Biology subjects

Silva, C.

Publications and source records attributed to Silva, C..

At least 19 recordsLinked to original sources

bioRxiv2025

Chromosomal evolution and polyploidy dynamics in tribe Andropogoneae (Poaceae: Panicoideae): insights from phylogenomic reconstruction

O_LIThe dissertation explored the chromosomal evolution of 230 species in the Andropogoneae tribe (Poaceae), which includes 1.224 species, using a detailed search of literature and databases. The phylogenetic analysis was based on complete plastome sequencing, and ancestral reconstruction utilized Bayesian inference and character optimization. C_LIO_LIResults indicated high diversity, with 46 variations in chromosome number (2n), ranging from 8 to 140, and 30% of species exhibiting polyploidy. This suggests multiple chromosomal alteration events occurred during the tribes evolution. C_LIO_LIThe chromosome number 2n = 20 was identified as the ancestral state for most internal nodes of the tree and confirmed as predominant in the Andropogoninae subtribe. However, more recently divergent taxa displayed higher chromosome numbers. C_LIO_LIThe research concludes that chromosomal variation is dynamic and complex. It emphasizes the importance of obtaining more chromosomal data to fill knowledge gaps and achieve a more complete understanding of the diversity and evolutionary mechanisms shaping the Andropogoneae tribe. C_LI

plant biology↗

bioRxiv2025

Deep White-Matter Pathways Mediate the Link Between Docosahexaenoic Acid (DHA) Status and Cognitive Performance in Adolescence

Docosahexaenoic acid (DHA) is a polyunsaturated fatty acid enriched in neuronal membranes and myelin and associated with cognitive performance. However, nutritional interventions show inconsistent cognitive effects, partly due to limited knowledge of the neural pathways linking DHA status to human cognition during sensitive periods of white-matter maturation, such as adolescence. We addressed this gap by studying 99 adolescents drawn from both extremes of performance on a national scholastic examination. Participants completed assessments of scholastic achievement (SA) and intellectual ability (IA), provided erythrocyte DHA samples, and underwent multimodal MRI, including diffusion, T1-weighted, and T2-weighted imaging. Independent component analysis and Bayesian multivariate LASSO models identified brain components jointly associated with DHA and cognition. Across four MRI modalities, a single deep white-matter component consistently emerged as the strongest shared pathway linking DHA with cognition. Tract-resolved analyses highlighted predominant contributions from the fornix and thalamus-temporal fasciculus, with additional subcortical and cortical involvement. In joint models, these components predicted SA and IA after accounting for DHA and other fatty acids, consistent with an indirect, mediation-like pathway. These findings move beyond DHA-behavior correlations by identifying specific neuroanatomical pathways through which a modifiable dietary factor relates to adolescent learning and intellectual performance, offering mechanistic insight relevant to neuroscience, nutrition, and education. Significance StatementAdolescence is a sensitive period for the maturation of white-matter pathways that support learning and reasoning. Docosahexaenoic acid (DHA), an essential dietary fatty acid enriched in neuronal membranes and myelin, has been linked to cognitive performance, yet the neural mechanisms underlying this association remain unclear. Using multimodal MRI and Bayesian multivariate modeling in adolescents with high or low scholastic performance, identify a specific deep white-matter pathway--centered on the fornix and the thalamus-temporal fasciculus--as the principal route connecting DHA status with scholastic achievement and intellectual ability. Additional subcortical and cortical contributions reveal a coordinated system-level architecture. These findings move beyond correlations by providing mechanistic insight into how a modifiable nutritional factor relates to cognitive development, with implications for neuroscience, public health, and education.

neuroscience↗

bioRxiv2025

Lateral flow cell-free transcriptional assay for contaminant detection

Cell free transcriptional biosensors are emerging as a powerful technology, offering enhanced capabilities for detecting chemical contaminants in settings where traditional analytical techniques fall short of societal needs. However, the sensitivity of these biosensors for many critical chemical contaminants often remains insufficient to meet regulatory detection limits, while maintaining portability and ensuring selectivity. In this work, an in vitro transcription (IVT) based lateral flow assay (LFA) is reported, which is 1000 times more sensitive than reported IVT portable detection methods. Through combining the amplification power of IVT with nucleic acid LFA-based avidity effects, we develop rapid, ultra-sensitive turn-on sensors. Our sensors meet regulatory detection limits for lead, a particularly challenging metal ion contaminant, in untreated spring water samples collected from a basin that exemplifies the environmental monitoring challenges. Additionally, we show that by optimizing the IVT conditions, we can tune the limit of detection to produce an on-off signal reaching the WHO regulation threshold and others. Finally, we evaluate the selectivity of different metal-responsive repressors in the context of in vitro biosensing and discuss how to identify potentially hazardous samples with an easy-to-use and point-of-care assay.

synthetic biology↗

bioRxiv2025

Coping with extremes: How Epigenetic and Molecular Adaptations Enable Earthworms to Thrive in Volcanic Soils

Earthworms thriving in naturally occurring geothermal soils offer rare insight into rapid adaptation to environmental extremes. Here, we show that the pantropical earthworm Amynthas gracilis survives and flourishes in soils of the Furnas Volcano (Sao Miguel Island, Azores), where conditions include elevated temperatures (up to 40 {degrees}C), high CO2 (88.6%), low O2 (10%), toxic metals, and mildly acidic pH. In a reciprocal-transplant, mesocosm-based experiment between soils overlying areas of active degassing volcanic gassing (hereafter active degassing soils) and reference soils, convergence of the epidermal thickness of the transplanted earthworms to the resident-soil phenotype (24 {+/-} 3.9 {micro}m active degassing soil, 43.8 {+/-} 8 {micro}m reference soil), was observed within 31 days. Combining RNA-Seq, DNA (5-cytosine) methylation mapping, and microRNA profiling, this phenotypic change results from coordinated transcriptional and epigenetic reprogramming. While gene-body methylation occurred at [~]98 % of loci, levels varied, and differentially methylated regions were enriched ffor genes with altered expression under volcanic stress. Multi-omics network analysis identified epithelial morphogenesis, circulatory system formation, and neural development as regulatory hubs, highlighted by a set of 41 epithelial-morphogenesis genes showing consistent methylation and miRNA patterns. Additional modules governing ion transport and signal transduction complemented the adaptive response. Collectively these findings demonstrate that A. gracilis employs dynamic DNA methylation and microRNA regulation alongside transcriptional reprogramming to generate a persistent phenotypic adjustment to a volcanic stress. This work advances our understanding of extremophile resilience and provides a scalable model for predicting organismal adaptive capacity in the face of environmental extremes.

molecular biology↗

bioRxiv2025

Gut3Gel: A High Throughput Mucus Model for Culturing Human Intestinal Microbiota

The human intestinal microbiota plays a crucial role in health and disease, yet recreating its complex interactions in vitro remains a significant challenge. Gut3Gel introduced herein as a novel in vitro mucus model, designed for culturing complex microbial communities without the need for anaerobic conditions. Intestinal microbiota samples from five donors were individually inoculated in Gut3Gel and cultured for 72 hours. Taxonomic composition assessment revealed that Gut3Gel sustains diverse microbial species and particularly promotes the growth of mucus-associated bacteria including Bifidobacterium, Lactobacillus, and Faecalibacterium. Microbial metabolic activity within Gut3Gel was confirmed by the increased production of acetate and butyrate, as well as of exopolysaccharides. Gut3Gel reproduces physiological features of intestinal mucus, providing a reproducible and scalable culturing platform. These features make Gut3Gel a promising tool for advancing microbiota research with potential applications in drug screening, microbiome mining, and high throughput testing of microbiome-modulating molecules.

microbiology↗

bioRxiv2024

Ccp1 depletion disrupts network integration of hippocampal parvalbumin interneurons

Post-translational modifications (PTMs) of microtubules (MTs) endow them with specific properties that are essential for key cellular functions, such as axonal transport. Polyglutamylation, a PTM that accumulates in long-lived MTs, has been linked to neurodegeneration in the cerebellum when in excess. While hyperglutamylation of MTs leads to neurodegeneration and disrupts the function of specific neuronal subtypes like Purkinje cells, cortical neurons, and hippocampal excitatory neurons, little is known about its impact on inhibitory interneurons and their functional integration into local networks. In this study, we generated a conditional knockout mouse model to deplete cytosolic carboxypeptidase 1 (Ccp1) in GABAergic neurons, a key MT deglutamylase expressed by hippocampal interneurons. Our findings reveal that the loss of Ccp1 has a profound effect on hippocampal parvalbumin (PV)-expressing interneurons, impairing their axonal transport and reducing their perisomatic inhibition of pyramidal cells (PCs) in the CA2 region of the hippocampus. Research TopicsMolecular Neuroscience, Cell Biology HighlightsO_LIDifferent subtypes of hippocampal interneurons express unique sets of (de)glutamylases and show varying levels of protein posttranslational glutamylation. C_LIO_LIParvalbumin interneurons become hyperglutamylated when Ccp1 activity is lost. C_LIO_LIThe loss of Ccp1 disrupts axonal transport in interneurons and is associated with decreased perisomatic inhibition of hippocampal pyramidal cells in the CA2 region. C_LI

neuroscience↗

bioRxiv2024

The kinetics of bedaquiline diffusion in tuberculous cavities opens a window for emergence of resistance.

Cavitary tuberculosis (TB) is difficult to cure and a site of relapse. Bedaquiline has been a wonder drug in the treatment of multidrug resistant TB, but emergence of resistance threatens its sustained success. To investigate the role of drug distribution in resistance development, we designed a novel laser-capture microdissection scheme to spatially resolve the penetration of bedaquiline in the necrotic center (caseum) of cavities, a recalcitrant site of disease. Working with preclinical models that form large necrotic lesions, we profiled bedaquiline and two next generation diarylquinolines TBAJ-587 and TBAJ-876. Drug concentrations were measured in laser-captured areas of cavity caseum as a function of time and distance from blood supply. To simulate drug coverage in patient cavities, the data were modeled, and drug penetration parameter estimates were linked to clinical plasma pharmacokinetics for bedaquiline and the new diarylquinolines. Pharmacokinetic-pharmacodynamic (PK-PD) simulations revealed that bedaquiline reaches efficacious concentrations in outer and deep caseum after several weeks to months and lingers at subtherapeutic concentrations up to 3 years after therapy ends. TBAJ-587 and TBAJ-876, currently in clinical development, achieve bactericidal concentrations in caseum more rapidly and shorten the window of suboptimal concentrations post treatment compared to bedaquiline. Simulations of clinically plausible dosing schemes were conducted to guide the design of clinical trials for cavitary TB and help mitigate resistance development. In summary, the slow kinetics of diffusion of bedaquiline into and out of cavity caseum creates spatio-temporal windows of subtherapeutic concentrations. Site-of-disease simulations of TBAJ-587 and TBAJ-876 predict reduced opportunities for resistance development. SIGNIFICANCEClinical resistance to bedaquiline has emerged faster than anticipated. Understanding potential contributing factors could help curb further resistance development, not only for bedaquiline but also for the next generation diarylquinolines currently in phase 2, TBAJ-587 and TBAJ-876. Here we hypothesized and confirmed that the extended time to reach steady state and slow clearance of bedaquiline leads to extremely slow diffusion into and out of cavity caseum, a recalcitrant site of TB disease and relapse. Through modeling of experimental data in a preclinical model of cavitary TB and clinical simulations, we show that the next generation diarylquinolines may reduce spatio-temporal windows of resistance development compared to bedaquiline. Our results can inform dosing schemes of diarylquinoline-based therapies that limit resistance development.

pharmacology and toxicology↗

bioRxiv2024

EMMPRIN confers metabolic advantage for monocytes and macrophages to promote disease in a model of multiple sclerosis

Monocytes and monocyte-derived macrophages have important roles in the initiation and progression of multiple sclerosis (MS). These cells undergo metabolic reprogramming to generate immunophenotypes that promote leukocyte infiltration, axonal degeneration and demyelination, worsening MS pathology. The mechanisms that dictate metabolic programs in monocytes and macrophages in MS remain unclear. We previously reported that extracellular matrix metalloproteinase inducer (EMMPRIN, CD147), a glycoprotein that acts as a chaperone of monocarboxylate transporter 4 (MCT4), assisted with glycolysis-driven pro-inflammatory phenotype in macrophages in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. Using newly-generated CCR2CreERT2:EMMPRINfl/fl (CCR2:EMMP) mice, we report that presymptomatic deletion of EMMPRIN in CCR2+ monocytes prevented or reduced clinical disability of EAE. This was correspondent with decreased infiltration of leukocytes into the CNS. Single cell RNA-seq of blood monocytes from EAE and proteomics analysis of macrophages from CCR2:EMMP-/- mice revealed significant alterations in metabolic programs, particularly reduced glycolysis and elevated mitochondrial electron transport and fatty acid oxidation, which were linked to their reduced pro-inflammatory traits. Our findings implicate EMMPRIN as a key regulator of metabolic pathways that exacerbate pro-inflammatory functions of monocytes in MS.

immunology↗

bioRxiv2023

Growth increases but regeneration declines in response to warming and drying at Arctic treeline in white spruce (Picea glauca)

1.As a temperature-delineated boundary, the Arctic treeline is predicted to shift northward in response to warming. However, the evidence for northward movement is mixed, with some sections of the treeline advancing while others remain stationary or even retreat. To identify the drivers of this variation, we need a landscape-level understanding of the interactions occurring between climate, tree growth, and population regeneration. In this study, we assessed regeneration alongside annual tree growth and climate during the 20th century. We used an ageheight model combined with tree height from aerial lidar to predict the age structure of 38,652 white spruce trees across 250 ha of Arctic treeline in the central Brooks Range, Alaska, USA. We then used age structure analysis to interpret the trends in regeneration and tree-ring analysis to interpret changes in annual tree growth. The climate became significantly warmer and drier circa 1975, coinciding with divergent responses of regeneration and tree growth. After 1975, regeneration of saplings (trees [≤] 2m tall) decreased compared to previous decades whereas annual growth in mature trees (trees >2m tall) increased by 54% (p<0.0001, Wilcoxon test). Tree-ring width was positively correlated with May-August temperature (p<0.01, Pearson coefficient) during the 20th century. However, after circa 1950, the positive correlation between temperature and growth weakened (i.e., temperature divergence) while the positive correlation with July precipitation strengthened (p<0.01, Pearson coefficient), suggesting that continued drying may limit future growth at this section of Arctic treeline. We conclude that while warmer temperatures appear to benefit annual growth in mature trees, the warmer and drier environmental conditions in spring and summer inhibit regeneration and therefore may be inhibiting the northward advance at this Arctic treeline site. Researchers should consider the interactions between temperature, water availability, and tree age when examining the future of treeline and boreal forest in a changing climate.

ecology↗

bioRxiv2022

The miR156-targeted SlSBP15 represses tomato shoot branching via modulating auxin transport and interacting with GOBLET and BRANCHED1b

The microRNA156 (miR156)/SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL/SBP) regulatory hub is highly conserved among phylogenetically distinct species, but how it interconnects multiple pathways to converge to common integrators controlling shoot architecture is still unclear. Here, we demonstrated that the miR156/SlSBP15 hub modulates tomato shoot branching (SB) by connecting phytohormones with important genetic pathways regulating both axillary bud (AB) development and outgrowth. We verified that plants overexpressing the miR156 (156-OE plants) display high SB, whereas plants overexpressing a miR156-resistant SlSBP15 alelle (rSBP15 plants) display arrested SB and are able to partially restore the wild-type (WT) phenotype in156-OE background. Although rSBP15 plants showed ABs smaller than MT, its activation is dependent on shoot apex-derived auxin transport inhibition. Additionally, hormonal measurements reveal that IAA and ABA concentrations were lower in 156-OE and higher in rSBP15-OE plants. SlSBP15 regulates AB development and outgrowth by inhibiting auxin transport and the activity of GOBLET (GOB), and by interacting with BRANCHED1b (SlBRC1b) at the protein level to control abscisic acid (ABA) levels within ABs. Our data provide a new mechanism by which the miR156/SPL/SBP hub regulates SB, and suggest that SlSBP15 has potential applications in improving tomato architecture.

developmental biology↗

bioRxiv2022

Targeting C5aR1 signaling reduced neutrophil extracellular traps and ameliorates COVID-19 pathology

Patients with severe COVID-19 develop acute respiratory distress syndrome (ARDS) that may progress to cytokine storm syndrome, organ dysfunction, and death. Considering that complement component 5a (C5a), through its cellular receptor C5aR1, has potent proinflammatory actions, and plays immunopathological roles in inflammatory diseases, we investigated whether C5a/C5aR1 pathway could be involved in COVID-19 pathophysiology. C5a/C5aR1 signaling increased locally in the lung, especially in neutrophils of critically ill COVID-19 patients compared to patients with influenza infection, as well as in the lung tissue of K18-hACE2 Tg mice (Tg mice) infected with SARS-CoV-2. Genetic and pharmacological inhibition of C5aR1 signaling ameliorated lung immunopathology in Tg-infected mice. Mechanistically, we found that C5aR1 signaling drives neutrophil extracellular trap (NET)s-dependent immunopathology. These data confirm the immunopathological role of C5a/C5aR1 signaling in COVID-19 and indicate that antagonist of C5aR1 could be useful for COVID-19 treatment.

immunology↗

bioRxiv2022

Botrytis cinerea infection accelerates ripening and cell wall disassembly to promote disease in tomato fruit

Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease. Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an ELISA-based glycomics technique to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening is dependent on the ability to infect the host and break down pectin. The B. cinerea double knockout{Delta} bcpg1{Delta}bcpg2 lacking two critical pectin degrading enzymes was found to be incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea. One-Sentence SummaryPhysiological, transcriptional, and glycomic evidence indicates Botrytis cinerea hastens tomato fruit ripening to facilitate infection by a mechanism dependent on the fungal enzymes Bcpg1 and Bcpg2.

plant biology↗

bioRxiv2021

Oligodendrocyte precursor cells guide the migration of cortical interneurons by unidirectional contact repulsion

The cerebral cortex is built by neural cells that migrate away from their birthplace. In the forebrain, ventrally-derived oligodendrocyte precursor cells (vOPCs) travel tangentially together with cortical interneurons (cINs) to reach the cortex. After birth, vOPCs form transient synapses with cINs before engaging later into myelination. Here we tested whether these populations interact during embryogenesis while migrating. By coupling histological analysis of mouse genetic models with live imaging, we showed that, while responding to the chemokine Cxcl12, vOPCs and cINs occupy mutually-exclusive forebrain territories. Moreover, vOPCs depletion selectively disrupts the migration and distribution of cINs. At the cellular level, we found that by promoting unidirectional contact-repulsion (UCoRe) of cINs, vOPCs steer their migration away from blood vessels and contribute to their allocation to proper migratory streams. UCoRe is thus an efficient strategy to spatially control the competition for a shared chemoattractant, thereby allowing cINs to reach proper cortical territories.

neuroscience↗

bioRxiv2021

Whole human genome 5'-mC methylation analysis using long read nanopore sequencing

DNA methylation is a type of epigenetic modification that affects gene expression regulation and is associated with several human diseases. Microarray and short read sequencing technologies are often used to study 5-methylcytosine (5-mC) modification of CpG dinucleotides in the human genome. Although both technologies produce trustable results, the evaluation of the methylation status of CpG sites suffers from the potential side effects of DNA modification by bisulfite and the ambiguity of mapping short reads in repetitive and highly homologous genomic regions, respectively. Nanopore sequencing is an attractive alternative for the study of 5-mC since the long reads produced by this technology allow to resolve those genomic regions more easily. Moreover, it allows direct sequencing of native DNA molecules using a fast library preparation procedure. In this work we show that 10X coverage depth nanopore sequencing, using DNA from a human cell line, produces 5-mC methylation frequencies consistent with those obtained by methylation microarray and digital restriction enzyme analysis of methylation. In particular, the correlation of methylation values ranged from 0.73 to 0.90 using an average genome sequencing coverage depth <2X or a minimum read support of 17X for each CpG site, respectively. We also showed that a minimum of 5 reads per CpG yields strong correlations (>0.89) between sequencing runs and an almost uniform variation in methylation frequencies of CpGs across the entire value range. Furthermore, nanopore sequencing was able to correctly display methylation frequency patterns according to genomic annotations, including a majority of unmethylated and methylated sites in the CpG islands and inter-CpG island regions, respectively. These results demonstrate that low coverage depth nanopore sequencing is a fast, reliable and unbiased approach to the study of 5-mC in the human genome.

genomics↗

bioRxiv2021

Adolescent social stress decrease of adult morphine-induced behavioral sensitization is dependent upon genetic background

1Deaths related to opioid use have skyrocketed in the United States, leading to a public health epidemic. Research has shown that both biological (genes) and environmental (stress) precursors are linked to opioid use. In particular, stress during adolescence - a critical period of frontal lobe development - influences the likelihood of abusing drugs. However, little is known about the biological mechanisms through which adolescent stress leads to long-term risk of opioid use, or whether genetic background moderates this response. Male and female C57BL/6J and BALB/cJ mice were exposed to chronic variable social stress (CVSS) or control conditions throughout adolescence and then tested for morphine locomotor sensitization or morphine consumption in adulthood. To examine possible mechanisms that underlie stress-induced changes in morphine behaviors, we assessed physiological changes in response to acute stress exposure and prefrontal cortex miRNA gene expression. Adolescent stress did not influence morphine sensitization or consumption in BALB/cJ animals, and there was limited evidence of stress effects in female C57BL/6J mice. In contrast, male C57BL/6J mice exposed to adolescent CVSS had blunted morphine sensitization compared to control animals; no differences were observed in the acute locomotor response to morphine administration or morphine consumption. Physiologically, C57BL/6J mice exposed to CVSS had an attenuated corticosterone recovery following an acute stressor and downregulation of twelve miRNA in the prefrontal cortex compared to control mice. The specificity of the effects for C57BL/6J versus BALB/cJ mice provides evidence of a gene by environmental interaction influencing opioid behaviors. Long-term differences in stress reactivity or miRNA expression suggests two possible biological mechanisms to evaluate in future research.

animal behavior and cognition↗

bioRxiv2020

Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains

Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.

genomics↗

bioRxiv2020

Specific quorum sensing molecules are possibly associated with responses to herbicide toxicity in a Pseudomonas strain

Pesticides contribute to pest control and increased agricultural production; however, they are toxic to non-target organisms and they contaminate the environment. The exposure of bacteria to these substances can lead to the need for physiological and structural changes for survival, which can be determined by genes whose expression is regulated by quorum sensing (QS). However, it is not yet clear whether these processes can be induced by herbicides. Thus, the aim of this work was to determine whether there is a QS response system in a Pseudomonas fluorescens strain that is modulated by herbicides. This strain was isolated from water storage tanks used for washing pesticide packaging and was tested against herbicides containing saflufenacil, glyphosate, sulfentrazone, 2,4-D, and dicamba as active molecules. We found that this strain possibly uses QS signaling molecules to control the production of reactive oxygen species, whether those produced by the bacteriums energy generating system or by molecules induced by the presence of saflufenacil and glyphosate. This strain used other signaling molecules for various stages of biofilm formation in the presence of herbicides containing sulfentrazone, 2,4-D, and dicamba. These findings, as an initial screening which will guide new studies, suggest that this strain has a flexibility in gene expression that allows survival in the presence of several stress-inducing molecules, regardless of previous exposure. This represents a model of metabolic and physiological plasticity. Biofilms made up of several bacterial species can use this model in agricultural environments, increasing the potential for degradation of xenobiotics, but with impacts on diversity and functionality of microbiotas in these environments.

microbiology↗

bioRxiv2020

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

A broad panel of potentially amplifiable microsatellite loci and a multiplex system were developed for the Amazonian symbol fish species Arapaima gigas, which is currently in high danger of extinction due to the disorderly fishing exploitation. Several factors have contributed to the increase of this threat, among which we highlight the lack of genetic information about the structure and taxonomic status of the species, as well as the lack of accurate tools for evaluation of the effectivity of current management programs. Based on Arapaima gigas whole genome, available at the NCBI database (ID: 12404), a total of 95,098 unique perfect microsatellites were identified, including their proposed primers. From this panel, a multiplex system containing 12 tetranucleotide microsatellite markers was validated. These tools are valuable for research in as many areas as bioinformatics, ecology, genetics, evolution and comparative studies, since they are able to provide more accurate information for fishing management, conservation of wild populations and genetic management of aquaculture.

genomics↗