Biology subjects

Weiss, M.

Publications and source records attributed to Weiss, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Insectivorous birds and bats outperform ants in the top-down regulation of arthropods across strata of a Japanese temperate forest

O_LIBirds, bats, and ants are recognized as significant arthropod predators. However, empirical studies reveal inconsistent trends in their relative roles in top-down control across strata. Here, we describe the differences between forest strata in the separate effects of birds, bats, and ants on arthropod communities and their cascading effects on plant damage. C_LIO_LIWe implemented a factorial design to exclude vertebrates and ants in both the canopy and understory. Additionally, we separately excluded birds and bats from the understory using diurnal and nocturnal exclosures. At the end of the experiments, we collected all arthropods and assessed herbivory damage. C_LIO_LIArthropods responded similarly to predator exclusion across forest strata, with a density increase of 81% on trees without vertebrates and 53% without both vertebrates and ants. Additionally, bird exclusion alone led to an 89% increase in arthropod density, while bat exclusion resulted in a 63% increase. Herbivory increased by 42% when vertebrates were excluded and by 35% when both vertebrates and ants were excluded. Bird exclusion alone increased herbivory damage by 28%, while the exclusion of bats showed a detectable but non-significant increase (by 22%). In contrast, ant exclusion had no significant effect on arthropod density or herbivory damage across strata. C_LIO_LIOur results reveal that the effects of birds and bats on arthropod density and herbivory damage are similar between the forest canopy and understory in this temperate forest. In addition, ants were not found to be significant predators in our system. Furthermore, birds, bats, and ants appeared to exhibit antagonistic relationships in influencing arthropod density. These findings highlight, unprecedentedly, the equal importance of birds and bats in maintaining ecological balance across different strata of a temperate forest. C_LI

ecology↗

bioRxiv2023

Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos

Early embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell division timing and the subsequent, mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo, without breaking its eggshell. Compressing embryos to about 2/3 of their unperturbed diameter only resulted in markedly slower cell divisions. In contrast, compressing embryos to half of their native diameter frequently resulted in a loss of cytokinesis, yielding a non-natural syncytium that still allowed for multiple divisions of nuclei. Although the orientation of mitotic axes was strongly altered in the syncytium, key features of division timing and spatial arrangement of nuclei remained surprisingly similar to unperturbed embryos in the first few division cycles. This suggests that few, very robust mechanisms provide a basic and resilient program for safeguarding the early embryogenesis of C. elegans. STATEMENT OF SIGNIFICANCEEarly embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell division timing and cell positioning seemingly runs on autopilot, yielding a stereotypical development. Compressive forces, a potential hazard in the nematodes native habitat, may jeopardize this. We show that compressing embryos to 2/3 of their native diameter results in markedly slower cell divisions but leaves the early embryonic program otherwise intact. Further compression of embryos impairs the formation of new cells while nuclei still divide in a common cytoplasm (syncytium) with basic features of division timing and spatial arrangement being surprisingly similar to unperturbed embryos. This suggests that few robust mechanisms provide a basic program for the early embryonic autopilot.

developmental biology↗

bioRxiv2023

Intermittent subdiffusion of short nuclear actin rods due to interactions with chromatin

The interior of cellular nuclei, the nucleoplasm, is a crowded fluid that is pervaded by protein-decorated DNA polymers, the chromatin. Due to the complex architecture of chromatin and a multitude of associated non-equilbrium processes, e.g. DNA repair, the nucleoplasm can be expected to feature non-trivial material properties and hence anomalous transport phenomena. Here, we have used single-particle tracking on nuclear actin rods, which are important players in DNA repair, to probe such transport phenomena. Our analysis reveals that short actin rods in the nucleus show an intermittent, anti-persistent subdiffusion with clear signatures of fractional Brownian motion. Moreover, the diffusive motion is heterogeneous with clear signatures of an intermittent switching of trajectories between at least two different mobilities, most likely due to transient associations with chromatin. In line with this interpretation, hyperosmotic stress is seen to stall the motion of nuclear actin rods, whereas hypoosmotic conditions yield a reptation-like motion. Our data highlight the local heterogeneity of the nucleoplasm, e.g. distinct biochemical microenvironments and chromosome territories, that need to be taken into account for an understanding of nucleoplasmic transport and the mechanobiology of nuclei.

biophysics↗

bioRxiv2023

Deletion of SMC renders FtsK essential in Corynebacterium glutamicum

Structural maintenance of chromosomes (SMC) are ubiquitously distributed proteins involved in chromosome organization. Deletion of smc causes severe growth phenotypes in many organisms. Surprisingly, smc can be deleted in Corynebacterium glutamicum, a member of the Actinomycetota phylum, without any apparent growth phenotype. Earlier work has shown that SMC in C. glutamicum is loaded in a ParB-dependent fashion to the chromosome and functions in replichore cohesion. The unexpected absence of a growth phenotype in the smc mutant prompted us to screen for unknown synthetic interactions within C. glutamicum. Therefore, we generated a high-density Tn-5 library based on wild-type and smc-deleted C. glutamicum strains. The transposon sequencing (Tn-seq) data revealed that the DNA-translocase FtsK is essential in a smc deletion strain. FtsK localized to the septa and cell poles in wild type cells, however deletion of smc resulted in a decreased polar FtsK localization. Single-particle tracking analysis further suggests that prolonged FtsK complex activity is both required and sufficient to make up for the absence of SMC, thus achieving efficient chromosome segregation in C. glutamicum. Further, single molecule dynamics of FtsK is influenced, albeit indirectly, by DNA-loaded SMC. Deletion of ParB results in an increased of both SMC and FtsK mobility. While the first change agrees with previous data that show how ParB is essential for SMC loading on DNA, the latter suggests that FtsK mobility is affected in cells with defects in chromosome organization. Based on our data we propose a simple, yet efficient mechanism for efficient DNA segregation in C. glutamicum, even in absence of SMC proteins. ImportanceFaithful DNA segregation is of fundamental importance for life. Bacteria have efficient systems to coordinate chromosome compaction, DNA segregation and cell division. A key factor in DNA compaction is the SMC-complex that is found to be essential in many bacteria. In members of the Actinomycetota smc is dispensable, but the reason for this was unclear. We show here that the divisome associated DNA-pump FtsK can compensate SMC loss and the subsequent loss in correct chromosome organization. In cells with distorted chromosomes, FtsK functions for an extended period of time at the septum, until chromosomes are segregated.

microbiology↗

bioRxiv2023

MOCHA: Advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human disease cohorts

Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) has been increasingly used to study gene regulation. However, major analytical gaps limit its utility in studying gene regulatory programs in complex diseases. We developed MOCHA (Model-based single cell Open CHromatin Analysis) with major advances over existing analysis tools, including: 1) improved identification of sample-specific open chromatin, 2) proper handling of technical drop-out with zero-inflated methods, 3) mitigation of false positives in single cell analysis, 4) identification of alternative transcription-starting-site regulation, and 5) transcription factor-gene network construction from longitudinal scATAC-seq data. These advances provide a robust framework to study gene regulatory programs in human disease. We benchmarked MOCHA with four state-of-the-art tools to demonstrate its advances. We also constructed cross-sectional and longitudinal gene regulatory networks, identifying potential mechanisms of COVID-19 response. MOCHA provides researchers with a robust analytical tool for functional genomic inference from scATAC-seq data.

bioinformatics↗

bioRxiv2023

Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens

Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from seven primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hyper-mutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues, and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein, RUVBL2, and the mitochondrial protein, HSPD1. Antibody titers to F-actin and HSPD1 were elevated in the plasma of PDAC patients, and also detectable in healthy donors. Thus, PCs in PDAC produce auto-antibodies reacting with intracellular self-antigens, which may result from promotion of pre-existing, autoreactive B cell responses. These observations indicate that the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.

cancer biology↗

bioRxiv2023

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency

SummaryStochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of specific genomic loci after targeted purification in their native chromatin context. Applying MATAC-Seq to selected early-efficient (EE) and late-inefficient (LI) budding yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an optimal 100-115bp nucleosome-free region in combination with surrounding well-positioned nucleosomes and open +2 linker region is a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during DNA replication of eukaryotic cells. Consequently, our single-molecule assay for chromatin accessibility will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.

biochemistry↗

bioRxiv2023

The CGG triplet repeat binding protein 1 counteracts DNA secondary structure-induced transcription-replication conflicts

Short tracts of trinucleotide repeats with less than 10 repeats are found frequently throughout the genome without any apparent negative impact on DNA replication fork progression or transcription elongation. CGG binding protein 1 (CGGBP1) binds to CGG triplet repeats and has been implicated in multiple cellular processes such as transcription, replication and DNA damage. Here, we show that CGGBP1 binds to human gene promoter sites prone to G-quadruplex and R-loop secondary structure formation. Altering CGGBP1 levels results in the accumulation of R-loops and causes a defect in transcriptional elongation by RNA polymerase II, which subsequently leads to replication fork stalling and transcription-replication conflicts. Together, our work shows that short trinucleotide repeats are a source of genome-destabilizing secondary structures and cells rely on specific DNA-binding factors to maintain proper transcription and replication progression at short trinucleotide repeats.

cell biology↗

bioRxiv2022

A novel nuclease is the executing part of a bacterial plasmid defense system

Cells are continuously facing the risk of taking up foreign DNA that can compromise genomic and cellular integrity. Therefore, bacteria are in a constant arms race with mobile genetic elements such as phages, transposons and plasmids. They have developed several active strategies against invading DNA molecules that can be seen as a bacterial innate immune system. Anti-phage systems are usually organized in defense islands and can consist of restriction-modification (R-M) systems, CRISPR-Cas, and abortive infection (Abi) systems. Despite recent advances in the field, much less is known about plasmid defense systems. We have recently identified the MksBEFG system in Corynebacterium glutamicum as a novel plasmid defense system which comprises homologues of the condensin system MukFEB. Here, we investigated the molecular arrangement of the MksBEFG complex. Importantly, we identified MksG as a novel nuclease that degrades plasmid DNA and is, thus, the executing part of the system. The crystal structure of MksG revealed a dimeric assembly through its DUF2220 C-terminal domains. This domain is homologous to the TOPRIM domain of the topoisomerase II family of enzymes and contains the corresponding divalent ion binding site that is essential for DNA cleavage in topoisomerases, explaining the in vitro nuclease activity of MksG. We further show that the MksBEF subunits exhibit an ATPase cycle similar to MukBEF in vitro and we reason that this reaction cycle, in combination with the nuclease activity provided by MksG, allows for processive degradation of invading plasmids. Super-resolution localization microscopy revealed that the Mks system is spatially regulated via to the polar scaffold protein DivIVA. Introduction of plasmids increases the diffusion rate and alters the localization of MksG, indicating an activation of the system in vivo.

microbiology↗

bioRxiv2022

SegVeg: Segmenting RGB images into green and senescent vegetation by combining deep and shallow methods

The pixels segmentation of high resolution RGB images into background, green vegetation and senescent vegetation classes is a first step often required before estimating key traits of interest including the vegetation fraction, the green area index, or to characterize the sanitary state of the crop. We developed the SegVeg model for semantic segmentation of RGB images into the three classes of interest. It is based on a U-net model that separates the vegetation from the background. It was trained over a very large and diverse dataset. The vegetation pixels are then classified using a SVM shallow machine learning technique trained over pixels extracted from grids applied to images. The performances of the SegVeg model are then compared to a three classes U-net model trained using weak supervision over RGB images with predicted pixels by SegVeg as groundtruth masks. Results show that the SegVeg model allows to segment accurately the three classes, with however some confusion mainly between the background and the senescent vegetation, particularly over the dark and bright parts of the images. The U-net model achieves similar performances, with some slight degradation observed for the green vegetation: the SVM pixel-based approach provides more precise delineation of the green and senescent patches as compared to the convolutional nature of U-net. The use of the components of several color spaces allows to better classify the vegetation pixels into green and senescent ones. Finally, the models are used to predict the fraction of the three classes over the grids pixels or the whole images. Results show that the green fraction is very well estimated (R2=0.94) by the SegVeg model, while the senescent and background fractions show slightly degraded performances (R2=0.70 and 0.73, respectively). We made SegVeg publicly available as a ready-to-use script, as well as the entire dataset, rendering segmentation accessible to a broad audience by requiring neither manual annotation nor knowledge, or at least, offering a pre-trained model to more specific use.

plant biology↗

bioRxiv2022

Probing local chromatin dynamics by tracking telomeres

Chromatin dynamics is key for cell viability and replication. In interphase, chromatin is decondensed, allowing the transcription machinery to access a plethora of DNA loci. Yet, decondensed chromatin occupies almost the entire nucleus, suggesting that DNA molecules can hardly move. Recent reports have even indicated that interphase chromatin behaves like a solid body on mesoscopic scales. To explore the local chromatin dynamics, we have performed single-particle tracking on telomeres under varying conditions. We find that mobile telomeres feature in all conditions a strongly subdiffusive, anti-persistent motion that is consistent with the monomer motion of a Rouse polymer in viscoelastic media. In addition, telomere trajectories show intermittent accumulations in local niches at physiological conditions, suggesting the surrounding chromatin to reorganize on these time scales. Reducing the temperature or exposing cells to osmotic stress resulted in a significant reduction of mobile telomeres and the number of visited niches. Altogether, our data indicate a vivid local chromatin dynamics, akin to a semi-dilute polymer solution, unless perturbations enforce a more rigid state of chromatin. Statement of SignificanceIn interphase cells, chromatin is decondensed and occupies almost the entire nucleus, suggesting DNA molecules to be fairly immobile. Recent reports even indicated chromatin to behave like a solid body on mesoscopic scales. Tracking individual telomeres, we have explored local chromatin dynamics under varying conditions. Our data reveal that telomeres show an antipersistent subdiffusion (fractional Brownian motion) at physiological conditions and at lower temperatures, indicating chromatin to be a viscoelastic fluid on submicron length scales. Telomeres also appear to visit local niches, supposedly provided by the constantly reorganizing chromatin. Applying osmotic stress significantly reduced the fraction of mobile telomeres and the number of visited niches, indicating that chromatin eventually assumes an elastic, solid-like behavior under these conditions.

biophysics↗

bioRxiv2022

Generic principles of space compartmentalization in protocell patterns

Self-organization of cells into higher-order structures is key for multicellular organisms, e.g. during embryonic epithelium formation via repetitive replication of template-like founder cells. Yet, very similar spatial arrangements of cell-like compartments (protocells) are also seen in cell extracts in the absence of template structures and genetic material. Here we show that protocell patterns are highly organized, featuring a spatial arrangement and coarsening like two-dimensional foams but without signatures of disordered hyperuniformity. These features even remain unaffected when enforcing smaller protocells by stabilizing microtubule filaments. Comparing our data to generic models, we conclude that protocell patterns emerge by simultanous formation of randomly placed seeds that grow at a uniform rate until fusion of adjacent protocells drives coarsening. The strong similarity of our observations to the recently reported organization of epithelial monolayers suggests common generic principles for space allocation in living matter.

biophysics↗

bioRxiv2021

Deformation-induced actuation of cells in asymmetric periodic flow fields

Analyzing and sorting particles and/or biological cells in microfluidic devices is a topical problem in soft-matter and biomedical physics. An easy and rapid screening of the deformation of individual cells in constricted microfluidic channels allows, for example, the identification of sick or aberrant cells with altered mechanical properties, even in vast cell ensembles. The subsequently desired softness-specific segregation of cells is, however, still a major challenge. Moreover, aiming at an intrinsic and unsupervised approach raises a very general question: How can one achieve a softnessdependent net migration of particles in a microfluidic channel? Here we show that this is possible by exploiting a deformation-induced actuation of soft cells in asymmetric periodic flow fields in which rigid beads show a vanishing net drift.

biophysics↗

bioRxiv2021

Autologous human immunocompetent white adipose tissue-on-chip

Obesity and associated diseases, such as diabetes, have reached epidemic proportions globally. In the era of diabesity and due to its central role for metabolic and endocrine processes, adipose tissue (specifically white adipose tissue; WAT) has become a target of high interest for therapeutic strategies. To gain insights in cellular and molecular mechanisms of adipose (patho-)physiology, researchers traditionally relied on animal models since in vitro studies on human WAT are challenging due to the large size, buoyancy, and fragility of mature white adipocytes. Leveraging the Organ-on-Chip technology, we introduce a next-generation microphysiological in vitro model of human WAT based on a tailored microfluidic platform featuring vasculature-like perfusion. The platform integrates a 3D tissue comprising all major WAT-associated cellular components in an autologous manner, including not only mature adipocytes but also organotypic endothelial barriers and stromovascular cells featuring tissue-resident innate immune cells, specifically adipose tissue macrophages. This microphysiological tissue model recapitulates pivotal WAT functions, such as energy storage and mobilization as well as endocrine and immunomodulatory activities. The combination of all individual cell types with extra cellular matrix-like hydrogels in a precisely controllable bottom-up approach enables the generation of a multitude of replicates from the same donors circumventing issues of inter-donor variability and paving the way for personalized medicine. Moreover, it allows to adjust the models degree of complexity to fit a specific purpose via a flexible mix- and-match approach with different cell component modules. This novel WAT-on-chip system constitutes a human-based, autologous and immunocompetent in vitro model of adipose tissue that recapitulates almost full tissue heterogeneity. In the future, the new WAT-on-chip model can become a powerful tool for human-relevant research in the field of metabolism and its associated diseases as well as for compound testing and personalized- and precision medicine applications.

bioengineering↗

bioRxiv2021

Fresh insights into Mediterranean biodiversity: Environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

The Mediterranean region with its islands is among top biodiversity hotspots. It houses numerous freshwater taxa with a high rate of endemism, but is heavily impacted by anthropogenic pressures and global climate change. To conserve biodiversity, reliable data on species and genetic diversity are needed especially for the scarcely known insular freshwater ecosystems. Environmental DNA metabarcoding provide a straight-forward opportunity to assess aquatic biodiversity. Therefore, we conducted the first eDNA metabarcoding study in one stream catchment on Sicily. Specifically, we aimed to i) investigate spatial diversity patterns of macroinvertebrate communities, ii) assess seasonal changes, and iii) check if dispersal barriers can be identified. Water samples were taken at 27 different sites in two seasons and eDNA metabarcoding performed using the COI gene. In total, we detected 98 macroinvertebrate species, including 28 taxa potentially new to Sicily. Exact sequence variant (ESV) and species composition data showed that diversity differed between seasons with less taxa detected in winter. We also detected a dispersal barrier, which had a stronger effect in autumn. Our findings show that eDNA metabarcoding provides valuable information on Sicilian freshwater biodiversity. We therefore encourage its application for understudied regions to better understand the state and dynamics of freshwater biodiversity.

ecology↗

bioRxiv2021

Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence

SARS-CoV-2 has infected over 200 million and caused more than 4 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID-19 beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive immune activation that differed in character by age (young vs. old). We then characterized signals associated with recovery and convalescence to define and validate a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).

immunology↗

bioRxiv2021

Human immunocompetent Choroid-on-Chip: a novel tool for studying ocular effects of biological drugs

Disorders of the eye leading to visual impairment are a major issue that affects millions of people. On the other side ocular toxicities were described for e.g. molecularly targeted therapies in oncology and may hamper their development. Current ocular model systems feature a number of limitations affecting human-relevance and availability. To find new options for pharmacological treatment and assess mechanisms of toxicity, hence, novel complex model systems that are human-relevant and readily available are urgently required. Here, we report the development of a human immunocompetent Choroid-on-Chip (CoC), a human cell-based in vitro model of the choroid layer of the eye integrating melanocytes and microvascular endothelial cells, covered by a layer of retinal pigmented epithelial cells. Immunocompetence is achieved by perfusion of peripheral immune cells. We demonstrate controlled immune cell recruitment into the stromal compartments through a vascular monolayer and in vivo-like cytokine release profiles. To investigate applicability for both efficacy testing of immunosuppressive compounds as well as safety profiling of immunoactivating antibodies, we exposed the CoCs to cyclosporine and tested CD3 bispecific antibodies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/443846v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@506402org.highwire.dtl.DTLVardef@1d5cdd3org.highwire.dtl.DTLVardef@1bc09d3org.highwire.dtl.DTLVardef@2909de_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

bioengineering↗

bioRxiv2021

Generation and mutational analysis of a transgenic mouse model of human SRY

SRY is the Y-chromosomal gene that determines male sex development in humans and most other mammals. After three decades of study, we still lack a detailed understanding of which domains of the SRY protein are required to engage pathway of gene activity leading to testis development. Some insight has been gained from the study of genetic variations underlying differences/disorders of sex determination (DSD), but the lack of a system of experimentally generating SRY mutations and studying their consequences in vivo has limited progress in the field. To address this issue, we generated a mouse model carrying a human SRY transgene able to drive male sex determination in XX mice. Using CRISPR-Cas9 gene editing, we generated novel genetic modifications in each of SRYs three domains (N-terminal, HMG box, and C-terminal) and performed detailed analysis of their molecular and cellular effects on embryonic testis development. Our results provide new functional insights unique to human SRY and the causes of DSD, and present a versatile and powerful system in which to demonstrate causality of SRY variations in DSD, to functionally study the SRY variation database, and to characterize new pathogenic SRY variations found in DSD.

developmental biology↗