Biology subjects

Clements, J.

Publications and source records attributed to Clements, J..

25 records · Page 2Linked to original sources

bioRxiv2020

neuPrint: Analysis Tools for EM Connectomics

Due to technological advances in electron microscopy (EM) and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the connections between them, for significant volumes of neural tissue. The limited scope of past reconstructions meant they were primarily used by domain experts, and performance was not a serious problem. But the new reconstructions, of common laboratory creatures such as the fruit fly Drosophila melanogaster, upend these assumptions. These natural neural networks now contain tens of thousands of neurons and tens of millions of connections between them, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. This requires new tools that are easy to use and efficiently handle large data. We introduce neuPrint to address these data analysis challenges. neuPrint is a database and analysis ecosystem that organizes connectome data in a manner conducive to biological discovery. In particular, we propose a data model that allows users to access the connectome at different levels of abstraction primarily through a graph database, neo4j, and its powerfully expressive query language Cypher. neuPrint is compatible with modern connectome reconstruction workflows, providing tools for assessing reconstruction quality, and offering both batch and incremental updates to match modern connectome reconstruction flows. Finally, we introduce a web interface and programmer API that targets a diverse user skill set. We demonstrate the effectiveness and efficiency of neuPrint through example database queries.

neuroscience↗

bioRxiv2019

Estimating the power of sequence covariation for detecting conserved RNA structure

Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long noncoding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures.

genomics↗

bioRxiv2019

Conjugated linoleic acid as a novel insecticide targeting the agricultural pest Leptinotarsa decemlineata

The Colorado Potato Beetle, Leptinotarsa decemlineata, is a major agricultural pest of solanaceous crops in the United States. Historically, a multitude of insecticides have been used to control problematic populations. Due to increasing resistance to insecticides, novel compounds and methodologies are warranted for the control of beetle populations. Mixed-isomer conjugated linoleic acid has been studied in-depth for its beneficial properties to mammalian systems. At the same time, studies have demonstrated that conjugated linoleic acid can manipulate fatty acid composition in non-mammalian systems, resulting in embryo mortality. Consequently, experiments were conducted to assess the effects of foliar-applied conjugated linoleic acid on larval growth, embryogenesis, and feeding preference in Colorado potato beetle. Both maternal and deterrent effects of dietary conjugated linoleic acid were assessed. Conjugated linoleic acid demonstrated desirable insecticidal properties, including increased larval mortality, slowed larval development, antifeedant effects, and decreased egg viability after maternal ingestion.

ecology↗

bioRxiv2018

Transcriptomic analysis reveals similarities in genetic activation of detoxification mechanisms resulting from imidacloprid and chlorothalonil exposure

The Colorado potato beetle, Leptinotarsa decemlineata (Say), is an agricultural pest of commercial potatoes in parts of North America, Europe, and Asia. Plant protection strategies within this geographic range employ a variety of pesticides to combat not only the insect, but also plant pathogens. Previous research has shown that field populations of Leptinotarsa decemlineata have a chronological history of resistance development to a suite of insecticides, including the Group 4A neonicotinoids. The aim of this study is to contextualize the transcriptomic response of Leptinotarsa decemlineata when exposed to the neonicotinoid insecticide imidacloprid, or the fungicides boscalid or chlorothalonil, in order to determine whether these compounds induce similar detoxification mechanisms. We found that chlorothalonil and imidacloprid induced similar patterns of transcript expression, including the up-regulation of a cytochrome p450 and a UDP-glucuronosyltransferase transcript, which are often associated with xenobiotic metabolism. Further, transcriptomic responses varied among individuals within the same treatment group, suggesting individual insects responses vary within a population and may cope with chemical stressors in a variety of manners. These results further our understanding of the mechanisms involved in insecticide resistance in Leptinotarsa decemlineata.\n\nAuthor Contribution StatementConceived and designed the experiments: JC, CB, RLG. Performed the experiments: JC, BSS. Analyzed the data: JC, BSS. Wrote the paper: JC, BSS, RLG.

genetics↗

bioRxiv2018

Agricultural fungicides inadvertently influence the fitness of Colorado potato beetles, Leptinotarsa decemlineata, and their susceptibility to insecticides

The Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say), is an agricultural pest of solanaceous crops which has developed insecticide resistance at an alarming rate. Up to this point, little consideration has been given to unintended, or inadvertent effects that non-insecticide xenobiotics may have on insecticide susceptibility in L. decemlineata. Fungicides, such as chlorothalonil and boscalid, are often used to control fungal pathogens in potato fields and are applied at regular intervals when L. decemlineata populations are present in the crop. In order to determine whether fungicide use may be associated with elevated levels of insecticide resistance in L. decemlineata, we examined phenotypic responses in L. decemlineata to the fungicides chlorothalonil and boscalid. Using enzymatic and transcript abundance investigations we also examined modes of molecular detoxification in response to both insecticide (imidacloprid) and fungicide (boscalid and chlorothalonil) application to more specifically determine if fungicides and insecticides induce similar metabolic detoxification mechanisms. Both chlorothalonil and boscalid exposure induced a phenotypic, enzymatic and transcript response in L. decemlineata which correlates with known mechanisms of insecticide resistance.\n\nKey MessagesO_LIPrior-exposure to a fungicidal application changes the phenotypic response of Leptinotarsa decemlineata to the insecticide imidacloprid\nC_LIO_LIBoth a fungicide and insecticide application activates similar molecular mechanisms of detoxification in Leptinotarsa decemlineata\nC_LIO_LIFungicidal xenobiotics may contribute to insecticide resistance in Leptinotarsa decemlineata\nC_LI\n\nAuthor Contribution StatementJC, SS, CB, AH, and RG conceived and designed research. JC, AC, DA, TD, and BS conducted experiments. JC and AC analyzed data. JC and RG wrote the manuscript. All authors read and approved the manuscript.

ecology↗

bioRxiv2017

Growth control through regulation of insulin-signaling by nutrition-activated steroid hormone

Growth and maturation are coordinated processes in all animals. Integration of internal cues, such as signalling pathways, with external cues such as nutritional status is paramount for an orderly progression of development in function of growth. In Drosophila, this coordination involves insulin and steroid signalling, but the mechanisms by which this occurs and how they are coordinated are incompletely understood. We show that production of the bioactive 20-hydroxyecdysone by the enzyme Shade in the fat body is a nutrient-dependent process. We demonstrate that during fed conditions, Shade plays a role in growth regulation, as knockdown of shade in the fat body resulted in growth defects and perturbed expression and release of the Drosophila insulin-like peptides from the insulin-producing cells (IPCs). We identify the trachea and IPCs as direct targets through which 20-hydroxyecdysone regulates insulin-signaling. The identification of the trachea-dependent regulation of insulin-signaling exposes an important variable that may have been overlooked in other studies focusing on insulin-signaling in Drosophila. Finally, we show with IPC-specific manipulations that 20E may both be a growth-promoting and growth-inhibiting signal in the IPCs acting through different nuclear receptors. Our findings provide a potentially conserved, novel mechanism by which nutrition can modulate steroid hormone bioactivation, reveal an important caveat of a commonly used transgenic tool to study IPC function and yield further insights as to how steroid and insulin signalling are coordinated during development to regulate growth and developmental timing.

developmental biology↗

bioRxiv2017

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

genomics↗