Biology subjects

Martin, M.

Publications and source records attributed to Martin, M..

At least 109 records · Page 6Linked to original sources

bioRxiv2021

NeuroSCORE: A Genome-wide Omics-Based Model to Identify Candidate Disease Genes of the Central Nervous System

To identify and prioritize candidate disease genes of the central nervous system (CNS) we created the Neurogenetic Systematic Correlation of Omics-Related Evidence (NeuroSCORE). We used five genome-wide metrics highly associated with neurological phenotypes to score 19,598 protein-coding genes. Genes scored one point per metric, resulting in a range of scores from 0-5. Approximately 13,000 genes were then paired with phenotype data from the Online Mendelian Inheritance in Man (OMIM) database. We used logistic regression to determine the odds ratio of each metric and compared genes scoring 1+ to cause a known CNS-related phenotype compared to genes that scored zero. We tested NeuroSCORE using microarray copy number variants (CNVs) in case-control cohorts, mouse model phenotype data, and gene ontology (GO) and pathway analyses. NeuroSCORE identified 8,296 genes scored [≥]1, of which 1,580 are "high scoring" genes (scores [≥]3). High scoring genes are significantly associated with CNS phenotypes (OR=5.5, p<2x10-16), enriched in case CNVs, and enriched in mouse ortholog genes associated with behavioral and nervous system abnormalities. GO and pathway analyses showed high scoring genes were enriched in chromatin remodeling, mRNA splicing, dendrite development, and neuron projection. OMIM has no phenotype for 1,062 high scoring genes (67%). Top scoring genes include ANKRD17, CCAR1, CLASP1, DOCK9, EIF4G2, G3BP2, GRIA1, MAP4K4, MARK2, PCBP2, RNF145, SF1, SYNCRIP, TNPO2, and ZSWIM8. NeuroSCORE identifies and prioritizes CNS-disease candidate genes, many not yet associated with any phenotype in OMIM. These findings can help direct future research and improve molecular diagnostics for individuals with neurological conditions.

genomics↗

bioRxiv2021

A Mycobacterium tuberculosis effector targets mitochondrion, controls energy metabolism and limits cytochrome c exit.

Host metabolism reprogramming is a key feature of Mycobacterium tuberculosis (Mtb) infection that enables the survival of this pathogen within phagocytic cells and modulates the immune response facilitating the spread of the tuberculosis disease. Here, we demonstrate that a previously uncharacterized secreted protein from Mtb, Rv1813c manipulates the host metabolism by targeting mitochondria. When expressed in eukaryotic cells, the protein is delivered to the mitochondrial intermembrane space and promotes the enhancement of host ATP production by boosting the oxidative phosphorylation metabolic pathway. Furthermore, the release of cytochrome c from mitochondria, an early apoptotic event in response to short-term oxidative stress, is delayed in Rv1813c expressing cells. This study reveals a novel class of mitochondria targeting effectors from Mtb which might participate in host cells metabolic reprogramming and apoptosis control during Mtb infections.

microbiology↗

bioRxiv2021

The impact of C-Tactile Low threshold mechanoreceptors on affective touch and social interactions in mice.

Affective touch is necessary for proper neurodevelopment and sociability. However, it is still unclear how the neurons innervating the skin detect affective and social behaviours. To clarify this matter, we targeted a specific population of somatosensory neurons in mice, named C-low threshold mechanoreceptors (C-LTMRs), that appears particularly well suited physiologically and anatomically to perceive affective and social touch but whose contribution to these processes has not yet been resolved. Our observations revealed that C-LTMRs functional deficiency from birth induced social isolation and reduced tactile interactions in adults. Conversely, transient increase in C-LTMRs excitability in adults using chemogenetics was rewarding, temporally promoted touch seeking behaviours and thus had pro-social effects on group dynamics. This work provides the first empirical evidence that specific peripheral inputs alone can drive complex social behaviour, demonstrating the existence of a specialised neuronal circuit originating from the skin wired to promote interaction with other individuals.

neuroscience↗

bioRxiv2020

Inherent population structure determines the importance of filtering parameters for reduced representation sequencing analyses

As technological advancements enhance our ability to study population genetics, we must understand how the intrinsic properties of our datasets influence the decisions we make when designing experiments. Filtering parameter thresholds, such as call rate and minimum minor allele frequency (MAF), are known to affect inferences of population structure in reduced representation sequencing (RRS) studies. However, it is unclear to what extent the impacts of these parameter choices vary across datasets. Here, we reviewed literature on filtering choices and levels of genetic differentiation across RRS studies on wild populations to highlight the diverse approaches that have been used. Next, we hypothesized that choices in filtering thresholds would have the greatest impact when analyzing datasets with low levels of genetic differentiation between populations. To test this hypothesis, we produced seven simulated RRS datasets with varying levels of population structure, and analyzed them using four different combinations of call rate and MAF. We performed the same analysis on two empirical RRS datasets (low or high population structure). Our simulated and empirical results suggest that the effects of filtering choices indeed vary based on inherent levels of differentiation: specifically, choosing stringent filtering choices was important to detect distinct populations that were slightly differentiated, but not those that were highly differentiated. As a result, experimental design and analysis choices need to consider attributes of each specific dataset. Based on our literature review and analyses, we recommend testing a range of filtering parameter choices, and presenting all results with clear justification for ultimate filtering decisions used in downstream analyses.

bioinformatics↗

bioRxiv2020

CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations

Systemic analysis of available large-scale biological and biomedical data is critical for developing novel and effective treatment approaches against both complex and infectious diseases. Owing to the fact that different sections of the biomedical data is produced by different organizations/institutions using various types of technologies, the data are scattered across individual computational resources, without any explicit relations/connections to each other, which greatly hinders the comprehensive multi-omics-based analysis of data. We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. As a use-case study, we constructed CROssBAR COVID-19 KGs (available at: https://crossbar.kansil.org/covid_main.php) that incorporate relevant virus and host genes/proteins, interactions, pathways, phenotypes and other diseases, as well as known and completely new predicted drugs/compounds. Our COVID-19 graphs can be utilized for a systems-level evaluation of relevant virus-host protein interactions, mechanisms, phenotypic implications and potential interventions.

bioinformatics↗

bioRxiv2020

Kinesin-4 KIF21B limits microtubule growth to allow rapid centrosome polarization in T cells.

When a T cell and an antigen-presenting cell form an immunological synapse, rapid dynein-driven translocation of the centrosome towards the contact site leads to reorganization of microtubules and associated organelles. Currently, little is known about how the regulation of microtubule dynamics contributes to this process. Here, we show that the knockout of KIF21B, a kinesin-4 linked to autoimmune disorders, causes microtubule overgrowth and perturbs centrosome translocation. KIF21B restricts microtubule length by inducing microtubule pausing typically followed by catastrophe. Catastrophe induction with vinblastine prevented microtubule overgrowth and was sufficient to rescue centrosome polarization in KIF21B-knockout cells. Biophysical simulations showed that a relatively small number of KIF21B molecules can restrict microtubule length and promote an imbalance of dynein-mediated pulling forces that allows the centrosome to translocate past the nucleus. We conclude that proper control of microtubule length is important for allowing rapid remodeling of the cytoskeleton and efficient T cell polarization.

cell biology↗

bioRxiv2020

The cytoskeleton adaptor protein Sorbs1 controls the development of lymphatic and venous vessels in zebrafish

Lymphangiogenesis, the formation of lymphatic vessels is tightly linked to the development of the venous vasculature, both at the cellular and molecular levels. Here, we identify a novel role for Sorbs1, the founding member of the SoHo family of cytoskeleton adaptor proteins, in vascular and lymphatic development in zebrafish. We show that Sorbs1 is required for secondary sprouting and emergence of several vascular structures specifically derived from the axial vein. Most notably, formation of the precursor parachordal lymphatic structures is affected in sorbs1 mutant embryos, severely impacting the establishment of a proper trunk lymphatic network and leading to edema development. We show that Sorbs1 is probably not part of the Vegfc signaling, but instead might interacts with the BMP pathways. Mechanistically, we show that Sorbs1 controls FAK/Src signaling to impact on Rac1 and RhoA GTPases-regulated cytoskeleton processes. Inactivation of Sorbs1 altered cell-extracellular matrix (ECM) contact rearrangement and cytoskeleton dynamics, leading to specific defects in endothelial cell migratory and adhesive properties. Our data thus establish Sorbs1 as an important regulator of lymphangiogenesis distinct from the Vegfc signaling axis, increasing our understanding of context-specific vascular and lymphatic development.

developmental biology↗

bioRxiv2020

Multi- and transgenerational disruption of maternal behavior and female puberty by Endocrine Disrupting Chemical (EDC) mixture exposure

Female reproductive development and maternal behavior are two intertwined phenotypes centrally controlled by the hypothalamus. Endocrine disrupting chemicals (EDC) can alter these processes especially when animals are exposed during development. We propose the concept that developmental exposure to a low environmentally relevant dose of EDC mixture induces a transgenerational alteration of female rat pubertal timing and ovarian physiology throughout epigenetic reprograming of hypothalamic Kiss1, Esr1 and Oxt1 loci. Such exposure also caused a multigenerational reduction of maternal behavior induced by the loss in hypothalamic dopaminergic signaling. Our results identify the hypothalamic Polycomb Group of epigenetic repressors as actors of this mechanism of transgenerational reproductive disruption. Using a cross-fostering approach, we identified that while the reduction in maternal phenotype was normalized in EDC exposed pups raised by unexposed dams, no reversal of the pubertal phenotype was achieved, suggesting a germline transmission of the reproductive phenotype.

neuroscience↗

bioRxiv2020

Functional and molecular early enteric biomarkers for Parkinson's disease in mice and men

Parkinsons disease (PD) usually has a late clinical onset. The lack of early biomarkers for the disease represents a major challenge for developing timely treatment interventions. Here, we use an -synuclein-overexpressing transgenic (Th-1-SNCA-A30P) mouse model of PD to identify appropriate candidate markers in the gut for early stages of PD before hallmark symptoms begin to manifest. A30P mice did not show alterations in gait parameters at 2 months of age, and these mice were therefore defined as pre-symptomatic A30P mice (psA30P). We discovered early functional motility changes in the gut and early molecular dysregulations in the myenteric plexus of psA30P mice by comparative protein and miRNA profiling and cell culture experiments. We found that the proteins neurofilament light chain, vesicle-associated membrane protein 2 and calbindin 2, together with the miRNAs that regulate them, are potential biomarkers of early PD that may facilitate timely treatment and/or prevention of PD in men.

neuroscience↗

bioRxiv2020

Concerted action of kinesin-1 KIF5B and kinesin-3 KIF13B promotes efficient transport of exocytotic vesicles to microtubule plus ends

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.

cell biology↗

bioRxiv2020

Loss of Activating Transcription Factor 3 prevents KRAS-mediated pancreatic cancer

The unfolded protein response (UPR) is activated in pancreatic pathologies and suggested as a target for therapeutic intervention. In this study, wxe examined Activating Transcription Factor 3 (ATF3), a mediator of the UPR which promotes acinar-to-ductal metaplasia (ADM) in response to pancreatic injury. Since ADM is an initial step in the progression to pancreatic ductal adenocarcinoma (PDAC), we hypothesized ATF3 is required for initiation and progression of PDAC. We generated mice carrying a germ line mutation of Atf3 (Atf3-/-) combined with acinar-specific induction of oncogenic KRAS (Ptf1acreERT/+KrasLSL-G12D). Atf3-/- mice with (termed APK) and without KRASG12D were exposed to cerulein-induced pancreatitis. In response to recurrent pancreatitis, Atf3-/- mice showed decreased ADM and enhanced regeneration based on morphological and biochemical analysis. Similarly, an absence of ATF3 reduced spontaneous pancreatic intraepithelial neoplasia formation and PDAC in Ptf1acreERT/+KrasLSL-G12D mice. In response to injury, KRASG12D bipassed the requirement for ATF3 with a dramatic loss in acinar tissue and PanIN formation observed regardless of ATF3 status. However, unlike Ptf1acreERT/+KrasLSL-G12D mice, APK mice exhibited a cachexia-like phenotype, did not progress through to PDAC, and showed altered pancreatic fibrosis and immune cell infiltration. These findings suggest a complex, multifaceted role for ATF3 in pancreatic cancer pathology.

cancer biology↗

bioRxiv2020

Driving factors of conifer regeneration dynamics in eastern Canadian boreal old-growth forests

Old-growth forests play a major role in conserving biodiversity, protecting water resources, sequestrating carbon, and these forests are indispensable resources for indigenous societies. To preserve the ecosystem services provided by these boreal ecosystems, it becomes necessary to develop novel silvicultural practices capable of emulating the natural dynamics and structural attributes of old-growth forests. The success of these forest management strategies depends on developing an accurate understanding of natural regeneration dynamics. Our goal was therefore to identify the main patterns and the drivers involved in the regeneration dynamics of old-growth forests, placing our focus on boreal stands dominated by black spruce (Picea mariana (L.) Mill.) and balsam fir (Balsam fir (L.) Mill.) in eastern Canada. We sampled 71 stands in a 2200 km2 study area located within Quebecs boreal region. For each stand, we noted tree regeneration (seedlings and saplings), structural attributes (diameter distribution, deadwood volume, etc.), and abiotic (topography and soil) factors. We observed that secondary disturbance regimes and topographic constraints were the main drivers of balsam fir and black spruce regeneration. Furthermore, the regeneration dynamics of black spruce appeared more complex than those of balsam fir. We observed distinct phases of seedling production first developing within the understory, then seedling growth when gaps opened in the canopy, followed by progressive canopy closure. Seedling density, rather than the sapling density, had a major role in explaining the ability of black spruce to fill the canopy following a secondary disturbance. The density of balsam fir seedlings and saplings was also linked to the abundance of balsam fir trees at the stand level. This research helps explain the complexity of old-growth forest dynamics where many ecological factors interact at multiple temporal and spatial scales. This study also improves our understanding of ecological processes within native old-growth forests and identifies the key factors to consider when ensuring the sustainable management of old-growth boreal stands.

ecology↗

bioRxiv2019

Single-Cell RNA-Seq Reveals Endocardial Defect in Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is one of the most challenging forms of congenital heart diseases. Previous studies were mainly focused on intrinsic defects in myocardium. However, this does not sufficiently explain the abnormal development of the cardiac valve, septum, and vasculature, known to originate from the endocardium. Here, using single-cell RNA profiling, induced pluripotent stem cells, and human fetal heart tissue with an underdeveloped left ventricle, we identified a developmentally impaired endocardial population in HLHS. The intrinsic endocardial deficits contributed to abnormal endothelial to mesenchymal transition, NOTCH signaling, and extracellular matrix organization, all of which are key factors in valve formation. Consequently, endocardial abnormalities conferred reduced proliferation and maturation of cardiomyocytes through a disrupted fibronectin-integrin interaction. Several recently described HLHS de novo mutations were associated with abnormal endocardial gene and FN1 regulation and expression. Our studies provide a rationale for considering endocardial function in future regenerative strategies for HLHS.

developmental biology↗

bioRxiv2019

Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon

Little is known about the relative contributions of selective and neutral forces on human-associated microbiota assembly. Here, we characterize microbial community assembly in 52 Tsimane infant-mother pairs, using longitudinally collected stool and tongue swab samples profiled with 16S rRNA gene amplicon sequencing. The Tsimane are an indigenous Bolivian population who practice infant care associated behaviors expected to increase mother-infant dispersal. Infant consumption of dairy products, vegetables, and chicha (a fermented drink inoculated with oral microbes) was significantly associated with gut microbiota composition. At both body sites, maternal microbes at higher relative abundance were more likely to be shared. Shared microbes were also higher in abundance in infants at both body sites, but decreased in average relative abundance with age and were not significantly higher by 12 months of age. Infant microbiotas were modeled using a neutral community model of assembly, which showed that the prevalence of more than two thirds of infant-colonizing microbes could be explained using neutral processes alone. The same method was applied to datasets from Finnish and Bangladeshi infants, confirming that the majority of microbes colonizing infants from different countries were neutrally distributed. Among the Tsimane infant and adult gut microbiota samples, neutral processes were less prominent in villages with more market access. These results underscore the importance of neutral processes during infant microbiota assembly, and suggest that cultural changes associated with market integration may be affecting traditional modes of microbiota assembly by decreasing the role of these neutral processes, perhaps through changes in diet, sanitation, or access to medical care.

microbiology↗

bioRxiv2019

Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease

Multiple myeloma (MM) progression and myeloma-associated bone disease (MBD) are highly dependent on the bone marrow (BM) microenvironment, in particular on mesenchymal stromal cells (MSCs). MSCs from MM patients exhibit an abnormal transcriptional profile, suggesting that epigenetic alterations could be governing the tumor-promoting functions of MSCs and their prolonged osteoblast (OB) suppression in MM. In this study, we analyzed the DNA methylome of BM-derived MSCs from patients with monoclonal gammopathy of undetermined significance, smoldering myeloma and symptomatic MM at diagnosis in comparison with their normal counterparts. DNA methylation alterations were found at each of the myeloma stage in association with deregulated expression levels of Homeobox genes involved in osteogenic differentiation. Moreover, these DNA methylation changes were recapitulated in vitro by exposing MSCs from healthy individuals to MM plasma cells. Pharmacological targeting of DNMTs and G9a with the dual inhibitor CM-272, reverted the expression of aberrantly methylated osteogenic regulators and promoted OB differentiation of MSCs from myeloma patients. Most importantly, in a mouse model of bone marrow-disseminated MM, administration of CM-272 prevented tumor-associated bone loss and reduced tumor burden. Our results demonstrated that not only was aberrant DNA methylation a main contributor to bone formation impairment found in MM patients, but also its targeting by CM-272 was able to reverse MM-associated bone loss.\n\nKEY POINTS- Bone marrow-derived mesenchymal stromal cells (MSCs) from monoclonal gammopathy of undetermined significance, smoldering myeloma and myeloma patients exhibit an aberrant DNA methylome compared to their healthy counterparts.\n- These DNA methylation changes are associated with an altered expression of genes of the Homeobox loci that orchestrate osteogenic differentiation of mesenchymal precursors.\n- MM plasma cell-exposed healthy MSCs recapitulate the DNA methylation alterations observed in MSCs isolated from myeloma patients.\n- Dual targeting of DNMTs and the histone methyltransferase G9a with CM-272 not only controls MM tumor burden but also prevents myeloma-associated bone loss.

cancer biology↗

bioRxiv2019

Privatization of biofilm matrix in structurally heterogeneous biofilms

ABSTRACTThe self-produced biofilm provides beneficial protection for the enclosed cells, but the costly production of matrix components makes producer cells susceptible to cheating by non-producing individuals. Despite detrimental effects of non-producers, biofilms can be heterogeneous, with isogenic non-producers being a natural consequence of phenotypic differentiation processes. For instance, in Bacillus subtilis biofilm cells differ in the two major matrix components production, the amyloid fiber protein TasA and exopolysaccharides (EPS), demonstrating different expression levels of corresponding matrix genes. This raises questions regarding matrix gene expression dynamics during biofilm development and the impact of phenotypic non-producers on biofilm robustness. Here, we show that biofilms are structurally heterogeneous and can be separated into strongly and weakly associated clusters. We reveal that spatiotemporal changes in structural heterogeneity correlate with matrix gene expression, with TasA playing a key role in biofilm integrity and timing of development. We show that the matrix remains partially privatized by the producer subpopulation, where cells tightly stick together even when exposed to shear stress. Our results support previous findings on the existence of ‘weak points’ in seemingly robust biofilms as well as on the key role of linkage proteins in biofilm formation. Furthermore, we provide a starting point for investigating the privatization of common goods within isogenic populations.IMPORTANCE Biofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of non-producing individuals on biofilm development raises questions about the dynamics between community members, especially when isogenic non-producers exist within wild-type populations. We asked ourselves whether phenotypic non-producers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression occurs. Based on our results we propose that the matrix remains partly privatized by the producing subpopulation, since producing cells stick together when exposed to shear stress. The important role of linkage proteins in robustness and development of the structurally heterogeneous biofilm provides an entry into studying the privatization of common goods within isogenic populations.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

bioRxiv2019

Xyloglucan homeostasis and microtubule dynamics synergistically maintain meristem geometry and robustness of phyllotaxis in Arabidopsis

The shoot apical meristem (SAM) gives rise to all aerial organs of the plant. The cell walls are supposed to play a central role in this process, translating molecular regulation into dynamic changes of growth rates and directions, although their precise role in morphogenesis during organ formation remains not well understood. Here we investigate the role of xyloglucans (XyGs), which form a major, yet functionally poorly characterized, wall component in the SAM. Using immunolabeling, biochemical analysis, genetic approaches, micro-indentation, laser ablations and live imaging, we show that XyGs are important for meristem shape and phyllotaxis, although no difference in cell wall stiffness could be observed when XyGs are perturbed. Mutations in enzymes required for XyG synthesis also affect other cell wall components such as cellulose content and the pectin methylation status. Interestingly, we show that the control of cortical microtubules dynamics by the severing enzyme KATANIN becomes vital when XyGs are perturbed or absent. This suggests an active role of the cytoskeleton in compensating for altered wall composition.

plant biology↗

bioRxiv2019

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

evolutionary biology↗