Biology subjects

Vieira, J.

Publications and source records attributed to Vieira, J..

9 recordsLinked to original sources

bioRxiv2026

Rp-vasa: a bona fide Primordial Germ Cell marker that drives embryonic expression in the Chagas disease vector Rhodnius prolixus

Rhodnius prolixus is an insect vector of the protozoan Trypanosoma cruzi, the causative agent of debilitating Chagas disease, which is transmitted to humans during blood feeding. Identifying germline markers is a critical step in advancing vector control and transgenic technologies of these medically important insects. Transmission of genetic traits to the next generation requires proper differentiation of the germline that gives rise to gametes. Germline precursors are established during early stages of development as the primordial germ cell (PGC) population. Among the genes required for this process, vasa homologues exert a conserved role in germline specification. Here, we characterize and validate the genomic structure of the R. prolixus Rp-vasa locus and assess its expression during early embryogenesis. We observe widespread Rp-vasa expression in preblastoderm embryos. Later, during the cellular blastoderm and at the beginning of gastrulation, Rp-vasa and Rp-piwi2 expression is restricted to PGCs, morphologically identifiable as a cluster of cells at the posterior of the embryo. We also report, for the first time, the use of R. prolixus regulatory sequences to drive the expression of exogenous genes. We identify the Rp-vasa regulatory region and show that these cis-regulatory sequences are sufficient to drive Cas9 and dsRed expression in the early embryo. Together, these findings demonstrate that Rp-vasa has great potential for use as a PGC marker and as a driver for gene expression in transgenic and gene editing approaches for Triatomine vectors.

developmental biology↗

bioRxiv2021

Deposition chamber technology as building blocks for a standardized brain-on-chip framework

In vitro modeling of human brain connectomes is key to explore the structure-function relationship of the central nervous system. The comprehension of this intricate relationship will serve to better study the pathological mechanisms of neurodegeneration, and hence to perform improved drug screenings for complex neurological disorders, such as Alzheimers and Parkinsons diseases. However, currently used in vitro modeling technologies lack potential to mimic physiologically relevant neural structures, because they are unable to represent the concurrent interconnectivity between myriad subtypes of neurons across multiple brain regions. Here, we present an innovative microfluidic design that allows the controlled and uniform deposition of various specialized neuronal populations within unique plating chambers of variable size and shape. By applying our design, we offer novel neuro-engineered microfluidic platforms, so called neurofluidic devices, which can be strategically used as organ-on-a-chip platforms for neuroscience research. Through the fine tuning of the hydrodynamic resistance and the cell deposition rate, the number of neurons seeded in each plating chamber can be tailored from a thousand up to a million, creating multi-nodal circuits that represent connectomes existing within the intact brain. These advances provide essential enhancements to in vitro platforms in the quest accurately model the brain for the investigation of human neurodegenerative diseases.

bioengineering↗

bioRxiv2021

Neurite growth kinetics regulation through hydrostatic pressure in a novel triangle-shaped neurofluidic system

Microfluidic neuro-engineering design rules have been widely explored to create in vitro neural networks with the objective to replicate physiologically relevant structures of the brain. Several neurofluidic strategies have been reported to study the connectivity of neurons, either within a population or between two separated populations, through the control of the directionality of their neuronal projections. Yet, the in vitro regulation of the growth kinetics of those projections remains challenging. Here, we describe a new neurofluidic chip with a triangular design that allows the accurate monitoring of neurite growth kinetics in a neuronal culture. This device permits to measure the maximum achievable length of projecting neurites over time and to report variations in neurite length under several conditions. Our results show that, by applying positive or negative hydrostatic pressure to primary rat hippocampal neurons, neurite growth kinetics can be tuned. This work presents a pioneering approach for the precise characterization of neurite length dynamics within an in vitro minimalistic environment.

neuroscience↗

bioRxiv2021

Microchannel patterning strategies for in vitro structural connectivity modulation of neural networks

Compartmentalized microfluidic chips have demonstrated tremendous potential to create in vitro minimalistic environments for the reproduction of the neural circuitry of the brain. Although the protocol for seeding neural soma in these devices is well known and has been widely used in myriad studies, the accurate control of the number of neurites passing through the microchannels remains challenging. However, the regulation of axonal density among different groups of neurons is still a requirement to assess the inherent structural connectivity between neuronal populations. In this work, we report the effect of microchannel patterning strategies on the modulation of neuronal connectivity by applying dimensional modifications on microchannel-connected microfluidic chambers. Our results show that those strategies can modulate the direction and the number of neuronal projections of passage, therefore regulating the strength of the structural connections between two populations of neurons. With this approach, we provide innovative microfluidic design rules for the engineering of in vitro physiologically relevant neural networks.

neuroscience↗

bioRxiv2020

The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here we report fourteen DNA viruses detected in a metagenomic analysis of approximately 6500 pool-sequenced Drosophila, sampled from 47 European locations between 2014 and 2016. These include three new Nudiviruses, a new and divergent Entomopox virus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of Galbut virus, a dsRNA Partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a Bidnavirus, may be composed of up to 12 segments and represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2% or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly-available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D. melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.

microbiology↗

bioRxiv2020

Multiple loci linked to inversions are associated with eye size variation in species of the Drosophila virilis phylad

The size and shape of organs is tightly controlled to achieve optimal function. Natural morphological variations often represent functional adaptations to an ever-changing environment. For instance, variation in head morphology is pervasive in insects and the underlying molecular basis is starting to be revealed in the Drosophila genus for species of the melanogaster group. However, it remains unclear whether similar diversifications are governed by similar or different molecular mechanisms over longer timescales. To address this issue, we used species of the virilis phylad because they have been diverging from D. melanogaster for at least 40 million years. Our comprehensive morphological survey revealed remarkable differences in eye size and head shape among these species with D. novamexicana having the smallest eyes and southern D. americana populations having the largest eyes. We show that the genetic architecture underlying eye size variation is complex with multiple associated genetic variants located on most chromosomes. Our genome wide association study (GWAS) strongly suggests that some of the putative causative variants are associated with the presence of inversions. Indeed, northern populations of D. americana share derived inversions with D. novamexicana and they show smaller eyes compared to southern ones. Intriguingly, we observed a significant enrichment of genes involved in eye development on the 4th chromosome after intersecting chromosomal regions associated with phenotypic differences with those showing high differentiation among D. americana populations. We propose that variants associated with chromosomal inversions contribute to both intra- and inter-specific variation in eye size among species of the virilis phylad.

evolutionary biology↗

bioRxiv2018

RBPMetaDB: A comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins

RNA-binding proteins may play a critical role in gene regulation in various diseases or biological processes by controlling post-transcriptional events such as polyadenylation, splicing, and mRNA stabilization via binding activities to RNA molecules. Due to the importance of RNA-binding proteins in gene regulation, a great number of studies have been conducted, resulting in a large amount of RNA-Seq datasets. However, these datasets usually do not have structured organization of metadata, which limits their potentially wide use. To bridge this gap, the metadata of a comprehensive set of publicly available mouse RNA-Seq datasets with perturbed RNA-binding proteins were collected and integrated into a database called RBPMetaDB. This database contains 278 mouse RNA-Seq datasets for a comprehensive list of 163 RNA-binding proteins. These RNA-binding proteins account for only [~]10% of all known RNA-binding proteins annotated in Gene Ontology, indicating that most are still unexplored using high-throughput sequencing. This negative information provides a great pool of candidate RNA-binding proteins for biologists to conduct future experimental studies. In addition, we found that DNA-binding activities are significantly enriched among RNA-binding proteins in RBPMetaDB, suggesting that prior studies of these DNA- and RNA-binding factors focus more on DNA-binding activities instead of RNA-binding activities. This result reveals the opportunity to efficiently reuse these data for investigation of the roles of their RNA-binding activities. A web application has also been implemented to enable easy access and wide use of RBPMetaDB. It is expected that RBPMetaDB will be a great resource for improving understanding of the biological roles of RNA-binding proteins.\n\nDatabase URL: http://rbpmetadb.yubiolab.org

bioinformatics↗

bioRxiv2018

Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

evolutionary biology↗

bioRxiv2017

Estimating DSM accuracy for Attention Deficit Hyperactivity Disorder Based on Neurophysiological, Psychological, and Behavioral Correlates

Background.Psychiatric nosology lacks objective biological foundation, as well as typical biomarkers for diagnoses, which raises questions about its validity. The problem is particularly evident concerning Attention Deficit/Hyperactivity Disorder (ADHD). The objective of this study is to estimate whether the \"Diagnostic and Statistical Manual of Mental Disorders\" (DSM) is biologically valid for ADHD diagnosis using a multivariate analysis for small samples from a large dataset concerning neurophysiological, behavioral, and psychological variables.\n\nMethodsTwenty typically developing boys and 19 boys diagnosed with ADHD, aged 10-13 years, were examined using the Attentional Network Test (ANT) with records of event-related potentials (ERPs). From 815 variables, a reduced number of latent variables (LVs) were extracted with a clustering method, for further reclassification of subjects using the k-means method. This approach allowed multivariate analysis to be applied to a significantly larger number of variables than the number of cases (E. Wigneau et al., 2003, 2015)\n\nResultsFrom datasets including ERPs from the mid-frontal, mid-parietal, right frontal, and central channels, only seven subjects were miss-reclassified by the LVs. An estimated specificity of 75.00% and sensitivity of 89.47% for DSM were found in the reclassification. The kappa index between DSM and behavioral/psychological/neurophysiological data was 0.75, which is regarded as a \"substantial level of agreement\".\n\nDiscussionResults showed that CLV is a useful method for diagnostic classification using a large dataset of small samples, suggesting the biological validity of DSM for ADHD diagnosis, in accordance to alterations in fronto-striatal networks previously related to ADHD.

neuroscience↗