Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 451 records · Page 25Linked to original sources

bioRxiv2022

Dynamics of Borrelia Burgdorferi Invasion and Intravasation in a Tissue Engineered Dermal Microvessel Model

Lyme disease is a tick-borne disease prevalent in North America, Europe, and Asia. Dissemination of vector-borne pathogens, such as Borrelia burgdorferi (Bb), results in infection of distant tissues and is the main contributor to poor outcomes. Despite the accumulated knowledge from epidemiological, in vitro, and in animal studies, the understanding of dissemination remains incomplete with several important knowledge gaps, especially related to invasion and intravasation at the site of a tick bite, which cannot be readily studied in animal models or humans. To elucidate the mechanistic details of these processes we developed a tissue-engineered human dermal microvessel model. Fluorescently-labeled Bb (B31 strain) were injected into the extracellular matrix (ECM) of the model to mimic tick inoculation. High resolution, confocal imaging was performed to visualize Bb migration in the ECM and intravasation into circulation. From analysis of migration paths we found no evidence to support adhesin-mediated interactions between Bb and components of the ECM or basement membrane, suggesting that collagen fibers serve as inert obstacles to migration. Transendothelial migration occurred at cell-cell junctions and was relatively fast, consistent with Bb swimming in ECM. In addition, we found that Bb alone can induce endothelium activation, resulting in increased immune cell adhesion but no changes in global or local permeability. Together these results provide new insight into the minimum requirements for dissemination of Bb at the site of a tick bite, and highlight how tissue-engineered models are complementary to animal models in visualizing dynamic processes associated with vector-borne pathogens. Significance StatementUsing a tissue-engineered human dermal microvessel model we reveal new insight into the invasion and intravasation of Borrelia burgdorferi (Bb), a causative agent of Lyme disease in North America, following a tick bite. These results show how tissue-engineered models enable imaging of dynamic processes that are challenging in animal models or human subjects.

bioengineering↗

bioRxiv2022

Cell size regulation and proliferation fluctuations in single-cell derived colonies

Exponentially growing cells regulate their size by controlling their timing of division. Since two daughter cells are born as a result of this cell splitting, cell size regulation has a direct connection with cell proliferation dynamics. Recent models found more clues about this connection by suggesting that division occurs at a size-dependent rate. In this article, we propose a framework that couples the stochastic transient dynamics of both the cell size and the number of cells in the initial expansion of a single-cell-derived colony. We describe the population from the two most common perspectives. The first is known as Single Lineage: where only one cell is followed in each colony, and the second is Population Snapshots: where all cells in different colonies are followed. At a low number of cells, we propose a third perspective; Single Colony, where one tracks only cells with a common ancestor. We observe how the statistics of these three approaches are different at low numbers and how the Single Colony perspective tends to Population Snapshots at high numbers. Analyzing colony-to-colony fluctuations in the number of cells, we report an intriguing find: the extent of fluctuations first increases with time and then decreases to approach zero at large numbers of cells. In contrast, in classical size-independent proliferation models, where cell division occurs based on a pure timing mechanism, fluctuations in cell number increase monotonically over time to approach a nonzero value. We systematically study these differences and the convergence speed using different size control strategies.

systems biology↗

bioRxiv2022

Selection for increased post-infection survival ameliorates mating induced immune suppression in Drosophila melanogaster females

Sexual activity (mating) negatively affects immune function in various insect species, in both sexes. In the experiments reported in this manuscript, we tested if hosts adapted to regular pathogen challenges are less susceptible to mating induced immune suppression, using experimentally evolved Drosophila melanogaster populations selected for increased post-infection survival when infected with a Gram-positive bacterium, Enterococcus faecalis. Mating increased susceptibility of females to bacterial pathogens, but in a pathogen specific manner. Mating-induced increase in susceptibility was also affected by host evolutionary history, with females from selected populations exhibiting similar post-infection survival irrespective of mating status, while females from control populations became more susceptible to bacterial infections after mating. Post-infection survival of males, irrespective of their evolutionary history, was not affected by their mating status. We therefore conclude that hosts evolved to better survive bacterial infections are also better at resisting mating-induced increase in susceptibility to infections in Drosophila melanogaster.

evolutionary biology↗

bioRxiv2022

Function and phylogeny support the independent evolution of acid-sensing ion channels in the Placozoa

Acid-sensing ion channels (ASICs) are proton-gated cation channels that are part of the Deg/ENaC ion channel family, which also includes neuropeptide-, bile acid-, and mechanically-gated channels. Despite sharing common tertiary and quaternary structures, strong sequence divergence within the Deg/ENaC family has made it difficult to resolve their phylogenetic relationships, and by extension, whether channels with common functional features, such as proton-activation, share common ancestry or evolved independently. Here, we report that a Deg/ENaC channel from the early diverging placozoan species Trichoplax adhaerens, named TadNaC2, conducts proton-activated currents in vitro with biophysical features that resemble those of the mammalian ASIC1 to ASIC3 channels. Through a combined cluster- based and phylogenetic analysis, we successfully resolve the evolutionary relationships of most major lineages of metazoan Deg/ENaC channels, identifying two subfamilies within the larger Deg/ENaC family that are of ancient, pre-bilaterian origin. We also identify bona fide Deg/ENaC channel homologues from filasterean and heterokont single celled eukaryotes. Furthermore, we find that ASIC channels, TadNaC2, and various other proton-activated channels from vertebrates and invertebrates are part of phylogenetically distinct lineages. Through structural modelling and mutation analysis, we find that TadNaC2 proton-activation employs fundamentally different molecular determinants than ASIC channels, and identify two unique histidine residues in the placozoan channel that are required for its proton-activation. Together, our phylogenetic and functional analyses support the independent evolution of proton-activated channels in the phylum Placozoa. Spurred by our discovery of pH sensitive channels, we discovered that despite lacking a nervous system, Trichoplax can sense changes in extracellular pH to coordinate its various cell types to locomote away from acidic environments, and to contract upon rapid exposure to acidic pH in a Ca2+-dependent manner. Lastly, via yeast 2 hybrid screening, we find that the Trichoplax channels TadNaC2 and TadNaC10, belonging to the two separate Deg/ENaC subfamilies, interact with the cytoskeleton organizing protein filamin, similar to the interaction reported for the human ENaC channels.

evolutionary biology↗

bioRxiv2022

Correlated responses to experimental evolution of increased post-infection survival in Drosophila melanogaster: Life-history trade-offs and reaction to novel stressors

Evolution of increased immune defence is often limited by costs: correlated changes in other traits (viz. life-history traits) that otherwise reduce the fitness of the host organisms. Experimental evolution studies are useful for understanding the evolution of immune function, and correlated changes in other traits. We experimentally evolved replicate Drosophila melanogaster populations to better survive infection challenge with an entomopathogenic bacteria, Enterococcus faecalis. Within 35 generations of forward selection, selected populations showed marked increase in post-infection survival compared to ancestrally paired controls. We next measured various life-history traits of these populations. Our results show that the selected populations do not differ from control populations for larval development time and body weight at eclosion. No difference is also observed in case of fecundity and longevity (following the acute phase of infection), either when the flies are subjected to infection or when the flies were uninfected; although infected flies from all populations die much earlier compared to uninfected flies. Selected flies and control flies are also equally good at surviving abiotic stressors (starvation and desiccation), although infected flies from all populations are more susceptible to stress than uninfected flies. Therefore, we conclude that (a) D. melanogaster populations can rapidly evolve to be more immune to infection with E. faecalis; (b) evolution of increased defence against E. faecalis entails no life-history cost for the hosts; and (c) evolving defence against a biotic threat (pathogen) does not make flies more resistant to abiotic stressors.

evolutionary biology↗

bioRxiv2022

Dynamic interplay of protrusive microtubule and contractile actomyosin forces drives tissue extension

In order to shape a tissue, cell-based mechanical forces have to be integrated into global force patterns. Over the last decades, the importance of actomyosin contractile arrays, which are the key constituents of various morphogenetic processes, has been established for many tissues. Intriguingly, recent studies demonstrate that the microtubule cytoskeleton mediates folding and elongation of the epithelial sheet during Drosophila morphogenesis, placing microtubule mechanics en par with actin-based processes. While these studies establish the importance of both cytoskeletal systems during cell and tissue rearrangements, a mechanistic explanation of their functional hierarchy is currently missing. Here, we dissect the individual roles of these two key generators of mechanical forces during epithelium elongation. We demonstrate that microtubules dictate cell shape changes and actomyosin refines them. Combining experimental and numerical approaches, we find that altering the microtubule and actomyosin functions results in predictable changes in tissue shape. We further show that planar polarized microtubule patterning is independent of cell geometry and actomyosin-based mechanics. These results support a hierarchical mechanism, whereby microtubule-based forces in some epithelial systems prime actomyosin-generated forces.

developmental biology↗

bioRxiv2022

Temperature Sensitive Contacts in Disordered Loops Tune Enzyme I Activity

Homologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic activities of thermophilic/mesophilic variants of the C-terminal domain of bacterial Enzyme I (EIC) are largely localized within disordered loops, offering a model system with which to investigate this phenomenon. In this work, we employ molecular dynamics simulations and mutagenesis experiments to reveal a mechanism of sequence-dependent activity tuning of EIC homologs. We find that a network of contacts in the catalytic loops is particularly sensitive to changes in temperature, with some contacts exhibiting distinct linear or non-linear temperature-dependent trends. Moreover, these trends define structurally clustered dynamical modes and can distinguish regions that tend toward order or disorder at higher temperatures. Assaying several thermophilic EIC mutants, we show that complementary mesophilic mutations to the most temperature-sensitive positions exhibit the most enhanced activity while mutations to relatively temperature insensitive positions exhibit the least enhanced activities. These results provide a mechanistic explanation of sequence-dependent temperature tuning and offer a computational method for rational enzyme modification. SignificanceTemperature affects the catalytic rates of all enzymes. The impact of temperature on the catalytic activity of an enzyme, however, is convoluted from contributions of protein sequence, structure, and dynamics. As such, understanding and designing the molecular features of enzymes which tune catalytic rates at different temperatures remains a fundamental challenge in biophysics. In this work we have employed molecular simulations and mutagenesis experiments to reveal the temperature tuning mechanism of mesophilic and thermophilic homologues of the C domain of bacterial Enzyme l. We find that enzymes can be tuned to their physiological temperatures through a network of temperature-sensitive residue contacts localized in the disordered loops. Furthermore, we find that among temperature-sensitive contacts some exhibit linear and others non-linear dependence on temperature. These clues offer a promising physics-based approach for tuning enzyme activity.

biophysics↗

bioRxiv2022

Disrupting cellular memory to overcome drug resistance

Plasticity enables cells to change their gene expression state in the absence of a genetic change. At the single-cell level, these gene expression states can persist for different lengths of time which is a quantitative measurement referred to as gene expression memory. Because plasticity is not encoded by genetic changes, these cell states can be reversible, and therefore, are amenable to modulation by disrupting gene expression memory. However, we currently do not have robust methods to find the regulators of memory or to track state switching in plastic cell populations. Here, we developed a lineage tracing-based technique to quantify gene expression memory and to identify single cells as they undergo cell state transitions. Applied to human melanoma cells, we quantified long-lived fluctuations in gene expression that underlie resistance to targeted therapy. Further, we identified the PI3K and TGF-{beta} pathways as modulators of these state dynamics. Applying the gene expression signatures derived from this technique, we find that these expression states are generalizable to in vivo models and present in scRNA-seq from patient tumors. Leveraging the PI3K and TGF-{beta} pathways as dials on memory between plastic states, we propose a " pretreatment" model in which we first use a PI3K inhibitor to modulate the expression states of the cell population and then apply targeted therapy. This plasticity informed dosing scheme ultimately yields fewer resistant colonies than targeted therapy alone. Taken together, we describe a technique to find modulators of gene expression memory and then apply this knowledge to alter plastic cell states and their connected cell fates.

systems biology↗

bioRxiv2022

Acute sleep deprivation induces synaptic remodeling at the soleus muscle neuromuscular junction in rats

Sleep is important for cognitive and physical performance. Sleep deprivation not only affects neural functions but also results in muscular fatigue. A good nights sleep reverses these functional derangements caused by sleep deprivation. The role of sleep in brain function has been extensively studied. However, its role in neuromuscular junction or skeletal muscle morphology is sparsely addressed although skeletal muscle atonia and suspended thermoregulation during rapid eye movement sleep possibly provides a conducive environment for the muscle to rest and repair; somewhat similar to slow-wave sleep for synaptic downscaling. In the present study, we have investigated the effect of 24 h sleep deprivation on the neuromuscular junction morphology and neurochemistry using electron microscopy and immunohistochemistry in the rat soleus muscle. Acute sleep deprivation altered synaptic ultra-structure viz. mitochondria, synaptic vesicle, synaptic proteins, basal lamina, and junctional folds needed for neuromuscular transmission. Further acute sleep deprivation showed the depletion of the neurotransmitter acetylcholine and the overactivity of its degrading enzyme acetylcholine esterase at the neuromuscular junction. The impact of sleep deprivation on synaptic homeostasis in the brain has been extensively reported recently. The present evidence from our studies shows new information on the role of sleep on neuromuscular junction homeostasis and its functioning. Statement of significanceSleep causes synaptic downscaling in the brain, and allows the brain to carry out various housekeeping functions. Here we have reported that the function of the sleep-wake cycle on the synaptic homeostasis extends beyond the brain. Acute sleep deprivation caused significant alteration at ultra and macrostructure of antigravity muscle and the neuromuscular junction along with adaptation to new fiber type in rats. These morpho-functional changes were well correlated with the biochemical assessment of the acetylcholine at the neuromuscular junction. These changes were partially recovered when the rats were allowed to recover from sleep deprivation. The findings suggest a new avenue for a sleep study; employing the neuromuscular junction for exploring the effect of sleep at energy and synaptic homeostasis levels.

neuroscience↗

bioRxiv2022

Threshold-crossing time statistics for gene expression in growing cells

Many intracellular events are triggered by attaining critical concentrations of their corresponding regulatory proteins. How cells ensure precision in the timing of the protein accumulation is a fundamental problem, and contrasting predictions of different models can help us understand the mechanisms involved in such processes. Here, we formulate the timing of protein threshold-crossing as a first passage time (FPT) problem focusing on how the mean FPT and its fluctuations depend on the threshold protein concentration. First, we model the protein-crossing dynamics from the perspective of three classical models of gene expression that do not explicitly accounts for cell growth but consider the dilution as equivalent to degradation: (birth-death process, discrete birth with continuous deterministic degradation, and Fokker-Planck approximation). We compare the resulting FPT statistics with a fourth model proposed by us (growing cell) that comprises size-dependent expression in an exponentially growing cell. When proteins accumulate in growing cells, their concentration reaches a steady value. We observe that if dilution by cell growth is modeled as degradation, cells can reach concentrations higher than this steady-state level at a finite time. In the growing cell model, on the other hand, the FPT moments diverge if the threshold is higher than the steady-state level. This effect can be interpreted as a transition between noisy dynamics when cells are small to an almost deterministic behavior when cells grow enough. We finally study the mean FPT that optimizes the timing precision. The growing cell model predicts a higher optimal FPT and less variability than the classical models.

systems biology↗

bioRxiv2022

Improved methods for bulk cultivation and fixation of Loxodes ciliates for fluorescence microscopy

Loxodes is one of the best ecologically characterized ciliate genera with numerous intriguing physiological abilities, including gravity-sensing organelles and nitrate respiration. However, these cells have been considered challenging to cultivate in bulk, and are poorly preserved by conventional fixatives used for fluorescence microscopy. Here we describe methods to grow and harvest Loxodes cells in bulk with liquid soil extract medium, as well as a new fixative called ZFAE (zinc sulfate, formaldehyde, acetic acid, ethanol) that can fix Loxodes cells more effectively than buffered formaldehyde or methanol. We show that ZFAE is compatible with immunofluorescence and the nuclear stain DAPI. Loxodes is thus now amenable to long-term maintenance, large-scale growth, and modern cell biology investigations of monoclonal strains in laboratory conditions.

cell biology↗

bioRxiv2022

Whole exome-sequencing of vitiligo lesions indicate lower burden of somatic variations: implications in risk for non-melanoma skin cancers

Mapping of somatic variations has enabled understanding the progression of clonal variations from healthy skin to cutaneous malignancies. Highlighting, the adaptive nature of pigmentation, germline mutations in albinism amplify skin cancer susceptibility. However, lower incidence of non-melanoma skin cancer among subjects with acquired depigmenting skin disorder vitiligo is enigmatic and a matter of longstanding debate. To address this, we performed high-coverage exome sequencing of matched non-lesional and lesional vitiligo skin along with whole blood to account for germline variations. Our analysis suggests lower burden of somatic cancer-associated variations in exposed depigmented lesional skin compared to the non-lesional skin. A detailed investigation of vitiligo skin transcriptome reveals elevation of DNA repair and cell-proliferation pathways. Validation by comet-assay for DNA damage and cell cycle analysis of epidermal cells suggest undamaged DNA in vitiligo lesions that could be attributed to higher proliferation-coupled repair. Endorsing this, UV-signature variations are not prominent, instead SBS5 associated with endogenous mutational processes is conspicuous in both the vitiligo tissues. Our systematic pilot study indicates lower somatic mutation burden in vitiligo skin and supports the earlier demographic observation on lower risk of non-melanoma skin cancer in vitiligo subjects, providing an opportunity to learn strategies for cancer prevention from vitiligo. Brief SummaryVitiligo skin harbors decreased somatic variation burden in cancer-associated genes and a concomitant augmentation in DNA repair response, explaining the lower incidence of cutaneous malignancies.

genomics↗

bioRxiv2022

When Citizen Science meets teaching: A storified citizen science computer game to teach and contribute to genomic data analysis

In the last decade, video games became a common vehicle for citizen science initiatives in life science, allowing participants to contribute to real scientific data analysis while learning about it. Since 2010, our scientific discovery game (SDG) Phylo enlists participants in comparative genomic data analysis. It is frequently used as a learning tool, but the activities were difficult to aggregate to build a coherent teaching activity. Here, we describe a strategy and series of recipes to facilitate the integration of SDGs in courses and implement this approach in Phylo. We developed new roles and functionalities enabling instructors to create assignments and monitor the progress of students. A story mode progressively introduces comparative genomics concepts, allowing users to learn and contribute to the analysis of real genomic sequences. Preliminary results from a user study suggest this framework may help to boost user motivation and clarify pedagogical objectives.

scientific communication and education↗

bioRxiv2022

Discovery of a new class of reversible TEA-domain transcription factor inhibitors with a novel binding mode

The TEA domain (TEAD) transcription factor forms a transcription co-activation complex with the key downstream effector of the Hippo pathway, YAP/TAZ. TEAD-YAP controls the expression of Hippo-responsive genes involved in cell proliferation, development, and tumorigenesis. Hyperactivation of TEAD-YAP activities is observed in many human cancers, and is associated with cancer cell proliferation, survival and immune evasion. Therefore, targeting the TEAD-YAP complex has emerged as an attractive therapeutic approach. We previously reported that the mammalian TEAD transcription factors (TEAD1-4) possess auto-palmitoylation activities and contain an evolutionarily conserved palmitate-binding pocket (PBP), which allows small molecule modulation. Since then, several reversible and irreversible inhibitors have been reported by binding to PBP. Here, we report a new class of TEAD inhibitors with a novel binding mode. Representative analog TM2 shows potent inhibition of TEAD auto-palmitoylation both in vitro and in cells. Surprisingly, the co-crystal structure of the human TEAD2 YAP-binding domain (YBD) in complex with TM2 reveals that TM2 adopts an unexpected binding mode by occupying not only the hydrophobic PBP, but also a new side binding pocket formed by hydrophilic residues. RNA-seq analysis shows that TM2 potently and specifically suppresses TEAD-YAP transcriptional activities. Consistently, TM2 exhibits strong anti-proliferation effects as a single agent or in combination with a MEK inhibitor in YAP-dependent cancer cells. These findings establish TM2 as a promising small molecule inhibitor against TEAD-YAP activities and provide new insights for designing novel TEAD inhibitors with enhanced selectivity and potency.

biochemistry↗

bioRxiv2022

A therapeutically targetable NOTCH1-SIRT1-KAT7 axis in T-cell Leukemia

T-cell Acute Lymphoblastic Leukemia (T-ALL) is a NOTCH1-driven disease in need of novel therapies. Here, we identify a NOTCH1-SIRT1-KAT7 link as a therapeutic vulnerability in T-ALL, in which SIRT1 is overexpressed downstream of a novel NOTCH1-bound enhancer. SIRT1 loss impairs leukemia generation, while SIRT1 overexpression accelerates leukemia and confers resistance to NOTCH1 inhibition in a deacetylase-dependent manner. Moreover, secondary SIRT1 loss extends survival and synergizes with NOTCH1 inhibition. Global acetyl-proteomics upon SIRT1 loss uncovered hyperacetylation of KAT7 and BRD1, subunits of a histone acetyltransferase complex targeting H4K12. Metabolic and gene expression profiling revealed a metabolic crisis together with a transcriptional signature resembling KAT7 deletion. Consistently, SIRT1 loss resulted in reduced H4K12ac, and overexpression of a non-acetylatable KAT7 mutant partly rescued SIRT1 loss-induced proliferation defects. The newly unveiled NOTCH1-SIRT1-KAT7 axis uncovers novel therapeutic targets in T-ALL and reveals a circular feedback mechanism balancing deacetylase/acetyltransferase activation with potentially broad relevance in cancer. Statement of significanceWe identified a novel axis in T-ALL whereby NOTCH1 activates SIRT1 through an enhancer region, and SIRT1 deacetylates and activates KAT7. Targeting SIRT1 shows antileukemic effects, partly mediated by KAT7 inactivation. Our results identify novel therapeutic targets and uncover a rheostat mechanism between deacetylase/acetyltransferase activities with potentially broader cancer relevance.

cancer biology↗

bioRxiv2022

Effects of netarsudil-family Rho kinase inhibitors on human trabecular meshwork cell contractility and actin remodeling using a bioengineered ECM hydrogel

Interactions between trabecular meshwork (TM) cells and their extracellular matrix (ECM) are critical for normal outflow function in the healthy eye. Multifactorial dysregulation of the TM is the principal cause of elevated intraocular pressure that is strongly associated with glaucomatous vision loss. Key characteristics of the diseased TM are pathologic contraction and actin stress fiber assembly, contributing to overall tissue stiffening. Among first-line glaucoma medications, the Rho-associated kinase inhibitor (ROCKi) netarsudil is known to directly target the stiffened TM to improve outflow function via tissue relaxation involving focal adhesion and actin stress fiber disassembly. Yet, no in vitro studies have explored the effect of netarsudil on human TM (HTM) cell contractility and actin remodeling in a 3D ECM environment. Here, we use our bioengineered HTM cell-encapsulated ECM hydrogel to investigate the efficacy of different netarsudil-family ROCKi compounds on reversing pathologic contraction and actin stress fibers. Netarsudil and all related experimental ROCKi compounds exhibited significant ROCK1/2 inhibitory and focal adhesion disruption activities. Furthermore, all ROCKi compounds displayed potent contraction-reversing effects on HTM hydrogels upon glaucomatous induction in a dose-dependent manner, relatively consistent with their biochemical/cellular inhibitory activities. At their tailored EC50 levels, netarsudil-family ROCKi compounds exhibited distinct effect signatures of reversing pathologic HTM hydrogel contraction and actin stress fibers, independent of the cell strain used. Netarsudil outperformed the experimental ROCKi compounds in support of its clinical status. In contrast, at uniform EC50-levels using netarsudil as reference, all ROCKi compounds performed similarly. Collectively, our data suggest that netarsudil exhibits high potency to rescue HTM cell pathobiology in a tissue-mimetic 3D ECM microenvironment, solidifying the utility of our bioengineered hydrogel model as a viable screening platform to further our understanding of TM pathophysiology in glaucoma.

cell biology↗

bioRxiv2022

MaLAdapt reveals novel targets of adaptive introgression from Neanderthals and Denisovans in worldwide human populations

Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, these outlier-based approaches are vulnerable to a high false-negative rate as the power of different methods vary, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals as AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present an ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selection sweeps, heterosis, and demographic misspecifications. Further, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and on a validation of empirical signals through visual impaction of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data, and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.

evolutionary biology↗

bioRxiv2022

Female factors are important for the seminal Sex Peptide's association with sperm in mated female D. melanogaster.

BackgroundMale-derived seminal fluid proteins (SFPs) enter and induce a myriad of physiological and behavioral changes in mated female flies optimizing fertility. Many post-mating changes in female Drosophila melanogaster persist for [~]10-14 days, because the seminal protein that induces them, Sex Peptide (SP), is retained long-term in females by binding to sperm, with gradual release of its active domain from sperm. Several other "long-term response SFPs" (LTR-SFPs) "prime" sperm to bind SP. Whether female factors play a role in this process is unknown, though it is important to study both sexes for a comprehensive physiological understanding of this reproductive process and for consideration in models of sexual conflict. ResultsWe report here that sperm in male ejaculates bind SP more weakly than sperm that have entered females, and that the amount of SP and other SFPs bound to sperm increases with time and transit of individual seminal proteins within the female reproductive tract. Thus, female contributions are needed for maximal and appropriate binding of SP, and other SFPs, to sperm. Towards understanding the molecular roles of the female, we found no dramatic change in pH of the female reproductive tract after mating and that initial binding of SP to sperm is normal in females with ablated or defective spermathecal secretory cells and/or parovaria, but that higher levels of SP (and sperm) are retained in the latter females. ConclusionThis study reveals that the SP pathway is not entirely male-biased and that females also contribute to regulating it.

physiology↗