Biology subjects

Sempere, G.

Publications and source records attributed to Sempere, G..

4 recordsLinked to original sources

bioRxiv2024

mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

We developed a python package called mbctools, designed to offer a cross-platform tool for processing amplicon data from various organisms in the context of metabarcoding studies. It can handle the most common tasks in metabarcoding pipelines such as paired-end merging, primer trimming, quality filtering, sequence denoising, zero-radius operational taxonomic unit (ZOTU) filtering, and has the capability to process multiple genetic markers simultaneously. mbctools is a menu-driven program that eliminates the need for expertise in command-line skills and ensures documentation of each analysis for reproducibility purposes. The software, designed to run in a console, offers an interactive experience, guided by keyboard inputs, assisting users along the way through data processing and hiding the complexity of command lines by letting them concentrate on selecting parameters to apply in each step of the process. In our workflow, VSEARCH is utilized for processing fastq files derived from amplicon-based Next-Generation Sequencing data. This software is a versatile open-source tool for processing amplicon sequences, offering advantages such as high speed, efficient memory usage, and the ability to handle large datasets. It provides functions for various tasks such as dereplication, clustering, chimera detection, and taxonomic assignment. VSEARCH is thus very efficient in retrieving the overall diversity of a sample. To adapt to the diversity of projects in metabarcoding, we facilitate the reprocessing of datasets with the possibility to adjust parameters. mbctools can also be launched in a headless mode, making it suited for integration into pipelines running on High-Performance Computing environments. mbctools is available at https://github.com/GuilhemSempere/mbctools, https://pypi.org/project/mbctools/.

bioinformatics↗

bioRxiv2022

Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense

Animal African trypanosomosis, caused by blood protozoan parasites transmitted mainly by tsetse flies, represents a major constraint for millions of cattle in sub-Saharan Africa. Exposed cattle include trypanosusceptible indicine breeds, severely affected by the disease, and West African taurine breeds called trypanotolerant owing to their ability to control parasite development, survive and grow in enzootic areas. Until now the genetic basis of trypanotolerance remains unclear. Here, to improve knowledge of the biological processes involved in trypanotolerance versus trypanosusceptibility, we identified bovine genes differentially expressed in five West African cattle breeds during an experimental infection by Trypanosoma congolense and their biological functions. To this end, whole blood genome-wide transcriptome of three trypanotolerant taurine breeds (NDama, Lagune and Baoule), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou) were profiled by RNA sequencing at four time points, one before and three during infection. As expected, infection had a major impact on cattle blood transcriptome regardless of the breed. The functional analysis of differentially expressed genes over time in each breed confirmed an early activation of the innate immune response, followed by an activation of the humoral response and an inhibition of T cell functions at the chronic stage of infection. More importantly, we highlighted overlooked features, such as a strong disturbance in host metabolism and cellular energy production that differentiates trypanotolerant and trypanosusceptible breeds. NDama breed showed the earliest regulation of immune response, associated with a strong activation of cellular energy production, also observed in Lagune, and to a lesser extent in Baoule. Susceptible Zebu Fulani breed differed from other breeds by the strongest modification in lipid metabolism regulation. Overall, this study provides a better understanding of the biological mechanisms at work during infection, especially concerning the interplay between immunity and metabolism that seems differentially regulated depending on the cattle breeds.

pathology↗

bioRxiv2020

Bacteriome diversity of blackflies gut and association with Onchocerca volvulus, the causative agent of onchocerciasis in Mbam valley (Center Region, Cameroon)

BackgroundVector control using larvicides is the main alternative strategy to address limits of preventive chemotherapy using ivermectin to fight onchocerciasis. However, it remains substantially limited by implementation difficulties, ecological concerns and resistance of vector populations. Therefore, efficient and environmentally safe alternative control strategies are still needed. This study explores the role of blackfly bacterial communities both on vector competence and refractoriness to O. volvulus infection in order to determine their potential as a novel vector control-based approach to fight onchocerciasis. Principal findingsA total of 1,270 blackflies were dissected and the infection rate was 10.1%, indicative of ongoing transmission of onchocerciasis in the surveyed communities. Sequencing process revealed 19 phyla and 210 genera, highlighting the diversity of gut blackflies bacterial communities. Wolbachia was the predominant genus with 70% of relative abundance of blackflies gut bacterial communities. Serratia sp and Acidomonas genera were significantly abundant among infected blackflies (p=0.043 and p=0.027, respectively), whereas other genera as Brevibacterium were associated with the absence of infection (p=0.008). Conclusion/SignificanceThis study revealed that blackfly native bacteria are potentially involved in infection by O. volvulus, either by facilitating or preventing the parasite infestation of the vector. These bacteria represent an interesting potential as a biological target for a novel approach of vector control to fight onchocerciasis. Author summaryStudies of arthropods involved in vector-borne diseases (tsetse flies, mosquitoes, and drosophila) demonstrated the importance of their native bacteria either to ease infection and transmission of human pathogenic microorganisms including parasites or on the contrary to induce host protective effects against these parasites. Indeed, some native bacteria of arthropod vectors are now recognized to be associated either with the resistance of their hosts to parasitic infections, or the reduction of their hosts viability in case of the parasite infestation, thus highlighting the potential of such bacteria to be used as biological tool for vector control strategies. However, such bacteria have never been described on blackfly, an arthropod transmitting Onchocerca volvulus, which is the parasite responsible of onchocerciasis commonly known as river blindness. This study aimed to fill this gap by investigating the bacterial diversity of blackfly bacteriome and describing the possible role of bacteria communities in susceptibility/resistance features of the blackflies to O. volvulus infection, and therefore their potential as biological targets or tool for vector control. The screening of these blackflies native bacteria during this study, highlighted some bacteria genera of interest with significant association either with the absence of O. volvulus in blackfly or with vector infection.

molecular biology↗

bioRxiv2019

Benchmarking Database Systems for Genomic Selection Implementation

MotivationWith high-throughput genotyping systems now available, it has become feasible to fully integration genotyping information into breeding programs [22]. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize them in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs one would need an efficient genotype data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems.\n\nResultsWe found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.\n\nAvailabilityhttp://gobiinx1.bti.cornell.edu:6083/projects/GBM/repos/benchmarking/browse\n\nContactyn259@cornell.edu

genomics↗