Biology subjects

Myers, B.

Publications and source records attributed to Myers, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Genetic and Epigenetic Landscape of Self-Identified Hispanics/Latino in All Of Us

Human genetic studies still underrepresent many populations, limiting discovery and interpretation of medically relevant variation. Extensive admixture in self-identified Hispanic/Latino populations increases the need for representative reference data and ancestry-aware interpretation of medically relevant variation. We used long-read sequencing to analyze genetic variation, ancestry, and DNA methylation in 1,490 self-identified Hispanic/Latino participants from the All of Us Research Program. We identified 10 million novel variants and more than 100 candidate phenotype associations, with fine-mapping prioritizing structural variants over nearby single-nucleotide variants in more than half. We linked 3,329 tandem repeats to DNA methylation, resolved widespread allele-specific methylation, and identified ancestry-linked regulation across paralogous genes. These results reveal previously inaccessible genetic and regulatory variation and show the value of long-read sequencing for diverse populations.

genetics↗

bioRxiv2026

Large disruptions to mammalian spermatogenesis downstream of genetic perturbations in meiotic double-strand break repair

Fertility in mammals relies on successful pairing of homologous chromosomes mediated by DNA double-strand breaks (DSBs). Here, we develop a system of mouse hybrids in which (a)symmetry of binding by the break-positioning protein PRDM9 to homologs varies over broad scales in the genome. Profiling transcription and chromatin in single nuclei, we trace how resulting delays in repair of variable subsets of meiotic DSBs propagate through spermatogenesis and drive large fertility differences in animals. We demonstrate that only asymmetry-generating mutations in PRDM9-binding motifs, not high average (~1%) divergence, disrupt chromosomal pairing. We observe substantial variation in animal-level sensitivity to asymmetry, and identify an interacting locus containing Dmc1 and Mei1 controlling (R2=0.64) this variation. Silencing of unpaired autosomes downstream of asynapsis and failure of normal sex chromosome silencing independently explain cell death in pachytene. Surprisingly, many cells with synaptic defects evade cell cycle arrest, and even those where physical division arrests still exhibit transcriptional progression to post-division states. Attrition of abnormal cells via arrest continues beyond the first division; nonetheless, cells that complete both meiotic divisions exhibit aneuploidy, especially of the sex chromosomes. This partly reflects de novo segregation errors explained by silencing of only chromosomes 16 and 19. Even "normal" euploid spermatids show crossovers redistributed at multi-megabase scales, indicating novel and potentially post-zygotic impacts of delays in meiotic DSB-repair. We thus elucidate cell-level and chromosome-specific impacts of regulatory variation in ~0.03% of the genome cascading through germline development, advancing our understanding of fertility and reproductive isolation.

genetics↗

bioRxiv2026

Sex-specific organization and synaptic signaling in prefrontal-hypothalamic circuitry

Top down signaling from the cortex to the hypothalamus is critical to link cognitive and emotional processing to homeostasis and motivation. This study investigates signaling from the medial prefrontal cortex (mPFC) to the posterior hypothalamus (PH), a region that modulates endocrine and autonomic stress responses and motivated behaviors. The function and anatomy of this circuit was examined with patch clamp electrophysiology and mapping studies in male and female rats. Spontaneous firing properties of PH neurons were determined in a cell-type specific manner by combining a transgenic glutamic acid decarboxylase-Cre rat with Cre-dependent colorswitch virus to determine postsynaptic cell-type identity. Overall, PH neurons were more excitable in females compared to males and, in both sexes, data indicated tonic inhibition within the PH, with significantly greater inhibition in males. Using Channelrhodopsin-assisted circuit mapping to query the mPFC-PH circuit, we found that a majority of PH neurons received input from the mPFC and mPFC synapses targeted glutamatergic cells over GABAergic PH cells. Retrograde tracing revealed more PH-projecting neurons in females, specifically within the tenia tecta and infralimbic regions of the mPFC, with significantly more stress-activated PH-projecting cells in the female prelimbic cortex. Anterograde tracing revealed, surprisingly, no sex differences in mPFC presynaptic terminal density in the PH, despite more PH-projecting cell bodies in the female mPFC. These data help to elucidate the sexual divergence in cortical-hypothalamic signaling and how cognitive and emotional information from the prefrontal cortex may differentially regulate homeostasis and motivation between sexes. Significance StatementNeural signaling between the prefrontal cortex and the hypothalamus is important for maintaining homeostasis, particularly during contextual challenges such as stressors. Here we find multiple aspects of sex-specific organization and neurophysiology in this circuitry. Excitatory inputs from the medial prefrontal cortex target both excitatory and inhibitory neurons within the posterior hypothalamic nucleus in both sexes. However, there are sex differences in the number of stress-activated neurons in the prefrontal cortex that innervate the posterior hypothalamus, as well as differences in hypothalamic inhibitory signaling and estrous cycle-dependent effects on neuronal excitability. Altogether, these data suggest that organizational, synaptic, and hormonal factors may contribute to sex-specific behavioral and physiological integration.

neuroscience↗

bioRxiv2026

Prefrontal-medullary circuitry is necessary for sex-specific responses to metabolic stress in rats

Chronic stress increases risk for metabolic disorders, including diabetes mellitus. Additionally, projections from the infralimbic cortex (IL) to the rostral ventrolateral medulla (RVLM) regulate endocrine stress responses. However, the neurobiological basis for chronic stress effects on glucose homeostasis has not been identified. The current study tests the hypothesis that the IL-RVLM circuit is necessary to prevent glucose intolerance. Accordingly, male and female rats with Cre-dependent expression of tetanus toxin light chain (TeLC) to inhibit neurotransmitter release from RVLM-projecting IL neurons were subject to chronic variable stress (CVS) or remained as No CVS controls. Animals were then acutely challenged with a fasted intraperitoneal glucose tolerance test (GTT). Endocrine metabolic function was evaluated during GTT via time courses of glucose, insulin, glucagon, and corticosterone. In No CVS females expressing TeLC, inhibition of IL-RVLM circuit signaling impaired glucose tolerance characterized by elevated glucose and decreased insulin sensitivity. Following chronic stress, females had impaired glucoregulation characterized by decreased glucose clearance and elevated corticosterone. When combined with TeLC, chronically-stressed females showed shifts in the ratio of insulin to glucagon compared to CVS GFP females, suggesting circuit function impacts the pancreatic mechanisms mediating glucose homeostasis during chronic stress. In No CVS males, TeLC increased glucagon only. However, CVS TeLC males had impaired glucose tolerance, reduced insulin sensitivity, and decreased corticosterone. These data indicate that the IL-RVLM circuit mediates glucoregulation in a manner dependent on both sex and stress history. Collectively, the IL-RVLM circuit is necessary for the sex-specific maintenance of glucose homeostasis following chronic stress.

neuroscience↗

bioRxiv2025

GENESIS: Generating scRNA-Seq data from Multiome Gene Expression

Single-cell technologies have significantly advanced our understanding of cellular heterogeneity by allowing the examination of individual cells at high resolution. Traditional single-cell RNA sequencing (scRNA-Seq) methods, which utilise whole cells, capture comprehensive RNA content. In contrast, emerging Multiome technologies, which simultaneously profile multiple omics such as gene expression (GEX) and chromatin accessibility, rely on nuclear RNA, potentially missing key cytoplasmic information. This discrepancy leads to substantial technical and biological differences between GEX and scRNA-Seq datasets, making it difficult to integrate data and perform downstream tasks like cell-type classification. To address this challenge, we introduce GENESIS (Gene Expression Normalisation and Enhancement for Single-cell Integrated Sequencing), a novel computational framework designed to transform GEX data from Multiome experiments into enhanced, scRNA-Seq like profiles. Utilising advanced generative models--including Variational Autoencoders, Generative Adversarial Networks, and a tailored VAE UNet architecture--GENESIS can generate high-quality data by modelling and compensating for the inherent differences between nuclear and cytoplasmic RNA. Our comprehensive evaluations show that GENESIS, particularly through the VAE UNet model, generates synthetic scRNA-Seq data that closely resembles the resolution and biological accuracy of whole-cell sequencing, improving downstream tasks, especially cell-type classification.

bioinformatics↗

bioRxiv2025

Infralimbic prefrontal cortical projections to the autonomic brainstem: Quantification of inputs to cholinergic and adrenergic/noradrenergic nuclei

The ventromedial prefrontal cortex regulates both emotional and physiological processes. The infralimbic cortex (IL), a prefrontal subregion in rodents, integrates behavioral, neuroendocrine, and autonomic responses to stress. However, the organization of cortical inputs to brainstem nuclei that regulate homeostatic responses are not well defined. We hypothesized that IL projections differentially target pre-ganglionic parasympathetic neurons and adrenergic/noradrenergic nuclei. To quantify IL projections to autonomic brainstem nuclei in male rats, we utilized viral-mediated gene transfer to express yellow fluorescent protein (YFP) in IL glutamatergic neurons. YFP-positive projections to cholinergic and adrenergic/noradrenergic nuclei were then imaged and quantified. Cholinergic neurons were visualized by immunohistochemistry for choline acetyltransferase (ChAT), the enzyme responsible for the synthesis of acetylcholine. Adrenergic/noradrenergic neurons were visualized with immunohistochemistry for dopamine beta-hydroxylase (DBH) which converts dopamine to norepinephrine. Our results indicate that IL glutamate neurons innervated the cholinergic dorsal motor nucleus of the vagus with greater density than the nucleus ambiguus. Furthermore, numerous DBH-positive cell groups received IL inputs. The greatest density was to the C2 and A2 regions of the nucleus of the solitary tract with intermediate levels of input to A6 locus coeruleus and throughout the C1 and A1 regions of the ventrolateral medulla. Minimal input was present in the pontine A5. Additionally, IL projections targeted the local GABAergic neurons that regulate activity within preautonomic nuclei. Collectively, our results indicate that IL pyramidal neurons project to vagal preganglionic parasympathetic neurons, presympathetic neurons of the ventrolateral medulla, as well as diffuse homeostatic modulators the nucleus of the solitary tract and locus coeruleus. Ultimately, these findings provide a roadmap for determining circuit-level mechanisms for neural control of homeostasis and autonomic balance.

neuroscience↗

bioRxiv2025

Proximity based proteomics reveals Git1 as a regulator of Smoothened signaling

The GPCR-like protein Smoothened (Smo) plays a pivotal role in the Hedgehog (Hh) pathway. To initiate Hh signaling, active Smo binds to and inhibits the catalytic subunit of PKA in the primary cilium, a process facilitated by G protein-coupled receptor kinase 2 (Grk2). However, the precise regulatory mechanisms underlying this process, as well as the events preceding and following Smo activation, remain poorly understood. To address this question, we leveraged the proximity labeling tool TurboID and conducted a time-resolved proteomic study of Smo-associated proteins over the course of Hh signaling activation. Our results not only confirmed previously reported Smo interactors but also uncovered new Smo-associated proteins. We characterized one of these new Smo interactors, Grk-interacting protein 1 (Git1), previously known to modulate GPCR signaling. We found that Git1 localizes to the base of the primary cilium, where it controls the cilium transport of Grk2, an early event in Hh signaling. Loss of Git1 impairs Smo phosphorylation by Grk2, a critical step for Smo-PKA interaction, leading to attenuated Hh signaling and reduced cell proliferation in granule neuron precursors. These results revealed a critical regulatory mechanism of Grk2 phosphorylation on Smo in the primary cilium. Our Smo-TurboID proteomic dataset provides a unique resource for investigating Smo regulations across different stages of Hh pathway activation.

cell biology↗

bioRxiv2024

Repeated presentation of visual threats drives innate fear habituation and is modulated by environmental and physiological factors

To survive predation, animals must be able to detect and appropriately respond to predator threats in their environment. Such defensive behaviors are thought to utilize hard-wired neural circuits for threat detection, sensorimotor integration, and execution of ethologically relevant behaviors. Despite being hard-wired, defensive behaviors (i.e. fear responses) are not fixed, but rather show remarkable flexibility, suggesting that extrinsic factors such as threat history, environmental contexts, and physiological state may alter innate defensive behavioral responses. The goal of the present study was to examine how extrinsic and intrinsic factors influence innate defensive behaviors in response to visual threats. In the absence of a protective shelter, our results indicate that mice showed robust freezing behavior following both looming (proximal) and sweeping (distal) threats, with increased behavioral vigor in response to looming stimuli, which represent a higher threat imminence. Repeated presentation of looming or sweeping stimuli at short inter-trial intervals resulted in robust habituation of freezing, which was accelerated at longer inter-trial intervals, regardless of contextual cues. Finally, physiological factors such as acute stress further disrupted innate freezing habituation, resulting in a delayed habituation phenotype, consistent with a heightened fear state. Together, our results indicate that extrinsic factors such as threat history, environmental familiarity, and physiological stressors have robust and diverse effects on defensive behaviors, highlighting the behavioral flexibility in how mice respond to predator threats.

animal behavior and cognition↗

bioRxiv2024

Sex-Specific Cardiac Remodeling in Aged Rats after Early-Life Chronic Stress: Associations with Endocrine and Metabolic Factors

BackgroundCardiovascular disease is a leading cause of death worldwide. Rates of cardiovascular disease vary both across the lifespan and between sexes. While multiple factors, including adverse life experiences, impact the development and progression of cardiovascular disease, the potential interactions of biological sex and stress history on the aged heart are unknown. To this end, we examined sex- and stress-specific impacts on left ventricular hypertrophy (VH) after aging. We hypothesized that early life chronic stress exposure impacts behavioral and physiologic responses that predict cardiac remodeling in a sex-specific manner. MethodsHistological analysis was conducted on hearts of male and female rats previously exposed to chronic variable stress during the late adolescent period (postnatal days 43-62). These animals were challenged with a forced swim test and a glucose tolerance test before aging to 15 months and again being challenged. Predictive analyses were then used to isolate factors that relate to cardiac remodeling among these groups. ResultsEarly-life chronic stress impacted cardiac remodeling in a sex-specific manner. Among rats with a history of chronic stress, females had increased inward VH. However, there were few associations within the female groups among individual behavioral and physiologic parameters and cardiac remodeling. While males as a group did not have VH after chronic stress, they exhibited multiple individual associations with cardiac susceptibility. Passive coping in young males and active coping in aged males related to VH in a stress history-dependent manner. Moreover, baseline corticosterone positively correlated with VH in unstressed males, while chronically-stressed males had positive correlations between VH and visceral adiposity. ConclusionsThese results indicate that females as a group are uniquely susceptible to the effects of early-life stress on cardiac remodeling later in life. Conversely, males have more individual differences in vulnerability, where susceptibility to cardiac remodeling relates to endocrine, metabolic, and behavioral measures depending on stress history. These results ultimately support a framework for accessing cardiovascular risk based on biological sex and prior adverse experiences. HighlightsO_LIAged female rats had greater left ventricular hypertrophy (VH) than males after early-life chronic variable stress. C_LIO_LITertile divisions based on susceptibility or resilience to inward VH indicated interactions between VH, sex, and stress on multiple behavioral and physiological measures. C_LIO_LIIn males, VH correlated with endocrine and metabolic parameters in a stress history-dependent manner. C_LIO_LIPrior adverse experience and biological sex interact across the lifespan to impact cardiovascular risk. C_LI Plain English SummaryCardiovascular disease is the leading cause of death worldwide. Multiple factors influence the incidence and severity of cardiovascular disease including adverse life experiences, biological sex, and age. Alterations of heart structure predict negative cardiovascular health by impacting blood circulation; however, the potential interactions of stress history and biological sex on the aged heart are unknown. In this study, we examined how chronic stress exposure impacts heart structure in male and female rats after aging. Adolescent male and female rats were chronically stressed and then acutely challenged to examine behavioral, endocrine, and metabolic parameters both immediately following chronic stress and after aging. Heart morphology was quantified to examine how behavioral and physiological responses related to cardiac remodeling. Our results indicate that, as a group, female rats previously exposed to chronic stress were uniquely susceptible to inward remodeling of the heart. Subjects were further divided into sub-groups based on the level of inward remodeling of the ventricle. While male rats did not exhibit group effects on heart structure, individual variability in male heart morphology related to endocrine and metabolic parameters in a stress history-dependent manner. Here, there were interactions with multiple systems including coping behavior, stress hormones, and body composition. Moreover, males without a prior history of chronic stress had correlations between stress hormones and the degree of heart remodeling. However, males that were exposed to chronic stress had correlations between heart structure and abdominal fat. Overall, our results indicate that biological sex and stress history interact to predict cardiovascular susceptibility.

physiology↗

bioRxiv2023

Cortical-brainstem circuitry attenuates stress reactivity

Exposure to stressful stimuli promotes multi-system biological responses to restore homeostasis. Catecholaminergic neurons in the rostral ventrolateral medulla (RVLM) facilitate sympathetic activity and promote physiological adaptations, including glycemic mobilization and corticosterone release. While it is unclear how brain regions involved in the cognitive appraisal of stress regulate RVLM neural activity, recent studies found that the rodent ventromedial prefrontal cortex (vmPFC) mediates stress appraisal and physiological stress responses. Thus, a vmPFC-RVLM connection could represent a circuit mechanism linking stress appraisal and physiological reactivity. The current study investigated a direct vmPFC-RVLM circuit utilizing genetically-encoded anterograde and retrograde tract tracers. Together, these studies found that stress-reactive vmPFC neurons project to catecholaminergic neurons throughout the ventrolateral medulla in male and female rats. Next, we utilized optogenetic terminal stimulation to evoke vmPFC synaptic glutamate release in the RVLM. Photostimulating the vmPFC-RVLM circuit during restraint stress suppressed glycemic stress responses in males, without altering the female response. However, circuit stimulation decreased corticosterone responses to stress in both sexes. Circuit stimulation did not modulate affective behavior in either sex. Further analysis indicated that circuit stimulation preferentially activated non-catecholaminergic medullary neurons in both sexes. Additionally, vmPFC terminals targeted medullary inhibitory neurons. Thus, both male and female rats have a direct vmPFC projection to the RVLM that reduces endocrine stress responses, likely through the recruitment of local RVLM inhibitory neurons. Ultimately, the excitatory/inhibitory balance of vmPFC synapses in the RVLM may regulate stress reactivity as well as stress-related health outcomes. First author profileSebastian Pace is a Ph.D. candidate in the laboratory of Brent Myers at Colorado State University. Before beginning his Ph.D., Sebastian completed his B.S. and M.S. at the University of Texas-El Paso. While completing his M.S. he worked in the Karine Fenelon Lab. Sebastians current research project focuses on understanding how corticolimbic inputs to the medullary brainstem regulate sympathetic and neuroendocrine stress responses. Key points summaryO_LIGlutamatergic efferents from the ventromedial prefrontal cortex target catecholaminergic neurons throughout the ventrolateral medulla. C_LIO_LIPartially segregated, stress-responsive ventromedial prefrontal cortex populations innervate the rostral and caudal ventrolateral medulla. C_LIO_LIStimulating ventromedial prefrontal cortex synapses in the rostral ventrolateral medulla decreases stress-induced glucocorticoid release in males and females. C_LIO_LIStimulating ventromedial prefrontal cortex terminals in the rostral ventrolateral medulla preferentially activates non-catecholaminergic neurons. C_LIO_LIVentromedial prefrontal cortex terminals target medullary inhibitory neurons. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/549781v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@c362acorg.highwire.dtl.DTLVardef@1830ca5org.highwire.dtl.DTLVardef@b3411borg.highwire.dtl.DTLVardef@779392_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Sex-specific prefrontal-hypothalamic control of behavior and stress responding

Depression and cardiovascular disease are both augmented by daily life stress. Yet, the biological mechanisms that translate psychological stress into affective and physiological outcomes are unknown. Previously, we demonstrated that stimulation of the ventromedial prefrontal cortex (vmPFC) has sexually divergent outcomes on behavior and physiology. Importantly, the vmPFC does not innervate the brain regions that initiate autonomic or neuroendocrine stress responses; thus, we hypothesized that intermediate synapses integrate cortical information to regulate stress responding. The posterior hypothalamus (PH) directly innervates stress-effector regions and receives substantial innervation from the vmPFC. In the current studies, circuit-specific approaches examined whether vmPFC synapses in the PH coordinate stress responding. Here we tested the effects of optogenetic vmPFC-PH circuit stimulation in male and female rats on social and motivational behaviors as well as physiological stress responses. Additionally, an intersectional genetic approach was used to knock down synaptobrevin in PH-projecting vmPFC neurons. Our collective results indicate that male vmPFC-PH circuitry promotes positive motivational valence and is both sufficient and necessary to reduce sympathetic-mediated stress responses. In females, the vmPFC-PH circuit does not affect social or preference behaviors but is sufficient and necessary to elevate neuroendocrine stress responses. Altogether, these data suggest cortical regulation of stress reactivity and behavior is mediated, in part, by projections to the hypothalamus that function in a sex-specific manner.

neuroscience↗

bioRxiv2022

Engineering Nanowires in Bacteria to Elucidate Electron Transport Structural Functional Relationships

Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells bioenergetic programming. Their role is thought to be linked to facilitating electron transfer with the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineered Cupriavidus necator H16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells for the first time. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using a CN chassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment. O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/510814v2_ufig1.gif" ALT="Figure 1"> View larger version (90K): org.highwire.dtl.DTLVardef@134d026org.highwire.dtl.DTLVardef@4d84f3org.highwire.dtl.DTLVardef@15379fcorg.highwire.dtl.DTLVardef@16d942c_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract displaying theoretical PilA monomer models (left), PeakForce TUNA atomic force microscopy contact current images (right) of wild-type (top) and modified with increased tyrosine content (bottom) PilA filaments expressed by Cupriavidus necator H16 cells.

bioengineering↗

bioRxiv2022

Prefrontal representation of affective stimuli: importance of stress, sex, and context

Major depressive disorder diminishes health-related quality-of-life and disproportionality impacts females. Negative life events predict the onset of depressive symptoms including negative mood, anhedonia, and social withdrawal. While the neurobiology of affective illness is not completely understood, structural and functional changes in the ventromedial prefrontal cortex (vmPFC) associate with mood and anxiety disorders. Rodent studies have investigated the prefrontal impact of chronic stress, a preclinical model of mood disruption. However, ex vivo slice and postmortem histological studies have focused largely on males and yielded mixed results. Although genetically-defined recordings in behaving animals of both sexes have not been reported. Here, we hypothesized that chronic variable stress (CVS) would reduce the neural processing of affective stimuli in the infralimbic region of rodent vmPFC region. To test this hypothesis, we targeted expression of a fluorescent calcium indicator, GCaMP6s, to infralimbic pyramidal cells. In males, CVS reduced infralimbic responses to social interaction and restraint stress but increased responses to novel objects and food reward. In contrast, females did not have CVS-induced changes in infralimbic activity, which was partially dependent on ovarian status. Collectively, these results indicate that both male and female vmPFC pyramidal cells encode social, stress, and reward stimuli. However, chronic stress effects are sex-dependent and behavior-specific. Ultimately, these findings extend the understanding of chronic stress-induced prefrontal dysfunction and indicate that sex is a critical factor for cortical processing of affective stimuli. SignificanceMood disorders are often preceded by stressful experiences and exhibit sex differences in prevalence. Further, affective illness is frequently accompanied by changes in prefrontal cortical function. However, the neurobiology that underlies sex-specific cortical processing of affective stimuli is poorly understood. Therefore, the current studies employ cell type-specific calcium photometry to determine the effects of chronic stress on ventromedial prefrontal cortex (vmPFC) activity in male and female rats. Our results indicate that chronic stress exposure differentially alters vmPFC encoding of social, stress, and reward stimuli. Moreover, the sex-specific effects of chronic stress are partially mediated by ovarian hormones. Ultimately, our results indicate that prolonged stress alters vmPFC function in a context-dependent and sex-specific manner, contributing to the biological bases for sex differences in emotional processing.

neuroscience↗

bioRxiv2021

Glucoregulation and coping behavior after chronic stress: sex differences across the lifespan

Exposure to prolonged stress during adolescence taxes adaptive and homeostatic processes leading to deleterious behavioral and metabolic outcomes. Although previous pre-clinical studies found effects of early life stress on cognition and stress hormone reactivity, these studies largely focused on males. The purpose of the current study was to determine how biological sex shapes behavioral coping and metabolic health across the lifespan after chronic stress. We hypothesized that examining chronic stress-induced behavioral and endocrine outcomes would reveal sex differences in the biological basis of susceptibility. During the late adolescent period, male and female Sprague-Dawley rats experienced chronic variable stress (CVS). Following completion of CVS, all rats experienced a forced swim test (FST) followed 3 days later by a fasted glucose tolerance test (GTT). The FST was used to determine coping in response to a stressor. Endocrine metabolic function was evaluated in the GTT by measuring glucose and corticosterone, the primary rodent glucocorticoid. Animals then aged to 15 months when the FST and GTT were repeated. In young animals, chronically stressed females exhibited more passive coping and corticosterone release in the FST. Additionally, chronically stressed females had elevated corticosterone and impaired glucose clearance in the GTT. Aging affected all measurements as behavioral and endocrine outcomes were sex specific. Furthermore, regression analysis between hormonal and behavioral responses identified associations depending on sex and stress. Collectively, these data indicate female susceptibility to the effects of chronic stress during adolescence. Further, translational investigation of coping style and glucose homeostasis may identify biomarkers for stress-related disorders.

animal behavior and cognition↗

bioRxiv2020

Sexually divergent cortical control of affective-autonomic integration

Depression and cardiovascular disease reduce quality of life and increase mortality risk. These conditions commonly co-occur with sex-based differences in incidence and severity. However, the biological mechanisms linking the disorders are poorly understood. In the current study, we hypothesized that the infralimbic (IL) prefrontal cortex integrates mood-related behaviors with the cardiovascular burden of chronic stress. In a rodent model, we utilized optogenetics during behavior and in vivo physiological monitoring to examine how the IL regulates affect, social motivation, neuroendocrine-autonomic stress reactivity, and the cardiac consequences of chronic stress. Our results indicate that IL glutamate neurons increase socio-motivational behaviors specifically in males. IL activation also reduced endocrine and cardiovascular stress responses in males, while increasing reactivity in females. Moreover, prior IL stimulation protected males from subsequent chronic stress-induced sympatho-vagal imbalance and cardiac hypertrophy. Our findings suggest that cortical regulation of behavior, physiological stress responses, and cardiovascular outcomes fundamentally differ between sexes.

neuroscience↗

bioRxiv2020

Deletion of the voltage-gated calcium channel, CaV1.3, causes deficits in motor performance and associative learning

L-type voltage-gated calcium channels are important regulators of neuronal activity and are widely expressed throughout the brain. One of the major L-type voltage-gated calcium channel isoforms in the brain is CaV1.3. Mice lacking CaV1.3 are reported to have impairments in fear conditioning and depressive-like behaviors, which have been linked to CaV1.3 function in the hippocampus and amygdala. Genetic variation in CaV1.3 has been linked to a variety of psychiatric disorders, including autism and schizophrenia, which are associated with altered motor learning, associative learning, and social function. Here, we explored whether CaV1.3 plays a role in these behaviors. We found that CaV1.3 knockout mice have deficits in rotarod learning despite normal locomotor function. Deletion of CaV1.3 is also associated with impaired gait adaptation and associative learning on the Erasmus Ladder. We did not observe any impairments in CaV1.3 knockout mice on assays of anxiety-like, depression-like, or social preference behaviors. Our results suggest an important role for CaV1.3 in neural circuits involved in motor learning and concur with previous data showing its involvement in associative learning.

neuroscience↗

bioRxiv2020

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3 end of LINE-1_Cfs (i.e., LINE-1_Cf 3-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation. SignificanceAdvancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.

genomics↗

bioRxiv2020

Pan-genome-wide analysis of Pantoea ananatis identified genes linked to pathogenicity in onion

Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion-virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-GWAS revealed a large core genome of 3,153 genes and a flexible accessory genome of [≤]5,065 genes. Phylogenomic analysis using pan-GWAS and presence and absence variants (PAVs) distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. The pan-GWAS also predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, TraR/DksA family transcriptional regulator, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. This is the first report of using pan-GWAS on P. ananatis for the prediction of novel genes contributing to pathogenicity in onion, which will be utilized for further functional analyses. Pan-genomic differences (using PAVs) differentiated onion pathogenic from non-pathogenic strains of P. ananatis, which has been difficult to achieve using single or multiple gene-based phylogenetic analyses. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the alt cluster that aid in P. ananatis colonization in onion bulbs. We concluded that HiVir/PASVIL genes are associated with pathogenic P. ananatis strains and the alt gene cluster alone is not responsible for pathogenicity on onion. The pan-genome also provides clear evidence of constantly evolving accessory genes in P. ananatis that may contribute to host-range expansion and niche-adaptation. Author summaryPantoea ananatis is a major bacterial pathogen that causes center rot of onion and diseases of a number of other plant species. In order to understand the genome architecture and identify genes responsible for pathogenicity in onion, a pan-genome analysis was performed. We used 81 strains of P. ananatis collected over 20 years from different regions of the state of Georgia, USA. The pan-genome study identified a core genome with a conserved set of genes and an accessory genome that displayed variation among strains. We conducted pan-GWAS (pan-genome-wide association study) using presence and absence variants (PAVs) in the genomes and associated onion-pathogenic phenotypes based on a red-onion scale necrosis assay. The study resulted in identification of genes, including a cluster of chromosomal HiVir/PASVIL genes, that are significantly associated with the onion pathogenic phenotype. In addition, we identified 28 novel genes, a majority of which (n = 20) have hypothetical functions. We concluded and further substantiated earlier findings that a cluster of genes is responsible for pathogenicity on onion. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the alt cluster that aid in bacterial colonization of onion bulbs by P. ananatis strains. We concluded that HiVir/PASVIL genes are associated with onion-pathogenic strains, and the alt gene cluster alone is not responsible for pathogenicity on onion. This study also provides potential evidence of constantly evolving accessory genes in P. ananatis which may help in host range expansion and adaptation to diverse niches.

genomics↗