kais ghedira - Academia.edu (original) (raw)

Papers by kais ghedira

InTech eBooks, Oct 11, 2017

Biomedical engineering, Sep 28, 2022

Infection, Genetics and Evolution, Nov 1, 2022

Saudi Journal of Biological Sciences, Feb 1, 2022

Graphical abstract

SARS-CoV-2 is one of the most common pathogens. SARS-CoV-2 has shown 80% genome identity with oth... more SARS-CoV-2 is one of the most common pathogens. SARS-CoV-2 has shown 80% genome identity with other Corona viruses. Due to the high rate of infection reported in the COVID-19 pandemic, in recent months, a lot of studies have been performed on the introduction of antiviral drugs. Secondary metabolites as alkaloids, essential oils, flavonoids, polyphenols and other natural compounds have shown promise as antiviral agents against several pathogenic viruses including SARS-CoV-2. The antimicrobial peptides display narrow-or broad spectrum activity against microbes including COVID-19 causative agent. The gathering of such data related to these molecules in one central database resource would therefore be of great benefit to the exploitation of these anti-coronavirus peptides and anti-COVID-19 secondary metabolites in the present context of increasing contagiousness in humans and its spread across the globe. The database AntiCov-DB has been developed to facilitate access to important infor...

Foods

Globally, Campylobacter is a significant contributor to gastroenteritis. Efficient pathogens are ... more Globally, Campylobacter is a significant contributor to gastroenteritis. Efficient pathogens are qualified by their virulence power, resistance to antibiotics and epidemic spread. However, the correlation between antimicrobial resistance (AR) and the pathogenicity power of pathogens is complex and poorly understood. In this study, we aimed to investigate genes encoding virulence and AR mechanisms in 177 Campylobacter isolates collected from layer hens and eggs in Tunisia and to assess associations between AR and virulence characteristics. Virulotyping was determined by searching 13 virulence genes and AR-encoding genes were investigated by PCR and MAMA-PCR. The following genes were detected in C. jejuni and C. coli isolates: tet(O) (100%/100%), blaOXA-61 (18.82%/6.25%), and cmeB (100%/100%). All quinolone-resistant isolates harbored the Thr-86-Ile substitution in GyrA. Both the A2074C and A2075G mutations in 23S rRNA were found in all erythromycin-resistant isolates; however, the er...

Journal of Medical Microbiology

Introduction. Candida spp. may cause opportunistic infections called vulvovaginal candidiasis (VV... more Introduction. Candida spp. may cause opportunistic infections called vulvovaginal candidiasis (VVC), which is estimated to be the second most common cause of vaginitis worldwide. Gap Statement. Under various circumstances, VVC could compromise pregnancy outcomes. Emerging data suggests that VVC during pregnancy may be associated with increased risk of complications and congenital cutaneous candidiasis. Aim. To assess the prevalence of Candida spp. in asymptomatic pregnant women and determine the susceptibility of the isolates to antifungal drugs. Methodology. In a prospective cohort, 65 high vaginal swab samples of consented pregnant women. Candida isolates were identified using both microbiological and molecular tools and drug susceptibilities were profiled. Results. The prevalence of VVC among our study participants was 37 %, 24 of the 65 asymptomatic pregnant women show Candida spp. colonization. C. albicans was the most common species 61 %, followed by C. glabrata 39 %. In addit...

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massiv... more Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

Biochemical and Biophysical Research Communications, 2022

Nowadays, a large number of databases have been developed gathering different types of therapeuti... more Nowadays, a large number of databases have been developed gathering different types of therapeutic peptides including antimicrobial, antiviral and scorpion toxins peptides facilitating the searching for these molecules and their structural characteristics and pharmacology. Disintegrins, a family of small non-enzymatic and cysteine-rich proteins found in the snake venom may have a potential role in terms of novel therapeutic leads for cancer treatment. Despite their therapeutic effect, no database dedicated to disintegrins is available yet. Indeed, accessible information related to disintegrins are either scattered or fragmented in different databases from which it becomes extremely difficult to collect all the properties related to a particular disintegrin without exploring numerous databases available through distinct websites. Here, we propose DisintegrinDB as a first unique resource centralizing data related to disintegrins from snake venom. DisintegrinDB aims to facilitate the search on a given disintegrin and centralizes all the information on these peptides, helping researchers to retrieve all relevant related information.

PLOS ONE, 2021

Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, wit... more Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses’ dates were e...

InTech eBooks, Oct 10, 2018

Cell cysteine (Cys) levels and/or the [Cys/CySS] redox potential have been shown to regulate mRNA... more Cell cysteine (Cys) levels and/or the [Cys/CySS] redox potential have been shown to regulate mRNA levels of the CTNS gene, which encodes for a lysosomal cystine (CySS) carrier that is defective in cystinosis. To investigate the mechanisms involved CTNS mRNA regulation, different portions of the CTNS promotor were cloned into a luciferase vector and transfected in HK2 cells. A 1.5-2.4-fold increase in luciferase activity was observed when cells were incubated in culture medium containing low CySS concentrations. Conversely, CTNS mRNA levels decreased by 47-56% in the presence of N-acetyl-L-cysteine (NAC). Chase experiments with actinomycin D (ActD) demonstrated a 3-fold stabilization of the CTNS mRNA when cells were cultured in low CySS medium for 48 h. Treatment of control cells with cyclohexamide (CHX) increased CTNS mRNA levels, suggesting that CHX blocked the synthesis of proteins involved in mRNA degradation or in repression of the CTNS gene. Finally, in vitro binding assays showed increased binding (30-110%) of the Sp-1 transcription factor to two regions of the CTNS promotor when cells were incubated in low CySS medium. These results indicate that the CTNS gene is actively regulated at the transcriptional and posttranscriptional levels and suggest that CTNS plays a pivotal role in regulating cell thiol concentrations.

Molecules

Snake venom contains a number of active molecules that have been shown to possess high anti-tumor... more Snake venom contains a number of active molecules that have been shown to possess high anti-tumor activities; disintegrins are an excellent example among these. Their ability to interact and bind with integrins suggests that they could be very valuable molecules for the development of new cancer therapeutic approaches. However, in the absence of a clear Lysine-Threonine-Serine (KTS) Disintegrins Integrin interaction model, the exact compound features behind it are still unknown. In this study, we investigated the structural characteristics of three KTS-disintegrins and the interaction mechanisms with the α1β1 integrin receptor using in silico bioinformatics approaches. Normal mode analysis showed that the flexibility of the KTSR motif and the C-terminal region play a key role and influence the KTS-Disintegrin-integrin interaction. Protein-protein docking also suggested that the interaction involving the KTSR motif is highly dependent on the residue following K21, S23 and R24. These ...

Background Proper usage of biomedical data can be useful in designing future research strategies ... more Background Proper usage of biomedical data can be useful in designing future research strategies and in patient management and care. Exploring the clinical data with text mining allow the prediction of healthcare costs, disease diagnosis and prognosis, and the discovery related healthcare pat terns from other databases establishing, relationships among diseases, and relationships among drugs. Moreover; clinical research on the data can allow discovering disease intervention strategies. However, exploration of clinical data can be hindered if the database is not properly designed, un-normalized or contain redundant data. We hereby describe the automated migration of a clinical database containing cohort data of Sickle cell disease (SCD) patients attending clinic at Muhimbili National Hospital, in Dar es Salaam, Tanzania. The main objective was to migrate in the old SCD database into a new consistent database. Methodology The new database was modeled using MySQL-Workbench by consulting the study case report forms (CRF) and the old database. Mapping of new database columns was matched with the new database columns to get a definitive column for migration. Values in the old database were checked against valid range of values and text values were recorded to uniform values for all clinical variables. Consistency check within and between tables was done and data cleaned. The definitive column mappings were made and these were used to guide the automated migration from old to new database. Consistency, range check and mapping were done using python scripts or VBA scripts. The input to the script was made via comma separated values (csv) files. Results In total 1768 columns in 33 tables of the old database were considered important to migrate into 622 columns within 27 new tables in the new database. Nine pairs out of the 33 tables were double entry tables, which were merged in the new database design. The resulting mapping comprised of 1712 column pairs where related old columns were migrated to the same new column. Conclusions The newly created repository will facilitate analyzing the clinical data and generate new interventions for SCD

New advances in the understanding of haloarchaea physiology, metabolism, biochemistry, and molecu... more New advances in the understanding of haloarchaea physiology, metabolism, biochemistry, and molecular biology show that these kinds of microorganisms produce several compounds in response to the extreme conditions of their ecosystems. Thus, the complete metabolic and genetic machineries are fully adapted to nutrient starvation, high sun radiation, and high ionic strength. Due to these adaptations, some of the primary and secondary metabolites produced by haloarchaea are of high interest in terms of potential biotechnological uses. The principal goal of the chapter is to present a review about the main characteristics of these biocompounds and their potential uses in biomedicine, pharmacy, and industry.

Current Research in Microbial Sciences

Antibiotics

Antibiotic resistance in foodborne pathogens is an emergent global health concern. The objectives... more Antibiotic resistance in foodborne pathogens is an emergent global health concern. The objectives of this study were to assess antimicrobial resistance (AMR) in Campylobacter isolates from chicken carcasses and to investigate the AMR molecular mechanisms as well as the presence of virulence determinants. The study was performed on 257 samples collected from abattoirs and retail shops in northeastern Tunisia. Forty-eight Campylobacter isolates were recovered and identified as C. jejuni (n = 33) and C. coli (n = 15). Antibiotic resistance was tested against eight antibiotics and high resistance rates were observed against tetracycline (100%), erythromycin (97.9%), ciprofloxacin (73%), nalidixic acid (85.4%), ampicillin (83.3%), amoxicillin/clavulanic acid (22.9%), chloramphenicol (75%), and gentamicin (27.1%). All isolates were multidrug-resistant, and 22 resistance patterns were found. All isolates were screened for AMR genes (tet(O), tet(A), tet(B), tet(L), cmeB, ermB, blaOXA-61, an...

Viruses

SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have... more SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since it holds mutations of concern. Here, we report additional lineage A.27 data and sequences from five African countries and describe the molecular characteristics, and the genetic history of this lineage worldwide. Based on the new sequences investigated, the most recent ancestor (tMRCA) of lineage A.27 was estimated to be from April 2020 from Niger. It then spread to Europe and other parts of the world with a peak observed between February and April 2021. The detection rate of A.27 then decreased with only a few cases reported during summer 2021. The phylogenetic analysis revealed many sub-lineages. Among them, one was defined by the substitution Q677H in the spike (S) gene, one was defined by the s...

BioMed Research International

Host-pathogen molecular cross-talks are critical in determining the pathophysiology of a specific... more Host-pathogen molecular cross-talks are critical in determining the pathophysiology of a specific infection. Most of these cross-talks are mediated via protein-protein interactions between the host and the pathogen (HP-PPI). Thus, it is essential to know how some pathogens interact with their hosts to understand the mechanism of infections. Malaria is a life-threatening disease caused by an obligate intracellular parasite belonging to the Plasmodium genus, of which P. falciparum is the most prevalent. Several previous studies predicted human-plasmodium protein-protein interactions using computational methods have demonstrated their utility, accuracy, and efficiency to identify the interacting partners and therefore complementing experimental efforts to characterize host-pathogen interaction networks. To predict potential putative HP-PPIs, we use an integrative computational approach based on the combination of multiple OMICS-based methods including human red blood cells (RBC) and Pl...

Viruses, 2022

Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is ... more Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were ...