Biology subjects

Straub, D.

Publications and source records attributed to Straub, D..

13 recordsLinked to original sources

bioRxiv2026

Tracking the hidden dynamics of proprioception

Every movement unfolds with a simple question: Where is my body? The nervous system answers through proprioception - the sense of limb position (static position sense) and movement (dynamic proprioception). Although position sense has been well characterized, dynamic proprioception has remained difficult to isolate and measure. Here we introduce a continuous proprioceptive tracking paradigm, coupled with computational modelling, that captures dynamic proprioception in real time. We first establish that this approach is sensitive, reliable and efficient. Leveraging this method, we then show that dynamic proprioception provides faster and more faithful estimates of limb state than vision, dominates multisensory state estimation when vision is also available, and is not correlated with conventional measures of position sense. Together, these findings provide a new quantitative framework for characterizing dynamic proprioception in health and disease.

neuroscience↗

bioRxiv2026

Tactile suppression during movement as optimal integration of somatosensory feedback across time

Goal-directed movements generate tactile signals from the moving body, yet many are perceptually suppressed. Prevailing accounts propose that the nervous system reduces tactile sensitivity by prioritizing internal predictions over somatosensory feedback, contrasting with the view that suppression reflects peripheral masking. However, both accounts lack quantitative explanations of temporal dynamics and dependence on the motor task. Here, we show that tactile suppression is a consequence of optimal state estimation during movement. Using optimal feedback control theory, we derived how the nervous system should dynamically weight uncertain internal predictions against noisy somatosensory feedback. Human participants performed goal-directed reaching movements while vibrotactile stimuli were delivered at different time points. Suppression weakened as internal uncertainty about hand distance to target increased, consistent with greater reliance on sensory feedback. Model comparison identifies tactile suppression as dynamic, uncertainty-dependent state estimation rather than peripheral masking, establishing a normative principle for tactile sensitivity during action.

neuroscience↗

bioRxiv2026

Towards understanding nitrate-reducing Fe(II) oxidation in Ferrigenium straubiae: spotlight on old and new key protein candidates

3.Autotrophic Fe(II) oxidation is a key microbial process linking iron cycling to global carbon and nitrogen turnover in anoxic and low-oxygen environments. While Fe(II) oxidation, and electron utilization by canonical denitrification or oxygen-reducing pathways have been proposed, the whole electron transport chain via the periplasm is unknown. To address this gap, we compared the transcriptome of Ferrigenium straubiae strain KS (= KCTC 25982; = DSM 118991) cultivated under autotrophic conditions using Fe(II) as the electron donor and either nitrate or oxygen as the terminal electron acceptor. Additionally, we reanalyzed the genome using bioinformatic tools (FeGenie, MHCScan, Foldseek, AlphaFold, COFACTOR, and InterProScan) to classify known, putative, and previously uncharacterized proteins. Using these analyses, we (i) identified a form II RubisCO-mediated, sedoheptulose-7-phosphate-forming transaldolase variant of the Calvin-Benson-Bassham cycle, (ii) revealed the metabolic possibility of a reversed oxidative TCA cycle and an alternative CO2 fixation route via 10-formyl-tetrahydrofolate, (iii) found novel structural features of the proposed Fe(II) oxidases (Cyc2 and MtoA/B: {beta}-barrel outer membrane cytochromes), (iv) uncovered a nitric oxide reductase (eNOR-family) and two redox complexes specifically upregulated under nitrate-reducing Fe(II)-oxidizing conditions, including one comprising a sphaeroides heme protein homolog, and (v) reveal a cytochrome c rich gene area encoding ten heme proteins and (iv) proposed a conserved nonaheme cytochrome c to link Fe(II) oxidation to quinone reduction. 2. RepositoriesGenBank whole genome sequence of strain KS: JAGRPI00000000 IMG Taxon ID of strain KS: 2878407288 NCBI BioProject ID of RNA-Seq data: PRJNA1399691 Strain availability: KCTC 25982 and DSM 118991 Normalized transcripts and Log2FoldChanges (Excel file), and supplementary information are available with the online version of this article.

microbiology↗

bioRxiv2025

Resistance Training Reshapes the Gut Microbiome for Better Health

ObjectivesThe gut microbiome plays a critical role in metabolism, immunity, and aging. While endurance training has been shown to beneficially modulate the microbiome, the effects of resistance training remain less clear, with some studies reporting minimal changes. This project aims to investigate whether structured resistance training elicits significant changes in gut microbiome composition and diversity in sedentary, healthy adults. Methods150 participants completed an 8-week supervised resistance training program. Session-level training data, including weights and repetitions, were recorded alongside metrics like load and compliance. Fecal samples were collected throughout the study period at designated timepoints for 16S rRNA gene amplicon sequencing to assess microbiome composition and for metabolomics analyses to evaluate microbial metabolic activity. ResultsNo differences in microbial diversity were observed, and there were no significant changes in microbial community composition or fecal metabolomics across all participants post-training. However, within-individual microbial community changes significantly correlated with strength improvement, and significantly stronger shifts in beta diversity were observed in participants with high average strength gains compared to those with smaller gains. In these high responders, differential abundance analysis revealed time-dependent microbial changes, with more taxa enriched or depleted by week 8 of training. Notably, Faecalibacterium and Roseburia hominis--both associated with a healthier, anti-inflammatory microbiome--were significantly enriched. Many differentially abundant taxa belonged to the Lachnospiraceae family. ConclusionResistance training drives significant, time-dependent gut microbiome changes, particularly in those demonstrating greater improvements in strength. These shifts mirror endurance training effects and may reflect improved overall health. SummaryWhile endurance training has been consistently shown to enhance gut microbiome composition, the effects of resistance training remain less well defined, with findings to date being variable. Our results indicate that resistance training can induce meaningful, time-dependent shifts in the gut microbiome, particularly among sedentary individuals who experience substantial strength gains. Notably, we observed enrichment of key health-associated taxa, including Faecalibacterium and Roseburia hominis, both linked to anti-inflammatory effects and improved gut function. These findings suggest that resistance training may contribute to gut health in conjunction with physical fitness, supporting its broader application in health promotion strategies and future microbiome-focused research.

microbiology↗

bioRxiv2025

nf-core/detaxizer: A Benchmarking Study for Decontamination from Human Sequences

Privacy is paramount in health data, particularly in human genetics, where information extends beyond individuals to their relatives. Metagenomic datasets contain substantial human genetic material, necessitating careful handling to mitigate data leakage risks when sharing or publishing. The same applies to genetic datasets from the environment or datasets from contaminated laboratory samples, although to a lesser extent. To address these topics, we developed nf-core/detaxizer, a nextflow-based pipeline that employs Kraken2 and bbmap/bbduk for taxonomic classification, identifying and optionally filtering Homo sapiens reads. Due to its generalized design, other taxa can also be classified and filtered. We benchmark its filtering efficacy for human reads against Hostile and CLEAN, demonstrating its utility for secure data preprocessing. The comparison revealed that the choice of tool and database can lead to an order of magnitude more human data not removed. As part of the nf-core initiative, nf-core/detaxizer adheres to best practices, leveraging containerized dependencies for streamlined installation. The source code is openly available under the MIT license: https://github.com/nf-core/detaxizer.

microbiology↗

bioRxiv2025

Intuitive sensorimotor decisions under risk take Newtonian physics into account

The success of our interactions with objects in natural tasks depends on generating motor actions, which are subject to sensorimotor variability, the objects physical properties, which are governed by the laws of kinematics, and the costs and benefits associated with the actions outcomes. Therefore, such interactions jointly involve sensorimotor control, intuitive physics, and decision-making under risk. Here, we devised a mixed reality experiment, which allows investigating human behavior involving the interaction of all three of these cognitive faculties. Participants slid pucks to target areas associated with monetary rewards and losses within an immersive, naturalistic virtual environment. In this task, signal-dependent variability inherent in motor control interacts non-linearly with the physical relationships governing objects motion under friction. By systematically testing generative models of behavior incorporating different assumptions about how participants may generate the slides, we find decisive evidence that participants decision under risk readily took their individual motor variability and Newtonian physics into account to gain monetary rewards without relying on trial by trial learning. Author summaryHumans are exceptionally proficient at manipulating objects in natural tasks. This skill requires integrating three cognitive faculties: 1. Sensorimotor-control, subject to inherent uncertainty and variability; 2. Intuitive physical reasoning as object manipulations are subject to physical dynamics; 3. Economic decision-making when actions have outcomes with monetary consequences. Here, we show that in a naturalistic, immersive object manipulation task, human participants plan their movements by taking into account how their sensorimotor variability interacts with the physical dynamics of object manipulation to optimize economic outcomes. Therefore, our findings suggest that in everyday naturalistic interactions with the world, humans can integrate these three cognitive faculties.

neuroscience↗

bioRxiv2024

A shade-responsive microProtein in the Arabidopsis ATHB2 gene regulates elongation growth and root development

Shade triggers widespread changes in transcript isoform production in Arabidopsis thaliana. Using 5' PEAT sequencing, we identified 377 candidate microprotein-encoding transcripts arising from alternative transcription start sites, including one located within the third exon of ATHB2, a class II HD-ZIP transcription factor central to shade avoidance. The encoded microprotein, ATHB2miP, lacks the DNA-binding homeodomain but retains the leucine zipper domain, through which it forms heterodimers with full-length ATHB2, inhibits its DNA-binding activity, and disrupts its localization to nuclear photobodies. Ectopic expression of ATHB2miP phenocopies loss of ATHB2, deregulating genes involved in auxin signaling, root development, and iron homeostasis. Complementation of the athb2 mutant with a construct carrying a silent mutation at the ATHB2miP start codon results in exaggerated hypocotyl elongation under both white light and shade, demonstrating that ATHB2miP is required to restrain excessive elongation growth. Immunoprecipitation mass spectrometry confirmed that this mutation redirects translation to alternative initiation sites, producing distinct proteoforms absent from wild-type plants. Additionally, ATHB2 suppresses iron uptake genes, and iron availability modulates shade growth responses in an ATHB2-dependent manner. Together, these findings establish ATHB2miP as a regulator of an ATHB2 feedback circuit that integrates light and nutritional signals to coordinate shoot elongation and root development.

plant biology↗

bioRxiv2023

How tool combinations in different pipeline versions affect the outcome in RNA-seq analysis

Data analysis tools are continuously changed and improved over time. In order to test how these changes influence the comparability between analyses, the output of different workflow options of the nf-core/rnaseq pipeline were compared. Five different pipeline settings (STAR+Salmon, STAR+RSEM, STAR+featureCounts, HiSAT+featureCounts, pseudoaligner Salmon) were run on three datasets (human, Arabidopsis, zebrafish) containing spike-ins of the External RNA Control Consortium (ERCC). Fold change ratios and differential expression of genes and spike-ins were used for comparative analyses of the different tools and versions settings of the pipeline. An overlap of 85% for differential gene classification between pipelines could be shown. Genes interpreted with a bias were mostly those present at lower concentration. Also, the number of isoforms and exons per gene were determinants. Previous pipeline versions using featureCounts showed a higher sensitivity to detect one-isoform genes like ERCC. To ensure data comparability in long-term analysis series it would be recommendable to either stay with the pipeline version the series was initialized with or to run both versions during a transition time in order to ensure that the target genes are addressed the same way.

bioinformatics↗

bioRxiv2022

The m6A writer FIONA1 methylates the 3'UTR of FLC and controls flowering in Arabidopsis

Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identified suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated mRNAs. We provide evidence that FIO1 is the elusive methylase responsible for the 3-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.

plant biology↗

bioRxiv2021

Putting perception into action: Inverse optimal control for continuous psychophysics

Psychophysical methods are a cornerstone of psychology, cognitive science, and neuroscience where they have been used to quantify behavior and its neural correlates for a vast range of mental phenomena. Their power derives from the combination of controlled experiments and rigorous analysis through signal detection theory. Unfortunately, they require many tedious trials and preferably highly trained participants. A recently developed approach, continuous psychophysics, promises to transform the field by abandoning the rigid trial structure involving binary responses and replacing it with continuous behavioral adjustments to dynamic stimuli. However, what has precluded wide adoption of this approach is that current analysis methods recover perceptual thresholds, which are one order of magnitude larger compared to equivalent traditional psychophysical experiments. Here we introduce a computational analysis framework for continuous psychophysics based on Bayesian inverse optimal control. We show via simulations and on previously published data that this not only recovers the perceptual thresholds but additionally estimates subjects action variability, internal behavioral costs, and subjective beliefs about the experimental stimulus dynamics. Taken together, we provide further evidence for the importance of including acting uncertainties, subjective beliefs, and, crucially, the intrinsic costs of behavior, even in experiments seemingly only investigating perception.

animal behavior and cognition↗

bioRxiv2021

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install - all dependencies are provided within containers -, portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All code is hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.

bioinformatics↗

bioRxiv2019

Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline.

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is DNA- or RNA-based 16S rRNA (gene) amplicon sequencing. Subsequent bioinformatics analyses are required to extract valuable information from the high-throughput sequencing approach. However, manifold bioinformatics tools complicate their choice and might cause differences in data interpretation, making the selection of the pipeline a crucial step. Here, we compared the performance of most widely used 16S rRNA gene amplicon sequencing analysis tools (i.e. Mothur, QIIME1, QIIME2, and MEGAN) using mock datasets and environmental samples from contrasting terrestrial and freshwater sites. Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times less false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), while there was still room for improvement e.g. imperfect sequence recovery (recall up to 87%) or detection of additional false sequences (precision up to 72%). Furthermore, we found that microbial diversity estimates and highest abundant taxa varied among analysis pipelines (i.e. only one in five genera was shared among all analysis tools) when analyzing environmental samples, which might skew biological conclusions. Our findings were subsequently implemented in a high-performance computing conformant workflow following the FAIR (Findable, Accessible, Interoperable, and Re-usable) principle, allowing reproducible 16S rRNA gene amplicon sequence analysis starting from raw sequence files. Our presented workflow can be utilized for future studies, thereby facilitating the analysis of high-throughput DNA- or RNA-based 16S rRNA (gene) sequencing data substantially. ImportanceMicroorganisms play an essential role in biogeochemical cycling events across the globe. Phylogenetic marker gene analysis is a widely used method to explore microbial community dynamics in space and time, to predict the ecological relevance of microbial populations, or to identify microbial key players in biogeochemical cycles. Several computational analysis methods were developed to aid 16S rRNA gene analysis but choosing the best method is not trivial. In this study, we compared popular analysis methods (i.e. Mothur, QIIME1 and 2, and MEGAN) using samples with known microbial composition (i.e. mock community samples) and environmental samples from contrasting habitats (i.e. groundwater, soil, sediment, and river water). Our findings provide guidance for choosing the currently optimal 16S rRNA gene sequencing analysis method and we implemented our recommended pipeline into a reproducible workflow, which follows highest bioinformatics standards and is open source and free to use.

microbiology↗

bioRxiv2018

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

MicroProteins have emerged as potent regulators of transcription factor activity. Here we use a combination of forward genetics and proteomics to dissect the miP1a/b microProtein complex that acts to delay the floral transition in Arabidopsis. The microProteins miP1a and miP1b can bridge an interaction between the flowering promoting factor CONSTANS (CO) and the TOPLESS (TPL) co-repressor protein to represses flowering. We find that the JUMONJI14 (JMJ14) histone demethylase is part of this repressor complex that can initiate chromatin changes in FLOWERING LOCUS T (FT) gene, the direct target of CO. Plants with mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on the activity of CO, supporting a role for CO in this repressive complex. When mis-expressed at the shoot apex, CO can induce early flowering only in the jmj14 background. Our results indicate that the repressor acts in the shoot apical meristem to keep it in an undifferentiated state until the leaf-derived florigen signal induces the conversion into a floral meristem.

plant biology↗