Biology subjects

Roder, T.

Publications and source records attributed to Roder, T..

4 recordsLinked to original sources

bioRxiv2023

Scoary2: Rapid association of phenotypic multi-omics data with microbial pan-genomes

Genomic screening of bacteria is common practice to select strains with desired properties. However, 40-60% of all bacterial genes are still unknown, making capturing the phenotype an important part of the selection process. While omics-technologies collect high-dimensional phenotypic data, it remains challenging to link this information to genomic data to elucidate the impact of specific genes on phenotype. To this end, we present Scoary2, an ultra-fast software for microbial genome-wide association studies (mGWAS), enabling integrative data exploration. As proof of concept, we explore the metabolome of 44 yogurts with different strains of Propionibacterium freudenreichii, discovering two genes affecting carnitine metabolism.

bioinformatics↗

bioRxiv2022

OpenGenomeBrowser: A versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

OpenGenomeBrowser is a self-hostable open-source platform that manages access to genomic data and drastically simplifies comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. The largest instance currently contains over 1,400 bacterial genomes. Source code, documentation, tutorials and a demo server are available at opengenomebrowser.github.io.

bioinformatics↗

bioRxiv2021

A beta-glucosidase of an insect herbivore determines both toxicity and deterrence of a dandelion defense metabolite

Gut enzymes can metabolize plant defense metabolites and thereby affect the growth and fitness of insect herbivores. Whether these enzymes also influence herbivore behavior and feeding preference is largely unknown. We studied the metabolization of taraxinic acid {beta}-D-glucopyranosyl ester (TA-G), a sesquiterpene lactone of the common dandelion (Taraxacum officinale) that deters its major root herbivore, the common cockchafer larva (Melolontha melolontha). We demonstrate that TA-G is rapidly deglycosylated and conjugated to glutathione in the insect gut. A broad-spectrum M. melolontha {beta}-glucosidase, Mm_bGlc17, is sufficient and necessary for TA-G deglycosylation. Using plants and insect RNA interference, we show that Mm_bGlc17 reduces TA-G toxicity. Furthermore, Mm_bGlc17 is required for the preference of M. melolontha larvae for TA-G deficient plants. Thus, herbivore metabolism modulates both the toxicity and deterrence of a plant defense metabolite. Our work illustrates the multifacteted roles of insect digestive enzymes as mediators of plant-herbivore interactions.

ecology↗

bioRxiv2019

Response of Bat Activity to Land-Cover and Land-Use Change in Savannas is Scale-, Season-, and Guild-Specific

Tropical savannas are biomes of global importance that are under severe pressure from anthropogenic change, including land-cover and land-use change. Bats, the second-most diverse group of mammals, are critical to ecosystem functioning, but may be vulnerable to such anthropogenic stresses. However, there is little information on the response of savanna bats to land-cover and land-use change, especially in Africa. This limits our ability to develop conservation strategies for bats and maintain the ecosystem functions and services they provide in this biome. Using acoustic monitoring, we measured how guild-specific (aerial, edge, and clutter forager) bat activity responded to both fine-scale metrics of vegetation structure and landscape-scale metrics of land-cover composition and configuration across the wet and dry seasons in a savanna in southern Africa undergoing rapid land-cover and land-use change. We found that all three guilds responded more strongly to landscape metrics than fine-scale vegetation structure, although the specific metrics varied between guilds. Aerial and edge bats responded most strongly to the percent savanna cover and savanna fragmentation in both seasons while clutter bats responded to percent rural cover in the wet season and percent water cover in the dry. All three guilds responded more strongly to the landscape in the dry season than the wet season. Our results show it is possible to conserve bats, and the ecosystem services they can provide, in savannas undergoing anthropogenic land-use and land-cover change but strategies to do so must consider foraging guild, large spatial scales, and seasonal variation in bat activity.\n\nHighlightsO_LIBats in savannas respond to land-cover and land-use change on large spatial scales\nC_LIO_LILandscape had a greater influence on bat activity in the dry season than the wet\nC_LIO_LIAerial and edge forager activity responded to savanna cover and fragmentation\nC_LIO_LIClutter forager activity was best explained by rural and water cover\nC_LIO_LIMinimizing fragmentation and maintaining water promotes bat activity in modified savannas\nC_LI

ecology↗