Design and implementation of a scalable high-performance computing (HPC) cluster for omics data analysis: achievements, challenges and recommendations in LMICs.

Background: The advent of high-throughput technologies, including cutting-edge sequencing devices, has revolutionized biomedical data generation and processing. Nevertheless, big data applications require novel hardware and software for parallel computing and management to handle the ever-growing data size and analysis complexity. On-premise, high-performance computing (HPC) is increasingly used in biomedical research for big data stewardship.

Uncovering the clinical relevance of unclassified variants in DNA repair genes: a focus on negative Tunisian cancer families.

Recent advances in sequencing technologies have significantly increased our capability to acquire large amounts of genetic data. However, the clinical relevance of the generated data continues to be challenging particularly with the identification of Variants of Uncertain Significance (VUSs) whose pathogenicity remains unclear. In the current report, we aim to evaluate the clinical relevance and the pathogenicity of VUSs in DNA repair genes among Tunisian breast cancer families.

PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries.

Hackathons are collaborative events that bring together diverse groups to solve predefined challenges. The COVID-19 pandemic caused by SARS-CoV-2 has emphasized the need for portable and reproducible genomics analysis pipelines to study the genetic susceptibility of the human host and investigate human-SARS-CoV-2 protein interactions. To build and strengthen institutional capacities in OMICS data analysis applied to host-pathogen interaction (HPI), the PHINDaccess project organized two hackathons in 2020 and 2021.

Effect of shading imposed by the algae Chaeotomorpha linum loads on structure, morphology and physiology of the seagrass Cymodocea nodosa.

In shallow coastal waters, seagrass and macroalgae occur together but under eutrophic conditions, bloom-forming algae can take over seagrasses causing an irreversible regime shift. Understanding the effect of macroalgae loads on seagrass meadows at an early stage can help prevent the loss of these ecosystems and the services they provide. In the present study, in situ experiments were conducted for 90 days in Bekalta (eastern coast of Tunisia) to assess the response of the seagrass Cymodocea nodosa when challenged with shading induced by filamentous macroalgae Chaetomorpha linum.

Spectrum of Genetic Diseases in Tunisia: Current Situation and Main Milestones Achieved.

Genetic diseases in Tunisia are a real public health problem given their chronicity and the lack of knowledge concerning their prevalence and etiology, and the high rates of consanguinity. Hence, we performed systematic reviews of the literature in order to provide a more recent spectrum of these disorders and to expose the challenges that still exist to tackle these kinds of diseases. A manual textual data mining was conducted using MeSH and PubMed databases.

Contribution of Nanotechnologies to Vaccine Development and Drug Delivery against Respiratory Viruses.

According to the Center for Disease Control and Prevention (CDC), the coronavirus disease 2019, a respiratory viral illness linked to significant morbidity, mortality, production loss, and severe economic depression, was the third-largest cause of death in 2020. Respiratory viruses such as influenza, respiratory syncytial virus, SARS-CoV-2, and adenovirus, are among the most common causes of respiratory illness in humans, spreading as pandemics or epidemics throughout all continents. Nanotechnologies are particles in the nanometer range made from various compositions.

Alpha-mannosidosis in Tunisian consanguineous families: Potential involvement of variants in GHR and SLC19A3 genes in the variable expressivity of cognitive impairment.

Alpha-Mannosidosis (AM) is an ultra-rare storage disorder caused by a deficiency of lysosomal alpha-mannosidase encoded by the MAN2B1 gene. Clinical presentation of AM includes mental retardation, recurrent infections, hearing loss, dysmorphic features, and motor dysfunctions. AM has never been reported in Tunisia.

Phylodynamic and phylogeographic analysis of the complete genome of the West Nile virus lineage 2 (WNV-2) in the Mediterranean basin.

Background: The West Nile virus is a highly contagious agent for a wide range of hosts. Its spread in the Mediterranean region raises several questions about its origin and the risk factors underlying the virus's dispersal.

Materials And Methods: The present study aims to reconstruct the temporal and spatial phylodynamics of West Nile virus lineage 2 in the Mediterranean region using 75 complete genome sequences from different host species retrieved from international databases.

Chemical composition of essential oils of eight Tunisian Eucalyptus species and their antibacterial activity against strains responsible for otitis.

Background: The chemical composition and biological activity of Eucalyptus essential oils have been studied extensively (EOs). A few of them were tested for antibacterial effectiveness against otitis strains. The chemical composition and antibacterial activity of the EOs of eight Tunisian Eucalyptus species were assessed in the present study.

Multi-Solvent Extraction Procedure for the Pioneer Fecal Metabolomic Analysis-Identification of Potential Biomarkers in Stable Kidney Transplant Patients.

Metabolic alteration plays a functional role in kidney allograft complications. Metabolomics is a promising high-throughput approach in nephrology but is still limited by the lack of overlap in metabolite coverage. We performed an untargeted fecal metabolomic analysis of forty stable kidney allograft recipients and twenty non-transplant controls.

Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein.

The COVID-19 pandemic is caused by SARS-CoV-2. Currently, most of the research efforts towards the development of vaccines and antibodies against SARS-CoV-2 were mainly focused on the spike (S) protein, which mediates virus entry into the host cell by binding to ACE2. As the virus SARS-CoV-2 continues to spread globally, variants have emerged, characterized by multiple mutations of the S glycoprotein.

New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations.

Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious questions. Thirteen VP1 structures with mutations mapping to the RNA entry site were analyzed using molecular dynamics simulations, and the results were combined with the experimental findings reported previously.

Identification of a CDH12 potential candidate genetic variant for an autosomal dominant form of transgrediens and progrediens palmoplantar keratoderma in a Tunisian family.

Molecular diagnosis of rare inherited palmoplantar keratoderma (PPK) is still challenging. We investigated at the clinical and genetic level a consanguineous Tunisian family presenting an autosomal dominant atypical form of transgrediens and progrediens PPK to better characterize this ultrarare disease and to identify its molecular etiology. Whole-exome sequencing (WES), filtering strategies, and bioinformatics analysis have been achieved.

Association of cytokine Th2 gene polymorphisms with autoimmune thyroid diseases in Tunisian population.

Autoimmune thyroid diseases (AITD) including Graves' disease (GD) and Hashimoto's thyroiditis (HT) are complex genetic diseases. Th2 cytokines act on the development of AITD. This study was conducted on Tunisian patients with AITD to investigate the association of Th2 cytokine gene polymorphisms and haplotype combination with GD or HT risk.

Astaxanthin inhibits aldose reductase activity in , a model of type 2 diabetes and diabetic retinopathy.

Astaxanthin (ATX) is a marine carotenoid known for its powerful antioxidant and neuroprotective properties. In this study, we investigated the in vitro and in vivo potential inhibitory effect of ATX on the aldose reductase (AR) activity, a key enzyme in the polyol pathway responsible for the pathogenesis of diabetic complications including diabetic retinopathy (DR). The gerbil (), an animal model for type 2 diabetes and DR has been used.

Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach.

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins.

A comparative study of trace elements in Cymodocea nodosa from three semi-enclosed coastal areas in Tunisia.

The present study quantifies the levels of five trace elements (TEs) Zn, Cu, Ni, Pb, and Cd in the leaves and rhizomes of Cymodocea nodosa as well as the surficial sediments from three semi-enclosed coastal areas in Tunisia, in the south Mediterranean Sea. Samples were taken from the Bizerte and Ghar El Melh lagoons and from marina Cap Monastir. The TE ranking was found to be Zn > Cu > Pb > Ni > Cd in sediments and Zn > Cu = Ni = Pb = Cd in C.

Study of retinal neurodegeneration and maculopathy in diabetic Meriones shawi: A particular animal model with human-like macula.

The purpose of this work was to evaluate a potentially useful animal model, Meriones shawi (M.sh)-developing metabolic X syndrome, diabetes and possessing a visual streak similar to human macula-in the study of diabetic retinopathy and diabetic macular edema (DME). Type 2 diabetes (T2D) was induced by high fat diet administration in M.

Biological, serological and molecular typing of potato virus Y (PVY) isolates from Tunisia.

In Tunisia, potato virus Y (PVY) currently presents a significant threat to potato production, reducing tuber yield and quality. Three hundred and eighty-five potato samples (six different cultivars) collected in autumn 2007 from nine regions in Tunisia were tested for PVY infection by DAS-ELISA. The virus was detected in all regions surveyed, with an average incidence of 80.