Biology subjects

Martinez, S.

Publications and source records attributed to Martinez, S..

34 records · Page 2Linked to original sources

bioRxiv2023

MAPK/MAK/MRK overlapping kinase (MOK) controls microglial inflammatory/type-I IFN responses via Brd4 and is involved in ALS pathophysiology

Amyotrophic lateral sclerosis (ALS) is a fatal and incurable neurodegenerative disease affecting motor neurons and characterized by microglia-mediated neurotoxic inflammation whose underlying mechanisms remain incompletely understood. In this work we reveal that MAPK/MAK/MRK overlapping kinase (MOK), with unknown physiological substrate, displays an immune function by controlling inflammatory and type-I IFN responses in microglia which are detrimental to primary motor neurons. Moreover, we uncover the epigenetic reader bromodomain-containing protein 4 (Brd4) as the first molecule regulated by MOK, by promoting Ser492-phospho-Brd4 levels. We further demonstrate that MOK regulates Brd4 functions by supporting its binding to cytokine gene promoters, therefore enabling innate immune responses. Remarkably, we show that MOK levels are increased in ALS spinal cord, particularly in microglial cells, and that administration of a chemical MOK-inhibitor to ALS model mice is able to modulate Ser492-phospho-Brd4 levels, suppress microglial activation and modify disease course, indicating a pathophysiological role of MOK kinase in ALS and neuroinflammation.

neuroscience↗

bioRxiv2022

A Re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling

Wheat blast, caused by the Triticum lineage of Pyricularia oryzae (PoT), is a serious disease that first emerged in Brazil and quickly spread to neighboring countries. The recent appearance of this disease in Bangladesh and Zambia highlights a need to understand the population biology and epidemiology of the disease so as to mitigate pandemic outbreaks. Current knowledge in these areas is largely based on analyses of wheat blast isolates collected in Brazil, and their comparison with isolates from non-wheat, endemic grasses. Those studies concluded that wheat blast is caused by a highly diverse P. oryzae population that lacks host specificity and, as a result, undergoes extensive gene flow with populations infecting non-wheat hosts. Additionally, based on genetic similarity between wheat blast and isolates infecting Urochloa species, it was proposed that the disease originally emerged via a host jump from this grass, and the widespread use of Urochloa as a pasture grass likely plays a central role in wheat blast epidemiology. Inconsistencies with earlier phylogenetic studies prompted us to re-analyze the Brazilian data in the context of a comprehensive, global, phylogenomic dataset. We now show that the seminal studies failed to sample the P. oryzae populations normally found on endemic grasses and, instead, repeatedly sampled PoT and P. oryzae Lolium (PoL) members that happened to be present in these hosts. The resulting lack of accurate and representative information about the grass-infecting populations in Brazil means that current conclusions about wheat blasts evolution, population biology and epidemiology are unsubstantiated and could be equivocal.

microbiology↗

bioRxiv2022

Exploring the adaptability and robustness of the central carbon metabolism of Mycoplasma pneumoniae

In this study we explored the adaptability and robustness of glycolysis and pyruvate metabolism of Mycoplasma pneumoniae (MPN). We used a dual approach, we analysed metabolomics data collected for a large number of OE and KO mutants and perturbation samples. Furthermore, we trained a dynamic model of central carbon metabolism and tested the models capacity to predict these mutants and perturbation samples as well as identify key controlling factors in central carbon metabolism. Our analysis of metabolite data as well as our model analysis indicate MPN metabolism is inherently robust against perturbations due to its network structure. Two key control hubs of central carbon metabolism were identified.

systems biology↗

bioRxiv2022

Binucleated cells generated by nuclear movement during neural transdifferentiation from human bone marrow-derived mesenchymal cells

Although it has been reported that bone marrow-derived cells (BMDCs) can transdifferentiate into neural cells, the findings are considered unlikely. It has been argued that the rapid neural transdifferentiation of BMDCs reported in culture studies is actually due to cytotoxic changes induced by the media. While transplantation studies indicated that BMDCs can form new neurons, it remains unclear whether the underlying mechanism is transdifferentiation or BMDCs-derived cell fusion with the existing neuronal cells. Cell fusion has been put forward to explain the presence of gene-marked binucleated neurons after gene-marked BMDCs transplantation. In the present study, we demostrated that human BMDCs can rapidly adopt a neural-like morphology through active neurite extension and binucleated human BMDCs can form with independence of any cell fusion events. We also showed that BMDCs neural transdifferentiation involves the formation of intermediate cells which can then redifferentiate into neural-like cells, redifferentiate back to the mesenchymal fate or even repeatedly switch lineages without cell division. Furthermore, we have discovered that nuclei from intermediate cells rapidly move within the cell, adopting different morphologies and even forming binucleated cells. Therefore, our results provide a stronger basis for rejecting the idea that BMDCs neural transdifferentiation is merely an artefact.

neuroscience↗

bioRxiv2022

In vivo CRISPR screens reveal SCAF1 and USP15 as novel drivers of pancreatic cancer

Functionally characterizing the genetic alterations that drive pancreatic cancer progression is a prerequisite for Precision Medicine. Here, we developed a somatic CRISPR/Cas9 mutagenesis screen to assess the transforming potential of 125 recurrently mutated long-tail pancreatic cancer genes, which revealed USP15 and SCAF1 as novel and potent Pancreatic ductal adenocarcinoma PDAC tumor suppressors, with USP15 functioning in a haplo-insufficient manner. Mechanistically, we found that loss of USP15 leads to reduced inflammatory responses associated with TNF, TGF-{beta} and IL6 signaling and sensitizes pancreatic cancer cells to PARP inhibition and gemcitabine. Similarly, genetic ablation of SCAF1 reduced inflammatory responses linked to TNF, TGF-{beta} and mTOR signaling and increased sensitivity to PARP inhibition. Furthermore, we identified that loss of SCAF1 resulted in the formation of a truncated inactive USP15 isoform at the expense of full length USP15, functionally coupling SACF1 and USP15. Notably, USP15 and SCAF1 mutations or copy number losses are observed in 31% of PDAC patients. Together, our results demonstrate the utility of in vivo CRISPR to integrate human cancer genomics with mouse modeling to delineate novel cancer driver genes USP15 and SCAF1 such as with potential prognostic and therapeutic implications.

cancer biology↗

bioRxiv2022

In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

How the genetic landscape of a tumor governs the tumors response to immunotherapy remains largely elusive. Here, we established a direct in vivo CRISPR/Cas9 gene editing methodology to assess the immune-modulatory capabilities of 573 putative cancer genes associated with altered cytotoxic activity in human cancers. Using KrasG12D- and BrafV600E-driven mouse lung cancer models, we identify Serpinb9 and Adam2 as our top immune suppressive and immune enhancing genes, respectively. Mechanistically, we show that Serpinb9 ablation in KrasG12D- and BrafV600E-mutant lung tumor cells greatly enhances the efficacy of cytotoxic T-cells in vitro and in vivo. ADAM2 is a cancer testis antigen broadly expressed in human cancers such as lung adenocarcinoma (13.9%), renal (74.7%), prostate (72.4%), uterine (28.6%) and invasive breast (9.5%) cancer. In our mouse models, we show that Adam2 expression is induced in KrasG12D- but not BrafV600E-driven murine lung tumors and that its expression is further enhanced by immunotherapy. We show that loss of Adam2 significantly decreases KrasG12D-lung tumor burden but blocks the efficacy of cytotoxic T-cells. Consistently, Adam2 overexpression dramatically increases tumor growth and enhances immunotherapy efficacy. Mechanistically, we find that Adam2s oncogenic function depends on modulating the tumor immune microenvironment by restraining productive type I and type II interferon responses as well as cytokine signaling, reducing the presentation of tumor-associated antigen, and modulating surface expression of several immunoregulatory receptors within Kras-driven lung tumors. Adam2 expression also leads to reduced levels of immune checkpoint inhibitors such as Pd-l1, Lag3, Tigit and Tim3. This reduced exhaustion within the tumor microenvironment may explain why ex vivo expanded and adoptively transferred cytotoxic T-cells show enhanced cytotoxic efficacy against Adam2 overexpressing lung tumors. Together, our study highlights the power of integrating cancer genomic with in vivo CRISPR/Cas9 screens to uncover how cancer-associated genetic alterations control responses to immunotherapies.

cancer biology↗

bioRxiv2021

Recombination of standing variation in a multi-hybrid swarm drove adaptive radiation in a fungal pathogen and gave rise to two pandemic plant diseases

Adaptive radiations fuel speciation and are characterized by rapid genetic diversification and expansion into new ecological niches. Historically, these processes were believed to be driven by selection on novel mutations but genomic analyses now indicate that standing variation and gene flow often have prominent roles. How "old" variation is combined, however, and its resulting genetic architecture within newly-adapted populations is not well understood. We reconstructed a recent radiation in the fungus, Pyricularia oryzae, that spawned a population pathogenic to eleven grass genera, and caused two new plant diseases: wheat blast - already a serious threat to global agriculture - and gray leaf spot of ryegrasses. We show that the new population evolved in a multi-hybrid swarm using only the standing variation that was present in seven individuals from five distinct, host-specialized lineages. Sexual and parasexual recombination within the swarm reassorted key host-specificity factors and generated more diversity in possibly just a few weeks than existing lineages had accumulated over hundreds to thousands of years. We suggest that the process was initiated by sexual opportunity arising when a fertile fungal strain was imported into Brazil on Urochloa introduced as forage for beef production; and we further contend that the host range expansion was largely fortuitous, with host selection playing little, if any, role in driving the process. Finally, we believe that our findings point to an overlooked role for happenstance in creating situations that allow organisms to skirt rules that would normally hold evolution in check. Commercial Endorsement DisclaimerMention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. Equal Opportunity/Non-Discrimination StatementUSDA is an equal opportunity provider and employer.

evolutionary biology↗

bioRxiv2021

Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay

Rice is an important crop in Uruguay associated mostly with livestock production in a rice and pasture rotation system since the 1920s. However, in recent years there has been interest in intensifying the production in some of these systems to satisfy market demands and increase income. Intensification occurs by augmenting the rice frequency in the rotation, including new crops like sorghum and soybean, or shortening the pasture phase. A long-term experiment was established in 2012 in the main rice producing area of Uruguay with the objective to study the impact of intensification in rice rotations. After the first cycle of rotation soils from seven rotation phases were sampled and microbial communities were studied by means of high-throughput sequencing of Illumina NovaSeq 6000. Archaeal/bacterial and fungal community composition were studied (16S rRNA and 18S gene regions) detecting 3662 and 807 bacterial and fungal Operational Taxonomic Units (OTUs), respectively. Actinobacteria, Firmicutes and Proteobacteria were the most common bacterial phyla. Among them, only Proteobacteria differed significantly between rotations. Although most fungal OTUs were unidentified, Ascomycota, Basidiomycota and Mucoromycota were the most abundant fungal classes within identified taxa. Bacterial communities differed between rotations forming three groups according to the percentage of rice in the system. Fungal communities clustered in four groups, although not well differentiated, and mostly associated with the antecessor crop. Only P and C:N varied between rotations among soil physicochemical variables after six years, and individual bacterial OTUs appeared weakly influenced by P, pH, Mg and fungal OTUs by P. The results suggest that after six years, bacteria/archaeal communities were influenced by the time with rice in the rotation, and fungal communities were more influenced by the antecessor crop. More studies are needed to associate fungal communities with certain rotational or environmental variables. Some taxa were associated with a particular rotation, and some bacterial taxa were identified as biomarkers. Fungal indicator taxa were not identified at the species level for any rotation.

microbiology↗

bioRxiv2021

Differentiation of human adult-derived stem cells towards a neural lineage involves a de-differentiation event prior to re-differentiation to neural phenotypes

Although it has been reported that mesenchymal stem cells isolated from adult tissues can be induced to overcome their mesenchymal fate and transdifferentiate into neural cells, the findings and their interpretation have been challenged. The main argument against this process is that the cells rapidly adopt neuron-like morphologies through retraction of the cytoplasm rather than active neurite extension. In this study, we examined the sequence of biological events during neural differentiation of human periodontal ligament-derived stem cells (hPDLSCs), human bone marrow-derived stem cells (hBMSCs) and human dental pulp-derived stem cells (hDPSCs) by time-lapse microscopy. We have demonstrated that hPDLSCs, hBMSCs and hDPSCs can directly differentiate into neuron-like cells without passing through a mitotic stage and that they shrink dramatically and change their morphology to that of neuron-like cells through active neurite extension. Furthermore, we observed micronuclei movement and transient cell nuclei lobulation concurrent to in vitro neurogenesis from hBMSCs and hDPSCs. Our results demonstrate that the differentiation of hPDLSCs, hBMSCs and hDPSCs towards a neural lineage occurs through a de-differentiation step followed by re-differentiation to neural phenotypes, and therefore we definitively confirm that the rapid acquisition of the neural phenotype is via a differentiation trait.

neuroscience↗

bioRxiv2020

A drug-screening platform based on organotypic cultures identifies vulnerabilities to prevent local relapse and treat established brain metastasis

Exclusion of brain metastases from clinical trials is a major cause of the limited therapeutic options for this growing population of cancer patients. Here, we report a medium-throughput drug-screening platform (METPlatform) based on organotypic cultures that allows to evaluate inhibitors against metastases growing in situ. By applying this approach to brain metastasis, we identified several hits from a library of FDA approved inhibitors and others being tested in clinical trials. A blood-brain barrier permeable HSP90 inhibitor showed high potency against mouse and human brain metastases at clinically relevant stages of the disease, including a novel model of local relapse after neurosurgery. Furthermore, in situ proteomic analysis applied to organotypic cultures with metastases treated with the chaperone inhibitor revealed novel biomarkers in human brain metastasis and actionable mechanisms of resistance. Our work validates METPlatform as a potent resource for metastasis research integrating drug-screening and unbiased omic approaches that is fully compatible with human samples. We envision that METPlatform could be established as a clinically relevant strategy to personalize the management of metastatic disease in the brain and elsewhere. SummarySystemic spread of cancer continues to be the key aspect associated with lethality. In this publication, Zhu et al. describes a drug-screening platform specifically designed to study vulnerabilities of metastasis when colonizing secondary organs and demonstrates its value in difficult-to-treat brain metastasis using new models and patient-derived samples.

cancer biology↗

bioRxiv2020

Status of the pillar coral Dendrogyra cylindrus in Los Roques National Park, Southern Caribbean

Information on the status of the pillar coral Dendrogyra cylindrus across its global distribution range is needed to plan and implement effective conservation interventions at both the national and regional level. Knowledge on the species distribution and abundance on the southernmost edge of its range was limited to qualitative data gathered in the 1980s. In 2014, we started using local ecological knowledge and extensive surveys to assess the status of the pillar coral in Archipelago Los Roques National Park, Venezuela; also evaluating the species representativeness within the MPA according to the level of protection established by the parks zoning. Between 2014 and 2016, we recorded over 1,000 colonies-the highest abundance reported to date for the species- within 14 different habitat types. Disease, bleaching and partial mortality prevalence were below 4%. Size frequency distribution was uni-modal for the MPA and dominated by medium size colonies (40cm -70cm height) suggesting potential for intrinsic population growth. However, the structure of size classes varied among reefs (Pseudo-F=2.70, p=0.03), indicating asynchronous dynamics mostly driven by reef-scale processes. Overall, our results indicate that Los Roques could be a stronghold for the species. But, to maintain the conservation value for coral reefs and the pillar coral, the MPAs zoning designation needs to be urgently revised and the extension of its high-protection zones expanded to increase habitat redundancy as well as the singular habitats composed by thickets of Acropora cervicornis and mounds of Madracis sp. This work confirms the species as extant in one of the four localities within its national range in Venezuela. However, further research on genetic diversity and connectivity among reefs within the MPA is needed to estimate effective population size and assess viability.

ecology↗

bioRxiv2020

Effect of different derivatization protocols on the calculation of trophic position using amino acids compound-specific stable isotopes

Amino acids compound-specific nitrogen stable isotope (AA-CSIA) is an emerging tool in ecology for understanding trophic system dynamics. While it has been successfully used for several independent studies across a range of environments and study locations, researchers have encountered calculation issues for determining trophic position values. Most studies introduce modifications to the constants of trophic position equation calculations, but then fail to account for the equation variations when comparing the results of separate research studies. The acceptance of this approach is related to the underlying presumption that no addition of the exogenous nitrogen atom occurs in the different methods and, therefore, such variations should not affect the outcome. In this paper, we evaluate the use of the EZfaast amino acid derivatization kit (chloroformate) and compare it to the isotopic results of two other derivatization methods. We highlight new considerations for working with AA-CSIA that might account for some of the variations in the results and lead researchers to modify constants in the equation. This likely requires developing the unique constants per derivatization method in order to be able to compare the trophic position results across different studies.

ecology↗

bioRxiv2019

Polyhydroxyalkanoate granule accumulation makes optical density measurement an unreliable method for bacterial growth assessment in Burkholderia thailandensis

Optical density (OD) measurement is the standard method used in microbiology for estimating bacterial concentrations in cultures. However, most studies do not compare these measurements with viable cell counts and assume that they reflect the real cell concentration. Burkholderia thailandensis was recently identified as a polyhydroxyalkanoate (PHA) producer. PHA biosynthesis seems to be coded by an ortholog of the Cupriavidus necator phaC gene. When growing cultures of wildtype strain E264 and an isogenic phaC- mutant, we noted a difference in their OD600 values, although viable cell counts indicated similar growth. Investigating the cellular morphologies of both strains, we found that under our conditions the wildtype strain was full of PHA granules, deforming the cells, while the mutant contained no granules. These factors apparently affected the light scattering, making the OD600 values no longer representative of cell density. We show a direct correlation between OD600 values and the accumulation of PHA. We conclude that OD measurement is unreliable for growth evaluation of B. thailandensis because of PHA production. This study also suggests that B. thailandensis could represent an excellent candidate for PHA bioproduction. Correlation between OD measurements and viable cell counts should be verified on any study realized in B. thailandensis.

microbiology↗

bioRxiv2019

Impact of within-tree organ distances on floral induction and fruit growth in apple tree: implication of carbon and gibberellin organ contents

In plants, organs are inter-dependent for growth and development. Here, we aimed to investigate the distance at which interaction between organs operates and the relative contribution of within-tree variation in carbohydrate and hormonal contents on floral induction and fruit growth, in a fruit tree case study. Manipulations of leaf and fruit numbers were performed in two years on Golden delicious apple trees, at the shoot or branch scale or one side of Y-shape trees. For each treatment, floral induction proportion and mean fruit weight were recorded. Gibberellins content in shoot apical meristems, photosynthesis, and non-structural carbohydrate concentrations in organs were measured. Floral induction was promoted by leaf presence and fruit absence but was not associated with non-structural content in meristems. This suggests a combined action of promoting and inhibiting signals originating from leaves and fruit, and involving gibberellins. Nevertheless, these signals act at short distance only since leaf or fruit presence at long distances had no effect on floral induction. Conversely, fruit growth was affected by leaf presence even at long distances when sink demands were imbalanced within the tree, suggesting long distance transport of carbohydrates. We thus clarified the inter-dependence and distance effect among organs, therefore their degree of autonomy that appeared dependent on the process considered, floral induction or fruit growth.

plant biology↗

bioRxiv2018

Nuclear polymorphism and non-proliferative adult neurogenesis in human neural crest-derived cells.

Self-renewal and lineage regulation of neural stem cells in the adult mammalian brain (aNSCs) are still far from been understood. Although previous studies have reported that some aNSCs in neurogenic niches showed irregular nuclei, their functional significance remains elusive. We used neural crest-derived human periodontal ligament stem cells (hPDLSCs) as an in vitro cell model of neurogenesis to investigate the functional significance of nuclear polymorphisms. Here, we show that hPDLSCs-derived neurons are not directly generated through cell division from stem cells. In fact, the cell shape of neural precursors is reset and start their neuronal development as round spheres. The hPDLSCs-derived neurons gradually adopted a complex morphology by forming several processes, that grew and arborized, adquiring dendritic-like and axonal-like identities, giving rise to a variety of neuron-like morphologies. To our knowledge, this article provides the first observation of these morphological events during in vitro neurogenesis and neuron polarization in human aNCSCs, and we have discovered a transient cell nuclei lobulation coincident to in vitro neurogenesis, without being related to cell proliferation. We observed that small DNA containing structures move within the cell to specific directions and temporarily form lobed nuclei. Morphological analysis also reveals that neurogenic niches in the adult mouse brain contains cells with nuclear shapes highly similar to those observed during in vitro neurogenesis from hPDLSCs. Our results provide strong evidence that neuronal differentiation from aNSCs may also occur during in vivo adult mammalian neurogenesis without being related to cell proliferation. In addition, we demonstrate that hPDLSCs-derived neurons display a sequence of morphologic development highly similar to those observed in primary neuronal cultures derived from rodent brains during neurogenesis, providing strong evidence that it is possible to reproduce neurogenic processes and obtain neurons from hPDLSCs. Beyond the central nervous system, the presence of lobed nuclei has been reported in most blood and immune cells, but the functional significance of multilobed nuclear structures is not yet stablished. Our results suggest that multilobed nuclear structures is associated to nuclear movement within the cell.

neuroscience↗

bioRxiv2018

Epidemiological Study of Autism Subgroups Using Autism Treatment Evaluation Checklist (ATEC) Score

Here we report the results of the subgroup analyses of an observational cohort of children whose parents completed the Autism Treatment Evaluation Checklist (ATEC) over the period of several years. A linear mixed effects model was used to evaluate longitudinal changes in ATEC scores within different patient subgroups. All groups decreased their mean ATEC score over time indicating improvement of symptoms, however there were significant differences between the groups. Younger children improved more than the older children. Children with milder ASD improved more than children with more severe ASD in the Communication subscale. There was no difference in improvement between females vs. males. One surprising finding was that children from developed English-speaking countries improved less than children from non-English-speaking countries.

epidemiology↗