. We validate our method using simulated evolution of a protein site under different scenarios and show that it has high specificity for a wide range of assumptions regarding the underlying changes in selection, while its sensitivity differs between scenarios. We apply our method to the env gene of two HIV-1 subtypes, A and B, and to the HA gene of two influenza A subtypes, H1 and H3, and show that the inferred fitness changes are consistent with the fitness differences observed in deep mutational scanning experiments. We find that changes in relative fitness of different amino acid variants within a site do not always trigger episodes of positive selection and therefore may not result in an overall increase in the frequency of substitutions, but can still be detected from changes in relative frequencies of different substitutions.
Author summaryWhich amino acids are acceptable at a certain protein site can change with time. In viruses, for example, this can be due to changes in mechanisms of drug resistance and immune escape in the course of evolution. Here, we develop a method for detecting such changes from how evolutionary events are distributed over an evolutionary tree. Informally, we infer that a certain amino acid is favored in a certain group of lineages if substitutions giving rise to it repeatedly occur in the evolution of this group, and disfavored if such substitutions are rare. In surface proteins of HIV-1 and influenza A, we find that changes in preferences detected with d-test match those observed in deep mutational scanning experiments. Our purely bioinformatic approach allows inference of changes in selection between lineages from sequences alone, shedding light on the functional differences between strains or species even in the absence of any structural or functional data. | evolutionary biology |
10.1101/590836 | Extensive genetic mixing within the clam genus Corbicula | AO_SCPLOWBSTRACTC_SCPLOW"Occasional" sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species. | evolutionary biology |
10.1101/590836 | Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula | AO_SCPLOWBSTRACTC_SCPLOW"Occasional" sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species. | evolutionary biology |