Three dimensional structure prediction of fatty acid binding site on human transmembrane receptor CD36

CD36 is an integral membrane protein which is thought to have a hairpin-like structure with alpha-helices at the C and N terminals projecting through the membrane as well as a larger extracellular loop. This receptor interacts with a number of ligands including oxidized low density lipoprotein and long chain fatty acids (LCFAs). It is also implicated in lipid metabolism and heart diseases. It is therefore important to determine the 3D structure of the CD36 site involved in lipid binding. In this study, we predict the 3D structure of the fatty acid (FA) binding site [127–279 aa] of the CD36 receptor based on homology modeling with X-ray structure of Human Muscle Fatty Acid Binding Protein (PDB code: 1HMT). Qualitative and quantitative analysis of the resulting model suggests that this model was reliable and stable, taking in consideration over 97.8% of the residues in the most favored regions as well as the significant overall quality factor. Protein analysis, which relied on the secondary structure prediction of the target sequence and the comparison of 1HMT and CD36 [127–279 aa] secondary structures, led to the determination of the amino acid sequence consensus. These results also led to the identification of the functional sites on CD36 and revealed the presence of residues which may play a major role during ligand-protein interactions

MatSAM: a Matlab implementation for Significance Analysis of Microarrays

Microarray experiments enable the simultaneous measure of expression levels of large amount of genes and have many applications. A widespread one is finding set of genes that are differentially expressed. Significance Analysis of Microarrays (SAM) helps to produce those sets using multiple testing techniques. There is unfortunately not yet a public tool enabling to do SAM using the Matlab platform. We here define MatSAM, a SAM implementation in Matlab, and show that it yields results of high confidence comparatively to those obtained by putative tools available in the R programming environment. MatSAM can be used in conjunction with Matlab Bioinformatics toolbox to perform further analysis.Availability: MatSAM is available as source code at  http://www.bioinfoindia.org/MatSA

Copper, zinc and selenium imbalance in Moroccan haemodialysis patients and its correlation to lipid peroxidation

Background: Haemodialysis patients are at risk of developing trace elements imbalance and lipid peroxidation. The present study was aimed to assess plasma levels of copper (Cu), zinc (Zn), selenium (Se) and malondialdehyde (MDA) of haemodialysis patients and to investigate the possible effect of haemodialysis on these trace elements and MDA imbalance.Methods: Blood samples of fifty hemodialysis patients and forty healthy controls subjects were analyzed for determination of hemoglobin, albumin, creatinine, urea and high-sensitivity C-reactive protein (hs-CRP). Cu, Zn and Se were determined in plasma (before and after hemodialysis) and erythrocytes and MDA in plasma before and after hemodialysis.Results: The study showed that, plasma Zn and Se concentrations were lower in haemodialysis patients compared to that of healthy controls, while plasma Cu, MDA and Cu/Zn ratio were higher.  Plasma Cu/Zn ratios were positively correlated to MDA and weakly correlated to hs-CRP levels whereas plasma Se concentrations were inversely correlated to MDA. In addition, MDA levels increased after haemodialysis session.Conclusions: Based on the results of the present study regarding the imbalance of trace elements in haemodialysis patients, it seems reasonable to periodically assess the trace elements status and consider possible correctional therapy in case of deficiency.

COMPARATIVE STUDY OF THE EFFICACY OF STEM CELLS IN CORNEAL REGENERATION IN A CHEMICAL BURN IN RABBITS

Objectives: This study compares the efficacy of stem cell transplantation in corneal regeneration and restoration of the limbic deficit in an experimental chemical burn in rabbits. Methods: Biopsy was performed of the limbus and the chemical burns for all rabbits, and we collected the amniotic membranes from a pregnant female rabbit. We kept a control group without transplantation, to study spontaneous and natural healing, and we transplanted the stem cells produced in vitro under the corneal epithelium burned. To compare the result, we tested a group for amniotic stem cell transplantation, a group for limbal stem cell graft, and another group for combined transplantation of both types of stem cells. Results: Transplanted rabbits develop permanent unilateral blindness due to a severe limbic deficit. The group receiving only amniotic stem cells shows temporary anatomical improvement without functional recovery. The two groups receiving limbal stem cells alone or combined with amniotic stem cells showed anatomical and functional satisfaction with quick recovery time for the combined transplantation. Conclusions: A simple chemical burn can establish permanent blindness. When the limbic deficit is important, spontaneous healing is not available. Transplantation of stem cell transplant is the only way to repair this deficit and regenerate the cornea. Only limbic stem cells can be sufficient. Amniotic stem cells can support and speed up the healing time when it combined to limbal stem cells graft.               Peer Review History: Received 23 July 2020; Revised 14 August; Accepted 28 August, Available online 15 September 2020 Academic Editor: Essam Mohamed Eissa, Beni-Suef University, Egypt, [email protected] UJPR follows the most transparent and toughest ‘Advanced OPEN peer review’ system. The identity of the authors and, reviewers will be known to each other. This transparent process will help to eradicate any possible malicious/purposeful interference by any person (publishing staff, reviewer, editor, author, etc) during peer review. As a result of this unique system, all reviewers will get their due recognition and respect, once their names are published in the papers. We expect that, by publishing peer review reports with published papers, will be helpful to many authors for drafting their article according to the specifications. Auhors will remove any error of their article and they will improve their article(s) according to the previous reports displayed with published article(s). The main purpose of it is ‘to improve the quality of a candidate manuscript’. Our reviewers check the ‘strength and weakness of a manuscript honestly’. There will increase in the perfection, and transparency. Received file:                Reviewer's Comments: Average Peer review marks at initial stage: 5.0/10 Average Peer review marks at publication stage: 7.5/10 Reviewer(s) detail: Dr. Mohamed Amin El-Emam, Department of Pharmacology and Therapeutics, Faculty of Pharmacy and Drug Manufacturing, Pharos University in Alexandria (PUA), Alexandria, Egypt, [email protected] Francesco Ferrara,USL Umbria 1, Perugia, Italy, [email protected] Maged Almezgagi, Department of Immunology, Medical College of Qinghai University, Qinghai Xining 810001, China, [email protected] Dr. Asia Selman Abdullah, University of Basrah, Iraq, [email protected]

In Vivo Potential Anti-Inflammatory Activity of Extracts from Calendula arvensis (CA) Flowers

Calendula arvensis (CA) had been reported in traditional Moroccan medicine to exhibit its extensive use to treat pain and inflammation. Therefore, the objective of this study was to evaluate the anti‐inflammatory activity of CA flowers. The methanol, aqueous, and hexane extracts (ME, AE, and HE) were investigated for inflammatory effects by using two methods, namely, carrageenan and experimental trauma‐induced hind paw edema in rats and using indomethacin (20 mg/kg body weight) as a standard drug. The results demonstrated that Calendula Arvensis CA extracts had significant anti‐inflammatory activity where the HE at the doses of 300 and 500 mg/kg p.o. (p < 0.001) had the best significant reduction and inhibition of edema with 51.08, 71.33 and 63.38, 67.33% induced by carrageenan and on experimental trauma induced rat paw edema at third hour, respectively, and similar as compared with standard drug indomethacin 20 mg/kg body weight p.o. (p < 0.001). These results indicate that it could be suggested as contributory effects to the use of CA flowers in the management of inflammation and pain conditions

Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing

Background: Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. The ancestry of present-day Moroccans is unknown and may be substantially different from Africans found South of the Sahara desert, Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans and suggested that North African individuals may be genetically distinct from previously studied African populations. Results: We present SNVs discovered by whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G and were not in the extensive gnomAD database. We summarise the SNVs by genomic position, type of sequence gene context and effect on proteins encoded by the sequence. Analysis of the overall genomic information of the Moroccan individuals to individuals from 1000G supports the Moroccan population being distinct from both sub-Saharan African and European populations. Conclusions: We conclude that Moroccan samples are genetically distinct and lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of novel SNVs and aid in functional characterisation of the genome

Acinetobacter infections prevalence and frequency of the antibiotics resistance: comparative study of intensive care units versus other hospital units

Introduction: This study aims to determine the Acinetobacter sp clinical isolates frequency and its antibiotic susceptibility pattern by comparing results obtained from the Intensive Care Units (ICUs) to that of other units at the Mohammed V Military Teaching Hospital in Rabat. Methods: This is a retrospective study over a 2-years period where we collected all clinical isolates of Acinetobacter sp obtained from samples for infection diagnosis performed on hospitalized patients between 2012 to 2014. Results: During the study period, 441 clinical and non-repetitive isolates of Acinetobacter sp were collected representing 6.94% of all bacterial clinical isolates (n=6352) and 9.6% of Gram negative rods (n=4569). More than a half of the isolates were from the ICUs and were obtained from 293 infected patients of which 65, 2% (191 cases) were males (sex ratio = 1.9) and the median age was 56 years (interquartile range: 42-68 years). Acinetobacter clinical isolates were obtained from respiratory samples (44.67%) followed by blood cultures (14.51%). The resistance to ciprofloxacin, ceftazidime, piperacillin / tazobactam, imipenem, amikacin, tobramycin, netilmicin, rifampicin and colistin was respectively 87%, 86%, 79%, 76%; 52%, 43%, 33% 32% and 1.7%. The difference in resistance between the ICUs and the other units was statistically significant (p &lt;0.05) except for colistin, tetracycline and rifampicin. Conclusion: This paper shows that solving the problem of prevalence and high rate of multidrug resistant Acinetobacter infection which represents a therapeutic impasse, requires the control of the hospital environment and optimizing hands hygiene and antibiotics use in the hospital.Pan African Medical Journal 2016; 2

Association between “cluster of differentiation 36 (CD36)” and adipose tissue lipolysis during exercise training: a systematic review

Fatty acid translocase (FAT/CD36) is a transmembrane glycoprotein belonging to the scavenger class B receptor family and is encoded by the cluster of differentiation 36 (CD36) gene. This receptor has a high affinity for fatty acids and is involved in lipid metabolism. An abundance of FAT/CD36 during exercise occurs in mitochondria and solitary muscles. As such, we aimed to systematically review the evidence for the relationship FAT/CD36 and adipose tissue lipolysis during exercise training. Five electronic databases were selected for literature searches until June 2022: PubMed, Web of Science, Scopus, science direct, and Google Scholar. We combined the different synonyms and used the operators (“AND”, “OR”, “NOT”): (CD36 gene) OR (CD36 polymorphism) OR (cluster of differentiation 36) OR (FAT/CD36) OR (fatty acid translocase) OR (platelet glycoprotein IV) OR (platelet glycoprotein IIIb) AND (adipose tissue lipolysis) OR (fatty acids) OR (metabolism lipid) OR (adipocytes) AND (physical effort) OR (endurance exercise) OR (high-intensity training). All published cross-sectional, cohort, case-control, and randomized clinical trials investigating CD36 polymorphisms and adipose tissue lipolysis during exercise in subjects (elite and sub-elite athletes, non-athletes, sedentary individuals and diabetics), and using valid methods to measure FAT/CD36 expression and other biomarkers, were considered for inclusion in this review. We initially identified 476 publications according to the inclusion and exclusion criteria, and included 21 studies investigating FAT/CD36 and adipose tissue lipolysis during exercise in our systematic review after examination of titles, abstracts, full texts, and quality assessments using the PEDro scale. There were nine studies with male-only participants, three with female-only participants, and nine studies included both female and male participants. There were 859 participants in the 21 selected studies. Studies were classified as either low quality (n = 3), medium quality (n = 13), and high quality (n = 5). In general, the data suggests an association between FAT/CD36 and adipose tissue lipolysis during exercise training. Improvements in FAT/CD36 were reported during or after exercise in 6 studies, while there were no changes reported in FAT/CD36 in 4 studies. An association between fat oxidation and FAT/CD36 expression during exercise was reported in 7 studies. No agreement was reached in 5 studies on FAT/CD36 content after dietary changes and physical interventions. One study reported that FAT/CD36 protein expression in muscle was higher in women than in men, another reported that training decreased FAT/CD36 protein in insulin-resistant participants, while another study reported no differences in FAT/CD36 in young, trained individuals with type 2 diabetes. Our analysis shows an association between FAT/CD36 expression and exercise. Furthermore, an association between whole-body peak fat oxidation and FAT/CD36 expression during exercise training was demonstrated.Systematic Review Registration: [PROSPERO], identifier [CRD42022342455

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants