Biology subjects

Starke, J.

Publications and source records attributed to Starke, J..

9 recordsLinked to original sources

bioRxiv2026

Automated refinement of metagenomic bins and estimation of binning success using itBins

Most prokaryotic genomes in public databases are genomes reconstructed from metagenomes, forming a compendium of multiple contiguous sequences (contigs) assembled from shotgun sequencing data. Binning algorithms for assigning contigs to metagenome assembled genomes (MAGs) are manifold and continuously improving in accuracy. However, binning errors, i.e. the incorrect assignment of a contig and coding sequence to a MAG, often propagate through various databases and confound taxonomic, metabolic and/or evolutionary analyses. Here we present itBins, a fully automated python-based software that enables ultra-fast refinement of metagenomic bins using a rule-based approach harnessing information from %GC content (%GC for brevity), coverage, and taxonomy of individual contigs. When applied to the low, medium, and high complexity data of the Critical Assessment of Metagenome Interpretation (CAMI I) challenge [1], itBins produced higher F1 scores (the harmonic mean of precision and recall) for all levels compared to other automated refinement tools, i.e., MDMcleaner and Rosella. Compared to manual refinement via uBin, itBins performed similarly well across all three complexity levels of the CAMI I dataset. With an average speed of 61 ms per bin, itBins is faster than all other refinement tools by at least three orders of magnitude when input data is accordingly available (%GC, coverage, and taxonomy), and was similarly fast when input data preparation was included in the processing time. Application to 64 real-world metagenomes from highly complex river mesocosms resulted in 259 medium-quality and 19 high-quality MAGs refined by itBins, while the other automated refinement tools failed in generating output at all or within 5000 hours of runtime. Finally, itBins also utilizes marker genes to determine the overall binning success for individual metagenomes, providing a crucial benchmark for the user to estimate the ecological relevance of their binned data. The herein introduced software itBins is broadly applicable to any type of metagenome data, integrates well with other software like DASTool, and enables swift and reliable refinement of genomes from metagenomes along with estimation of the overall binning success. itBins is distributed via EUPL 1.2 license and available at Codeberg (codeberg.org/JMK/itBins), GitHub (github.com/ProbstLab/itBins) and through Bioconda [2](bioconda.github.io/recipes/itbins/README.html).

bioinformatics↗

bioRxiv2025

Differential Effects of Short-term and Long-term Deep Brain Stimulation on Striatal Neuronal Excitability in a Dystonia Animal Model

Deep brain stimulation (DBS) is, by now, one of the standard treatment options for movement disorders like dystonia or Parkinsons Disease. Although its clinical effectiveness is established, the exact mechanisms by which DBS influences neural motor networks are not fully understood. The present study explores the development of adaptive network mechanisms with DBS in the dtsz hamster model, an in-vivo model exhibiting spontaneous dystonic episodes, by comparing functional impacts of short-term and long-term DBS on medium spiny neurons (MSNs) and synaptic transmission in the striatum. In this electrophysiological study, we uncovered contrasting changes in neuronal excitability and synaptic dynamics following short-term versus long-term DBS. Short-term DBS enhanced neuronal firing responses, while long-term DBS diminished them. Regarding synaptic alterations, both short-term and long-term DBS significantly shifted spontaneous EPSC occurrences to longer intervals, with this effect, however, being more pronounced in short-term DBS, leading to a significant decrease in mEPSC frequency. Notably, acetylcholine application effectively reversed this effect, restoring mEPSC frequency more efficiently again in tissue subjected to short-term DBS compared to long-term DBS. These observations indicate that the therapeutic benefits of DBS in dystonia may involve both immediate and adaptive mechanisms, which has implications for improving stimulation parameters and treatment protocols. The findings shed light on the temporal specificity of DBS effects and highlight the importance of understanding synaptic mechanisms to enhance therapeutic outcomes for dystonia patients.

neuroscience↗

bioRxiv2025

A uniform stress response of stream microbiomes in the hyporheic zone across North America

BackgroundStream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental stressors. ResultsBased on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies. ConclusionsThe hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems.

microbiology↗

bioRxiv2024

Complex compositional and cellular response of river sediment microbiomes to multiple anthropogenic stressors

Rivers face constant anthropogenic stressors, resulting in significant changes in microbial community composition. What remains unclear is whether these changes render the microbiome better adapted to the stressed environment. Here, by subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to lowered flow velocity resulting in substantially altered community compositions not fully capable of compensating for the stressor effect within two weeks albeit having stable functions encoded in metagenomes. Transcriptomics revealed a systematic heat shock response in the community and a highly active, previously unknown anaerobic key stone species with great metabolic versatility. Increases in temperature (+3.5 {degrees}C) or salinity (+0.5 mS/cm) were outcompeted by lowered flow and elicited only minor responses at community or transcriptomic level with, e.g., upregulation of the photosystem of chloroplasts. Following a two-week recovery period, transcriptomic stress responses vanished completely compared to control mesocosms, exemplifying the river microbiomes resilience. We conclude that, given the complex community responses at both the cellular and compositional level, maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.

ecology↗

bioRxiv2024

Utilising activity patterns of a complex biophysical network model to optimise intra-striatal deep brain stimulation

AO_SCPLOWBSTRACTC_SCPLOWIn this study, we develop a large-scale biophysical network model for the isolated striatal body to optimise potential intrastriatal deep brain stimulation applied in, e.g. obsessive-compulsive disorder by using spatiotemporal patterns produced by the network. The model uses modified Hodgkin-Huxley models on small-world connectivity, while the spatial information, i.e. the positions of neurons, is obtained from a detailed human atlas. The model produces neuronal activity patterns segregating healthy from pathological conditions. Three indices were used for the optimisation of stimulation protocols regarding stimulation frequency, amplitude and localisation: the mean activity of the entire network, the mean activity of the ventral striatal area (emerging as a defined community using modularity detection algorithms), and the frequency spectrum of the entire network activity. By minimising the deviation of the aforementioned indices from the normal state, we guide the optimisation of deep brain stimulation parameters regarding position, amplitude and frequency.

neuroscience↗

bioRxiv2023

Metaproteogenomics resolution of a high-CO2 aquifer community suggests an active symbiotic lifestyle of groundwater Gracilibacteria

BackgroundBacteria of the Candidate Phyla Radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. However, besides genomic evidence, little is known about the lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, where they were initially been genomically resolved. Therefore, we here aimed to investigate Gracilibacteria activity in situ and to discern expressed genes involved in their lifestyle, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany. ResultsWe coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 670 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Galionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria encoded for a high number of proteins related to a symbiotic or even predatory lifestyle, e.g., type IV and type II secretion system subunits and features related to cell-cell interactions and cell motility, which were also detected on protein level. ConclusionsCoupling metagenomics to metaproteomics enabled us to identify microbial keystone taxa in a high-CO2 aquifer, and to reveal microbial dynamics of Gracilibacteria. We posit that Gracilibacteria might be successful microbial predators in this ecosystem, potentially aiding in population control of this highly perturbed microbial geyser community from the deep biosphere.

ecology↗

bioRxiv2021

Glycerol-driven Denitratation: Process Kinetics, Microbial Ecology, and Operational Controls

Denitratation, the selective reduction of nitrate to nitrite, is a novel process when coupled with anaerobic ammonium oxidation (anammox) could achieve resource-efficient biological nitrogen removal of ammonium- and nitrate-laden waste streams. Using a fundamentally-based, first principles approach, this study optimized a stoichiometrically-limited, glycerol-driven denitratation process and characterized mechanisms supporting nitrite accumulation with results that aligned with expectations. Glycerol supported selective nitrate reduction to nitrite and near-complete nitrate conversion, indicating its viability in a denitratation system. Glycerol-supported specific rates of nitrate reduction (135.3 mg-N/g-VSS/h) were at least one order of magnitude greater than specific rates of nitrite reduction (14.9 mg-N/g-VSS/h), potentially resulting in transient nitrite accumulation and indicating glycerols superiority over other organic carbon sources in denitratation systems. pH and ORP inflection points in nitrogen transformation assays corresponded to maximum nitrite accumulation, indicating operational setpoints to prevent further nitrite reduction. Denitratation conditions supported enrichment of Thauera sp. as the dominant genus. Stoichiometric limitation of influent organic carbon, coupled with differential nitrate and nitrite reduction kinetics, optimized operational controls, and a distinctively enriched microbial ecology, was identified as causal in glycerol-driven denitratation.

bioengineering↗

bioRxiv2020

V. longisporum elicits media-dependent secretome responses with a further capacity to distinguish between plant-related environments

Verticillia cause a vascular wilt disease affecting a broad range of economically valuable crops. The fungus enters its host plants through the roots and colonizes the vascular system. It requires extracellular proteins for a successful plant colonization. The exoproteome of the allodiploid Verticillium longisporum was analyzed upon cultivation in different media. Secreted fungal proteins were identified by label free LC-MS/MS screening. V. longisporum induced two main secretion patterns. One response pattern was elicited in various non-plant related environments. The second pattern includes the exoprotein responses to the plant-related media, pectin-rich simulated xylem medium and pure xylem sap, which exhibited similar but additional distinct features. These exoproteomes include a shared core set of 223 secreted and similarly enriched fungal proteins. The pectin-rich medium significantly induced the secretion of 144 proteins including a number of pectin degrading enzymes, whereas xylem sap triggered a smaller but unique fungal exoproteome pattern with 32 enriched proteins. The latter pattern included proteins with domains of known effectors, metallopeptidases and carbohydrate-active enzymes. The most abundant and uniquely enriched proteins of these different groups are the necrosis and ethylene inducing-like proteins Nlp2 and Nlp3, the cerato-platanin proteins Cp1 and Cp2, the metallopeptidases Mep1 and Mep2 and the CAZys Gla1, Amy1 and Cbd1. Deletion of the majority of the corresponding genes caused no phenotypic changes during ex planta growth or invasion and colonization of tomato plants. However, we discovered that the NLP2 and NLP3 deletion strains were compromised in plant infections. Overall, our exoproteome approach revealed that the fungus induces specific secretion responses in different environments. The fungus has a general response to non-plant related media whereas it is able to fine-tune its exoproteome in the presence of plant material. Importantly, the xylem sap-specific exoproteome pinpointed Nlp2 and Nlp3 as single effectors required for successful V. dahliae colonization. Author SummaryVerticillium spp. infect hundreds of different plants world-wide leading to enormous economic losses. Verticillium wilt is a disease of the vasculature. The fungus colonizes the xylem of its host plant where it exploits the vascular system to colonize the whole plant. Therefore, the fungus spends part of its lifetime in this nutrient-low and imbalanced environment where it is inaccessible for disease control treatments. This lifestyle as well requires the fungus to react to plant defense responses by secreting specific effector molecules to establish a successful infection. We addressed the differences in media-dependent secretion responses of Verticillium longisporum. We identified a broad response pattern induced by several media, and a similar response (but with some distinct differences) for the plant-related environments: the pectin-rich medium SXM and xylem sap from the host rapeseed. Importantly, we show that the necrosis and ethylene inducing-like proteins Nlp2 and Nlp3 are xylem sap-specific proteins that are required for full V. dahliae pathogenicity on tomato. These factors play a role during the colonization phase and represent potential targets for new control strategies for Verticillium wilt.

genetics↗

bioRxiv2020

Unfolded protein response and scaffold independent pheromone MAP kinase signalling control Verticillium dahliae growth, development and plant pathogenesis

O_LIDevelopment and virulence of the vascular plant pathogen Verticillium dahliae are connected and depend on a complex interplay between the unfolded protein response, a Ham5 independent pheromone MAP kinase module and formation of precursors for oxylipin signal molecules. C_LIO_LIGenes coding for the unfolded protein response regulator Hac1, the Ham5 MAPK scaffold protein, and the oleate {Delta}12-fatty acid desaturase Ode1 were deleted and their functions in growth, differentiation, and virulence on plants were studied using genetic, cell biology, and plant infection experiments. C_LIO_LIThe unfolded protein response transcription factor Hac1 is required for initial root colonization, fungal conidiation and propagation inside the host and is essential for resting structure formation. Microsclerotia development, growth and virulence require the pheromone response MAPK pathway, but without the Ham5 scaffold function. Single ER-associated enzymes for linoleic acid production make important contributions to fungal growth but have only a minor impact on the pathogenicity of V. dahliae. C_LIO_LIFungal growth, sporulation, dormant structure formation and plant infection require a network of the Hac1-regulated unfolded protein response, a scaffold-independent pheromone response MAPK pathway and formation of precursors for signalling. This network includes interesting targets for disease management of the vascular pathogen V. dahliae. C_LI

genetics↗