Biology subjects

Koch, M. A.

Publications and source records attributed to Koch, M. A..

16 recordsLinked to original sources

bioRxiv2026

Inherited maternal memory T cells protect offspring from respiratory viral infection through disease tolerance

Maternal immune transfer is a powerful mechanism for early-life protection from infection, yet the full repertoire of protective factors remains unknown. We discovered that maternal memory T cells are both necessary and sufficient to protect offspring from lethal respiratory infection. This antigen-specific protection operated independently of maternal antibodies and offspring T cell responses and required IL-10 produced by maternal T cells. Transfer of protective maternal T cells reduced offspring inflammatory responses and lung tissue damage without affecting viral burdens, indicating that maternal memory T cells directly suppress pathogenic innate inflammatory responses to preserve offspring health. Critically, maternal vaccination similarly protected offspring in a T cell-dependent manner. These findings reveal maternal antigen-specific T cell transfer as a complementary immunological defense mechanism to protect offspring against pathogens that escape maternal antibodies, with broad implications for maternal vaccination strategies.

immunology↗

bioRxiv2026

Why woodiness repeatedly evolves--and disappears

Derived woodiness--the evolution of woody growth from herbaceous ancestors--has arisen hundreds of times across flowering plants, yet the environmental conditions associated with its repeated evolution remain poorly understood. Here, we analyse woodiness evolution in the mustard family (Brassicaceae; ~4,150 species) using a time-calibrated phylogeny of 2,927 species, including 374 of the 385 known woody species, together with global growth-form and climatic niche data. We infer 231 independent origins of woodiness alongside 176 reversals to herbaceousness, indicating that woodiness evolves repeatedly but remains evolutionarily unstable. Although woody species are enriched on islands, most occur on the mainland, where woodiness is consistently associated with drought and reduced frost. Correlated-evolution analyses reveal that drought is associated primarily with the persistence of woodiness, whereas reduced frost is associated with gains of woodiness and increased frost with its loss. These findings identify distinct climatic associations with the gain, persistence, and loss of woody growth forms.

evolutionary biology↗

bioRxiv2026

Evolutionary history and polyploidization lead to rapid shifts in chemodiversity of Hypericum

Polyploidization can profoundly affect plant metabolite biosynthesis, yet its influence on chemodiversity remains poorly understood, despite the central role of chemodiversity in mediating plant interactions with the environment. The coexistence of facultative apomictic and sexual reproductive systems across ploidy levels in Hypericum provides an excellent model for investigating the evolution of chemodiversity following polyploidization. We analyzed ploidy levels and leaf metabolic fingerprints across selected populations of three Hypericum taxa, H. maculatum, H. perforatum subsp. perforatum and H. perforatum subsp. veronense. Polyploidization was common across all three taxa. Leaf metabolic fingerprints were more pronouncedly differentiated by the ploidy level of the mother plant (F0) than that of the offspring (F1). Although unique metabolic features emerged in plants of most ploidy levels, diploid plants exhibited fewer metabolic features than polyploid plants. Higher Shannon diversity, functional Hill diversity, and intensities of features belonging to specific chemical families were associated with higher F0 ploidy levels in H. perforatum subsp. perforatum, but not in H. maculatum and H. perforatum subsp. veronense. Our findings demonstrate that polyploidization can lead to rapid shifts in chemodiversity across generations in Hypericum. The fast divergence in chemodiversity associated with polyploidization in H. perforatum may contribute to its remarkable invasive potential.

plant biology↗

bioRxiv2026

Drowning in a sandy ocean: Epiarenic growth of Tillandsia in the hyperarid Atacama Desert

The Atacama Desert hosts a unique ecosystem formed by the sand-dwelling Tillandsia landbeckii, which extends over hundreds of square kilometers. This vegetation relies primarily on fog as its main water source; however, aeolian sand also plays a crucial role in the long-term persistence of both the species and the overall plant community. The terrain is sloped and exposed to the prevailing wind direction. Tillandsia forms regular banding patterns oriented orthogonally to these landscape features. In this study, we aim to elucidate the abiotic-biotic interactions between sand properties and vegetation characteristics through a comparative approach. Three populations - Caldera, Oyarbide and Arica -, each spanning several square kilometers in the southern, central, and northern regions of the Chilean Atacama Desert, were selected to compare wind regimes, terrain structure, sand and substrate properties, and vegetation structure in order to identify common principles that maintain vegetation integrity. Data were collected from six climate stations, 1,246 substrate samples, population genomic data from 718 individuals, as well as satellite imagery and digital terrain models. Our findings demonstrate that regional wind systems transport sand from distant source areas, while near the ground, Tillandsia vegetation reduces wind velocity and traps sand, leading to the formation of moderately sorted sandy substrates that are similar across all three populations. Sites lacking or containing dead Tillandsia individuals often differ significantly in substrate characteristics. Genetic analyses indicate that Tillandsia populations exhibit strong spatial structure albeit recruiting high genetic diversity and an excess of heterozygosity, reflecting adaptation to the dynamic environmental conditions. We conclude that sand represents an essential component of this ecosystem, while Tillandsia, as the dominant biotic factor, actively shapes and maintains this distinctive desert environment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/707457v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@14529eforg.highwire.dtl.DTLVardef@1c42435org.highwire.dtl.DTLVardef@25147aorg.highwire.dtl.DTLVardef@639128_HPS_FORMAT_FIGEXP M_FIG C_FIG Generated based on own drawings and iterative improvements using ChatGPT while providing own peer-reviewed research contributions as input and baseline information (MAK). Short summaryWe exemplify unimodal regional wind systems facilitating sand transport toward Tillandsiales. Tillandsiales show a low-energy wind system allowing sand accumulation of predominant grain sizes available at each site. Thereby Tillandsia landbeckii modifies and maintains its own microenvironment. Genomic data reveal high clonality and excess of heterozygosity promoting fitness in a hyperarid environment, and abiotic factors drive the selection of diverse and adaptive Tillandsia phenotypes.

plant biology↗

bioRxiv2025

Discovery Stack Pilot: Feasibility and Outcomes of a Scientist-Designed Peer Review Model Separating Quality and Impact

Peer review serves as the cornerstone of scientific quality control. Yet, the current journal-centric system is hindered by long timelines, high publication costs, inconsistent review quality, systemic biases, and editorial gatekeeping. Notably, the system relies on misaligned measures of impact that are tethered to journal branding and conflate scientific rigor (Quality) with perceived significance (Impact). Here, we report findings from the Discovery Stack Pilot Study, which tested a scientist-designed, journal-independent peer review model. The Discovery Stack model integrates in-line reviewer comments to promote constructive feedback and separately evaluates scientific Quality and Impact using defined criteria. To examine feasibility and effectiveness, manuscripts were reviewed in parallel with traditional journal review. A total of 162 reviews were completed, and survey data from 86 participants were analyzed. The results showed that reviewers effectively evaluated Quality and Impact as separate dimensions, with Quality scores being more consistent across reviewers than Impact scores. Participants strongly supported the core elements of the Discovery Stack model and expressed enthusiasm for its broader adoption to enhance transparency, efficiency, and value in peer review. Future studies will explore integrating this model into a digital platform for reviewing and curating scientific discoveries to improve the production and dissemination of high-quality research.

scientific communication and education↗

bioRxiv2025

Split or spread - A spatio-temporal framework for the evolution of annual Arabis (Brassicaceae) in Eurasia

Life history in plants appears to be an important determining factor for the capacity to cope with major environmental change. Consequently, the evolutionary history of life form may have constrained significantly present-day biogeographic distribution patterns of phylogenetically related species, which had either to adapt or migrate during Pleistocene climatic fluctuations. In particular in Brassicaceae the molecular basis of monocarpic and polycarpic flowering behavior is well understood, and it is thought that both traits are reciprocally conversed. The Brassicaceae consist in total of c. 25% of monocarpic species. However, species-rich tribes such as Arabideae consist of only 8% monocarpic species indicating evolutionary and environmental constrain towards life history transition. Here we utilized whole plastid genome sequencing through next-generation sequencing (NGS) to investigate the spatio-temporal timing of the evolution of annual species in the tribe Arabideae (Brassicaceae). Based on these data, we conducted phylogenetic reconstructions, divergence time estimations, and plastid haplotype distribution analyses. Past and present ecological niche modeling was performed for monocarpic taxa from three different Arabideae clades, Arabis auriculata, Arabis nova subsp. iberica, and Arabis montbretiana. With the integration of these approaches, we test the hypothesis that the evolution of monocarpic species in tribe Arabideae at low frequency is associated with large-scale biogeographic patterns reflecting migration rather than adaptation or reversals.

evolutionary biology↗

bioRxiv2024

Breastmilk IgG engages the neonatal immune system to instruct host-microbiota mutualism

Maternal antibodies fundamentally regulate infant immunity to the developing gut microbiota, yet the mechanisms underlying this process remain elusive. Here, we show that maternal IgG, ingested in the first week of life, functions to restrain microbiota-dependent adaptive immune responses and reduce offspring susceptibility to intestinal inflammation weeks later, following weaning. To exert these functions, efficient binding of IgG to gut bacterial antigens and engagement of Fc and complement dependent effector functions in offspring was required. These discoveries reveal a novel mechanism wherein maternal IgG engages the offspring immune system to calibrate responses to gut microbes. This mode of maternal immune instruction may provide adaptability to developmental shifts in microbiota necessary for establishing host-microbiota mutualism and limiting susceptibility to inflammatory disease. One sentence abstractIngestion of maternal IgG during a discrete postnatal window calibrates neonatal immunity to the gut microbiota.

immunology↗

bioRxiv2024

Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data

Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing paralog status of targeted loci and incorporating them into tree reconstruction methods. Using a target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of paralogous sequences into a diploid tree. We call this approach Paralog PhyloGenomics (PPG), and show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach will be a valuable addition to phylogenomic methods available for the study of polyploids.

evolutionary biology↗

bioRxiv2023

Impact of whole-genome duplications on structural variant evolution in the plant genus Cochlearia

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated plant species. Despite its centrality in evolution, WGD is a hugely disruptive mutation, and we still lack a clear understanding of its fitness consequences. Here, we study whether WGD results in greater diversity of genomic structural variants (SVs) and how this influences evolutionary dynamics in nature. Using a set of long-read sequenced samples from the plant genus Cochlearia (Brassicaceae), which contains diploids and a recent ploidy series up to octoploid, we show that masking of recessive mutations due to WGD has led to a substantial and progressive accumulation of genic SVs across four ploidy levels. Such SVs likely constitute a genetic load and thus reduce the adaptive potential of polyploid populations. However, this SV accumulation also provides a rich pool of standing genetic variation upon which selection may act in novel environments. By constructing a graph-based pangenome for Cochlearia, we identify SVs in hundreds of samples and study the genomic basis of environmental adaptation. We find putatively beneficial SVs involved in pathogen resistance, root development, and salt tolerance, many of which are unique to polyploids. Finally, we explore the adaptive landscapes of SVs and SNPs, identify geographical regions where SVs make novel contributions to adaptive variation, and predict that the role of SVs in environmental adaptation increases due to rapid climate change.

evolutionary biology↗

bioRxiv2023

Kinetochore and ionomic adaptation to whole genome duplication

Transforming genomic and cellular landscapes in a single generation, whole genome duplication (WGD) brings fundamental challenges, but is also associated with diversification. How is WGD tolerated, and what processes commonly evolve to stabilize the resulting polyploid? Here we study this in Cochlearia spp., which have experienced multiple WGDs in the last 300,000 years. We first generate a chromosome-scale genome and sequence 113 individuals from 33 diploid, tetraploid, hexaploid, and outgroup populations. We detect the clearest post-WGD selection signatures in functionally interacting kinetochore components and ion transporters. We structurally model these derived selected alleles, identifying striking WGD-relevant functional variation, and then compare these results to independent recent post-WGD selection in Arabidopsis arenosa and Cardamine amara. Most prominent in these results is genetic evidence of at least four functionally interacting kinetochore complex subunits in adaptation to WGD at the centromere among our very top selective sweep outliers. In addition, some of the same biological processes evolve in all three WGDs, but specific genes recruited are flexible. This points to a polygenic basis for modifying systems that control the kinetochore, meiotic crossover number, DNA repair, ion homeostasis, and cell cycle. Given that DNA management (especially repair) is the most salient category with the strongest selection signal, we speculate that the generation rate of structural genomic variants may be altered by WGD in young polyploids, contributing to their occasionally spectacular adaptability observed across kingdoms. Significance StatementWhole-genome duplication (WGD) occurs in all kingdoms and is linked to adaptation, speciation, domestication, and even cancer outcome. But WGD is a shock to the system, and commonly disrupts cell division due to increased DNA management burden and transformed cell physiology. Nevertheless, the hopeful monster that survives WGD is special, occasionally experiencing runaway success. Why do some thrive but others die? Here we introduce a powerful new model, Cochlearia, which has benefitted from multiple WGDs, and we provide the first genetic evidence of rapid adaptation of functionally interacting components of the cell division machinery, the kinetochore. We also compare which processes and genes evolve to stabilize the new polyploid in three independent cases and highlight common mechanisms.

evolutionary biology↗

bioRxiv2023

Genetic diversity of the Atacama Desert shrub Huidobria chilensis in the context of geography and climate

Survival in hyperarid deserts is a major challenge for plant life, requiring the development of evolutionary strategies. The Atacama Desert presents harsh conditions such as limited rainfall, crusted soils, high soil salinity, high altitude, and intense solar radiation. These conditions, together with paleoclimatic variability since the past millions of years, have influenced the genetic structure and connectivity of plant populations, resulting in a diverse flora with high endemism. However, the diversification of most lineages appears to be relatively recent, in contrast to proposed age of the Atacama Desert and the onset, evolution and expansion of hyperarid conditions since the Late Oligocene and Early Miocene. A prominent exception is the Atacama paleoendemic Huidobria chilensis (Loasaceae), which is thought to be adapted to such conditions since the Eocene. Still, the environmental limits and thresholds for life in the Atacama remain poorly understood. To investigate the genetic structure in relation to the history of the Atacama Desert, we studied 186 individuals from 11 populations using genotyping-by-sequencing (GBS). Genome-wide single nucleotide polymorphisms (SNPs) were analyzed for population structure and genetic diversity. We identified three genetic clusters corresponding to geographic regions: the coastal region south of Tocopilla, the Coastal Cordillera around Chanaral, and the Copiapo watershed in the south. These clusters as well as genetic diversity were analyzed alongside rainfall, altitude, and landscape data. Although the genetic data generally supports isolation by distance as a major factor for genetic variation between populations, the study also reveals the influence of the topography on the distribution of H. chilensis and highlights the role of hydrologically connected watersheds and rivers in plant migration and colonization. This shapes the species evolutionary trajectory and genetic diversity. Understanding these patterns provides insights into the adaptation and survival strategies of plants in extreme desert environments such as the Atacama.

genetics↗

bioRxiv2022

Single-cell profiling uncovers a Muc4-expressing metaplastic gastric cell type sustained by Helicobacter pylori-specific inflammation

AbstractMechanisms for Helicobacter pylori (Hp)-driven stomach cancer are not fully understood. In a transgenic mouse model of gastric preneoplasia, concomitant Hp infection and induction of constitutively active KRAS (Hp+KRAS+) alters metaplasia phenotypes and elicits greater inflammation than either perturbation alone. Gastric single-cell RNA-seq showed that Hp+KRAS+ mice had a large population of metaplastic pit cells that expressed the intestinal mucin Muc4 and the growth factor amphiregulin. Metaplastic pit cells were associated with macrophage and T cell inflammation and prevented by gastric immunosuppression. Lineage tracing showed that Muc4 was not dependent on cell-intrinsic KRAS activity, and lineage-derived cells had a limited propensity for growth as organoids, demonstrating that metaplastic pit cells are largely not self- renewing. Finally, MUC4 expression was significantly associated with proliferation in human gastric cancer samples. These studies identify an Hp-associated metaplastic pit cell lineage, also found in human gastric cancer tissues, whose expansion is driven by Hp-dependent inflammation. Statement of SignificanceUsing a mouse model, we have delineated metaplastic pit cells as a pre-cancerous cell type whose expansion requires H. pylori-driven inflammation. In humans, metaplastic pit cells show enhanced proliferation as well as enrichment in precancer and early cancer tissues, highlighting an early step in the gastric metaplasia to cancer cascade.

microbiology↗

bioRxiv2022

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

evolutionary biology↗

bioRxiv2021

Evolutionary footprints of a cold relic in a rapidly warming world

With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This rapid change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed ancestral central carbon metabolism responses to cold in diverse ecotypes, likely due to continuous connections to cold habitats that we hypothesize facilitated widespread parallel adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.

evolutionary biology↗

bioRxiv2020

Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

Convergent evolution is observed broadly across the web of life, but the degree of evolutionary constraint during adaptation of core intracellular processes is not known. High constraint has been assumed for conserved processes, such as cell division and DNA repair, but reports of nimble evolutionary shifts in these processes have confounded this expectation. Whole genome duplication (WGD) necessitates the concerted adjustment of a wide range of fundamental intracellular functions but nevertheless has been repeatedly survived in all kingdoms. Given this repeated adaptation to WGD despite obvious intracellular challenges to core processes such as meiosis, we asked: how do lineages not only survive WGD, but sometimes ultimately thrive? Are the solutions employed constrained or diverse? Here we detect genes and processes under selection following WGD in the Cochlearia species complex by performing a scan for selective sweeps following WGD in a large-scale survey of 73 resequenced individuals from 23 populations across Europe. We then contrast our results from two independent WGDs in Arabidopsis arenosa and Cardamine amara. We find that while WGD does require the adaptation of particular functional processes in all three cases, the specific genes recruited to respond are highly flexible. We also observe evidence of varying degrees of convergence between different cases. Our results point to a polygenic basis for the distributed adaptive systems that control meiotic crossover number, ionomic rewiring, cell cycle control, and nuclear regulation. Given the sheer number of loci under selection post-WGD, we surmise that this polygenicity may explain the general lack of convergence between these species that are ~30 million years diverged. Based on our results, we speculate that adaptive processes themselves - such as the rate of generation of structural genomic variants--may be altered by WGD in nascent autopolyploids, contributing to the occasionally spectacular adaptability of autopolyploids observed across kingdoms.

evolutionary biology↗

bioRxiv2017

Fetal death certificate data quality: A tale of two US counties

PurposeDescribe the relative frequency and joint effect of missing and misreported fetal death certificate (FDC) data and identify variations by key characteristics.\n\nMethodsStillbirths were prospectively identified during 2006-2008 for a multi-site population-based case-control study. For this study, eligible mothers of stillbirths were not incarcerated residents of DeKalb County, Georgia, or Salt Lake County, Utah, aged > 13 years, with an identifiable FDC. We identified the frequency of missing and misreported (any departure from the study value) FDC data by county, race/ethnicity, gestational age, and whether the stillbirth was antepartum or intrapartum.\n\nResultsData quality varied by item, and was highest in Salt Lake County. Reporting was generally not associated with maternal or delivery characteristics. Reasons for poor data quality varied by item in DeKalb County: some items were frequently missing and misreported; however, others were of poor quality due to either missing or misreported data.\n\nConclusionsFDC data suffer from missing and inaccurate data, with variations by item and county. Salt Lake County data illustrate that high quality reporting is attainable. The overall quality of reporting must be improved to support consequential epidemiologic analyses for stillbirth, and improvement efforts should be tailored to the needs of each jurisdiction.\n\nAbbreviations and Acronyms

epidemiology↗