Biology subjects

Lemke, S.

Publications and source records attributed to Lemke, S..

14 recordsLinked to original sources

bioRxiv2026

Deep learning enables direct HLA typing from immunopeptidomics data

The immune system eliminates malignant and infected cells through T-cell-mediated recognition of peptides presented by human leukocyte antigen molecules. Mass spectrometry-based immunopeptidomics enables unbiased identification of naturally presented HLA-restricted peptides and has become central to the development of T-cell-based immunotherapies. However, immunopeptidomics data reflects the combined peptide presentation of multiple HLA alleles, and determining which allotypes are represented in this multi-allelic complexity remains an unmet computational challenge. Here, we introduce immunotype, a deep learning-based ensemble predictor for HLA class I allotyping directly from immunopeptidomics data. Immunotype integrates peptide and HLA protein sequence information through transformer encoders and a graph neural network, complemented by a curated mono-allelic reference of known peptide-HLA binding preferences. Immunotype achieves an overall accuracy of 87.2% at protein-level resolution across diverse tissues and thereby enables rapid, cost-effective HLA typing of large-scale immunopeptidomics datasets.

bioinformatics↗

bioRxiv2025

Anchors for Homology-Based Scaffolding

Homology-based scaffolding orders contigs based on conserved collinearity of homologous sequences across related species. Existing methods often rely on costly whole-genome alignments or show limited robustness when integrating multiple references. Here, we introduce an anchor-based scaffolding framework that adapts synteny anchors to efficiently infer contig order and orientation relative to one or more reference genomes. Our approach leverages precomputed, sufficiently unique anchors and their respective high-confidence homology matches in a greedy approach, combining single-reference to multi-reference scaffolds using a maximum matching. Across simulated and real datasets, anchor-based scaffolding achieves accuracy comparable to state-of-the-art methods. Notably, the approach shows particular strengths in multi-reference settings. These results demonstrate that synteny-anchor-based scaffolding provides an additional tool for homology-based scaffolding with robust accuracy and superior performance in multi-reference scenarios.

bioinformatics↗

bioRxiv2025

Recently evolved, stage-specific genes are enriched at life stage transitions in flies

Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster has been extensively studied, less is known about the evolutionary dynamics that could govern stage-specific gene expression. To address this question, we compared the distribution of stage-specific genes, i.e., genes expressed in temporally restricted developmental stages, across development of D.melanogaster and Aedes aegypti. Using tau-scoring, a computational method to determine gene expression specificity, we found that, on average, a large proportion of genes (20 to 30% of all protein-coding genes) in both species exhibit restricted expression to specific developmental stages. Phylostratigraphy analysis, a method to date the age of genes, further revealed that stage-specific genes fall into two major categories: highly conserved and recently evolved. Notably, many of the recently evolved and stage-specific genes identified in A.aegypti and D.melanogaster are restricted to Diptera order (20 to 35% of all stage-specific genes), highlighting ongoing evolutionary processes that continue to shape life-stage transitions. Overall, our findings underscore the complex interplay between gene evolutionary age, expression specificity, and morphological transformations in development. These results suggest that the attraction of genes to critical life stage transitions is an ongoing process that may not be constant across evolutionary time or uniform between different lineages, offering new insights into the adaptability and diversification of dipteran genomes. Research HighlightsMetazoan genomes contain instructions for a single cell to develop into a complete adult organism. We investigated stage-specific genes, i.e. genes that expressed only during certain developmental stages, in two dipteran species. We found that between 20 to 35% of stage-specific genes are active during transitions between major life stages and have emerged recently, suggesting an ongoing evolutionary process shaping life-stage transitions.

evolutionary biology↗

bioRxiv2025

Telomerase RNA gene duplications drive telomeric repeatdiversity and evolution in Andrena bees

Most organisms in the animal kingdom require a non-coding telomerease RNA (TR) in conjunction with the telomerase reverse transcriptase (TERT) to add telomere tandem repeats to chromosome ends to genomic instability. Recent studies reported an extensive diversity in the sequence of telomeric repeats in some insect species. Our investigation of TR genes in the Andrena genus provides convincing evidence for the presence of multiple TR gene copies with different template sequences for synthesis of distinct telomeric repeat sequences in several species. In this study we describe the structure, genomic coordinates and abundance of these TR genes, and correlate our findings with the levels of tandem repeats found in DNAseq data. Based on an analysis of the synthenic context of these newly predicted TR genes, we show evidence for the existence of multiple TR paralogs that diverged during the evolution of the genus Andrena. To our knowledge this is the first time such a phenomenon is observed in animals, although recently reported for plants. Interestingly, the comprehensive annotation of all TERT genes found in yet unannotated Andrena species shows no corresponding evolutionary changes in related TERT proteins encoded by a single copy gene. Our study suggests an evolutionary mechanism for diversification of telomeric repeat sequences in certain insect species through telomerase RNA gene duplication.

bioinformatics↗

bioRxiv2024

Minimal-invasive 3D laser printing of microimplants in organismo

Multi-photon 3D laser printing has gathered much attention in recent years as a means of manufacturing biocompatible scaffolds that can modify and guide cellular behavior in vitro. However, in vivo tissue engineering efforts have been limited so far to the implantation of beforehand 3D printed biocompatible scaffolds and in vivo bioprinting of tissue constructs from bioinks containing cells, biomolecules, and printable hydrogel formulations. Thus, a comprehensive 3D laser printing platform for in vivo and in situ manufacturing of microimplants raised from synthetic polymer-based inks is currently missing. Here we present a platform for minimal-invasive manufacturing of microimplants directly in the organism by one-photon photopolymerization and multi-photon 3D laser printing. Employing a commercially available elastomeric ink giving rise to biocompatible synthetic polymer-based microimplants, we demonstrate first applicational examples of biological responses to in situ printed microimplants in the teleost fish Oryzias latipes and in embryos of the fruit fly Drosophila melanogaster. This provides a framework for future studies addressing the suitability of inks for in vivo 3D manufacturing. Our platform bears great potential for the direct engineering of the intricate microarchitectures in a variety of tissues in model organisms and beyond.

bioengineering↗

bioRxiv2023

Divergent evolutionary strategies preempt tissue collision in fly gastrulation

Metazoan development proceeds through a series of morphogenetic events that sculpt body plans and organ structures. In the early embryonic stages, morphogenetic processes involving growth and deformation occur concurrently. Forces generated in one tissue can thus increase mechanical stress in the neighboring tissue, potentially disrupting spatial patterning, morphological robustness, and consequently decreasing organismal fitness. How organisms evolved mechanisms to reduce or release inter-tissue stresses remains poorly understood. Here we combined phylogenetic survey across a whole insect order (Diptera), quantitative live imaging, and functional mechanical perturbation to investigate the evolution of mechanical stress management during epithelial expansions in the gastrulating fly embryos. We find that two distinct cellular mechanisms exist in Diptera to prevent the accumulation of compressive stress that can arise when the expanding head and trunk tissues collide. In Cyclorrhapha, a monophyletic dipteran subgroup including the fruit fly Drosophila melanogaster, the head-trunk boundary undergoes active out-of-plane deformation to form a transient epithelial fold, called the cephalic furrow (CF), which acts as a mechanical sink to preempt head-trunk collision. Genetic or optogenetic elimination of the CF leads to tissue buckling, yielding deleterious effects of axial distortion that likely results from unmitigated release of compressive stress. Non-cyclorrhaphan flies, by contrast, lack CF formation and instead display widespread out-of-plane division in the head, which shortens the duration of its expansion and reduces surface area increase. Reorienting head mitosis in Drosophila from in-plane to out-of-plane partially suppresses the need for epithelial out-of-plane deformation, suggesting that out-of-plane division can act as an alternative mechanical sink to prevent tissue collision. Our data suggest that programs of mechanical stress management can emerge abruptly under selective pressure of inter-tissue mechanical conflict in early embryonic development.

developmental biology↗

bioRxiv2023

Elevated temperature fatally disrupts nuclear divisions in the early Drosophila embryo.

Temperature variations can challenge animal survival, with elevated temperatures presenting distinct vulnerabilities at different stages of the animal life cycle. Embryonic development is known to be especially vulnerable, though the molecular mechanisms that underlie this vulnerability remain unclear. Here we investigate how elevated temperature affects embryogenesis in Drosophila melanogaster, an insect model known for extensively characterized genetic makeup and developmental processes. We identify the first three hours as a critical window in which Drosophila embryos are particularly vulnerable to elevated temperature. This period includes the formation of a syncytial blastoderm, which involves 4 rounds of meta-synchronous nuclear divisions at the embryonic cortex, and cellularization that leads to the formation of the cellular blastoderm. Embryos exposed to elevated temperature during this period subsequently exhibited developmental defects at the gastrulation stage, leading to increased lethality. At elevated temperature, we observed an increase in mitotic failures causing a loss of cortical nuclei during cellularization. There is also a local crowding of nuclei and an increase in asynchrony between the nuclear cycles in the center vs. the poles. Interestingly, these features cooperatively amplify the frequency of mitotic failures, leading to holes in the blastoderm epithelium. Further mechanistic analysis of mitotic failures revealed that they trigger DNA damage response. Focusing on cell biological causes of mitotic failures, we found that the interaction between F-actin and microtubules is weakened at elevated temperature. We performed functional tests to determine whether known regulators of mitosis could rescue mitotic failures, blastoderm hole formation, and improve embryo survival. We further analyzed genomic datasets from wild populations to determine whether these regulators also carry signatures of adaptation in wild populations. Our genetic rescue experiments show that in Drosophila embryos, the interaction between cortical F-actin and astral microtubules of mitotic spindle is vulnerable to disruption at elevated temperatures, leading to mitotic failures that can be potentially rescued by modulating the expression of just a few factors. We propose that levels of expression of corresponding genes could be used as indicators to predict the effects of increasing temperature variations on insect populations.

developmental biology↗

bioRxiv2022

PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma

Current therapeutic management of advanced melanoma patients largely depends on their BRAF mutation status. However, the vast heterogeneity of the tumors hampers the success of therapies targeting the MAPK/ERK pathway alone. Dissecting this heterogeneity will contribute to identifying key players in the oncogenic progression to tailor more effective therapies. We performed a comprehensive molecular and phenotypic characterization of a panel of patient-derived BRAFV600E-positive melanoma cell lines. Transcriptional profiling was used to identify groups of coregulated genes whose expression relates to an increased migratory potential and a higher resistance. A decrease in sensitivity to MAPK/ERK pathway inhibition with vemurafenib or trametinib corresponded with an increasing quiescence and migratory properties of the cells. This was accompanied by the loss of transcriptional signatures of melanocytic differentiation, and the gain of stem cell features that conferred highly-resistant/mesenchymal-like cells with increased xenobiotic efflux capacity. Nevertheless, targeting of the implicated ABC transporters did not improve the response to vemurafenib, indicating that incomplete BRAF inhibition due to reduced drug uptake is not a main driver of resistance. Rather, indifference to MAPK/ERK pathway inhibition arose from the activation of compensatory signaling cascades. The PI3K/AKT pathway in particular showed a higher activity in mesenchymal-like cells, conferring a lower dependency on MAPK/ERK signaling and supporting stem-like properties that could be reverted by dual PI3K/mTOR inhibition with dactolisib. In case of MAPK/ERK independency, therapeutic focus may be shifted to the PI3K/AKT pathway to overcome late-stage resistance in melanoma tumors that have acquired a mesenchymal phenotype.

cancer biology↗

bioRxiv2022

Composition of a low erucic acid, low fiber field pennycress (Thlaspi arvense L.) grain referred to as CoverCress™ developed through breeding and gene editing

Field pennycress (Thlaspi arvense L.) can be domesticated and cultivated as an annual in a corn / pennycress / soybean rotation where pennycress is sown and harvested as a cash cover crop. To improve the nutritional profile, pennycress was modified in two ways to achieve the same alterations in characteristics: 1) through selection of mutants and 2) through gene editing. These alterations resulted in a low erucic acid, lower fiber phenotype and the resulting products from these combinations are referred to as CoverCress CCWG-1 and CoverCress CCWG-2, respectively. CCWG-1 and CCWG-2 were planted as cover crops in five U.S. locations in the fall and the grain was harvested in the subsequent June. The grain was treated with 83 mM copper sulfate solution as a potential palatability agent for the naturally high glucosinolate levels, and was subsequently analyzed for nutrient (proximates, minerals, fatty acids, amino acids, and vitamins) and anti-nutrient (sinapine, glucosinolates, mold) content. The low erucic acid, lower fiber phenotype was consistently achieved across five lots. Generally, the nutrient content for both CCWG-1 and CCWG-2 were similar to canola grain. Canola grain contains the anti-nutrient sinapine but is significantly reduced to below the level of detection in CoverCress grain. As expected, CoverCress grain contains about 10 times more glucosinolates than canola. Based on the composition of CoverCress grain, it may provide a source of energy and amino acids to animals with restricted inclusion based on the glucosinolate content.

plant biology↗

bioRxiv2021

Single gene initiates evolution of epithelial architecture and function

Epithelial monolayers are a hallmark of the architecture of metazoan tissues: they provide stability, serve as barriers, and fold into organs. Epithelial cells vary in shape, ranging from flat and spread out to tall and slim. Dynamic epithelial shape changes have been explored in the context of tissue folding, where local cytoskeletal modulations cause epithelial bending and folding. Comparatively little is known about how entire tissues are transformed from a short to tall architecture. Here we show that shape regulation in epithelia can be governed by the activity of a single gene. We use a comparative approach in distantly related flies to experimentally decode the developmental program that directs the formation of columnar epithelia in the blastoderm and thus determines the physiological features of the resulting epithelium. We uncover an evolutionary novel, membrane-associated protein that emerged in flies and triggered a new development program, the cuboidal-to-columnar transformation of epithelial tissues. slow-as-molasses (slam) encodes a Dia/F-actin regulator that exploits an intrinsic morphological plasticity of cells to transform tissues. Our findings demonstrate that a single, newly emerged factor that amplifies its activity in epithelia provides the basis for adaptation and initiates the evolution of novel developmental programs.

evolutionary biology↗

bioRxiv2021

Impaired sleep-dependent consolidation after stroke - interaction of slow waves, rehabilitation and GABA

Sleep is known to be important for promoting recovery after brain injuries such as stroke. Yet, it remains unclear how such injuries affect neural processing during sleep and how to precisely enhance sleep-dependent memory processing during recovery. Using an experimental model of focal cortical stroke in rats along with long-term electrophysiological monitoring of neural firing and sleep microarchitecture, here we show that sleep-dependent neural processing is altered after stroke induction. Specifically, we found that the precise coupling of spindles to global slow- oscillations (SO), a phenomenon that is known to be important for memory consolidation, appeared to be disrupted by a pathological increase in "isolated" local delta waves. The transition from this pathological to a more physiological sleep state - with both a reduction in isolated delta waves and increased spindle coupling to SO - was associated with sustained performance gains after task training during recovery. Interestingly, post-injury sleep processing could be pushed towards a more physiological state via a pharmacological reduction of tonic GABA. Together, our results suggest that sleep processing after cortical brain injuries may be impaired due to an increase in local delta waves and that restoration of physiological processing is important for recovery of task performance.

neuroscience↗

bioRxiv2020

An economic dilemma between weapon systems may explain an arachno-atypical venom in wasp spiders (Argiope bruennichi)

Spiders use venom to subdue their prey, but little is known about the diversity of venoms in different spider families. Given the limited data available for orb-weaver spiders (Araneidae) we selected the wasp spider Argiope bruennichi for detailed analysis. Our strategy combined a transcriptomics pipeline based on multiple assemblies with a dual proteomics workflow involving parallel mass spectrometry techniques and electrophoretic profiling. We found that the remarkably simple venom of A. bruennichi has an atypical composition compared to other spider venoms, prominently featuring members of the CAP superfamily and other, mostly high-molecular-weight proteins. We also detected a subset of potentially novel toxins similar to neuropeptides. We discuss the potential function of these proteins in the context of the unique hunting behavior of wasp spiders, which rely mostly on silk to trap their prey. We propose that the simplicity of the venom evolved to solve an economic dilemma between two competing yet metabolically expensive weapon systems. This study emphasizes the importance of cutting-edge methods to encompass smaller lineages of venomous species that have yet to be characterized in detail, allowing us to understand the biology of their venom systems and to mine this prolific resource for translational research.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2020

Cellular-scale silicon probes for high-density, precisely-localized neurophysiology

Neural implants with large numbers of electrodes have become an important tool for examining brain functions. However, these devices typically displace a large intracranial volume compared to the neurons they record. This large size limits the density of implants, provokes tissue reactions that degrade chronic performance, and impedes the ability to accurately visualize recording sites within intact circuits. Here we report next-generation silicon-based neural probes at cellular-scale (5x10{micro}m cross-section), with ultra-high-density packing (as little as 66{micro}m between shanks) and 64 or 256 closely-spaced recording sites per probe. We show that these probes can be inserted into superficial or deep brain structures and maintain high-quality spike recordings in freely behaving rats for many weeks. Finally, we demonstrate a slice-in-place approach for the precise registration of recording sites relative to nearby neurons and anatomical features, including striatal {micro}-opioid receptor patches. This scalable technology provides a valuable tool for examining information processing within neural circuits, and potentially for human brain-machine interfaces.

bioengineering↗

bioRxiv2017

In toto fluorescence live imaging in scuttle fly Megaselia abdita reveals gradual transitions towards a novel extraembryonic architecture.

Extraembryonic tissues contribute to animal development, which often entails spreading over embryo or yolk. Apart from changes in cell shape, the requirements for this tissue spreading are not well understood. Here we analyze spreading of the extraembryonic serosa in the scuttle fly Megaselia abdita. The serosa forms from a columnar blastoderm anlage, becomes a squamous epithelium, and eventually spreads over the embryo proper. We describe the dynamics of this process in long-term, whole-embryo time-lapse recordings, demonstrating that free serosa spreading is preceded by a prolonged pause in tissue expansion. Closer examination of this pause reveals mechanical coupling to the underlying yolk sac, which is later released. We find mechanical coupling prolonged and serosa spreading impaired after knockdown of M. abdita Matrix metalloprotease 1. We conclude that tissue-tissue interactions provide a critical functional element to constrain spreading epithelia.\n\nImpact StatementExtraembryonic tissue spreading in the scuttle fly Megaselia abdita requires mechanical decoupling from the underlying yolk sac.

evolutionary biology↗