Biology subjects

Keller, M.

Publications and source records attributed to Keller, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbreaks throughout Europe, beginning with the pestis secunda. Despite its significance, the post-Black Death epidemiology of Yersinia pestis remains poorly understood. Here, we report 23 new Y. pestis genomes recovered from Second Plague Pandemic contexts across Scandinavia, the Netherlands, Iceland, and Armenia, spanning approximately 270 years. Applying a reproducible mutation-filtering pipeline to assess genetic diversity, we report both Black Death and post-Black Death lineages and document multiple waves of plague at individual cemetery sites. We identify four pestis secunda genomes, including three from Armenia, supporting the eastward dissemination of this lineage prior to its disappearance from Europe. We also resolve a previously under-characterised Branch 1A sub-lineage of Y. pestis and provide the first genomic evidence of plague in Iceland, resolving longstanding uncertainty over its presence on the island. Finally, by calling variants against a reconstructed ancestral reference, we identify clade-defining mutations, including nonsynonymous changes in metabolic and biofilm-related genes with predicted structural effects that may have contributed to shaping the epidemiological dynamics of the Second Plague Pandemic.

genetics↗

bioRxiv2026

V-ATPase-Driven Lysosomal Activation Orchestrates MEK2-Induced Endothelial Reprogramming

Direct lineage reprogramming holds therapeutic promise but often depends on transcription factor overexpression, resulting in unstable phenotypes. Here, we describe a novel strategy to convert fibroblasts into endothelial-like cells by activating lysosomal activity. Constitutively active MEK2 induces an endothelial gene program via sustained MAPK/ERK signaling, leading to enhanced vacuolar ATPase (V-ATPase) activity, lysosomal acidification, extracellular matrix degradation, and angiogenic behavior. V-ATPase inhibition impairs these effects, whereas pharmacologic activation with EN6 recapitulates key features of reprogramming and promotes nuclear translocation of TFEB, a master lysosomal regulator. Consistently, TFEB overexpression-particularly a phospho-deficient mutant-boosts lysosomal function and endothelial gene expression. These findings define a MAPK-V-ATPase-TFEB axis that drives endothelial reprogramming and highlight the lysosome as a central hub for cell fate transitions, offering an organelle-centric framework for regenerative medicine. HighlightsO_LISustained MEK2 activation reprograms fibroblasts into endothelial-like cells C_LIO_LIMEK2 enhances lysosomal acidification by upregulating V-ATPase subunits C_LIO_LIV-ATPase drives acidification and ECM remodeling for endothelial reprogramming C_LIO_LIV-ATPase activation promotes TFEB nuclear entry and endothelial gene expression C_LI

cell biology↗

bioRxiv2026

Preoperative biliary stenting is associated with functional dysbiosis and impaired bile acid metabolism in pancreatic cancer - Impact of preoperative biliary stenting on gut microbiota

Recent evidence suggests that the gut microbiome plays a role in the development and treatment response of pancreatic ductal adenocarcinoma (PDAC). However, the functional impact of tumor location and preoperative biliary stenting (PBS) on microbial composition and metabolism remains poorly understood. In this prospective study, preoperative stool specimens were collected from patients undergoing surgery for PDAC at Heidelberg University Hospital, Germany, between March 2020 and July 2021. Whole-genome shotgun metagenomic sequencing was performed to characterize microbial composition and functional pathways. A total of 63 preoperative stool samples were analyzed, including 40 patients with pancreatic head tumors (63.5%) and 23 with body/tail tumors (36.5%). Microbial community composition differed significantly according to tumor location (Bray-Curtis, p=0.005), with enrichment of Ruminococcus bromii in body/tail tumors. Among patients with pancreatic head tumors, PBS was associated with reduced alpha diversity (Shannon index, p=0.04), depletion of taxa including members of the Eubacteriales and Clostridiales orders as well as the genera Raoultella and Prevotella, and reduced abundance of selected genes involved in secondary bile acid metabolism. PBS was also associated with a higher rate of major postoperative complications according to Clavien-Dindo >3a (28.6% vs 3.8%; p=0.04). These findings suggest that biliary intervention may induce functional dysbiosis characterized by reduced microbial diversity and impaired bile acid metabolism, potentially disrupting host- microbiome crosstalk and contributing to adverse postoperative outcomes in pancreatic cancer.

microbiology↗

bioRxiv2026

Identification of key Y4R residues enables the discovery of selective non-peptide small-molecule agonists

G protein-coupled receptors (GPCRs) are central regulators of human physiology and disease, classifying them as relevant targets for therapeutic interventions. As transmembrane proteins, they convert extracellular signals into intracellular responses through agonist-induced conformational changes. Understanding how agonists stabilize active receptor conformations is decisive for rational drug design. In this study, we used the endogenous ligand pancreatic polypeptide (PP) and the cyclic hexapeptides UR-AK95c and UR-AK86c as molecular tools to determine key interactions critical for Y4R activation, which plays a crucial role in metabolic diseases. Guided by molecular docking, we systematically replaced Y4R residues and assessed activation. The in vitro and in silico studies delineated a key Y4R activation interface centered around the conserved C-terminal RXRY-NH2 motif of the peptides and, separately, identified receptor residues with distinct peptide-specific functional effects. Next, we performed an ultra-large library screening (ULLS) and experimentally validated three predicted hits as selective Y4R agonists that engage in a substantial subset of the identified critical receptor contacts. This study demonstrates how GPCR activation interface knowledge can be translated into the discovery of novel small-molecule agonists and outlines a general strategy for advanced GPCR drug discovery.

biochemistry↗

bioRxiv2026

SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data

Spatially resolved single-cell technologies enable profiling of cells in situ, yet computational approaches that jointly discover multicellular spatial patterns and characterize their molecular programs remain limited. Here we introduce SpatialQuery, a framework that can both identify cellular motifs, i.e. recurrent multicellular co-localization patterns, and perform molecular analyses focused on the motifs. It uncovers genes modulated by spatial contexts through differential expression analysis, and detects coordinated expression changes through covariation analysis. SpatialQuery can identify functional tissue units, and goes beyond pairwise analyses to characterize multicellular interactions. Applications to both spatial transcriptomics and proteomics data uncover cross-germ-layer signaling in gut tube patterning, disease-specific fibrotic and immunosuppressive niches in kidney and colon, and regional determinants of motif-associated transcriptional programs in a mouse brain atlas. SpatialQuery is available as a Python package, and we demonstrate how its light computational footprint enables integration into web-based cell atlas portals for interactive visualization and exploration.

bioinformatics↗

bioRxiv2026

Interferon-α and -β subtypes have temporally distinct roles in containing viral spread and protecting vital organs.

Type I interferons (IFN-Is), including a single IFN-{beta} and over a dozen IFN-s, induce the anti-viral state. In vitro, IFN-{beta} transcription requires the assembly of the "enhanceosome" composed of the constitutive transcription factors NF-{kappa}B and AP-1, and either constitutive IRF3 or IFN-I-inducible IRF7. IRF3 and IRF7 transcribe mouse IFN-4 and human IFN-1/13. Only IRF7 transcribes other IFN-s. How IFN-I subtype multiplicity and their differential constitutive/IFN-I-inducible versus only IFN-I-inducible transcription help control viruses in vivo remains unknown. Using novel genetically modified mice, we demonstrate that most or all IFN-I subtypes, regardless of their transcriptional control, are necessary to curb the systemic dissemination of lymph-borne ectromelia virus (ECTV) but do not necessarily suppress ECTV or West Nile Virus (WNV) replication in the liver or the brain, or promote survival to their infection. Individually, the most critical IFN-I subtype to survive ECTV and WNV infections is IFN-{beta}. IFN-4 potentiates IFN-{beta} but is not essential. PRDII, the IFN-{beta} promoters NF-{kappa}B binding site, which is required for enhanceosome assembly, is dispensable for in vivo IFN-{beta} production but complements IRF7-IFN-{beta} transcription to restrain ECTV and WNV. IFN-{beta} alone protects IFN--deficient mice from ECTV but not from WNV lethality. Control of WNV replication in the brain successively requires IFN-, IFN-{beta}, and then PRDII-dependent IFN-{beta}, suggesting that brain protection requires IFN-I production by various cell types and pathways. Thus, contrary to the prevailing view, in vivo, IFN-{beta} does not function earlier than IFN-, and IFN-I subtypes non-redundantly cooperate to restrain viruses in the periphery and in vital organs.

immunology↗

bioRxiv2026

Sex-specific remodeling of the human adipose tissue vascular niche in obesity

AO_SCPLOWBSTRACTC_SCPLOWObesity remodels the subcutaneous adipose tissue (SAT) vasculature and contributes to cardiometabolic risk, yet potential sex differences in this process remain poorly defined. Here, we integrated single-nucleus transcriptomics and histological analyses of human SAT to reveal pronounced sexual dimorphism within the vascular niche. Obese males exhibit mural cell loss, increased collagen deposition, and inflammatory endothelial activation, including enhanced antigen presentation programs. In contrast, females display preserved mural coverage and increased lipid-handling and redox-adaptive pathways. These coordinated structural and transcriptional differences position the adipose endothelium as a sex-divergent regulator of obesity-associated cardiometabolic vulnerability.

cell biology↗

bioRxiv2026

RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation

Alternative splicing, regulated by RNA-binding proteins (RBPs), enables the generation of diverse transcript isoforms critical for cellular function. However, how RNA secondary structure impacts RBP binding and function remains poorly understood. Here, we unravel how RNA G-quadruplexes (rG4s) facilitate cooperativity in splicing regulation by the RBP heterogeneous nuclear ribonucleoprotein H (HNRNPH). Through high-throughput in vivo and in vitro studies combined with theoretical modeling, we dissect how rG4s mediate cooperative HNRNPH binding to RNA, ultimately modulating the splicing of hundreds of exons. rG4 unfolding by HNRNPH exposes multiple G-rich binding sites, thereby establishing indirect cooperativity, which is further amplified to achieve switch-like splicing regulation. HNRNPH-mediated regulation is evident in breast cancer patients, with tumors showing rG4-disrupting variants and global HNRNPH alterations, driving distinct splicing patterns that distinguish tumor subtypes. Overall, our findings offer valuable insights into the mechanistic role of RNA secondary structures in cooperative RBP binding and splicing regulation and highlight the clinical relevance of HNRNPH-dependent splicing in cancer. HighlightsO_LIHundreds of cassette exons are cooperatively regulated by HNRNPH. C_LIO_LIUnfolding of RNA G-quadruplexes (rG4s) at HNRNPH binding sites facilitates indirect cooperativity in RNA binding. C_LIO_LIMulti-step splicing amplifies the response into highly switch-like regulation. C_LIO_LIrG4-disrupting variants and changing HNRNPH expression are associated with breast cancer phenotypes. C_LI

molecular biology↗

bioRxiv2026

Co-occurrence of Yersinia pestis and other zoonoses during European prehistory

The infection of humans by the causal agent of Plague, Yersinia pestis, has been attested as far back as 5,500 BP. Although the specific patho-mechanism and ultimate origin of the disease caused by these prehistoric genomes remains unclear, the bacterium spread through Europe, likely during the Late Neolithic to Bronze Age (LNBA). In this study, we analysed 9 genomic samples originating from 8 different human individuals dating to around 4950 cal BP from the site of Grotta della Spinosa, Tuscany, Italy. Metagenomic screening of these samples reveals one individual (GSP013) to be co-infected by Yersinia pestis, Erysipelothrix rhusiopathiae, and Hepatitis B virus (HBV). At least three further individuals from the site were infected with HBV, indicating its wider presence within the community. The phylogenetic placement of Y. pestis in GSP013 shows that this strain is closely related to the earliest LNBA Caucasus genomes of the bacterium, basal to later European diversity. This represents the earliest evidence of Y. pestis in the Italian peninsula (and Southern Europe more widely) to date, predating previously discovered genomes by at least 200 years. Furthermore, we retrieved 60 newly reported ancient genomes of Erysipelothrix rhusiopathiae and Erysipelothrix tonsillarum from animals and humans, dating back from 8,300 BP to 100 BP. Of these new genomes, 15 of which stem from individuals known to be infected by Y. pestis. This contributes to our understanding of Y. pestis transmission in prehistoric Europe and possible reservoirs, and offers insights into disease dynamics in communities during the 3rd millennium BCE.

evolutionary biology↗

bioRxiv2026

AncientMetagenomeDir dating metadataset highlights need for standardised radiocarbon reporting in ancient DNA

Ancient DNA is a valuable data source for the understanding of our past. However, to effectively interpret this data, it is essential to know the age of the samples from which the DNA is obtained. Although the field of palaeogenomics has been recognised for its robust open data sharing practices, dating information associated with analysed samples is not reported consistently across palaeogenomic studies, nor is it included as metadata in most genetic data repositories. Here, we describe the addition of standardised precise dating information for ancient microbial genomes into the AncientMetagenomeDir metadata repository of published ancient metagenomic samples. This extension currently includes dating information for over 700 ancient microbial genomic datasets, of which 333 are dated using historical, contextual, or stratigraphic methods, and 405 are radiocarbon dated. We quantitatively assess the quality of radiocarbon date reporting and find that, despite established reporting conventions, radiocarbon dating information is often reported inconsistently across ancient metagenomic studies. This new resource provides ancient microbial researchers with standardised dating information that facilitates more accurate and consistent analysis of metagenomic sequencing data. The dataset also highlights the need for greater standardisation of radiocarbon date reporting in original publications in order to allow effective reuse of this and future ancient microbial data.

bioinformatics↗

bioRxiv2026

Mismatch repair MLH complexes make distinct contributions to post-replicative mismatch repair versus trinucleotide repeat expansions

Mismatch repair (MMR) is a highly conserved DNA repair pathway that promotes genome stability by directing the repair of errors in DNA replication. In Saccharomyces cerevisiae, MMR is initiated by either Msh2-Msh3 or Msh2-Msh6, via recognition of insertion deletion loops (IDLs; up to [~] 17 nucleotides) and misincorporation events, respectively. Both complexes recognize and bind small (1-2 nucleotide) IDLs. Once bound, MSH complexes recruit one or more downstream MLH complexes to continue repair: Mlh1-Pms1, Mlh1-Mlh2 and/or Mlh1-Mlh3. Msh2-Msh3 also promotes CAG trinucleotide repeat (TNR) expansions through specific DNA-binding to TNR DNA structures, followed by recruitment of MLH complexes. These expansions lead to genome instability that causes neurodegenerative diseases such as Huntingtons Disease in humans. Here, we defined a hierarchy of MLH function in these Msh2-Msh3-mediated pathways in vivo in S. cerevisiae. We determined that Mlh1-Pms1 is the primary MLH complex required in Msh2-Msh3-mediated MMR. In contrast, all three MLH complexes were required to promote CAG expansions, with loss of Mlh1-Pms1 or Mlh1-Mlh2 exhibiting the strongest effects. Mutations in PMS1 and MLH3 were synergistic. We propose a model in which Mlh1-Pms1 is primarily responsible for "appropriate" Msh2-Msh3-mediated MMR, while all three MLH complexes collaborate specifically in the presence of CAG structure, to promote a "pathogenic" Msh2-Msh3-mediated pathway that leads to expansions. Our model highlights the importance of DNA structure-dependent conformations in modulating MLH function.

genetics↗

bioRxiv2025

REFLEX, a Novel Immune Profiling Assay, Combining TCR Repertoire and Multiome at Massively Scalable Single-cell Resolution to Catapult Exploration of T-cell Derived Immunity

Single-cell profiling of T cell state with immune repertoire is critical for understanding heterogenous T cell phenotypes and responses to antigen, however, existing technologies struggle to generate this information at sufficient throughput to match biological complexity. We present "REFLEX", a novel single-cell method enabling highly scalable, cost-efficient, multiomic profiling with paired-chain TCR sequencing. REFLEX utilizes in-situ reverse transcription with integrated sample multiplexing barcodes in a way that merges seamlessly with the commonly used 10x FLEX platform to allow capture of TCR sequences at unprecedented scale and depth. We profile >2 million cells from CMV-peptide-pulsed T cell expansions, capturing TCR sequences and rich multiomic information from 1.4M T cells, identifying many putative novel CMV reactive clonotypes and illustrating the scale and transformative impact on our understanding of T cell mediated adaptive immunity achievable with REFLEX.

immunology↗

bioRxiv2025

Evolutionary history and recurrent host adaptation in ancient Salmonella enterica

Salmonella enterica subsp. enterica is an extremely diverse bacterial pathogen causing frequent infections and foodborne disease among human populations. More than 1500 different bacterial strains (serovars) have been described, many with a wide host range. A small number of serovars are adapted to infect specific hosts: of these, serovars Typhi and Paratyphi A, B, and C cause primate-specific systemic infections (typhoid and paratyphoid fever). Although Paratyphi C is one of the rarest human-specific serovars today, it was once widespread, and all ancient Salmonella genomes published to date belong to or are ancestral to this lineage. Here, we present 53 new ancient Salmonella genomes spanning Eurasia and dating between 3500 BCE and 1300 CE. This rich genomic dataset allows us to reconstruct the evolutionary history of this pathogen in unprecedented detail. We identify multiple extinct prehistoric lineages that caused infections throughout Eurasia. Multiple lineage replacement events are observed throughout prehistoric and historic times, and Bayesian phylogenetic analysis is used to date and identify host adaptation events within this lineage. We find that host-adapted sublineages Paratyphi C, Choleraesuis, and Typhisuis continued to evolve host specificity independently from each other. We reconstruct signals of convergent host adaptation in the studied lineages and other host-adapted strains by analysing shared pseudogenes and recurrent gene gain and loss events. This analysis demonstrates a role for host interactions as a particular target of selection, highlighting the gradual adaptation of this S. enterica lineage to humans that coincides with the intensification of animal husbandry in pastoralist and sedentary farming societies.

genetics↗

bioRxiv2025

Active learnings impact on student course performance in STEM varies by type and intensity

We updated a recent meta-analysis of active learnings impact on student achievement in undergraduate STEM courses by following the same protocol to evaluate studies published from 2010-2017. We screened 1659 papers, coded 1294, and found 210 that met five pre-established inclusion criteria and six pre-established criteria for methodological quality. After further dropping 76 studies with no exam scores data, 134 of these studies contained data on student performance on identical or equivalent exams. We found that on average, active learnings effect size on exam scores was 0.519 {+/-} 0.049, meaning that when students are in active learning classes, they perform roughly half a standard deviation higher on an identical exam. Funnel plots and sensitivity analyses indicated that these results were not due to sampling bias. Active learning had a positive impact on student outcomes regardless of class size, course level, or STEM discipline, though there was heterogeneity in the effects. All of these results are very similar when compared to earlier meta-analyses, however increased resolution in the studies analyzed here revealed two novel results. First, student performance was significantly better in courses that employed high-intensity active learning, defined as students being on task at least two-thirds of class time, versus lower-intensities. Additionally, there was significant heterogeneity in efficacy across different types of active learning employed. These results suggest that most, if not all types of active learning are effective, and that when innovating in their classes, instructors should continually work to increase active learning intensity. We urge caution in interpreting the results on active learning types, however, and propose a preliminary framework for making more-sophisticated and reliable analyses of variation in course design. Finally, the evidence presented here for active learnings impact on student outcomes creates a strong foundation for faculty professional development and administration.

scientific communication and education↗

bioRxiv2025

Probing the zooarchaeological record across time and space for ancient pathogens

Zoonoses are among the greatest threats to human health, with many zoonotic pathogens believed to have emerged during prehistory. Palaeomicrobiological investigations of the zooarchaeological record hold potential to uncover the reservoirs, host ranges, and host adaptations of zoonotic pathogens but face challenges in identifying promising specimens and pathogen DNA preservation. We performed palaeopathological and genetic examinations of 346 skeletal elements from domesticated and wild animals collected from 34 Eurasian sites dating across the last six millennia. We identified 68 signatures of ancient (opportunistic) pathogens, including the important zoonotic pathogen Salmonella enterica, and found support that palaeopathological lesions provide guidance for specimen selection. For two pathogen species, Erysipelothrix rhusiopathiae and Streptococcus lutetiensis, we confirmed their ancient authenticity using phylogenetics, showcasing an approach to explore the relationship between ancient low-coverage genomes and their modern-day relatives. Our work presents a pathway to understanding prehistoric zoonotic diseases by integrating zooarchaeological, palaeopathological, and genetic data.

microbiology↗

bioRxiv2025

Regulation of early-stage tomato fruit growth by the splicing factor RS2Z36

Fruit growth is mediated by cell division and expansion. In tomato, the model for fleshy fruit development, both processes are tightly linked to changes in gene expression, including transcriptional regulation and RNA processing. While several transcription factors are implicated in fruit developmental programs, the role of splicing regulators remains largely unexplored. Expression profiling of splicing-related genes revealed expression patterns. The serine/arginine-rich splicing factor RS2Z36 is expressed in ovaries and during early fruit development. Loss-of-function mutations in RS2Z36 result in ovaries with altered patterning and in smaller, ellipsoid fruits. rs2z36 mutants display elongated pericarp cells along the longitudinal axis of pre-anthesis ovaries, indicating that RS2Z36-dependent expansion patterns are established before anthesis. RNA-seq uncovered widespread alternative splicing of genes across diverse biological processes, while proteome analysis revealed altered protein abundance and peptides derived from novel splice variants. In addition, rs2z36-1 pericarps show increased deposition of LM6-recognized arabinan and AGP epitopes. Together, these findings identify RS2Z36 as a regulator of ovary and fruit development and highlight a previously underappreciated role for splicing control in shaping early fruit morphology.

developmental biology↗

bioRxiv2025

Affiliative behaviours regulate allostasis development and shape biobehavioural trajectories in horse

Social interactions shape both physiological and behavioural development of offspring and poor care/early caregiver loss are known to promote negative outcomes in adulthood in both animals and humans. How affiliative behaviours impact future development of offspring remains unknown. Here, we used Equus caballus (domestic horse) as a model to investigate this question. By coupling magnetic resonance imaging, longitudinal biobehavioural assessment and advanced multivariate statistical modelling we found that maternal presence during childhood promotes maturation of brain territories involved in both social behaviour (anterior cingulate, retrosplenial cortex) and physiological regulation (hypothalamus, amygdala). Additionally, we found that offsprings benefiting from prolonged maternal presence showed higher default mode network (DMN) connectivity, improved social competences, more efficient feeding behaviours, and metabolic profiles. The present study underscores the salient role of social interactions for the development of allostatic regulation in offspring.

neuroscience↗

bioRxiv2024

Lysosomal calcium signalling contributes to the acute α-adrenergic response via calcium-stimulated adenylyl cyclase 1 and 8

Inositol trisphosphate (IP3), a calcium (Ca2+)-mobilizing second messenger, releases Ca2+ from the sarcoplasmic reticulum (SR) via IP3 receptors and modulates adenylyl cyclase (AC) activity in atrial myocytes. Lysosomes participate in Ca2+ homeostasis by mobilising Ca2+ in response to Nicotinic Acid Adenine Dinucleotide Phosphate (NAADP). We postulate that both downstream activation of Ca2+ sensitive AC (AC1 and AC8) and lysosomal Ca2+ signalling in response to IP3R activation contribute to atrial myocyte function and pacemaking. Ectopic application of phenylephrine (PE) increased chronotropy and inotropy and this response was reduced in the presence of NAADP pathway inhibitors (BZ-194 and SAN4825) and Bafilomycin A1. PE increased cyclic adenosine 3-5 monophosphate (cAMP) activity in neonatal rat atrial myocytes (NRAMs) and this was inhibited by NAADP pathway inhibitors. This inhibition was not observed in neonatal rat ventricular myocytes (NRVMs), revealing specificity of this response to NRAMs. We investigated expression of AC1 and AC8 as a possible explanation to these observations. Genetic perturbation of AC1 and AC8 by double-knockout of Adcy1 and Adcy8 in a mouse model showed a decrease in positive chronotropic and inotropic response upon cumulative dose of PE in atrial tissue, reduced PE stimulated amplitude of Ca2+ transient in isolated atrial myocytes and presented decreased cytosolic cAMP levels in response to PE in neonatal atrial myocytes that was not inhibited by NAADP pathway inhibitors. Our data identifies a link between NAADP and -adrenergic signalling pathways in atrial myocytes, highlighting that lysosomal Ca2+ is an important component of -adrenergic stimulation in the cardiac atria and warrants further investigation.

physiology↗