Biology subjects

Richter, L.

Publications and source records attributed to Richter, L..

13 recordsLinked to original sources

bioRxiv2026

Structural mechanism of Gasdermin E-mediated mtDNA release from apoptotic mitochondria

During apoptosis, the permeabilization of the mitochondrial inner membrane (MIM) through still-unclear mechanisms releases mtDNA into the cytosol, triggering the inflammatory cGAS/STING pathway under low caspase activity. Here, we report that, in apoptosis, the active form of the pore-forming protein Gasdermin E (GSDME-N) damages mitochondria before plasma membrane disruption. We visualize GSDME-N pore-like nano-assemblies in the MIM of apoptotic cells and of isolated mitochondria, which we bridge with the cryo-EM structure of the GSDME-N pore in mitochondria-like membranes. Deep membrane insertion of the anchor domain, which acts as a determinant of GSDME-N cardiolipin binding preferences, supports a role in pore formation. Notably, GSDME depletion results in a reduction in cristae swelling, MIM extrusion and mtDNA release during apoptosis. Subsequently, this decreases STING activation and inflammatory responses under caspase inhibition. Our findings reveal that GSDME mediates MIM permeabilization and mtDNA release during apoptosis and define the mechanism of GSDME-mediated membrane damage.

molecular biology↗

bioRxiv2026

Resolving Sub-Microsecond Conformational Dynamics of Vertical Nucleic Acids on Graphene

The function of nucleic acids is governed not only by their structure but also by their dynamics. At the molecular scale, transitions between functional structural states are superimposed on rapid thermal fluctuations, resulting in an intricate interplay that is challenging to resolve experimentally, particularly at the single-molecule level. Here, we introduce a novel approach for unraveling sub-microsecond dynamics in oligonucleotides, enabling direct observation of fluctuations in single DNA molecules. By immobilizing nucleic acids vertically on graphene and exploiting distance-dependent graphene energy transfer of fluorescent molecules attached to the DNA, we relate fluctuations in fluorescence intensity to biomolecular dynamics. We show that ionic strength modulates the fluctuations and that structural defects in DNA, such as nucleotide gaps or mismatches, alter the measured dynamics. The experimental findings are complemented by atomistic molecular dynamics simulations and kinetic Monte Carlo simulations, establishing a direct link between theoretical predictions of structure and dynamics and experimentally accessible fluctuation timescales. Overall, our findings advance the understanding of how thermal fluctuations affect oligonucleotides and are modulated by both external and internal stimuli.

biophysics↗

bioRxiv2026

From Growth Faltering to Recovery: Gut Microbial and Body Composition Signatures of Early Childhood Malnutrition Phenotypes

BackgroundChronic malnutrition in early childhood is a multifactorial condition associated with long-term impairments, yet the physiological and gut microbial pathways underlying differential growth trajectories remain poorly understood. ObjectiveWe aimed to characterize phenotypic growth trajectories and identify the associated gut microbial and body composition signatures in infants during the first year of life. MethodsWe analyzed longitudinal data from birth to 12 months in a South African cohort (Soweto, n=45). Individual linear growth trajectories were modeled using the Jenss-Bayley equation, and children were clustered based on model parameters to identify phenotypic subgroups. Body composition (fat-free mass and fat mass) was measured via deuterium dilution at 6 and 12 months, and gut microbiome development was assessed using 16S rRNA gene amplicons at 4, 6, and 12 months. ResultsWe identified distinct phenotypic subgroups including healthy growth, catch-up growth, and growth faltering, that were obscured at the cohort level. These trajectories diverged most dynamically within the first 6 months of life. Integrated analysis revealed that in the growth faltering cluster, height-for-age and fat-free mass z-scores stabilized between 6 and 12 months, whereas fat mass z-scores (FMZ) declined. This trade-off is consistent with a catabolic state where energy reserves are prioritized for lean tissue and bone growth. Furthermore, at 6 months, the growth faltering cluster was enriched with opportunistic pathobionts (e.g., Paraclostridium). In contrast, the catch-up cluster exhibited a transient enrichment of facultative anaerobes (e.g., Enterobacter), supporting a hypothesis that these oxygen-tolerant taxa may help bridge a transitional microbial state in partially oxygenated or inflamed environments to enable physiological recovery. ConclusionsEarly childhood chronic malnutrition phenotypes in South African infants can be defined by distinct microbial and body composition signatures that diverge within six months of life. Integrated interventions should target both host anabolic state and microbiome transitions to support recovery.

microbiology↗

bioRxiv2024

Modeling the spatio-temporal annual changes in human tick-borne encephalitis (TBE) risk in Europe

IntroductionTick-borne encephalitis (TBE), caused by tick-borne encephalitis virus (TBEV), is a zoonotic disease that can cause severe neurological symptoms. Given the increasing number of reported human TBE cases in Europe, a spatio-temporal predictive model to infer the year-to-year probability of human TBE occurrence across Europe at the regional and municipal administrative levels was developed. MethodsThe distribution of human TBE cases at the regional (NUTS-3) level during the period 2017-2022, was derived by using data provided by the European surveillance system (TESSy, ECDC), and at the municipal level by using data from Austria, Finland, Italy, Lithuania, and Slovakia. The probability of presence of human TBE cases at the regional and municipal levels for the period 2017-2024 was modeled with a boosted regression trees model, including covariates that affect both the natural hazard of virus circulation and human exposure to tick bites. ResultsAreas with the highest probability of human TBE infections are primarily located in central-eastern Europe, the Baltic states, and along the coastline of Nordic countries up to the Bothnian Bay. Our results also highlight a statistically significant rising trend in the probability of human TBE infections not only in north-western, but also in south-western European countries, offering a spatio-temporal predictive framework for the assessment of areas where human TBE infection are most likely to occur. The model showed good predictive performance, with a mean AUC of 0.85 (SD = 0.02), sensitivity of 0.82, and specificity of 0.80 at the regional level, and a mean AUC of 0.82 (SD = 0.03), sensitivity of 0.80, and specificity of 0.69 at the municipal level. DiscussionWith ongoing climate and land use changes, the number of human TBE cases is likely to increase and expand into new areas, as trends are already indicating. This underscores the need for predictive models that can help prioritize intervention efforts. The approach adopted, by leveraging lagged covaries, enables timely one-year-ahead predictions, thus supporting surveillance, prevention, and control of human TBE infections by public health authorities. StatementsO_ST_ABSEthical statementC_ST_ABSEthical approval was not needed. Funding statementThis project has received funding from the European Unions Horizon 2020 research and innovation programme under grant agreement No 874850 and is catalogued as MOOD 081. The contents of this publication are the sole responsibility of the authors and dont necessarily reflect the views of the European Commission. Conflict of interestNone. Authors contributionsFrancesca Dagostin: Conceptualization, Methodology, Data Curation, Formal Analysis, Writing - Original Draft. Diana Erazo: Conceptualization, Methodology, Writing - Review & Editing. Giovanni Marini: Conceptualization, Methodology, Writing - Review & Editing. Daniele Da Re: Conceptualization, Methodology, Writing - Review & Editing. Valentina Tagliapietra: Conceptualization, Methodology, Writing - Review & Editing. Maria Avdicova: Resources, Writing - Review & Editing. Tatjana Av[s]i[c] - [Z]upanc: Resources, Writing - Review & Editing. Timothee Dub: Conceptualization, Resources, Writing - Review & Editing. Nahuel Fiorito: Resources, Writing - Review & Editing. Nata[s]a Knap: Resources, Writing - Review & Editing. Celine M. Gossner: Resources, Writing - Review & Editing. Jana Kerlik: Resources, Writing - Review & Editing. Henna Makela: Resources, Writing - Review & Editing. Mateusz Markowicz: Resources,Writing - Review & Editing. Roya Olyazadeh: Resources, Writing - Review & Editing. Lukas Richter: Resources, Writing - Review & Editing. William Wint: Resources, Writing - Review & Editing. Maria Grazia Zuccali: Resources, Writing - Review & Editing. Milda [Z]ygutiene: Resources, Writing - Review & Editing. Simon Dellicour: Methodology, Writing - Review & Editing. Annapaola Rizzoli: Conceptualization, Methodology, Writing - Review & Editing. Data availabilityThe data that support the findings of this study were provided by ECDC, Azienda Provinciale per i Servizi Sanitari Provincia Autonoma di Trento (APSS), Unita Locale Socio Sanitaria Dolomiti (ULSS N.1 Dolomiti), Public Health Authority of the Slovak Republic, Austrian Agency for Health and Food Safety (AGES), Finnish Institute for Health and Welfare (THL), National Public Health Center under the Ministry of Health (Lithuania) and University of Ljubljana. Restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. The interactive risk maps can be explored in detail at https://mood-platform.avia-gis.com. DisclaimerThe views and opinions of the authors expressed herein do not necessarily state or reflect those of ECDC. The accuracy of the authors statistical analysis and the findings they report are not the responsibility of ECDC. ECDC is not responsible for conclusions or opinions drawn from the data provided. ECDC is not responsible for the correctness of the data and for data management, data merging and data collation after provision of the data. ECDC shall not be held liable for improper or incorrect use of the data.

ecology↗

bioRxiv2024

Redirecting full-length FLT1 expression towards its soluble isoform promotes postischemic angiogenesis

Vascular endothelial growth factors and their tyrosine kinase receptors are key mediators of vasculogenesis and angiogenesis with FLT1 (VEGFR1) serving as a decoy receptor. A truncated mRNA transcript encoding soluble (s) FLT1 can be generated by premature cleavage and polyadenylation (APA). Although a shortening of transcripts is described in pathological settings, including heart diseases, the functional in vivo impact of FLT1 gene isoform generation and relevance for angiogenesis remain unknown. Here, we show that specific splice site mutations within Flt1 inhibit telescripting and activate APA in vivo to efficiently modulate gene isoform expression, inducing a complete loss of full-length (fl) Flt1 and a switch towards sFlt1 in mice. FLT1 is a high-affinity decoy receptor of VEGF limiting vessel overgrowth. We show that sFLT1 was sufficient for developmental vasculogenesis, whereas flFLT1 controlled ischemia-driven angiogenesis. Our results demonstrate that telescripting is essential in vivo for controlling Flt1 isoform expression and angiogenesis and can be harnessed to improve reparative revascularization. Furthermore, given the widespread abundance of APA signals, our approach may serve as a blueprint for studying telescripting and generating other truncated gene isoforms in vivo.

cell biology↗

bioRxiv2024

Identification of a novel myosin antigen activating CD8+ T cells in C57BL/6 mice

Heart-specific T cells play important roles in myocardial diseases, including myocarditis, myocardial infarction, and heart failure. However, only few cardiac antigens and their respective specific T cell receptors (TCRs) have been validated so far. Therefore, we sought to identify new cardiac T cell epitopes in C57BL/6 mice and to characterize the specific TCRs. Antigen mapping of myosin heavy chain alpha (MYHCA) led to the identification of a 9-mer epitope (MYHCA724-732) recognized by CD8+ T cells. Single-cell TCR sequencing (scTCR-seq) analysis of MYHCA-stimulated CD8+ T cells enabled the identification of distinct TCRs enriched on specific T cells. Selected TCRs inferred from scTCR-seq data were then expressed on reporter cell lines and functionally validated. Our study expands the toolkit required to study heart-directed immune responses by revealing a new cardiac antigen and specific TCRs. These tools will enable in vivo characterization of myosin-specific CD8+ T cells in murine models of myocardial diseases.

immunology↗

bioRxiv2023

Real-Time Structural Biology of DNA and DNA-Protein Complexes on an Optical Microscope

The intricate interplay between DNA and proteins is key for biological functions such as DNA replication, transcription, and repair. To better understand these interactions, it is crucial to develop tools to study DNA-protein complexes with high spatial and temporal resolution. Here, we use the vertical orientation that DNA adopts on graphene and investigate its interactions with proteins via energy transfer from a probe dye to graphene, achieving spatial resolution down to the [A]ngstrom scale. We measured the bending angle of DNA induced by adenine tracts, bulges, abasic sites and the binding of Escherichia coli endonuclease IV with unprecedented precision and millisecond time resolution. Additionally, we observed the translocation of the O6-alkylguanine DNA alkyltransferase along double-stranded DNA, reaching single-base pair resolution and detecting an affinity for adenine tracts. Overall, we foresee that this method will become a widespread tool for the dynamical study of nucleic acid and nucleic acid-protein interactions.

biophysics↗

bioRxiv2022

Development and Validation of the Vanderbilt PRS-KS, an Instrument to Quantify Polygenic Risk Score Knowledge

PurposeAs polygenic risk scores (PRS) enter clinical practice, healthcare providers and the publics comprehension of PRS results are of great importance, yet poorly understood. We present the Vanderbilt Polygenic Risk Scores Knowledge Score (Vanderbilt PRS-KS), a tool to quantify PRS knowledge. MethodsThe Vanderbilt PRS-KS was developed by a team of genetic counselors and physicians to cover key conceptual facts pertaining to PRSs. We recruited (n=500) individuals with demographics representative of a U.S. sample and graduate-level healthcare students (n=74) at a large academic medical center to participate in this validation study. We evaluated the Vanderbilt PRS-KSs psychometric properties using confirmatory factor analysis (CFA) and item response theory (IRT). ResultsThe 7-item Vanderbilt PRS-KS correlated to a single latent construct on CFA ({Lambda}=0.31-0.61). The scale showed promising reliability (Cronbachs =0.66) with IRT summed scores of [≥]2 to [≤]5, demonstrating reliability > 0.70. The Vanderbilt PRS-KS significantly correlated with genetic knowledge and applied PRS knowledge (r=0.55, r=0.29), and graduate-level healthcare students had significantly higher scores compared to the representative sample (p<0.01). ConclusionsThe Vanderbilt PRS-KS is a rigorously validated measure to quantify PRS knowledge.

genetics↗

bioRxiv2022

Brain-wide imaging of an adult vertebrate with image transfer oblique plane microscopy

Optical imaging is a powerful tool to visualise and measure neuronal activity. However, due to the size and opacity of vertebrate brains it has until now been impossible to simultaneously image neuronal circuits at cellular resolution across the entire adult brain. This is true even for the smallest known vertebrate brain in the teleost Danionella, which is still too large for existing volumetric imaging approaches. Here we introduce image transfer oblique plane microscopy, which uses a new optical refocusing solution via a custom fibre-optical faceplate, enabling a large field-of-view of up to 4 mm3 at a volume rate of 1 Hz. We demonstrate the power of this method with the first brain-wide recording of neuronal activity in an adult vertebrate.

neuroscience↗

bioRxiv2022

The mycotoxin Beauvericin exhibits immunostimulatory effects on dendritic cells via activating the TLR4 signaling pathway

Beauvericin (BEA), a mycotoxin of the enniatin family produced by various toxigenic fungi, has been attributed multiple biological activities such as anti-cancer, anti-inflammatory, and anti-microbial functions. However, effects of BEA on dendritic cells remain unknown so far. Here, we identified effects of BEA on murine granulocyte-macrophage colony-stimulating factor (GM-CSF)-cultured bone marrow derived dendritic cells (BMDCs) and the underlying molecular mechanisms. BEA potently activates BMDCs as signified by elevated IL-12 and CD86 expression. Multiplex immunoassays performed on myeloid differentiation primary response 88 (MyD88) and toll/interleukin-1 receptor (TIR) domain containing adaptor inducing interferon beta (TRIF) single or double deficient BMDCs indicate that BEA induces inflammatory cytokine and chemokine production in a MyD88/TRIF dependent manner. Furthermore, we found that BEA was not able to induce IL-12 or IFN{beta} production in Toll-like receptor 4 (Tlr4)-deficient BMDCs, whereas induction of these cytokines was not compromised in Tlr3/7/9 deficient BMDCs. This suggests that TLR4 might be the functional target of BEA on BMDCs. Consistently, in luciferase reporter assays BEA stimulation significantly promotes NF-{kappa}B activation in mTLR4/CD14/MD2 overexpressing but not control HEK-293 cells. RNA-sequencing analyses further confirmed that BEA induces transcriptional changes associated with the TLR4 signaling pathway. Together, these results identify TLR4 as a cellular BEA sensor and define BEA as a potent activator of BMDCs, implying that this compound can be exploited as a promising candidate structure for vaccine adjuvants or cancer immunotherapies.

immunology↗

bioRxiv2020

Addressable Nanoantennas with Cleared Hotspots for Single-Molecule Detection on a Portable Smartphone Microscope

The advent of highly sensitive photodetectors1,2 and the development of photostabilization strategies3 made detecting the fluorescence of a single molecule a routine task in many labs around the world. However, to this day, this process requires cost-intensive optical instruments due to the truly nanoscopic signal of a single emitter. Simplifying single-molecule detection would enable many exciting applications, e.g. in point-of-care diagnostic settings, where costly equipment would be prohibitive.4 Here, we introduce addressable NanoAntennas with Cleared HOtSpots (NACHOS) that are scaffolded by DNA origami nanostructures and can be specifically tailored for the incorporation of bioassays. Single emitters placed in the NACHOS emit up to 461-fold brighter enabling their detection with a customary smartphone camera and an 8-US-dollar objective lens. To prove the applicability of our system, we built a portable, battery-powered smartphone microscope and successfully carried out an exemplary single-molecule detection assay for DNA specific to antibiotic-resistant Klebsiella pneumonia "on the road ".

biophysics↗

bioRxiv2019

Moving Targets: Monitoring Target Trends in Drug Discovery by Mapping Targets, GO Terms, and Diseases

Drug Discovery is a lengthy and costly process and has faced a period of declining productivity within the last two decades. As a consequence, integrative data-driven approaches are nowadays on the rise in pharmaceutical research, making use of an inter-connected (network) view on diseases. In addition, evidence-based decisions are alleviated by studying the time evolution of innovation trends in drug discovery.\n\nIn this paper a new approach leveraging data mining and data integration for inspecting target innovation trends protein family-wise is presented. The study highlights protein families which are receiving emerging interest in the drug discovery community (mainly kinases and G protein coupled receptors) and those with areas of interest in target space that have just emerged in the scientific literature (mainly kinases and transporters) highlighting novel opportunities for drug intervention.\n\nIn order to delineate the evolution of target-driven research interest from a biological perspective, trends in biological process annotations from Gene Ontology (GO) and disease annotations from DisGeNet for major target families are captured. The analysis reveals an increasing interest in targets related to immune system processes, and a recurrent trend for targets involved in circulatory system processes. At the level of disease annotations, targets associated to e.g., cancer-related pathologies as well as to intellectual disability and schizophrenia are increasingly investigated nowadays.\n\nCan this knowledge be used to study the \"movement of targets\" in a network view and unravel new links between diseases and biological processes? We tackled this question by creating dynamic network representations considering data from different time periods. The dynamic network for immune system process-associated targets suggest that e.g. breast cancer as well as schizophrenia are linked to the same targets (cannabinoid receptor CB2 and VEGFR2) thus suggesting similar treatment options which could be confirmed by literature search. The methodology has the potential to identify other drug repurposing candidates and enables researchers to capture trends in research attention in target space at an early stage.\n\nThe KNIME workflows and R scripts used in this study are publicly available from https://github.com/BZdrazil/Moving_Targets.\n\nAuthor summaryIn this study we have investigated target innovation in drug discovery over a period of 22 years (1995-2016) by extracting time trends of research interest (as published in the scientific literature and stored in the ChEMBL database) in certain protein classes inspecting different measures (numbers of pharmacological measurements, targets, papers, and drugs). Focusing on the most relevant protein classes in drug discovery (G protein-coupled receptors, kinases, ion channels, nuclear receptors, proteases, and transporters), we further linked single targets to Gene Ontology (GO) biological process annotations and inspected steep increasing or decreasing trends of GO annotations within target families over time. We also tracked trends in disease annotations from DisGeNET by filtering out diseases linked to targets with emerging trends in research interest. Finally, targets, GO terms, and diseases are interconnected in network representations and shifts in research foci are investigated over time. This new methodology which utilizes data mapping and data analysis can be used to explore trends in research attention target family-wise, to uncover previously unknown links between diseases and biological processes and to identify potential candidates for drug repurposing.

bioinformatics↗

bioRxiv2019

Resident memory CD8 T cells persist for years in human small intestine

In human small intestine, most CD8 T cells in the lamina propria and epithelium express a resident memory (Trm) phenotype and persist for at least one year in transplanted tissue. Intestinal CD8 Trm cells have a clonally expanded immune repertoire that is stable over time and exhibit enhanced protective capabilities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/553792v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@10c19aaorg.highwire.dtl.DTLVardef@168e86forg.highwire.dtl.DTLVardef@73f0f5org.highwire.dtl.DTLVardef@1d08d10_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe vast majority of CD8 T cells in the human small intestine are Trm cells C_LIO_LICD8 Trm cells persist for >1 year in transplanted duodenum C_LIO_LIIntraepithelial and lamina propria CD8 Trm cells show highly similar TCR repertoire C_LIO_LIIntestinal CD8 Trm cells efficiently produce cytokines and cytotoxic mediators C_LI

immunology↗