Biology subjects

Richter, C.

Publications and source records attributed to Richter, C..

16 recordsLinked to original sources

bioRxiv2026

AGROtools: A comprehensive modular cloning toolset for Agrobacterium strain engineering

Agrobacterium-mediated transformation is a cornerstone of plant genetic engineering, yet many crops remain recalcitrant to transformation and its efficiency is highly species- and genotype-dependent. The limited diversity of disarmed agrobacterial strains available for biotechnology, and the technically challenging workflows typically required for strain modification, constrain efforts to develop improved plant transformation platforms. Here, we describe the development of AGROtools-a versatile, expandable, and user-friendly modular cloning plasmid collection comprising more than 75 individual components, that is designed to simplify genetic engineering of agrobacteria. Constructs assembled with this toolkit couple visual reporters with selectable and counterselectable markers to facilitate identification of recombinant clones, thereby reducing reliance on PCR-based screening. We constructed and tested reporter cassettes that are functional across diverse agrobacterial strains and genomic contexts. By linking a visual reporter combinatorially with various antibiotic resistance markers and orthogonal site-specific recombinase recognition sequences, AGROtools can enable marker removal and recycling for up to four successive genomic modifications. We demonstrate the utility of AGROtools by disarming 10 novel wild-type strains, and accomplishing serial modifications within individual strain backgrounds. In addition to conventional recA-mediated homologous recombination, the collection incorporates components for applying contemporary strain engineering approaches, including CRISPR/dCas9 base editing, INTEGRATE-mediated targeted insertion, and phage-derived recombineering systems. Constructs can be assembled and deployed rapidly, enabling isolation of strains carrying an intended modification in less than two weeks. AGROtools provides a broadly applicable resource for accelerating strain development and genetic studies in agrobacteria, with potential to advance plant biotechnology by aiding improvement of disarmed strains.

plant biology↗

bioRxiv2026

Integrated risk assessment reveals low biological activity of RNA-based crop protection formulations across plant and non-target systems

RNA-based crop protection products are considered promising alternatives to conventional pesticides due to their high target specificity and selectivity profile. While current risk assessments mainly focus on sequence-dependent off-target effects, potential sequence-independent effects of RNA molecules and formulation components remain poorly understood. Here, we assessed the potential of naked and formulated RNA molecules to induce unintended biological responses in plants and non-target organisms using complementary plant stress and cellular toxicity assays. Single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), circular RNA (circRNA), and chitosan-based RNA formulations were evaluated for their ability to induce early stress responses in plants and adverse effects in insect cells. Cytosolic Ca{superscript 2} signaling and reactive oxygen species (ROS) production were monitored in barley and Arabidopsis, while impedance-based phenotypic profiling (ECIS) was used to assess cellular responses in Spodoptera frugiperda (Sf21) cells. Neither naked nor formulated RNA preparations triggered pronounced Ca{superscript 2} influxes or ROS bursts, indicating an absence of substantial activation of early plant defense signaling. Likewise, RNA formulations caused only minor effects on insect cell attachment and spreading as a measure for cell viability. Observable responses occurred primarily at elevated concentrations of RNA formulations and were formulation-dependent rather than RNA-dependent. Overall, the investigated RNA molecules exhibited low biological activity across the tested non-target systems. Our results highlight the importance of evaluating RNA active ingredients and delivery matrices separately and demonstrate the value of integrated screening approaches for the early hazard assessment of RNA-based crop protection products.

Plant Biology↗

bioRxiv2026

Immunoengineered Chitosanase-Produced Chitosan Oligomers for Elevating Plant Resistance to Viral Infection

Chitooligomers can act as plant biostimulants or biopesticides, but todays chitosan-based agro-biologics often lack sufficient efficacy. This is due to a lack of scalable production processes for structurally well-controlled chitosans combined with a limited understanding of structure-function relationships. Chitosans differ in their degree of polymerization (DP), fraction and pattern of acetylation (FA and PA). While the influence of DP and FA on antimicrobial and phytostimulatory properties is at least partially known, this is not yet the case for PA. PA can be partially controlled by using enzymatic rather than acid hydrolysis for oligomer production. We have used recombinant chitinases and chitosanases to hydrolyse a well-characterised chitosan polymer, and purified oligomers with different DP. We have structurally characterised the products and tested their abilities to protect tobacco from viral disease. Chitinase products were dominated by GlcNAc units at their reducing and non-reducing ends, with GlcN units dominating their centers, and v.v. for chitosanase products. While the chitinase-derived hydrolysates were inactive, the chitosanase-derived oligomers possessed elicitor and priming activities and protected plants from disease, and their activity increased with increasing DP. Clearly, the Bacillus chitosanase used is well-suited to set up a scalable production process for chitosan oligomers with promising agro-biologic properties. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/731087v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@b50b59org.highwire.dtl.DTLVardef@1fc35c3org.highwire.dtl.DTLVardef@12db91aorg.highwire.dtl.DTLVardef@d3732f_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2026

Cytosine base editing workflow for quality-controlled multiplex-knockout hiPSC lines

Dissecting polygenic disease mechanisms requires human cell models that harbour multiple targeted genetic modifications in a defined background. However, generating and rigorously validating such models remains difficult. We developed a cytosine base editing workflow to generate multiplex-knockout (KO) human induced pluripotent stem cell (hiPSC) lines. First, we assessed six cytosine base editor (CBE) variants and selected evoBE4max. We then combined sgRNA-guided introduction of premature termination codons and splice-site mutations with fluorescence-based enrichment. This yielded a median on-target C-to-T editing efficiency of 77.5% (range, 27.0-86.5%) across six loci. We generated single-, double-, and triple-KO hiPSC lines for endolysosomal Ca{superscript 2} signalling components (OCaR2, TPC1, TPC2) and confirmed loss-of-function at transcript and protein levels. We performed extensive quality control, including pluripotency assessment, SNP-array karyotyping, and whole-genome sequencing, which indicated minimal guide-directed off-target editing. We further extended multiplex editing to ORAI Ca{superscript 2} channel paralogs. This framework supports scalable production of quality-controlled multiplex-KO hiPSC lines.

genetics↗

bioRxiv2026

Chromosome axis protein SYCP2 recruits HORMAD2 to enable meiotic synapsis quality control in mice

Faithful chromosome segregation during meiosis depends on accurate recombination and synapsis of homologous chromosomes. These processes are monitored in mammals by checkpoint mechanisms involving the meiotic HORMA-domain proteins HORMAD1 and HORMAD2, which bind unsynapsed chromosome axes and promote activation of the DNA damage-response kinase ATR independently of DNA double-strand breaks (DSBs). However, no mechanism for axis recruitment of HORMAD1 or HORMAD2 had been demonstrated, nor had its role in checkpoint function been tested. We establish that a putative HORMAD-interacting region--the closure motif (CM)--within the chromosome-axis component SYCP2 is selectively required for HORMAD2, but not HORMAD1, localization. Deletion of the SYCP2 CM disrupts SYCP2-HORMAD2 complexes and prevents HORMAD2 axis binding without affecting axis assembly or recombination. Consequently, ATR accumulation and signaling on unsynapsed axes are reduced, and the prophase checkpoint malfunctions in a sexually dimorphic manner--causing aberrant elimination of synapsis-proficient spermatocytes and persistence of asynaptic oocytes. The phenotypes of SYCP2-CM-deficient and HORMAD2-null mice are indistinguishable, establishing the requirement for HORMAD2 axis recruitment in synapsis surveillance. We propose that axial recruitment generates a HORMAD2 scaffold that drives clustering-mediated ATR network activation independently of DSBs, thereby linking chromosome-axis architecture to synapsis quality control in mammalian meiosis.

cell biology↗

bioRxiv2025

Adenosine-specific transcriptional programs in murine connective tissue type mast cells

Mast cells are tissue-resident immune cells that are critical for the pathogenesis of allergic and inflammatory disorders. In addition to classic host defense against parasites, food quality control through antigen avoidance has been recently elucidated as additional physiological mast cell function. The purine nucleoside adenosine (ADO), like other mast cell activators, such as antigens or Mrgprb2 agonists, increases intracellular Ca2+ concentration; however, it fails to induce degranulation of preformed mediators when applied to isolated mast cells alone, and there is limited knowledge of whether ADO evokes the de novo synthesis and release of inflammatory mediators such as cytokines in tissue mast cells. An unbiased genome-wide analysis of gene expression triggered by various mast cell activators should enable identification of the gene program specifically activated by adenosine in mast cells and thereby reveal new components of the associated inflammatory responses. To this end, we performed bulk RNA sequencing (RNA-Seq) in primary murine peritoneal mast cells (PMCs) as connective tissue mast cells. By comparing responses evoked by ADO stimulation with those of the Mrgprb2 compound 48/80 and antigens that activate Fc{varepsilon}RI receptors, we identified 393 genes whose expression was uniquely regulated by ADO, including upregulation of genes encoding de novo synthesized mediators such as Tgfa and Il7. Transcription factor activity inference, protein classification, functional enrichment analysis, protein-protein interaction network, and topology analysis revealed that these genes play roles in phosphoinositide signaling, vesicle trafficking, glycolysis, mitochondrial activity, and cell cycle arrest. In summary, our work elucidates a distinct ADO-triggered response and identifies a set of proteins including de novo synthesized mediators whose functional relevance in adenosine-evoked mast cell activation and inflammatory reactions can be evaluated in future studies.

pharmacology and toxicology↗

bioRxiv2025

Selective breeding enhances coral heat tolerance even over small spatial scales

Coral reefs globally are experiencing escalating mass bleaching and mortality. Reefs along the western Indian Ocean have been relatively unimpacted. We assessed heat tolerance baselines in two widespread reef-building Acropora species and used selective breeding from two thermally distinct (present day and stress histories) northern (Mean Monthly Maximum 27.9 {degrees}C) and southern (26.6 {degrees}C) reefs along the Ningaloo World Heritage Reef. Fitness responses were measured in control and heat stress temperatures (adults = 31.0 {degrees}C, larvae = 35.5 {degrees}C), including survival, tissue necrosis, bleaching, and photosynthesis. Larvae with one parent from the warmer population exhibited >2.2-fold higher survival under heat stress, while those with both parents from the warmer population survived 1.6-fold better (compared to control larvae with two parents from the cooler population). Photosynthesis was maintained in both species and both populations, suggesting heat responses were host driven. Adults from both populations from one species (A. tenuis) exhibited similar responses to heat, while the other (A. millepora) was more variable. These findings are the first to demonstrate that selective breeding can provide heat tolerance enhancement for corals in the Indian Ocean and will be critical to preparing for future marine heatwaves.

ecology↗

bioRxiv2025

TARP γ-8 is a target of ethanol that regulates self-administration and relapse in mice

BackgroundBehavioral pathologies that characterize alcohol use disorder (AUD) are driven by the powerful reinforcing, or rewarding, properties of the drug. We have shown that glutamate AMPA receptor (AMPAR) activity is both necessary and sufficient for alcohol (ethanol) reinforcement. Transmembrane AMPAR regulatory protein (TARP) {gamma}-8 is an essential auxiliary protein that regulates AMPAR expression and activity; however, the role of TARP {gamma}-8 in AUD or other forms of addiction remains largely unexplored. ObjectivesThis study investigated the mechanistic role of TARP {gamma}-8 in operant ethanol self-administration (model of primary reinforcement) and cue-induced reinstatement of ethanol-seeking behavior (model of conditioned reinforcement) using TARP {gamma}-8 heterozygous null (+/-) mice. To determine if TARP {gamma}-8 signaling is targeted by ethanol use, we evaluated protein expression of TARP {gamma}-8, GluA1, CaMKII, and PSD-95 following ethanol self-administration. ResultsA battery of tests evaluating food and water intake, taste reactivity, anxiety-like behavior, and object recognition memory showed no fundamental behavioral deficits in TARP {gamma}-8 (+/-) mice, and no differences in response to acute ethanol or home-cage drinking as compared to wild-types. However, TARP {gamma}-8 (+/-) mice exhibited significantly reduced acquisition and escalation of operant ethanol self-administration and reduced cue-induced reinstatement of ethanol-seeking behavior, with no differences in parallel sucrose-only controls. In wild-type mice, ethanol self-administration increased TARP {gamma}-8 expression in the amygdala, nucleus accumbens, and hippocampus, and increased GluA1 expression in the amygdala and prefrontal cortex, compared to sucrose controls. ConclusionThese findings highlight the specificity of TARP {gamma}-8 regulation of ethanol reinforcement mechanisms and identify this crucial AMPAR auxiliary protein as a target of ethanol in reward-related brain regions, highlighting its potential for development of novel pharmacotherapies for AUD.

neuroscience↗

bioRxiv2022

Sexual dimorphic regulation of recombination by the synaptonemal complex

In sexually reproducing organisms, germ cells faithfully transmit the genome to the next generation by forming haploid gametes, such as eggs and sperm. Although most meiotic proteins are conserved between eggs and sperm, many aspects of meiosis are sexually dimorphic. The mechanisms regulating recombination display sex-specific differences in multiple organisms such that the same proteins in each sex are being utilized in different ways to produce sexually dimorphic outcomes. The synaptonemal complex (SC), a large ladder-like structure that forms between homologous chromosomes, is essential for regulating meiotic chromosome organization and promoting recombination. To assess whether sex-specific differences in the SC underpin sexually dimorphic aspects of meiosis, we examined two Caenorhabditis elegans SC central region proteins, SYP-2 and SYP-3, in oogenesis and spermatogenesis and uncovered sex-specific roles for the SYPs in regulating meiotic recombination. We find that SC composition is regulated by sex-specific mechanisms throughout meiotic prophase I. During pachytene, both oocytes and spermatocytes differentially regulate the stability of SYP-2 and SYP-3 within an assembled SC, with increased SYP-2 dynamics in spermatocytes and increased SYP-3 dynamics in oocytes. Further, we uncover that the relative amount of SYP-2 and SYP-3 within the SC is independently regulated in both a sex-specific and a recombination-dependent manner. Specifically, we find that SYP-2 regulates the early steps of recombination in both sexes, while SYP-3 controls the timing and positioning of crossover recombination events across the genomic landscape in only oocytes. Taken together, we demonstrate dosage-dependent regulation of individual SC components with sex-specific functions in recombination. These sexual dimorphic features of the SC provide insights into how spermatogenesis and oogenesis adapted similar chromosome structures to differentially regulate and execute recombination.

developmental biology↗

bioRxiv2022

Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria

Microorganisms contribute to the biology and physiology of eukaryotic hosts and affect other organisms through natural products. Xenorhabdus and Photorhabdus (XP) living in mutualistic symbiosis with entomopathogenic nematodes produce a myriad of natural products to mediate bacteria-nematode-insect interactions. However, a lack of systematic analysis of the biosynthetic gene clusters (BGCs) has limited the understanding of how natural products justify the bacterial niche specificity. Here we combine pangenome and sequence similarity networks to analyze BGCs from 45 XP species. The identified 1,000 BGCs belong to 176 families, over half of which are unknown. Eleven BGCs represent the most conserved families. We then homologously express the ubiquitous and unique BGCs and identify compounds featuring unusual architectures. The bioactivity evaluation demonstrates that the prevalent compounds are eukaryotic proteasome inhibitors, insect virulence factors, or insect immune suppressors. These findings account for the functional basis of bacterial natural products in this tripartite relationship.

biochemistry↗

bioRxiv2021

CREB5 reprograms nuclear interactions to promote resistance to androgen receptor targeting therapies

Metastatic castration resistant prostate cancers (mCRPC) are treated with therapies that antagonize the androgen receptor (AR). Nearly all patients develop resistance to AR-targeted therapies (ART). Our previous work identified CREB5 as an upregulated target gene in human mCRPC that promoted resistance to all clinically-approved ART. The mechanisms by which CREB5 promotes progression of mCRPC or other cancers remains elusive. Integrating ChIP-seq and rapid immunoprecipitation and mass spectroscopy of endogenous proteins (RIME), we report that cells overexpressing CREB5 demonstrate extensive reprogramming of nuclear protein-protein interactions in response to the ART agent enzalutamide. Specifically, CREB5 physically interacts with AR, the pioneering actor FOXA1, and other known co-factors of AR and FOXA1 at transcription regulatory elements recently found to be active in mCRPC patients. We identified a subset of CREB5/FOXA1 co-interacting nuclear factors that have critical functions for AR transcription (GRHL2, HOXB13) while others (TBX3, NFIC) regulated cell viability and ART resistance and were amplified or overexpressed in mCRPC. Upon examining the nuclear protein interactions and the impact of CREB5 expression on the mCRPC patient transcriptome, we found CREB5 was associated with TGF{beta} and Wnt signaling and epithelial to mesenchymal transitions, implicating these pathways in ART resistance. Overall, these observations define the molecular interactions among CREB5, FOXA1, and pathways that promote ART resistance.

cancer biology↗

bioRxiv2021

Alpha and beta rhythms differentially support the effect of symbols on visual object recognition

Hearing spoken words can enhance visual object recognition, detection and discrimination. Yet, the mechanisms that underpin this facilitation are incompletely understood. On one account, words do not bias early visual processing, but rather affect later semantic or decision-making stages. However, recent proposals suggest that words can alter early visual processes by activating category-specific priors in sensory regions. A prediction of this account is that top-down priors evoke changes in occipital areas in anticipation of visual stimuli. Here, we tested the hypothesis that neural oscillations serve as a mechanism to activate language-generated visual priors. Participants performed a cue-picture matching task where cues were either spoken words, in their native or second language, or natural sounds, while their EEG and reaction times were recorded. Behaviorally, we replicated the previously reported label-advantage effect, with images cued by words being recognized faster than those cued by natural sounds. A time-frequency analysis of cue-target intervals revealed that this behavioral label-advantage was associated with enhanced power in posterior alpha (9-11 Hz) and beta oscillations (17-19 Hz), both of which were larger when the image was preceded by a word compared to a natural sound. Importantly, object recognition performance improved with high alpha power but slowed down with enhancement of beta synchronization. These results suggest that alpha and beta rhythms play distinct functional roles to support language-mediated visual object recognition: alpha might function to amplify sensory priors in posterior regions, while beta may (re)activate the network states elicited by the auditory cue.

neuroscience↗

bioRxiv2020

The Chemical Structure of Widespread Microbial Aryl Polyene Lipids

Biosynthetic gene clusters (BGC) involved in aryl polyene (APE) biosynthesis are supposed to represent the most widespread BGC in the bacterial world.[1-3] Still, only hydrolysis products[4-8] and not the full-length product(s) have been identified, hindering studies on their biosynthesis and natural function. Here, we apply subsequent chromatographic separations to purify the aryl polyene-containing lipids (APELs) from the entomopathogenic bacterium Xenorhabdus doucetiae. Structure elucidation using a combination of isotope labeling, nuclear magnetic resonance techniques, and tandem mass spectrometry reveals an array of APELs featuring an all-trans C26:5 conjugated fatty acyl and a galactosamine-phosphate-glycerol moiety. In combination with extensive genetic studies, this research broadens the bacterial natural product repertoire and paves the way for future functional characterization of this almost universal microbial compound class. Due to their protective function against reactive oxygen species,[5,9] APELs might be important for virulence or symbiosis, mediating organismic interactions in several ecological niches.

microbiology↗

bioRxiv2020

Biologically informed deep neural network for prostate cancer classification and discovery

Determination of molecular features that mediate clinically aggressive phenotypes in prostate cancer (PrCa) remains a major biological and clinical challenge. Here, we developed a biologically informed deep learning model (P-NET) to stratify PrCa patients by treatment resistance state and evaluate molecular drivers of treatment resistance for therapeutic targeting through complete model interpretability. Using a molecular cohort of 1,238 prostate cancers, we demonstrated that P-NET can predict cancer state using molecular data that is superior to other modeling approaches. Moreover, the biological interpretability within P-NET revealed established and novel molecularly altered candidates, such as MDM4 and FGFR1, that were implicated in predicting advanced disease and validated in vitro. Broadly, biologically informed fully interpretable neural networks enable preclinical discovery and clinical prediction in prostate cancer and may have general applicability across cancer types.

bioinformatics↗

bioRxiv2020

Drift and termination of spiral waves in optogenetically-modified cardiac tissue at sub-threshold illumination

The development of new approaches to control cardiac arrhythmias requires a deep understanding of spiral wave dynamics. Optogenetics offers new possibilities for this. Preliminary experiments show that sub-threshold illumination affects electrical wave propagation in the mouse heart. However, a systematic exploration of these effects is technically challenging. Here, we use state-of-the-art computer models to study the dynamic control of spiral waves in a two-dimensional model of the adult mouse ventricle, using stationary and non-stationary patterns of sub-threshold illumination. Our results indicate a light intensity-dependent increase in cellular resting membrane potentials, which together with diffusive cell-cell coupling leads to the development of spatial voltage gradients over differently illuminated areas. A spiral wave drifts along the positive gradient. These gradients can be strategically applied to ensure drift-induced termination of a spiral wave, both in optogenetics and in conventional methods of electrical defibrillation.

biophysics↗

bioRxiv2018

Analyzing Human Movements - Introducing A Framework To Extract And Evaluate Biomechanical Data

This study discusses possible sources of discrepancy between findings of previous human motion studies and presents a framework that seeks to address these issues. Motion analysis systems are widely employed to identify movement deficiencies - e.g. patterns that potentially increase the risk of injury or inhibit performance. However, findings across studies are often conflicting in respect to what a movement deficiency is or the magnitude of the relationship to a specific injury. To test the information content of movement data, a framework was build to differentiate between movements performed by a control (NORM) and abnormal (IMP-L and IMP-C) cohort using solely movement data. Movement data was recorded during jumping, hopping and change of direction exercises and was mathematically decomposed into subject scores. Subjects scores were then used to identify the most appropriate machine learning technique, which was subsequently utilized to create a prediction model that classified if a movement was performed by: IMP-L, IMP-C or NORM. The Monte Carlo method was used to obtain a measure of expected accuracy for each step within the analysis. Findings demonstrate that even the worst classification model outperformed the best guess observed and that not all members of the NORM group represent a NORM pattern as they were repeatedly classified as IMP-L or IMP-C. This highlights that some NORM limbs share movement characteristics with the abnormal group and consequently should not be considered when describing NORM.

scientific communication and education↗