Biology subjects

Allen, C.

Publications and source records attributed to Allen, C..

54 records · Page 3Linked to original sources

bioRxiv2021

Network-Based Discovery of Opioid Use Vulnerability in Rats Using the Bayesian Stochastic Block Model

Opioid use disorder is a psychological condition that affects over 200,000 people per year in the U.S., causing the Centers for Disease Control and Prevention to label the crisis as a rapidly spreading public health epidemic. It has been found that the behavioral relationship between opioid exposure and development of opioid use disorder varies greatly between individuals, implying existence of sup-populations with varying degrees of opioid vulnerability. In this study, we assessed several behavioral variables across heroin taking, refraining and seeking to establish how these factors interact with one another resulting in a heroin dependent, resilient, or vulnerable behavioral phenotype. Over 400 (male and female) heterogeneous stock rats were used in these two studies, and data were collected from two geographically distinct locations. Rats underwent heroin self-administration training, followed by a progressive ratio and heroin-primed reinstatement test. Next, rats underwent extinction training and a cue-induced reinstatement test. To assess how these variables contribute to heroin addiction vulnerability, we developed a network-based data analysis workflow. Specifically, we integrated different cohorts of rats, remove possible batch effects, and constructed a rat-rat similarity network based on their behavioral patterns. We then implemented community detection on this similarity network using a Bayesian degree-corrected stochastic block model to uncover sub-populations of rats with differing levels of opioid vulnerability. We discovered three distinct behavioral sub-populations, each with significantly different behavioral outcomes that allowed for unique characterization of each cluster in terms of vulnerability to opioid use and seeking. We implement this analysis workflow as an open source R package, named mlsbm.

animal behavior and cognition↗

bioRxiv2021

A Bayesian Multivariate Mixture Model for Spatial Transcriptomics Data

High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seek to identify sub-populations within a tissue sample that reflect distinct cell types or states. Existing methods either ignore the spatial heterogeneity in gene expression profiles, fail to account for important statistical features such as skewness, or are heuristic network-based clustering methods that lack the inferential benefits of statistical modeling. To address this gap, we develop SPRUCE: a Bayesian spatial multivariate finite mixture model based on multivariate skew-normal distributions, which is capable of identifying distinct cellular sub-populations in HST data. We further implement a novel combination of Polya-Gamma data augmentation and spatial random effects to infer spatially correlated mixture component membership probabilities without relying on approximate inference techniques. Via a simulation study, we demonstrate the detrimental inferential effects of ignoring skewness or spatial correlation in HST data. Using publicly available human brain HST data, SPRUCE outperforms existing methods in recovering expertly annotated brain layers. Finally, our application of SPRUCE to human breast cancer HST data indicates that SPRUCE can distinguish distinct cell populations within the tumor microenvironment.

bioinformatics↗

bioRxiv2021

Imipramine and olanzapine block apoE4-catalyzed polymerization of Aβ and show evidence of improving Alzheimer's disease cognition

The apolipoprotein E (APOE) {varepsilon}4 allele confers the strongest risk for late-onset Alzheimers disease (AD) besides age itself, but the mechanism(s) underlying this risk are debated. The critical test of any proposed AD mechanism is whether it leads to effective treatments. We developed a high-throughput assay to identify inhibitors of apoE4-catalyzed polymerization of the amyloid {beta} (A{beta}) peptide into neurotoxic fibrils. Screening a human drug library, we identified five non-toxic, blood-brain-barrier-permeable hit compounds that reduced apoE4-promoted A{beta} and tau neuropathology in cultured neurons. Two hit compounds, imipramine and olanzapine, but not other (non-hit) antipsychotics or antidepressants, when prescribed to AD patients for their normal clinical indications, led to improvements in cognition and clinical diagnosis. Imipramine and olanzapine have no structural, functional, or clinical similarities other than their ability to inhibit apoE4-catalyzed A{beta} polymerization, thus identifying this mechanism as an essential contribution of apoE4 to AD. One Sentence SummaryHigh-throughput drug screens, studies in Alzheimers disease cell culture models, and analyses of human clinical data identified inhibitors of the apoE4-A{beta} interaction as a novel class of Alzheimers disease therapeutics.

neuroscience↗

bioRxiv2021

Characterisation of a novel ACE2-based therapeutic with enhanced rather than reduced activity against SARS-CoV2 variants

The human angiotensin-converting enzyme 2 acts as the host cell receptor for SARS-CoV-2 and the other members of the Coronaviridae family SARS-CoV-1 and HCoV-NL63. Here we report the biophysical properties of the SARS-CoV-2 spike variants D614G, B.1.1.7 and B.1.351 with affinities to the ACE2 receptor and infectivity capacity, revealing weaknesses in the developed neutralising antibody approaches. Furthermore, we report a pre-clinical characterisation package for a soluble receptor decoy engineered to be catalytically inactive and immunologically inert, with broad neutralisation capacity, that represents an attractive therapeutic alternative in light of the mutational landscape of COVID-19. This construct efficiently neutralised four SARS-CoV-2 variants of concern. The decoy also displays antibody-like biophysical properties and manufacturability, strengthening its suitability as a first-line treatment option in prophylaxis or therapeutic regimens for COVID-19 and related viral infections.

immunology↗

bioRxiv2020

IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis

SummarySingle-cell RNA-Seq (scRNA-Seq) data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases. Specifically, the investigation of functional gene modules (FGM) can help to understand gene interactive networks and complex biological processes. QUBIC2 is recognized as one of the most efficient and effective tools for FGM identification from scRNA-Seq data. However, its limited availability to a C implementation restricted its application to only a few downstream analyses functionalities. We developed an R package named IRIS-FGM (Integrative scRNA-Seq Interpretation System for Functional Gene Module analysis) to support the investigation of FGMs and cell clustering using scRNA-Seq data. Empowered by QUBIC2, IRIS-FGM can effectively identify co-expressed and co-regulated FGMs, predict cell types/clusters, uncover differentially expressed genes, and perform functional enrichment analysis. It is noteworthy that IRIS-FGM can also takes Seurat objects as input, which facilitate easy integration with existing analysis pipeline. Availability and ImplementationIRIS-FGM is implemented in R environment (as of version 3.6) with the source code freely available at https://github.com/OSU-BMBL/IRIS-FGM Contactqin.ma@osumc.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2020

Nitric Oxide Regulates the Ralstonia solanacearum Type 3 Secretion System

Ralstonia solancearum causes bacterial wilt disease on diverse plant hosts. R. solanacearum cells enter a host from soil or infested water through the roots, then multiply and spread in the water-transporting xylem vessels. Despite the low nutrient content of xylem sap, R. solanacearum grows very well inside the host, using denitrification to respire in this hypoxic environment. R. solanacearum growth in planta also depends on the successful deployment of protein effectors into host cells via a Type III Secretion System (T3SS). The T3SS is absolutely required for R. solanacearum virulence, but it is metabolically costly and can trigger host defenses. Thus, the pathogens success depends on optimized regulation of the T3SS. We found that a byproduct of denitrification, the toxic free-radical nitric oxide (NO), positively regulates the R. solanacearum T3SS both in vitro and in planta. Using chemical treatments and R. solanacearum mutants with altered NO levels, we show that the expression of a key T3SS regulator is induced by NO in culture. Analyzing the transcriptome of R. solanacearum responding to varying levels of NO both in culture and in planta revealed that the T3SS and effectors were broadly upregulated with increasing levels of NO. This regulation was specific to the T3SS and was not shared by other stressors. Our results suggest that R. solanacearum experiences an NO-rich environment in the plant host and may use this NO as a signal to activate T3SS during infection.

microbiology↗

bioRxiv2020

Skeletal muscle tissue secretes more extracellular vesicles than white adipose tissue and myofibers are a major source ex vivo but not in vivo.

Circulating extracellular vesicles (EVs) are biomarkers of and contributors to the etiology of disease. Skeletal muscle (SkM) and white adipose tissue (WAT) are the two largest organs by mass in humans and rodents but the relative contribution of EVs from these tissues is unknown. We hypothesized that SkM tissue secretes more EVs than WAT and that a dual fluorescent reporter mouse could be used to detect SkM myofiber-derived EVs in vivo. Human Protein Atlas data and directly measuring EV secretion in mouse SkM and WAT using an ex vivo tissue explant model confirmed that SkM tissue secretes more EVs than WAT. Differences in EV secretion between SkM and WAT were not due to SkM contraction but may be explained by differences in tissue metabolic capacity. A SkM myofiber-specific dual fluorescent reporter mouse was created. Spectral flow cytometry revealed that SkM myofibers are a major source of SkM tissue-derived EVs ex vivo but few reach the circulation in vivo. Our findings demonstrate that SkM secretes more EVs than WAT and many come from SkM myofibers, but our in vivo data indicate that EVs secreted by SkM myofibers may remain primarily in their local extracellular environment.

physiology↗

bioRxiv2020

Lamprey Lecticans Link New Vertebrate Genes to the Origin and Elaboration of Vertebrate Tissues

The evolution of vertebrates from an invertebrate chordate ancestor involved the evolution of new organs, tissues, and cell types. It was also marked by the origin and duplication of new gene families. If, and how, these morphological and genetic innovations are related is an unresolved question in vertebrate evolution. Hyaluronan is an extracellular matrix (ECM) polysaccharide important for water homeostasis and tissue structure. Vertebrates possess a novel family of hyaluronan binding proteins called Lecticans, and studies in jawed vertebrates (gnathostomes) have shown they function in many of the cells and tissues that are unique to vertebrates. This raises the possibility that the origin and/or expansion of this gene family helped drive the evolution of these vertebrate novelties. In order to better understand the evolution of the lectican gene family, and its role in the evolution of vertebrate morphological novelties, we investigated the phylogeny, genomic arrangement, and expression patterns of all lecticans in the sea lamprey (Petromyzon marinus), a jawless vertebrate. Though both P. marinus and gnathostomes have four lecticans, our phylogenetic and syntenic analyses suggest lamprey lecticans are the result of one or more cyclostome-specific duplications. Despite the independent expansion of the lamprey and gnathostome lectican families, we find highly conserved expression of lecticans in vertebrate-specific and mesenchyme-derived tissues. We also find that, unlike gnathostomes, lamprey expresses its lectican paralogs in distinct subpopulations of head skeleton precursors, potentially reflecting an ancestral diversity of skeletal tissue types. Together, these observations suggest that the ancestral pre-duplication lectican had a complex expression pattern, functioned to support mesenchymal histology, and likely played a role in the evolution of vertebrate-specific cell and tissue types.

evolutionary biology↗

bioRxiv2020

Bacterial processing of glucose modulates C. elegans lifespan and healthspan

Intestinal microbiota play an essential role in the health of a host organism. Here, we define how commensal Escherichia coli (E. coli) alters its host after long term exposure to glucose using a C. elegans-E. coli system. Our data reveal that bacterial processing of glucose, rather than direct ingestion by the animal, results in reduced lifespan and healthspan, including reduced locomotion, oxidative stress resistance, and heat stress resistance in C. elegans. Chronic exposure of E. coli to glucose produces growth defects and increased advanced glycation end products within the E. coli. These negative effects are abrogated when the E. coli is not able to process the additional glucose and by the addition of the anti-glycation compound carnosine. Physiological changes of the host C. elegans are accompanied by dysregulation of detoxifying genes including glyoxalase, glutathione-S-transferase, and superoxide dismutase. Loss of gst-4 shortens C. elegans lifespan and blunts the animals response to a glucose-fed bacteria diet. Taken together, we reveal that added dietary sugar may alter intestinal microbial E. coli to decrease lifespan and healthspan of the host and define the critical role of detoxification genes in maintaining health during a chronic high-sugar diet.

genetics↗

bioRxiv2020

Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles

Vascular pathogens travel long distances through host veins leading to life-threatening, systemic infections. In contrast, non-vascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and non-vascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the Xanthomonadaceae family and absent in most non-vascular species. CbsA expression allowed non-vascular Xanthomonas to cause vascular blight while cbsA mutagenesis resulted in reduction of vascular or enhanced non-vascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple non-vascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.

microbiology↗

bioRxiv2020

Low contribution of rare species to resilience and adaptive capacity in novel spatial regimes arising from biome shifts caused by global change

Human activity causes biome shifts that alter biodiversity and spatial resilience patterns, ultimately challenging conservation. Rare species, often considered vulnerable to change and endangered, can be a critical element of resilience by providing adaptive capacity in response to disturbances. However, little is known about changes in rarity and dominance patterns of communities once a biome transitions into a novel spatial regime, and how this affects conservation. We used time series modeling to identify species rarity and dominance patterns in an expanding terrestrial (southern) spatial regime in the North American Great Plains and another (northern) regime that will become encroached by the southern regime in the near future. In this approach, presumably rare and abundant species show stochastic and deterministic dynamics, respectively. We specifically assessed how stochastic species of the northern spatial regime influence the resilience and adaptive capacity of a novel spatial regime once it has been encroached by the southern regime by either becoming deterministic or staying stochastic. Using 47 years (1968 - 2014) of breeding bird survey data and a space-for-time substitution, we found half of the stochastic species from the northern regime to be either deterministic or stochastic in the southern regime. However, the overall contribution of these species to the community of the southern regime was low, manifested in marginal contributions to resilience and adaptive capacity of this regime. Also, none of these species were of conservation concern, suggesting limited need for revised species conservation action in the novel spatial regime. From a systemic perspective our result suggest that while stochastic species can potentially compensate for the loss of dominant species after disturbances and maintain the system in its current regime, they may only marginally contribute to resilience and adaptive capacity in a new spatial regime after fundamental ecological changes have occurred.

ecology↗

bioRxiv2020

Tumor control via targeting PD-L1 with chimeric antigen receptor modified NK cells

Failed T cell-based immunotherapies in the presence of genomic alterations in antigen presentations pathways may be overcome by NK cell-based immunotherapy. This approach may still be limited by the presence of immunosuppressive myeloid populations. Here we demonstrate that NK cells (haNKs) engineered to express a PD-L1 chimeric antigen receptor (CAR) haNKs killed a panel of human and murine head and neck cancer cells at low effector-to-target ratios in a PD-L1-dependent fashion. Treatment of syngeneic tumors resulted in CD8 and PD-L1-dependent tumor rejection or growth inhibition and a reduction in myeloid cells endogenously expressing high levels of PD-L1. Treatment of xenograft tumors resulted in PD-L1 dependent tumor growth inhibition. PD-L1 CAR haNKs reduced levels of macrophages and other myeloid cells endogenously expressing high PD-L1 in peripheral blood from patients with head and neck cancer. The clinical study of PD-L1 CAR haNKs is warranted.

immunology↗

bioRxiv2019

Roq1 confers resistance to Xanthomonas, Pseudomonas syringae and Ralstonia solanacearum in tomato

Xanthomonas species, Pseudomonas syringae and Ralstonia solanacearum are bacterial plant pathogens that cause significant yield loss in many crop species. Current control methods for these pathogens are insufficient but there is significant potential for generating new disease-resistant crop varieties. Plant immune receptors encoded by nucleotide-binding, leucine-rich repeat (NLR) genes typically confer resistance to pathogens that produce a cognate elicitor, often an effector protein secreted by the pathogen to promote virulence. The diverse sequence and presence / absence variation of pathogen effector proteins within and between pathogen species usually limits the utility of a single NLR gene to protecting a plant from a single pathogen species or particular strains. The NLR protein Recognition of XopQ 1 (Roq1) was recently identified from the plant Nicotiana benthamiana and mediates perception of the effector proteins XopQ and HopQ1 from Xanthomonas and P. syringae respectively. Unlike most recognized effectors, alleles of XopQ/HopQ1 are highly conserved and present in most plant pathogenic strains of Xanthomonas and P. syringae. A homolog of XopQ/HopQ1, named RipB, is present in many R. solanacearum strains. We found that Roq1 also mediates perception of RipB and confers immunity to Xanthomonas, P. syringae, and R. solanacearum when expressed in tomato. Strong resistance to Xanthomonas perforans was observed in three seasons of field trials with both natural and artificial inoculation. The Roq1 gene can therefore be used to provide safe, economical and effective control of these pathogens in tomato and other crop species and reduce or eliminate the need for traditional chemical controls. SummaryA single immune receptor expressed in tomato confers strong resistance to three different bacterial diseases.

plant biology↗

bioRxiv2019

Ralstonia solanacearum depends on catabolism of myo-inositol, sucrose, and trehalose for virulence in an infection stage-dependent manner

The soilborne pathogen Ralstonia solanacearum (Rs) causes lethal bacterial wilt disease of tomato and many other crops by infecting host roots and then colonizing the xylem vessels. Tomato xylem sap is nutritionally limiting but it does contain sucrose and trehalose. Transcriptomic analyses revealed that Rs expresses distinct sets of catabolic pathways at low cell density (LCD) and high cell density (HCD). To investigate the links between bacterial catabolism, infection stage, and virulence, we measured the in planta fitness of bacterial mutants lacking carbon catabolic pathways expressed at either LCD or HCD. We hypothesized that the bacterium needs LCD carbon sources early in disease (root infection) while HCD carbon sources are required during late disease (stem colonization). An Rs {Delta}iolG mutant unable to use the LCD nutrient myo-inositol was defective in root colonization but once it reached the stem, this strain colonized and caused symptoms as well as wild type. In contrast, Rs mutants unable to use sucrose ({Delta}scrA), trehalose ({Delta}treA), or both ({Delta}scrA/treA), infected roots as well as wild type but were defective in colonization and competitive fitness in tomato mid-stems and were reduced in bacterial wilt virulence. Additionally, xylem sap from tomato plants colonized by{Delta} scrA, {Delta}treA, or {Delta}scrA/treA contained more sucrose than sap from plants colonized by wild-type Rs. Together, these findings suggest Rs metabolism is specifically adapted for success in the different nutritional environments of plant roots and xylem sap.

microbiology↗

bioRxiv2018

DGEN: A Test Statistic for Detection of General Introgression Scenarios

When two species hybridize, one outcome is the integration of genetic material from one species into the genome of the other, a process known as introgression. Detecting introgression in genomic data is a very important question in evolutionary biology. However, given that hybridization occurs between closely related species, a compli-cating factor for introgression detection is the presence of incomplete lineage sorting, or ILS. The D-statistic, famously referred to as the \"ABBA-BABA\" test, was pro-posed for introgression detection in the presence of ILS in data sets that consist of four genomes. More recently, DFOIL--a set of statistics--was introduced to extend the D-statistic to data sets of five genomes.\n\nThe major contribution of this paper is demonstrating that the invariants underly-ing both the D-statistic and DFOIL can be derived automatically from the probability mass functions of gene tree topologies under the null species tree model and alterna-tive phylogenetic network model. Computational requirements aside, this automatic derivation provides a way to generalize these statistics to data sets of any size and with any scenarios of introgression. We demonstrate the accuracy of the general statistic, which we call DGEN, on simulated data sets with varying rates of introgression, and apply it to an empirical data set of mosquito genomes.\n\nWe have implemented DGEN and made it available, both as a graphical user interface tool and as a command-line tool, as part of the freely available, open-source software package ALPHA (https://github.com/chilleo/ALPHA).

evolutionary biology↗

bioRxiv2018

Predicting and Analyzing the Response to Selection on Correlated Characters

The breeders equation generally provides robust predictions for the short-term evolution of single characters. When selection targets two or more characters simultaneously, there are often large discrepancies between predicted and observed responses. We assessed how well this standard model predicts responses to bivariate selection on wing color pattern characteristics in the tropical butterfly Bicyclus anynana. In separate laboratory selection experiments, two sets of serially repeated eyespots were subjected to ten generations of concerted and antagonistic selection for either size or color composition. We compared predicted and actual selection responses over successive generations, using the phenotypic data, selection differentials, and estimates of the genetic variance-covariance matrix G. We found differences in the precision of predictions between directions of selection but did not find any evidence of systematic biases in our predictions depending on the direction of selection. Our investigation revealed significant environmental effects on trait evolution across generations. When these were accounted for, predictions using the standard model improved considerably. In the experiment on eyespot size, secondary splitting of selection lines allowed the estimation of changes in G after nine generations of selection. Changes were not in general agreement with expectations from the breeders equation. A contour plot of prediction errors across trait space suggests that directional epistasis in the eyespot genotype-phenotype map might occur but estimates of changes in G are too model-dependent to verify whether they agree with that hypothesis. Altogether, our results underscore the need for quantitative genetics to investigate and estimate potential effects of multivariate non-linear genotype-phenotype maps and of environmental effects on G.

evolutionary biology↗

bioRxiv2017

Partial restoration of mutational robustness after addition of genetic polymorphism and in the presence of sexual selection

The interaction between mutational (i.e. genetic) robustness, cryptic genetic variation and epistasis is currently under much debate, as is the question whether mutational robustness evolved under direct selection or as a by-product of environmental robustness. Here we report that mutational robustness was restored in a mutant line of the butterfly Bicyclus anynana after the spontaneous mutation, comet, appeared in a genetically polymorphic wild type population. The comet mutation modified two phenotypic traits known to be under sexual selection in this butterfly: the dorsal forewing eyespot, which is normally round, but became comet-shaped, and the androconia, the structures producing the male sex pheromone, which were reduced in size. The comet mutant line remained phenotypically stable for [~]7 seven years, but when outcrossed to the genetically polymorphic wild type population, the outcrossed comet line surprisingly recovered the wild type phenotype within 8 generations. This suggests that mutational robustness against the comet mutation was recovered in the comet outcrossed line by epistatic interactions with the genetic polymorphism originating from wild types. The extent of wild type phenotype recovery in the comet outcrossed line was trait- and developmental temperature-dependent, such that mutational robustness was partially recovered at high, but not at low developmental temperatures. We hypothesized that sexual selection through mate choice, which is sex-reversed between developmental temperatures in this butterfly, could produce mutational robustness at a high (but not at a low) temperature. Females are the choosy sex and exert stabilizing or directional selection on male secondary sexual wing traits but only at higher temperatures. Male mating success experiments under semi-natural conditions then revealed that males with the typical comet mutant phenotype suffered from lower mating success compared to wild type males, while mating success of comet males resembling wild types was partially restored. Altogether, we document the roles of cryptic genetic variation and epistasis in restoration of mutational robustness against a spontaneous mutation with known fitness effects, and we provide experimental evidence, for the first time to our knowledge, that sexual selection can produce mutational robustness.

evolutionary biology↗

bioRxiv2017

The separation of auditory experience and the temporal structure of MEG recorded brain activity

Do brain oscillations limit the temporal dynamics of experience? This pre-registered study used the separation of auditory stimuli to track perceptual experience and related this to oscillatory activity using magnetoencephalography. The rates at which auditory stimuli could be individuated matched the rates of oscillatory brain activity. Stimuli also entrained brain activity at the frequencies at which they were presented and a progression of high frequency gamma band events appeared to predict successful separation. These findings support a generalised function for brain oscillations, across frequency bands, in the alignment of activity to delineate representations.

physiology↗