Biology subjects

Schulte, L.

Publications and source records attributed to Schulte, L..

13 recordsLinked to original sources

bioRxiv2026

Dynamic anatomy of the replisome under stress

When exposed to replication stress, the factors involved in DNA replication display differing responses that in many cases remain unexplained. In this study, we generated a series of genomically engineered embryonic stem cell lines with fluorescently tagged replication factors to track their spatiotemporal dynamics in live-cell microscopy during and after treatment with the replication inhibitors aphidicolin and hydroxyurea. All 3 replicative polymerases were found to accumulate upon stress, with the primase subunits of polymerase alpha retaining catalytic activity. This accumulation was dependent on new origin firing and accompanied by 9-1-1 clamp loading in the vicinity of stalled forks. Pulse-stress-pulse experiments and spatial correlation analyses of replicons indicated that, after stress is removed, replication preferentially restarts at new sites surrounding previously stalled forks. These findings shed light on the replisomes immediate reaction to stalled replication forks and provide comprehensive kinetic maps of the replisome under stress. Highlights- Comprehensible atlas of the replisome under stress - DNA polymerases accumulate during stress, with clamp switch near stalled forks - In the absence of DNA synthesis, new adjacent origins fire with active priming - During stress recovery, replication restart predominantly at new fired origins

cell biology↗

bioRxiv2026

Ontogenetic variation in composition and bioactivity of common adder (Vipera berus) venom revealed by genome-guided proteomics and in vitro functional assays

1Ontogenetic shifts in diet are well documented in snakes and are increasingly linked to age-related venom variation. The common adder, Vipera berus, exhibits a dietary transition from predominantly ectothermic prey in its early life to increasingly incorporating endothermic prey as an adult. Here, we investigate whether this dietary shift is reflected in age-related changes in the venom composition and bioactivity of V. berus. Venoms from captive-bred V. berus from Germany were obtained and pooled across five age groups, from neonates to adults. Venom profiles were assessed by SDS-PAGE and genome-guided shotgun proteomics, with quantification based on normalized spectral abundance factors (NSAF) using a toxin-gene catalogue generated from a novel V. berus genome assembly. In parallel, we assayed general protease and PLA2 activities, as well as FXa-, thrombin-, and plasmin-like activities, and cytotoxicity toward mammalian cell lines. We identified two distinct age-related venom phenotypes (ontotypes): an svMP/CTL-rich ontotype A ([≤]1 year) and an svSP/PLA2-rich ontotype B ([≥]2 years). Functionally, protease activity decreased with age, whereas thrombin-like, plasmin-like and PLA2 activities, and cytotoxicity, increased. Our findings indicate an ontogenetic shift in composition and activities of V. berus venom that parallels dietary transitions and potentially reflect adaptation to differing prey physiologies.

biochemistry↗

bioRxiv2025

Dynamic connectivities of plant metacommunities at a millennial time-scale: the Beringia testbed

Ecological connectivity shapes ecosystem responses to climate change and is thought to underpin stability, yet its millennial-scale dynamics remain poorly resolved. We asked how spatial and temporal connectivity of plant metacommunities changed over the last 40 ka and which processes drove it. We analysed and compiled plant sedimentary DNA from 20 lake cores across Beringia (Siberia, Alaska) to investigate community dynamics and, for a high-resolution subset, applied beta- and zeta-diversity to track connectivity. Vegetation changed coherently across the glacial-Holocene transition, with trait shifts mirroring functional composition. Connectivity peaked during the late MIS3 and Last Glacial Maximum--likely aided by the Bering Land Bridge, mass effects and facilitation--collapsed during the Deglacial with rapid turnover, and rebounded in the Holocene as shrub and boreal communities expanded. Temporal zeta within sites exceeded spatial zeta, indicating strong local persistence and resilience. Tundra sites uninvaded by forest maintained continuous species pools. Overall, these patterns underscore the value of a metacommunity perspective for assessing millennial-scale connectivity changes.

ecology↗

bioRxiv2025

A genome-guided atlas to the composition, activity, and β-bungarotoxin dimerization in many-banded krait venom inferred by functional venomics

1Snakebite is a neglected tropical disease claiming [~]140,000 lives every year. One of the most medically relevant snakes of Asia is the many-banded krait (Bungarus multicinctus). Approximately 8% of the global human population is at risk of being envenomated by this species, able to cause fatal neurotoxicity. Here, we present a proteogenomic and functional assessment of the B. multicinctus venom via genome-guided bottom-up and top-down proteomics, combined with traditional protein profiling and bioassays. We report its venom profile alongside the primary structures of its toxins, revealing a relatively simple venom containing 55 components from 16 protein families. It is largely composed by three-finger toxins and phospholipase A2, besides acetylcholinesterase and snake venom metalloprotease. Top-down data unveiled the diversity of the highly lethal {beta}-bungarotoxins and allowed us to infer the complex dimerization patterning of these multi-domain neurotoxins. Our functional analysis revealed that B. multicinctus venom exerts potent phospholipase A2 and acetylcholinesterase activities, but protease activity as well as effects on cell viability and release of second messengers were virtually absent. This suggests, that B. multicinctus venom causes its devastating neurotoxic symptoms due to a heavy reliance on phospholipase A2 and acetylcholinesterase, but without impairing viability of neurons nor via interference of second messenger release. Antibacterial and antiviral screens further revealed activity against some pathogenic microbes that warrant further translational investigations. A comparison to previously published venom proteomes of B. multicinctus and its congeners suggests, that intraspecific venom variation occurs more widely in kraits than previously acknowledged and deserves higher attention. Overall, our investigation provides pivotal new insights into the biochemistry and pathophysiology of one of earths most lethal snakes and represents an important resource to inform future proteogenomic and functional studies in krait venom and beyond.

molecular biology↗

bioRxiv2025

Low extent of sex-based venom variation in Earth's most widespread viper, the common adder (Vipera berus)

Snake venom is an ecologically critical functional trait, primarily applied for foraging and accordingly shaped by selective pressures. Recent insights underpinned the high variability of snake venoms down to the intraspecific level, with regional, ontogenetic, and seasonal variation being mostly investigated. In contrast, sex-based venom variation has received considerably less attention so far, and its influence on venom compositions in vipers is virtually unknown. The common adder (Vipera berus) is a promising model species to explore this subject because of a described sexual dimorphism and its wide distribution, which promises a noteworthy degree of adaptability and venom plasticity. Here, we tested for sex-based venom variation in Central European V. berus by comparing venom profiles and bioactivity. Proteomics, paired with SDS-PAGE and RP-HPLC, revealed highly similar venom profiles. Likewise, phospholipases A2 and proteases bioactivity profiling, and bioassays targeting the coagulation cascade and mammalian cell lines revealed similar activity spectra. Hence, our analysis does not show a noteworthy extent of sex-based intraspecific venom variation in V. berus. We further discuss our data in light of the species venom profile at larger geographic scales, its clinical relevance, and the need for more standardized approaches when investigating venom variability. Our work provides novel insights into the venom biology of Earths most widespread viper, and serves as a foundation upon which future works can build.

biochemistry↗

bioRxiv2025

From larval stage to adulthood? Habitat type-specific chemical fingerprints of fire salamander larvae might give first indication for adult mate preference

Assortative mating can play a major role in the divergence of a population with gene flow. In a fire salamander population near Bonn, Germany, the larvae differ genetically according to the habitat type they are found in, i.e. ponds or streams. Neither sound nor vision are a source for assortative mating in fire salamanders, but it is known that females can discriminate between sexes and habitat types of the males based on chemical cues. The adults share the same terrestrial habitat which leads to the question whether there is a habitat type-specific chemical fingerprint already existing in the larvae that may be used in the adult stage as the base for assortative mating. We took water samples and captured larvae at two ponds and two streams and used polydimethylsiloxane and TD-GC-MS to collect and analyze samples of the environmental background as well as from the surface of the larvae. We found a significantly different composition of chemical features in the environmental back-ground samples. Additionally, we found the larvae to carry habitat type-specific chemical features. These finding allow to speculate that the features on the larval surface may be used

ecology↗

bioRxiv2024

Comparative venom analysis between melanistic and normally-colored phenotypes of the common adder (Vipera berus)

1Snake venom is an ecologically-relevant functional trait directly linked with a snakes fitness and survival, facilitating predation and defense. Snake venom variation occurs at all taxonomic levels, but the study of variation at intraspecific level is still in its early stages. The common adder (Vipera berus) exhibits considerable variation in color phenotypes across its distribution range. Melanistic (fully black) individuals are the subject of myths and fairytales, and in German folklore such "hell adders" are considered more toxic than their normally-colored conspecifics. However, these claims have never been formally tested. Here, we provide the first comparative analysis of venoms from melanistic and normally-colored common adders. Specifically, we compared the venom profiles by SDS-PAGE and RP-HPLC, and tested the protease, phospholipase A2 and cytotoxic activities of the venoms of both phenotypes. Phospholipase A2 activity was similar in both phenotypes, whereas general protease activity was higher in the melanistic venom, which was also more cytotoxic at two concentrations (6.25 and 12.5 {micro}g/ml). These minor differences between the venoms of melanistic and normally-colored adders are unlikely to be of clinical relevance in the context of human envenomation. In light of our results, the claim that melanistic adders produce more toxic venom than their normally-colored conspecifics appears rooted entirely in folklore.

molecular biology↗

bioRxiv2023

Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics

Glacier and permafrost shrinkage and land-use intensification threaten diverse mountain wildlife and affect nature conservation strategy. Our understanding of alpine ecological dynamics is, however, insufficient because time series portraying ecosystem complexity adequately are missing. Here, we present an ancient metagenomic record tracing 317 terrestrial and aquatic taxa, including mammals, fish, plants, and microorganisms retrieved from a lake sediment core from the southeastern Tibetan Plateau covering the last 18,000 years. We infer that steppe-meadow turned into woodland at 14 ka (cal BP) controlled by warming-induced cryosphere loss, further driving a change of herbivore dominance from wild yak to deer. Network analyses reveal that root hemiparasitic and cushion plants are keystone taxa, likely altering the terrestrial ecosystem via facilitation. These findings refute the hypothesis of top-down control by large herbivores in the alpine ecosystem. We also find that glacier mass loss significantly contributes to considerable turnover in the aquatic community at 14 ka, transitioning from glacier-related (blue-green) algae to abundant non-glacier-preferring picocyanobacteria, macrophytes, fish, and fish-eating otters. Human impact contributes little to shaping the alpine ecosystems. By applying network analysis, we provide the first sedaDNA-based assessment of the stress-gradient hypothesis. As cryosphere loss is ongoing due to climate warming, prioritizing the protection of habitats with rich nurse plants that aid neighbors in adapting to stressful conditions is likely to be a more beneficial conservation measure than livestock reduction in the Tibetan Plateau. Significance statementMerging ancient metagenomics and network analysis gives new insights into conserving the Tibetan alpine ecosystem under ongoing warming and human perturbations. We investigated the assembly of the Yak steppe-meadow ecosystem and an alpine lake system in response to cryosphere changes over the past [~]18,000 years on the Tibetan Plateau. Large herbivores cannot be a cost-effective natural climate solution to stabilize the Tibetan alpine ecosystem because they are not keystone taxa at the ecosystem scale. Furthermore, there is no support that land use considerably shapes the alpine communities and ecosystems. Protection policy should thus prioritize focus on alpine areas with intense land use and rich in root hemiparasitic and cushion plants because these taxa act as facilitators in the ecosystem.

ecology↗

bioRxiv2023

Stress response of fire salamander larvae differs between habitat types

Different habitats can impose varying selection pressures on individuals of the same species. Larvae of the European fire salamander (Salamandra salamandra) can inhabit two different habitats: streams and ponds. Streams are characterised by lower predation risk and intraspecific density and higher food availability than ponds. Thus, ponds are considered a less suitable habitat. To investigate the differential impacts of the two habitats on larval physiology, we measured the stress response of larvae living in the two different habitats. After successfully validating the measure of water-borne corticosterone (CORT) concentrations in fire salamander larvae, we measured the baseline and stress-induced CORT of 64 larvae from two pond and two stream locations in the field. We found larvae in ponds to be more stressed than larvae in streams. Additionally, we performed a reciprocal transplant experiment and tested whether larvae can adapt their stress response to changing habitat conditions. After two weeks of transfer, we did not find an increase in CORT when comparing stress-induced CORT values with baseline CORT values in larvae transferred into ponds. However, larvae transferred into streams exhibited an increase in the stress-induced CORT response. Moreover, transfer into ponds as well as larvae originating from ponds showed reduced growth rates, indicating that ponds might be the more stressful habitat, as it negatively affected larval physiology. These results show that noninvasive hormone measurements can provide information on habitat quality and potential adaptation and thus emphasis the potential for its use in conservation efforts.

ecology↗

bioRxiv2023

Genomic characterization of a nematode tolerance locus in sugar beet

BackgroundInfection by beet cyst nematodes (BCN, Heterodera schachtii) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under adverse conditions are among the main breeding objectives. Breeding of BCN tolerant sugar beet cultivars offering high yield in the presence of the pathogen is therefore of high relevance. ResultsTo identify causal genes providing tolerance against BCN infection, we combined several experimental and bioinformatic approaches. Relevant genomic regions were detected through mapping-by-sequencing using a segregating F2 population. DNA sequencing of contrasting F2 pools and analyses of allele frequencies for variant positions identified a single genomic region which confers nematode tolerance. The genomic interval was confirmed and narrowed down by genotyping with newly developed molecular markers. To pinpoint the causal genes within the potential nematode tolerance locus, we generated long read-based genome sequence assemblies of the tolerant parental breeding line Strube U2Bv and the susceptible reference line 2320Bv. We analyzed continuous sequences of the potential locus with regard to functional gene annotation and differential gene expression upon BCN infection. A cluster of genes with similarity to the Arabidopsis thaliana gene encoding nodule inception protein-like protein 7 (NLP7) was identified. Gene expression analyses confirmed transcriptional activity and revealed clear differences between susceptible and tolerant genotypes. ConclusionsOur findings provide new insights into the genomic basis of plant-nematode interactions that can be used to design and accelerate novel management strategies against BCN.

plant biology↗

bioRxiv2021

Long-term fungus-plant co-variation from multi-site sedimentary ancient DNA metabarcoding in Siberia

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the palaeo-ecosystems at selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. After bioinformatic processing with the OBItools pipeline, we obtained 706 unique fungal operational taxonomic units (OTUs) and 243 amplicon sequence variants (ASVs) for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedbacks between fungus compositional and plant diversity changes which will affect forest advance and stability in arctic regions.

ecology↗

bioRxiv2021

Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only one fast-evolving satellite DNA

In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 gigabasepairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers accumulative genome evolution mode. For this, we applied low coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carriere and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

plant biology↗

bioRxiv2020

Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests

Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches, in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA - metabarcoding - focuses on small fragments which cannot resolve Larix to species level nor allow the detailed study of population dynamics. Here we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back up to 6700 years in age from the Taymyr region in northern Siberia. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborate an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.

ecology↗