Biology subjects

Gut, M.

Publications and source records attributed to Gut, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions

The reference genome of Gluvia dorsalis is the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of the Northern chamois (Rupicapra rupicapra): Europe's most abundant mountain ungulate

The reference genome of Rupicapra rupicapra (subsp. rupicapra) provides insights into the genetic makeup that enabled this iconic mountain ungulate to adapt to its harsh environment, including its ability to survive in extreme weather and high altitudes--factors that are increasingly important in the face of climate change. A total of 29 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.62 Gb, composed of 124 contigs and 76 scaffolds, with contig and scaffold N50 values of 77 Mb and 101 Mb, respectively.

genomics↗

bioRxiv2024

Tag with Caution - How protein tagging influences the formation of condensates

Fluorescent proteins and peptide tags are essential tools in cellular biology, but can alter the biochemical properties of target proteins. Biomolecular condensates, which have emerged as key principles of cellular organization, are suggested to provide robustness to cells, yet they can also respond sensitively to small changes in environmental conditions--or tagging of their components, as our findings suggest. Here, we investigated the effects of sixteen widely used tags on condensate formation in various model organisms, in vitro, in cells and by computational modelling. We find that tagging strongly influenced condensation for some proteins, while others remained unaffected. Effects varied, with some tags enhancing and others decreasing condensation, and depended on the protein being tagged. Coarse-grained simulations suggest that the charge of the fluorescent protein tags is a critical factor modulating condensation behavior. Together, our results underscore the importance of rigorous experimental design and interpretation in condensate experiments.

molecular biology↗

bioRxiv2024

The Draparnaldia genome: alternative mechanisms for multicellularity and terrestrialization in green plants

Green plants contain two algal lineages: Streptophyte algae that diverged into land plants and Chlorophyte algae that are mostly aquatic. Draparnaldia is a Chlorophyte alga morphologically resembling mosses and living in both, the aquatic and terrestrial habitats. Because of its complex morphology and terrestrial adaptations, Draparnaldia can provide new insights into the evolution of multicellularity and terrestrialization in green plants. To develop Draparnaldia into a model, we de novo sequenced its genome and transcriptomes, and profiled its phytohormone repertoire. We found that 1) Expanded gene families in Draparnaldia with respect to unicellular Chlamydomonas are linked to multicellularity and abiotic stresses. 2) Draparnaldias terrestrial adaptations are reflected at both the morphological and molecular levels. 3) Draparnaldia synthesizes most of the phytohormones used by land plants to thrive in terrestrial habitats. All of this makes Draparnaldia a powerful model to uncover and study alternative evolutionary trajectories towards multicellularity and terrestrialization in plants.

evolutionary biology↗

bioRxiv2024

Mitochondrial leakage and mtDNA damage trigger early immune response in Inclusion Body Myositis.

Polymyositis with mitochondrial pathology (PM-Mito) was first identified in 1997 as a subtype of idiopathic inflammatory myopathy. Recent findings demonstrated significant molecular similarities between PM-Mito and Inclusion Body Myositis (IBM), suggesting a trajectory from early to late IBM and prompting the inclusion of PM-Mito as an IBM precursor (early IBM) within the IBM spectrum. Both PM-Mito and IBM show mitochondrial abnormalities, suggesting mitochondrial disturbance is a critical element of IBM pathogenesis. The primary objective of this cross-sectional study was to characterize the mitochondrial phenotype in PM-Mito at histological, ultrastructural, and molecular levels and to study the interplay between mitochondrial dysfunction and inflammation. Skeletal muscle biopsies of 27 patients with PM-Mito and 27 with typical IBM were included for morphological and ultrastructural analysis. Mitochondrial DNA (mtDNA) copy number and deletions were assessed by qPCR and long-range PCR, respectively. In addition, full-length single-molecule sequencing of the mtDNA enabled precise mapping of deletions. Protein and RNA levels were studied using unbiased proteomic profiling, immunoblotting, and bulk RNA sequencing. Cell-free mtDNA (cfmtDNA) was measured in the serum of IBM patients. We found widespread mitochondrial abnormalities in both PM-Mito and IBM, illustrated by elevated numbers of COX-negative and SDH-positive fibers and prominent ultrastructural abnormalities with disorganized and concentric cristae within enlarged and dysmorphic mitochondria. MtDNA copy numbers were significantly reduced, and multiple large-scale mtDNA deletions were already evident in PM-Mito, compared to healthy age-matched controls, similar to the IBM group. The activation of the canonical cGAS/STING inflammatory pathway, possibly triggered by the intracellular leakage of mitochondrial DNA, was evident in PM-Mito and IBM. Elevated levels of circulating cfmtDNA also indicated leakage of mtDNA as a likely inflammatory trigger. In PM-Mito and IBM, these findings were accompanied by dysregulation of proteins and transcripts linked to the mitochondrial membranes. In summary, we identified that mitochondrial dysfunction with multiple mtDNA deletions and depletion, disturbed mitochondrial ultrastructure, and defects of the inner mitochondrial membrane are features of PM-Mito and IBM, underlining the concept of an IBM-spectrum disease (IBM-SD). The activation of inflammatory pathways related to mtDNA release indicates a significant role of mitochondria-associated inflammation in the pathogenesis of IBM-SD. Thus, mitochondrial abnormalities precede tissue remodeling and infiltration by specific T-cell subpopulations (e.g., KLRG1+) characteristic of late IBM. This study highlights the critical role of early mitochondrial abnormalities in the pathomechanism of IBM, which may lead to new approaches to therapy.

neuroscience↗

bioRxiv2024

ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp

The reference genome of Valencia hispanica, a critically endangered actinopterygian species endemic to the Iberian Peninsula, is key to unravelling its genetic architecture and adaptation to freshwater ecosystems. This genomic resource will enable targeted conservation efforts and shed light on the species essential role in ecological dynamics, including its contributions to algal biomass regulation and role in the aquatic food web while also highlighting the challenges it faces from habitat degradation and invasive species. Furthermore, it offers opportunities to gain valuable insights into the evolutionary paths within the Valenciidae family, significantly advancing our comprehension of genetic diversity and adaptability in aquatic ecosystems. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.29Gb, composed of 99 contigs and 28 scaffolds, with contig and scaffold N50 values of 38.3Mb and 56.9Mb, respectively.

evolutionary biology↗

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management of C. rubrum. Significance StatementThe Mediterranean red coral, Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly, C. rubrum is increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated to C. rubrum.

genomics↗

bioRxiv2023

The hepatocyte Epidermal Growth Factor Receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic niche

Background & AimsLiver fibrosis is the consequence of chronic liver injury in the presence of an inflammatory component. Although the main executors of this activation are known, the mechanisms that lead to the inflammatory process that mediates the production of profibrotic factors are not well characterized. The Epidermal Growth Factor Receptor (EGFR) signaling in hepatocytes is essential for the regenerative process of the liver; however, its potential role in regulating the fibrotic niche is not yet clear. Approach & ResultsOur group generated a mouse model that expresses an inactive truncated form of the EGFR specifically in hepatocytes ({Delta}EGFR mice). Here, we have analyzed the response of WT and {Delta}EGFR mice to chronic treatment with CCl4. Resultsindicated that the hallmarks of liver fibrosis were attenuated in CCl4-treated {Delta}EGFR mice when compared to WT mice, coinciding with a faster resolution of the fibrotic process and an ameliorated damage. The absence of EGFR activity in hepatocytes induced changes in the pattern of immune cells in the liver, with a notable change in the population of M2 macrophages, more related to fibrosis resolution, as well as an increase in the population of lymphocytes related to eradication of the damage. Transcriptomic analysis of hepatocytes and secretome studies from extracellular media in in vitro studies allowed to elucidate the specific molecular mechanisms regulated by EGFR that mediate hepatocyte production of both pro-inflammatory and pro-fibrotic mediators. ConclusionsOur results support a pro-inflammatory and pro-fibrogenic role for the hepatocyte EGFR pathway during chronic liver damage.

pathology↗

bioRxiv2023

Whole genome approach to the structure and dynamics of Cacajao wild populations

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into bald and black uakaris, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of uakari populations. Beyond increasing their representation, with this work we explored the effects of the Amazon rainforests dynamism on platyrrhine species.

evolutionary biology↗

bioRxiv2023

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution

Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. They are one of the less scientifically studied animal phyla, and many aspects of their biology and evolution are still unknown, partially due to the lack of genomic resources for this phylum. As part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity, we present the taxonomic description and chromosome-level genome assembly of a newly described species of Nematomorpha (Gordionus montsenyensis Schmidt-Rhaesa & Fernandez sp. nov.). The final assembly has a total length of 288 Mb in 396 scaffolds with an N50 of 64.4 Mb, 97% of which is scaffolded into 5 pseudochromosomes. The circular mitochondrial genome was also assembled into a 15-kilobases sequence. Gene annotation predicted 10,320 protein-coding genes in the nuclear genome. In this study, we contribute a key genomic resource to not only explore the evolution of Ecdysozoa, but also to further our understanding on the genomic basis of parasitic lifestyles. In addition, we describe a species new to science from this enigmatic animal phyla.

evolutionary biology↗

bioRxiv2023

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly is available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n=30 chromosomes. Comparisons with other octopus species genomes show a conserved octopus karyotype, and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.

genomics↗

bioRxiv2023

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

genomics↗

bioRxiv2023

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human-specific. This study will open a wide range of research avenues for future primate genomic research. One-Sentence SummaryThe whole genome sequences of 233 primate species provide insight into the determinants of genetic diversity, phylogenomics, and human uniqueness.

genomics↗

bioRxiv2023

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Gunther, 1874) from the Balearic Islands (Spain)

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes, assigning 72% to known functions. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.

genomics↗

bioRxiv2023

Designed Ankyrin Repeat Proteins for detecting prostate-specific antigen expression in vivo

Late-stage prostate cancer often acquires resistance to conventional chemotherapies and transforms into a hormone-refractory, drug-resistant, and non-curative disease. Developing non-invasive tools to detect the biochemical changes that correlate with drug efficacy and reveal the onset of drug resistance would have important ramifications in managing the treatment regimen for individual patients. Here, we report the selection of new Designed Ankyrin Repeat Proteins (DARPins) that show high affinity toward prostate-specific antigen (PSA), a biomarker used in clinical monitoring of prostate cancer. Ribosome display and in vitro screening tools were used to select PSA-binding DARPins based on their binding affinity, selectivity, and chemical constitution. Surface plasmon resonance measurements demonstrated that the four lead candidates bind to PSA with nanomolar affinity. DARPins were site-specifically functionalised at a unique C-terminal cysteine with the hexadentate aza-nonamacrocyclic chelate (NODAGA) for subsequent radiolabelling with the positron-emitting radionuclide 68Ga. [68Ga]GaNODAGA-DARPins showed high stability toward transchelation and were stable in human serum for >2 h. Radioactive binding assays using streptavidin-loaded magnetic beads confirmed that the functionalisation and radiolabelling did not compromise the specificity of [68Ga]GaNODAGA-DARPins toward PSA. Biodistribution experiments in athymic nude mice bearing subcutaneous prostate cancer xenografts derived from the LNCaP cell line revealed that three of the four [68Ga]GaNODAGA-DARPins displayed specific tumour-binding in vivo. For DARPin-6, tumour-uptake in the normal group reached 4.16 {+/-} 0.58 %ID g-1 (n = 3; 2 h post-administration) and was reduced by [~]50% in the blocking group (2.47 {+/-} 0.42 %ID g-1; n = 3; P-value = 0.018). Collectively, the experimental results support the future development of new PSA-specific imaging agents for potential use in monitoring the efficacy of androgen receptor (AR)-targeted therapies.

biochemistry↗

bioRxiv2022

A TetR-like transcriptional regulator in Stenotrophomonas maltophilia involved in fatty acid metabolism is controlled by quorum sensing signals

Stenotrophomonas maltophilia is an environmental bacterium and it is also an emerging opportunistic multidrug-resistant pathogen. It uses the endogenous DSF quorum sensing (QS) system to coordinate population behaviors and to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. Whole-transcriptome sequencing analyses were performed for S. maltophilia K279a in the exponential and stationary phases as well as in exponential cultures after treatment with exogenous DSF or AHLs. The results revealed that at the beginning of the stationary phase 1673 genes are differentially expressed. COG analysis showed that most of these genes were enriched for energetic metabolism processes and regulation of gene expression. After adding DSF or AHLs, 28 or 82 genes were found deregulated, respectively, 22 of which upregulated by both autoinducers. Interestingly, among these later genes, 14 were also upregulated in the stationary phase. Gene functions regulated by all conditions include lipid and amino acid metabolism, stress response and signal transduction, nitrogen and iron metabolism, and adaptation to microoxic conditions. Among the common top upregulated QS core genes, a putative TetR-like regulator (Smlt2053) was selected for functional characterization. This regulator has been shown to control a narrow regulon, including its own operon. It was found to sense long-chain fatty acids, including the QS signal DSF, and regulate a {beta}-oxidation catabolic pathway. Overall, our findings provide clues on the role that the QS could have in S. maltophilia in the transition from the exponential to the stationary phase and bacterial fitness under high-density growth. IMPORTANCEThe quorum sensing system in Stenotrophomonas maltophilia, in addition to coordinating the bacterial population, controls virulence-associated phenotypes, such as biofilm formation, motility, protease production, and antibiotic resistance mechanisms. Biofilm formation is frequently associated with the persistence and chronic nature of nosocomial infections. In addition, biofilms exhibit high resistance to antibiotics, making treatment of these infections extremely difficult. The importance of studying the metabolic and regulatory systems controlled by quorum sensing autoinducers will make it possible to discover new targets to control pathogenicity mechanisms in S. maltophilia.

microbiology↗

bioRxiv2022

Novel method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Long-read whole genome sequencing is prohibitively expensive for mtDNA heteroplasmy detection and often does not recapitulate the full mtDNA length. Here we describe a method to target, multiplex and sequence full-length, native single-molecule the human mitochondrial genome utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks as barcodes with long-read sequencing, we implemented a protocol in an optimal setting for both high or low integrity genomic DNA to target the circular mitochondrial genome with extremely high coverage. Our analytical pipeline efficiently detects single nucleotide heteroplasmy, physically determines phase and can accurately disentangle complex deletion patterns. This workflow is a unique tool for studying mtDNA variation in health and disease, and will accelerate mitochondrial research.

genomics↗

bioRxiv2021

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

genetics↗