Biology subjects

Bishop, S.

Publications and source records attributed to Bishop, S..

8 recordsLinked to original sources

bioRxiv2025

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae

Background and AimsThe flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite the available transcriptomic data, no focused phylotranscriptomic study has been conducted to characterize the patterns of molecular evolution in this group. In this study, we leverage a dataset composed predominately of publicly available transcriptomes to infer relationships within Apocynaceae and explore the molecular processes that have shaped their divergences. MethodsWe extracted nuclear, chloroplast, and mitochondrial genes from 47 publicly available and one newly sequenced transcriptome to assemble and infer species relationships across Apocynaceae. Leveraging the gene-rich nuclear phylotranscriptomic data, we inferred molecular dates and investigated the complex history of gene tree conflict, molecular rate shifts, and gene duplications. To investigate the genomic basis of adaptations, we analyzed the inferred 14,838 gene duplications at the base of Apocynaceae for shared functional enrichment of genes related to evolutionary innovations. Key ResultsThe Apocynaceae topology inferred from our phylotranscriptomic analysis is highly concordant with the current consensus. Notably, a genome-wide acceleration in molecular rate subtends the Ceropegieae tribe. We observed that a decreased time between divergences is associated with a higher rate of gene tree conflict, a pattern especially prevalent across the Apocynaceaes historically recalcitrant backbone relationships. Furthermore, gene duplications may underlie evolutionary innovations, such as immunity-related gene expansion in the genus Asclepias and duplications associated with trichome modifications in the epiphytic Hoya. Finally, we discuss the contentious history of whole-genome duplication (WGD) within the Apocynaceae and emphasize the need for further investigation into the placement of WGDs. ConclusionsRepurposing transcriptomes is a powerful means of accumulating data for novel insights in plant evolution, especially during uncertain funding and cases where budget restrictions exist. Leveraging this gene-dense dataset, we obtained novel insights into the molecular evolution of Apocynaceae and identified areas for future investigations.

evolutionary biology↗

bioRxiv2023

A highly resolved multiplex network reveals the structural role of insects and plants in terrestrial food webs

Comparative studies suggest remarkable similarities among food webs across habitats, including systematic changes in their structure with diversity and complexity (scale-dependence). However, historic aboveground terrestrial food webs (ATFWs) have coarsely grouped plants and insects such that these webs are generally small, and herbivory is disproportionately underrepresented compared to vertebrate predator-prey interactions. Furthermore, terrestrial herbivory is thought to be structured by unique processes compared to size-structured feeding in other systems. Here, we present the richest ATFW to date, including [~]580,000 feeding links among [~]3,800 taxonomic species, sourced from [~]27,000 expert-vetted interaction records annotated as feeding upon one of six different resource types: leaves, flowers, seeds, wood, prey, and carrion. By comparison to historical ATFWs and null ecological hypotheses, we show that our temperate forest web displays a potentially unique structure characterized by two properties: a) a large fraction of carnivory interactions dominated by a small number of hyper-generalist, opportunistic bird and bat predators, and b) a smaller fraction of herbivory interactions dominated by a hyper-rich community of insects with variably-sized but highly-specific diets. We attribute our findings to the large-scale, even resolution of vertebrate, insect, and plant guilds in our food web.

ecology↗

bioRxiv2023

Metabolic Interactive Nodular Network for Omics (MINNO): Refining and investigating metabolic networks based on empirical metabolomics data

Metabolomics is a powerful tool for uncovering biochemical diversity in a wide range of organisms, and metabolic network modeling is commonly used to frame results in the context of a broader homeostatic system. However, network modeling of poorly characterized, non-model organisms remains challenging due to gene homology mismatches. To address this challenge, we developed Metabolic Interactive Nodular Network for Omics (MINNO), a web-based mapping tool that takes in empirical metabolomics data to refine metabolic networks for both model and unusual organisms. MINNO allows users to create and modify interactive metabolic pathway visualizations for thousands of organisms, in both individual and multi-species contexts. Herein, we demonstrate an important application of MINNO in elucidating the metabolic networks of understudied species, such as those of the Borrelia genus, which cause Lyme disease and relapsing fever. Using a hybrid genomics-metabolomics modeling approach, we constructed species-specific metabolic networks for three Borrelia species. Using these empirically refined networks, we were able to metabolically differentiate these genetically similar species via their nucleotide and nicotinate metabolic pathways that cannot be predicted from genomic networks. These examples illustrate the use of metabolomics for the empirical refining of genetically constructed networks and show how MINNO can be used to study non-model organisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/548964v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@8cdee6org.highwire.dtl.DTLVardef@7de3ddorg.highwire.dtl.DTLVardef@fac57forg.highwire.dtl.DTLVardef@1bc2efe_HPS_FORMAT_FIGEXP M_FIG MINNO tool facilitates refining of metabolic networks, multi omics integration and investigation of cross-species interactions. C_FIG

bioinformatics↗

bioRxiv2021

Compositional forecasting of Chinook Salmon Evolutionarily Significant Units in bycatch for Pacific Hake fisheries

Bycatch impacts on non-target species present significant management problems in diverse fisheries throughout the world. Despite successful efforts to minimize bycatch in US West Coast Pacific Hake fisheries, these impacts remain a concern, particularly for sensitive populations of Chinook Salmon. NOAA Fisheries needed predictive models to estimate proportions of Chinook Salmon Evolutionarily Significant Units (ESUs) expected in bycatch. We used genetic mixture analysis to estimate ESU proportions from at-sea bycatch between 2008 and 2015. Using latitude as a predictor and applying jackknife cross validation, we found Dirichlet regression more accurately estimated abundant ESUs, whereas multinomial logistic regression performed better with rare ESUs. This targeted, ESU-specific approach showed the spatial distribution of sensitive stocks in bycatch and supported NOAAs obligations to forecast impacts on listed ESUs. The overarching goal of this continuing work is to maximize sustainable harvest while protecting threatened and endangered Chinook Salmon ESUs.

genetics↗

bioRxiv2018

Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk

We present the largest exome sequencing study to date focused on rare variation in autism spectrum disorder (ASD) (n=35,584). Integrating de novo and case-control variation with an enhanced Bayesian framework incorporating evolutionary constraint against mutation, we implicate 99 genes in ASD risk at a false discovery rate (FDR) [≤] 0.1. Of these 99 risk genes, 46 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 50 show higher frequencies in individuals ascertained for ASD, and comparing ASD cases with disruptive mutations in the two groups shows differences in phenotypic presentation. Expressed early in brain development, most of the risk genes have roles in neuronal communication or regulation of gene expression, and 12 fall within recurrent copy number variant loci. In human cortex single-cell gene expression data, expression of the 99 risk genes is also enriched in both excitatory and inhibitory neuronal lineages, implying that disruption of these genes alters the development of both neuron types. Together, these insights broaden our understanding of the neurobiology of ASD.

genetics↗

bioRxiv2017

Prefrontal cortex regulates amygdala response to threat in trait anxiety

BackgroundHighly co-morbid mood and anxiety disorders are associated with aberrant fronto-limbic signalling during emotional processing. Animal models suggest that hypoactive prefrontal cortex weakens top-down control of limbic structures, causing heightened limbic and behavioural reactivity to negative information. Here we tested for this causal mechanism in human trait anxiety. We reasoned that if dorsolateral prefrontal cortex controls amygdala response to affective information, then stimulation of that brain region should reduce the hyperactive amygdala threat responsivity seen in trait anxiety.\n\nMethodsUsing a within-subjects design, sixteen high-trait anxious females received active and sham transcranial direct current stimulation (tDCS) of the dorsolateral prefrontal cortex, in counterbalanced order, with sessions timed to be at least one month apart. Each session was followed immediately by a functional magnetic resonance imaging (fMRI) scan during which participants performed an attentional task with threat-related distractors.\n\nResultsAs predicted, compared to sham stimulation, active prefrontal cortex stimulation reduced amygdala threat reactivity and simultaneously increased activity in cortical regions associated with attentional control and improved task accuracy.\n\nConclusionsThese results demonstrate a causal role for impoverished frontal regulation of amygdaloid function in attentional capture by threat in trait anxiety. The finding that prefrontal stimulation reduces amygdala threat reactivity acutely indicates a neurocognitive mechanism that could contribute to tDCS treatment effects in affective disorders.

neuroscience↗

bioRxiv2017

Kek-6: A Truncated Trk-Like Receptor For Drosophila Neurotrophin 2 Regulates Structural Synaptic Plasticity

Neurotrophism, structural plasticity, learning and long-term memory in mammals critically depend on neurotrophins binding Trk receptors to activate tyrosine kinase (TyrK) signalling, but Drosophila lacks full-length Trks, raising the question of how these processes occur in the fly. Paradoxically, truncated Trk isoforms lacking the TyrK predominate in the adult human brain, but whether they have neuronal functions independently of full-length Trks is unknown. Drosophila has TyrK-less Trk-family receptors, encoded by the kekkon (kek) genes, suggesting that evolutionarily conserved functions for this receptor class may exist. Here, we asked whether Keks function together with Drosophila neurotrophins (DNTs) at the larval glutamatergic neuromuscular junction (NMJ). Starting with an unbiased approach, we tested the evelen LRR and Ig-containing (LIG) proteins encoded in the Drosophila genome for expression in the central nervous system (CNS) and potential interaction with DNTs. Kek-6 was expressed in the CNS, could interact genetically with DNTs and could bind DNT2 both in signaling essays and in co-immunoprecipitations. There is promiscuity in ligand binding, as Kek-6 could also bind DNT1, and Kek-5 could also bind DNT2. In vivo, Kek-6 is found presynaptically in motoneurons, and binds DNT2 produced by the muscle, which functions as a retrograde factor at the NMJ. Kek-6 and DNT2 regulate NMJ growth, bouton formation and active zone homeostasis. Kek-6 does not antagonise the alternative DNT2 receptor Toll-6, but rather the two receptors contribute in distinct manners to NMJ structural plasticity. Using pull-down assays, we identified and validated CaMKII and VAP33A as intracellular partners of Kek-6, and show that together they regulate NMJ growth and active zone formation. These functions of Kek-6 could be evolutionarily conserved, raising the intriguing possibility that a novel mechanism of structural synaptic plasticity involving truncated Trk-family receptors independently of TyrK signaling may also operate in the human brain.\n\nAUTHOR SUMMARYA long-standing paradox had been to explain how brain structural plasticity, learning and long-term memory might occur in Drosophila in the absence of canonical Trk receptors for neurotrophin (NT) ligands. NTs link structure and function in the brain enabling adjustments in cell number, dendritic, axonal and synaptic patterns, in response to neuronal activity. These events are essential for brain development, learning and long-term memory, and are thought to depend on the tyrosine-kinase function of the NT Trk receptors. However, paradoxically, the most abundant Trk isoforms in the adult human brain lack the tyrosine kinase, and their neuronal function is unknown. Remarkably, Drosophila has kinase-less receptors of the Trk family encoded by the kekkon (kek) genes, suggesting that deep evolutionary functional conservation for this receptor class could be unveiled. Here, we show that Kek-6 is a receptor for Drosophila neurotrophin 2 (DNT2) that regulates structural synaptic plasticity via CaMKII and VAP33A, well-known factors regulating synaptic structure and plasticity, and vesicle release. Our findings suggest that in mammals truncated Trk-family receptors could also have synaptic functions in neurons independently of Tyrosine kinase signalling. This might reveal a novel mechanism of brain plasticity, with important implications for understanding also the human brain, in health and disease.

developmental biology↗

bioRxiv2016

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

Autism spectrum disorder (ASD) risk is influenced by both common polygenic and de novo variation. The purpose of this analysis was to clarify the influence of common polygenic risk for ASDs and to identify subgroups of cases, including those with strong acting de novo variants, in which different types of polygenic risk are relevant. To do so, we extend the transmission disequilibrium approach to encompass polygenic risk scores, and introduce the polygenic transmission disequilibrium test. Using data from more than 6,400 children with ASDs and 15,000 of their family members, we show that polygenic risk for ASDs, schizophrenia, and greater educational attainment is over transmitted to children with ASDs in two independent samples, but not to their unaffected siblings. These findings hold independent of proband IQ. We find that common polygenic variation contributes additively to risk in ASD cases that carry a very strong acting de novo variant. Lastly, we find evide ...

genetics↗