Biology subjects

Richter, F.

Publications and source records attributed to Richter, F..

13 recordsLinked to original sources

bioRxiv2026

Encephalitic alphavirus infection reduces neurite outgrowth and downregulates Rho GTPase pathways in human iPSC-derived neurospheres

Venezuelan equine encephalitis virus (VEEV) is a re-emerging neurotropic arbovirus, which affects the developing human brain, potentially leading to miscarriage, stillbirth, or long-term neurological sequelae. Currently, the mechanisms underlying these sequelae remain largely elusive. Using human induced pluripotent stem cell (iPSC)-derived neurospheres as a model for brain development, we show that both human neurons and glial cells are susceptible to VEEV infection. Microscopy-based quantification reveals that VEEV impairs neurite outgrowth in the human neurospheres. To mechanistically assess these observations, we performed multi-omics analyses of VEEV-infected neurospheres and demonstrate translational shutoff including downregulation of Rho GTPase pathways. The transcriptional and proteome profile is indicative of reduced actin cytoskeleton dynamics and consequently migratory defects of cells in the neurospheres. Shotgun secretomics moreover revealed downmodulation of neurite outgrowth associated proteins including midkine (MDK), amyloid-beta precursor protein (APP) and microtubule-associated protein 1B (MAP1B). Our findings reveal mechanistic insights into how VEEV infection impairs neuronal development and demonstrate that neurospheres are a powerful platform for assessing teratogenic effects of viruses on brain development.

neuroscience↗

bioRxiv2026

Where the tree of life is empirically resolved, and where it is not: an open atlas of species-level phylogenies and their archival uncertainty

Comparative and macroevolutionary biology depends on knowing two things at once: where the species-level tree of life is empirically resolved, and where it is not. Yet the phylogenies that anchor downstream inference are routinely treated as fixed inputs, even though their empirical substrate is heterogeneous in ways that vanish once a tree is downloaded. Trees differ in inference framework, in dating regime, and in the balance between species supported by direct molecular data and species inserted by taxonomic constraint. They also differ in whether per-node uncertainty estimated during inference survives the path from primary analysis to deposited derivative. These choices accumulate silently into cross-clade analyses, and no existing resource maps the current state of phylogenetic knowledge uniformly across Bacteria, Archaea, and Eukaryota. We offer a starting point: a first systematic inventory of what is, and is not, empirically resolved. We assemble an atlas of 264 species-level phylogenies, mapped onto a single global species dictionary of roughly 637,000 labels and organised into 62 partitions of described biodiversity, with 36 further partitions explicitly retained as unrepresented so that phylogenetic dark matter remains visible at the same resolution as the represented clades. For every canonical tree, a per-tree provenance ledger records inference framework, dating regime, the fraction of tips anchored in molecules rather than in taxonomy, and an audit of how much inferred uncertainty survived deposition; an explicit sensitivity envelope of inclusion criteria, from permissive to strictest, brackets every coverage statement against its own auditable rule. Because knowledge of the tree of life is itself moving, the atlas is released as a versioned, continuously updated resource through the companion R package phyloatlas and a per-partition wiki, so that downstream comparative analyses can propagate provenance and inclusion-criterion uncertainty into their own inferences rather than silently committing to one set of choices.

evolutionary biology↗

bioRxiv2026

A bioluminescence resonance energy transfer (BRET) assay to detect telomere length in S. cerevisiae

A method to measure telomere length in S. cerevisiae was developed based on bioluminescence resonance energy transfer (BRET). The system uses energy transfer between a luciferase-Rif2 fusion protein and fluorescently tagged Rap1. The study demonstrates that the BRET ratio correlates with the Rap1/Rif2 complex at the telomeres and thus the availability of telomeric Rap1 binding sites. This enables the measurement of telomere length in living cells. The system was able to reproduce reported deviations in telomere length in mutants lacking telomere length regulators, cells treated with telomere length modifying compounds and strains expressing inducible telomerase. The BRET ratio linearly correlated with the average number of telomeric nucleotides derived from long-read sequencing data using a novel algorithm for telomere length calculation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/711003v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@105f2c0org.highwire.dtl.DTLVardef@1842e3dorg.highwire.dtl.DTLVardef@f7bc16org.highwire.dtl.DTLVardef@5d5b50_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

Intricate asymbiotic hyphal interactions of Rhizophagus irregularis revealed with single-plane observations in a new microfluidic device

Arbuscular mycorrhizal fungi (AMF) are essential symbionts to most land plants. There is great interest in using AMF inoculation treatments to enhance restoration or agricultural efforts. However, little is known about AMF asymbiotic interactions that could shape soil ecosystems and inoculation outcomes. Studying these early traits is challenging given the obligate nature of AMF. Microfluidic devices enable high-resolution, single-plane, time-resolved observation of AMF hyphal traits in controlled, plant-less environments. The AMF-AnastomosisChip, introduced in this work, additionally separates spores and hyphae into lanes for detailed observations prior to entering a shared interaction zone. Using this device with Rhizophagus irregularis, we phenotyped key hyphal traits from germination to anastomosis. We compared the effect of a fatty acid (FA) treatment to other environmental factors in shaping AMF growth and fusion (anastomosis). Among our results, we confirm known effects of the FA treatment in increasing hyphal branching and longevity but interestingly show that multiple hyphae in a lane can negate FA effects. We also newly reveal that anastomosis occurs for 100% of interactions among hyphae from different lanes, but only for 50% of in-lane interactions, potentially linked to spore origin. Our findings validate the AMF-AnastomosisChip as a versatile platform for increasing discovery in trait-based microbial ecology, including for asymbiotic AMF interactions with environmental factors. This work sets the foundation for future studies with the AMF-AnastomosisChip on the effects of nutrient content, plant-derived molecules, or microbial community members on the AMF traits characterized in this study.

microbiology↗

bioRxiv2024

A probabilistic view of forbidden links: their prevalence and their consequences for the robustness of mutualistic networks

The presence in ecological communities of unfeasible species interactions, termed forbidden links, due to physiological or morphological exploitation barriers has been long debated, but little direct evidence has been found. Forbidden links are likely to make ecological communities less robust to species extinctions, stressing the need to assess their prevalence. Here, we used a dataset of plant-hummingbird interactions, coupled with a Bayesian hierarchical model, to assess the importance of exploitation barriers in determining species interactions. We found evidence for exploitation barriers between flowers and hummingbirds across the 32 studied communities, however, the proportion of forbidden links changed drastically among communities, because of changes in trait distributions. The higher the proportion of forbidden links, the more they decreased network robustness, because of constraints on interaction rewiring. Our results suggest that exploitation barriers are not rare in plant-hummingbird communities and have the potential to limit the rescue of species experiencing partner extinction.

ecology↗

bioRxiv2023

AMF-SporeChip provides new insights into arbuscular mycorrhizal fungal pre-symbiotic hyphal growth dynamics at the cellular level.

O_LIArbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants and deliver a wide range of soil-based ecosystem services. Due to their conspicuous belowground lifestyle in a dark environment surrounded by soil particles, much is still to be learned about the influence of environmental (i.e., physical) cues on spore germination, hyphal morphogenesis and hyphopodium formation in AMF. C_LIO_LITo fill existing gaps in AMF knowledge, we developed a new microfluidic platform - termed the AMF-SporeChip - to immobilise Rhizophagus and Gigaspora spores and confront pre-symbiotic hyphae with physical obstacles. In combination with timelapse microscopy, the fungi could be examined at the cellular level and in real-time. C_LIO_LIThe AMF-SporeChip allowed us to acquire movies with unprecedented visual clarity and therefore identify various exploration strategies of AMF pre-symbiotic hyphae. We witnessed anastomosis formation involving directed hyphal growth in a "stop-and-go" manner, yielding visual evidence of pre-anastomosis signalling and decision-making. Remarkably, we also revealed a so-far undescribed reversible cytoplasmic retraction as part of a highly dynamic space navigation. C_LIO_LIOur findings demonstrated how AMF employ an intricate mechanism of space searching, involving reversible cytoplasmic retraction, branching and directional changes. In turn, the AMF-SporeChip is expected to open many future frontiers for AMF research. C_LI

microbiology↗

bioRxiv2022

Gene expression patterns associated with fin shape differ between two lamprologine cichlids

Comparing gene regulatory patterns between seemingly similar phenotypic traits can provide important insights on the molecular mechanisms underlying the evolution of those traits. In this study, we investigate the molecular basis of the formation of a spade-shaped caudal fin, which is a rare phenotype among teleost fish characterized by an elongated medial region of the fin. We examined the expression patterns of candidate fin-shape genes in the spade-shaped caudal fin of the related species Lamprologus tigripictilis, an East African cichlid in the tribe Lamprologini. The candidate gene set consisted of a previously identified gene regulatory network (GRN) associated with the elongation of fin regions in another Lamprologini cichlid species and further genes selected on the basis of co-expression data and transcription factor prediction. Unexpectedly, the anatomical features of elongated fin rays differed and gene expression patterns associated with fin elongation were only weakly conserved between the two related species. We report 20 genes and transcription factors (including angptl5, cd63, csrp1a, cx43, esco2, gbf1 and rbpj), whose expression levels differed between the elongated and the short caudal fin regions of L. tigripictilis, and which are therefore candidates for the regulation of the spade-like fin shape.

evolutionary biology↗

bioRxiv2021

DETECTING PHYLODIVERSITY-DEPENDENT DIVERSIFICATION WITH A GENERAL PHYLOGENETIC INFERENCE FRAMEWORK

AO_SCPLOWBSTRACTC_SCPLOWDiversity-dependent diversification models have been extensively used to study the effect of ecological limits and feedback of community structure on species diversification processes, such as speciation and extinction. Current diversity-dependent diversification models characterise ecological limits by carrying capacities for species richness. Such ecological limits have been justified by niche filling arguments: as species diversity increases, the number of available niches for diversification decreases. However, as species diversify they may diverge from one another phenotypically, which may open new niches for new species. Alternatively, this phenotypic divergence may not affect the species diversification process or even inhibit further diversification. Hence, it seems natural to explore the consequences of phylogenetic diversity-dependent (or phylodiversity-dependent) diversification. Current likelihood methods for estimating diversity-dependent diversification parameters cannot be used for this, as phylodiversity is continuously changing as time progresses and species form and become extinct. Here, we present a new method based on Monte Carlo Expectation-Maximization (MCEM), designed to perform statistical inference on a general class of species diversification models and implemented in the R package emphasis. We use the method to fit phylodiversity-dependent diversification models to 14 phylogenies, and compare the results to the fit of a richness-dependent diversification model. We find that in a number of phylogenies, phylogenetic divergence indeed spurs speciation even though species richness reduces it. Not only do we thus shine a new light on diversity-dependent diversification, we also argue that our inference framework can handle a large class of diversification models for which currently no inference method exists.

evolutionary biology↗

bioRxiv2020

Mouse model for testing SARS-CoV-2 antivirals: Pharmacokinetics

Background and ObjectivesRemdesivir and hydroxychloroquine are or were among the most promising therapeutic options to tackle the current SARS-CoV-2 pandemic. Besides the use of the prodrug remdesivir itself, the direct administration of GS-441 524, the resulting main metabolite of remdesivir, could be advantageous and even more effective. All substances were not originally developed for the treatment of COVID-19 and especially for GS-441 524 little is known about its pharmacokinetic and physical-chemical properties. To justify the application of new or repurposed drugs in humans, pre-clinical in vivo animal models are mandatory to investigate relevant PK and PD properties and their relationship to each other. In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness. MethodsGS-441 524 and HCQ were administered intravenously as a single injection to male mice. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. In vitro experiments were conducted to investigate the degradation of remdesivir in human plasma and blood. All pharmacokinetic analyses were performed with R Studio using non-compartmental analysis. ResultsHigh tissue to plasma ratios for GS-441 524 and HCQ were found, indicating a significant distribution into the examined tissue, except for the central nervous system and fat. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. For HCQ, relatively high in vitro EC50 values are reported, which were not reached in all tissues. Facing its slow tissue distribution, HCQ might not lead to sufficient tissue saturation for a reliable antiviral effect. ConclusionThe mouse model was able to characterise the PK and tissue distribution of both model substances and is a suitable tool to investigate early drug candidates against SARS-CoV-2. Furthermore, we could demonstrate a high tissue distribution of GS-441 524 even if not administered as the prodrug remdesivir.

systems biology↗

bioRxiv2020

Whole Genome De Novo Variant Identification with FreeBayes and Neural Network Approaches

MotivationDe novo variant (DNV) calling typically relies on heuristic filters intrinsic to specific platforms and variant calling algorithms. FreeBayes and neural network approaches have overcome this limitation for variant calling, and we implemented a similar approach for DNV identification. ResultsWe developed a DNV calling framework that uses Genome Analysis Toolkit (GATK), FreeBayes and a neural network trained on Integrative Genomics Viewer pile-up plots (IGV-bot). We identified DNVs in 2,390 WGS trios and benchmarked results against heuristics based on GATK parameters. Results were validated in silico and with Sanger sequencing, with the latter showing true positive rates of 98.4% and 97.3% for SNVs and indels, respectively. Taken together we describe a scalable framework for DNV identification based on both FreeBayes and neural network methods. AvailabilitySource code and documentation are available at https://github.com/ShenLab/igv-classifier and https://github.com/frichter/dnv_pipeline under the MIT license. Contactys2411@cumc.columbia.edu

genomics↗

bioRxiv2018

Healthy ageing reduces the precision of episodic memory retrieval

Episodic memory declines with older age, but it is unresolved whether this decline reflects reduced probability of successfully retrieving information from memory, or decreased precision of the retrieved information. Here, we used continuous measures of episodic memory retrieval in combination with computational modelling of participants retrieval errors to distinguish between these two potential accounts of age-related memory deficits. In three experiments, young and older participants encoded stimuli displays consisting of everyday objects varying along different perceptual features (e.g., location, colour and orientation) in a circular space. At test, participants recreated the features of studied objects using a continuous response dial. Across all three experiments, we observed age-related declines in the precision of episodic memory retrieval, whereas age differences in retrieval success were limited to the most challenging task condition. Reductions in mnemonic precision were evident for retrieval of both item-based and contextual information, and persisted after controlling for age-related decreases in the fidelity of perception and working memory. The findings highlight impoverished precision of memory representations as one factor contributing to age-related episodic memory loss, and suggest that the cognitive and neural changes associated with older age can differentially affect distinct aspects of episodic retrieval.

neuroscience↗

bioRxiv2018

Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons

Isolation of cell populations is untangling complex biological interactions, but studies comparing methodologies lack in vivo complexity and draw limited conclusions about the types of transcripts identified by each technique. Furthermore, few studies compare FACS-based techniques to ribosomal affinity purification, and none do so genome-wide. We addressed this gap by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification in the context of D1 or D2 dopamine receptor-expressing medium spiny neuron (MSN) subtypes of the nucleus accumbens (NAc), a key brain reward region. We find that nuclear-FACS-seq generates a substantially longer list of differentially expressed genes between these cell types, and a significantly larger number of neuropsychiatric GWAS hits than the other two methods. RiboTag-seq has much lower coverage of the transcriptome than the other methods, but very efficiently distinguishes D1- and D2-MSNs. We also demonstrate differences between D1- and D2-MSNs with respect to RNA localization, suggesting fundamental cell type differences in mechanisms of transcriptional regulation and subcellular transport of RNAs. Together, these findings guide the field in selecting the RNAseq method that best suits the scientific questions under investigation.

neuroscience↗

bioRxiv2017

Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors

Multiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs). Using our Mendelian Error Method (MEM), we identified 127 deletions (inherited and de novo) in 2,601 WES trios from the Pediatric Cardiac Genomics Consortium, with a validation rate of 88% by digital droplet PCR. MEM identified additional de novo deletions compared to XHMM, and also identified sample switches, DNA contamination, a significant enrichment of 15q11.2 deletions compared to controls and eight cases of uniparental disomy. We applied MEM to WGS data from the Genome In A Bottle Ashkenazi trio and identified deletions with 97% specificity. MEM provides a robust, computationally inexpensive method for identifying deletions, and an orthogonal approach for verifying deletions called by other tools.

genetics↗