Dipartimento di Biotecnologie

RNA-Seq is a powerful technology for gene expression profilìng. The sequence read length and coverage allowed by current sequencing technologies also permits an estimation of RNA isoforms generateti by alternative splicing (AS). Recent studies have demonstrated that significant changes in AS events are reiated to breast cancer (BC), suggesting that an understanding of these events could increase prognostic accuracy ancf open new frontiers in molecular oncology. Genomics and proteomics studies revealed the different biological activity of estrogen receptor with respect to a relìes also on the components of the splicing machinery, confirming the relationship between ERbeta and mRNA splicing

The widespread adoption of NGS technologies has created in recent years an unparalleled inflow of sequence data, which can be leveraged to obtain clear information on the genetics and transcriptome of various organisms. In agronomics, these new methods can be used to gather information on cultivars of sequenced organisms. In particular we were interested in identifying putative specific genes represented in Vitis vinifera cv Corvina and not in the sequence grape clone (Pinot Noir 40024). These genes could be of interest in order to investigate the molecular bases of specific quality characteristics. To this end, we have pooled RNA of Vitis vinifera cv. Corvina samples taken from 45 different tissues and/or development stages, and sequenced it with an Illumina HiSeq platform. We obtained more than 100 million reads, which were filtered and assembled with the Velvet/Oases software suite. To facilitate the assembly, we provided the software with the alignment of the reads against the V...

Vitis vinifera, ROC, sensitivity ,specificity, significantly differentially expressed genes The recent development of transcriptomic approaches based on Next Generation Sequencing is gaining popularity as they provide a genome-wide, precise, quantitative measure of gene expression. However microarray still are a valuable tool for differential gene expression studies as they are cheap, easy to manage and to analyze. In this work we have assessed the performances of two microarray platforms (Combimatrix and Nimblegen) and two strategies of probe design (single or multiple probes per transcript) in gene expression analysis across two Vitis vinifera berry developmental stages. The same samples were analyzed by RNASeq analysis using an Illumina GAIIx sequencer. In order to assess sensitivity and specificity of the four microarray designs in detecting significantly differentially expressed genes, assuming RNASeq data as reference, Receive Operating Characteristic (ROC) analysis has been p...

1 Department of Biochemistry and Genetic, Pedagogic Research Unit of Genetic, Peleforo Gon Coulibaly University Korhogo, Côte d’Ivoire. 2 Division of General Medicine and Cardiology, Korhogo General Regional Hospital (Centre Hospitalier Régional de Korhogo), Côte d’Ivoire. 3 Department of Animal Biology, Peleforo Gon Coulibaly University Korhogo, Côte d’Ivoire. 4 Laboratoire de Biologie et Santé de l'UFR Biosciences, Université Félix Houphouët Boigny Abidjan, Côte d’Ivoire. 5 Département de Sociologie et d’Anthropologie, Université Peleforo Gon Coulibaly Korhogo, Côte d’Ivoire. 6 Unité de Formation et de Recherche (UFR) des Sciences Médicales, Université Alassane Ouattara de Bouaké, Côte d’Ivoire.

Background: Inflammatory bowel diseases (IBDs) are complex, multifactorial disorders that comprise Crohn’s disease (CD) and ulcerative colitis (UC). Recent discoveries have brought much attention to the genetic predisposition of patients with IBD. Here we evaluate the interaction between IBD genetic risk factors susceptibility and CD occurrence in an IBD pediatric patient population, performing a clinical exome survey. Methods: From February 2018 to April 2019, we collected blood samples from 7 pediatric patients with IBD concerns from several collaborating health centers and/or hospitals. Blood samples were processed by extracting and sequencing DNA for a clinical exome survey. Shophia-DDM-v3-4 platform allowed sequenced reads alignment on hg19 genome as well as genetic variant calling. Both IBD risk and pathogenic genetic variants covered by at least 20 reads were selected for subjacent analysis. Results: Normality and Bartlett tests of both risk and pathogenic genetic variants su...

Peanut (Arachis species) plants originated in South America where they have existed for thousands of years. Successively, peanut culture has been introduced in many African countries and was incorporated into local traditional food cultures. Numerous studies showed peanut nutritive importance and capacity to prevent several human diseases. The target of the present survey aimed to create a germplasm benchmark of peanut varieties in the north region of Cote d’Ivoire (West Africa country) since this plant is weakly studied in this geographic area. For this purpose, six peanut varieties were processed and pre and/or post-harvest measurements have been brought on seedlings. In addition, biochemical composition of peanut seed for each considered varieties were measured. Statistical analysis based on several R software functions showed a good quality of collected peanut data and proposed post-harvest parameters as an adequate factor clustering the present analyzed peanut varieties. Then, ...

The spatiotemporal activities of straw-colored fruit bats, Eidolon helvum (Kerr, 1792) a near-threatened species has been studied in the Commune of Plateau in Abidjan from August 2012 to July 2013. The present survey carried out by direct observations aimed in monitoring the straw-colored fruits bats population with the purpose to discriminate their circadian rhythm activities patterns in terms of time and space by processing behavioural pattern frequencies as well as by identifying distribution discriminant factors. Results showed that daily activity pattern was characterized by (i) sleeping activity from 07:00 Am to 05:00 Pm, (ii) awaking (05:00 Pm-05:30 Pm) and (iii) grooming in the early evening (05:30 Pm-06:00 Pm) and (iv) dispersion from 06:00 to Pm-07:00 Pm. Activities patterns varied with food availability, reproduction and season. A right integration of presently processed data into the biodiversity system preservation strategy should contribute to ensure and guarantee a ra...