Biology subjects

Idris, A. B.

Publications and source records attributed to Idris, A. B..

10 recordsLinked to original sources

bioRxiv2022

Whole-genome sequencing of Bacillus thuringiensis strain SY49.1 reveals the detection of novel candidate pesticidal and bioactive compounds isolated from Turkey

BackgroundBacillus thuringiensis SY49.1 (Bt SY49.1) strain is a new strain isolated from a soil sample in Adana city which is nestled in the most fertile agricultural area in Turkey. This strain has insecticidal activity against insect pests from different orders. Also, it is characterized by its significant activity against plant fungal infections and as plant growth promotion. AimsTo report the whole genome sequencing (WGS) and annotation of the Bt SY49.1 strain. Materials and MethodsThe Bt SY49.1 strain was isolated from the soil sample in Adana city by using a sodium acetate enriched medium. Bacterial DNA was extracted then sequenced using Illumina HiSeq technology. After data filtering and quality control, de novo assembly and genomic annotation were applied. Evolutionary and comparative genomic analysis and variant calling were performed using various in silico tools. ResultsThe WGS of strain Bt SY49.1 is 6. 32 Mbp long with a GC content of 34.68%. It reveals large numbers of single nucleotide polymorphisms (SNPs) and InDels. The assembled genome contains 6,562 protein-encoding genes. In addition, it encodes various gene inventories for the biosynthesis of bioactive compounds such as insecticidal delta endotoxins, growth stimulatory deaminase and phosphatases, fungicidal thuricin, bacillibactin, petrobactin, fengycin / plipastin, and zwittermycin A. ConclusionThe strain Bt SY49.1 could have several potential utilities as a source of antibiotics compounds, plant growth promoting metabolites, and biocontrol agents for fungal phytopathogens, and insects. We expect that the draft genome of the Bt SY49.1 strain may provide a model for proper understanding and studying of antimicrobial compound mining, genetic diversity among the B. cereus group, and pathogenicity against insect pests and plant diseases, and growth-promoting activity.

genomics↗

bioRxiv2021

New Insights into Molecular Basis Identification of Three Novel Strains of the Bacillus Subtilis Group Produce Cry Proteins Isolated from Soil Samples in Adana, Turkey

AimsThis study aimed to analyze the evolutionary relationship between Bacillus species isolated from agricultural soil using in-silico tools. Methods and ResultsAcross-sectional study was conducted in Adana province, in Turkey. A total of 120 Bacillus species were isolated from 80 soil samples. However, the phylogenetic tree diverged into two lineages; one belongs to B. subtilis group while the other belongs to B. cereus group. Interestingly, three native strains (SY27.1A, SY35.3A, and SY58.5A), which produce Cry proteins, shared high similarity with B. subtilis group (over 99%) and less than 95% similarity with known B. thuringiensis and other species of B. cereus group. Furthermore, 11 canonical SNPs (canSNPs) were identified in strains that belong to B. pumilus group when compared with B. subtilis reference sequences. ConclusionsPhylogenetic analysis of 16S rRNA sequences was found valuable for differentiation between Bacillus species isolated from soil samples. In addition, SNPs analysis provided more intra-specific information in the cases of B. subtilis group. Significance and Impact of StudyA detailed analysis was provided for the SNPs present in a conserved region of 16S rRNA gene of Bacillus species. Also, we proposed three novel Bacillus strains that produce Cry proteins and belong to B. subtilis group.

microbiology↗

bioRxiv2021

Epitope-Based Peptide prediction of vaccine against European bat lyssaviruses type 2 Glycoprotein G with Immunoinformatic Approach

ObjectiveEuropean bat lyssaviruses (EBLV) type 2 is present in many European countries. Infection is usually seen in bats, the primary reservoirs of the viruses. Human deaths have been documented within few days following bat exposures. So, it is very useful to design an insilco peptide vaccine for European bat lyssaviruses type 2 virus using glycoprotein G as an immunogen to stimulate protective immune response ResultsB cell tests were conducted for Bepipred with 15 conserved epitopes, Emini surface accessibility prediction with 7 conserved epitopes in the surface and Kolaskar and Tongaonkar antigenicity tested with three conserved epitopes being antigenic. 357 conserved epitopes were predicted to interact with different MHC-1 alleles with (IC50) [≤]500 while 282 conserved epitopes found to interact with MHC-II alleles with IC50[≤] 1000. Among all tested epitopes for world population coverage the epitope VFSYMELKV binding to MHC11 alleles was 97.94% and it found to bind 10 different alleles that indicate strong potential to formulate peptide vaccine for lyssaviruses type 2 virus. To the best of our knowledge this is the first study to propose peptide vaccine for European bat lyssavirus type 2.

bioinformatics↗

bioRxiv2020

Epitope-Based Peptide Vaccine Design Against Fructose Bisphosphate Aldolase of Candida Glabrata: An Immunomics Approach

Background Candida glabrata is a human opportunistic pathogen that can cause life-threatening systemic infections. Although, there are multiple effective vaccines against fungal infections, and some of these vaccines were engaged in different stages of clinical trials, none of them yet approved by (FDA).Aim To predict the most conserved and immunogenic B- and T-cell epitopes from the Fructose Bisphosphate aldolase (Fba1) protein of C. glabrata.Materials and Methods 13 C. glabrata Fructose bisphosphate aldolase protein sequences (361amino acid) were retrieved from NCBI and several in silico tools presented in the IEDB server for predicting peptides were used and homology modeling and molecular docking were performed.Result The promising B-cell Epitopes were AYFKPH, VDKESLYTK, and HVDKESLYTK. While, promising peptides which have the high affinity to MHC I binding were: AVHEALAPI, KYFKRMAAM, QTSNGGAAY, RMAAMNQWL and YFKEHGEPL. Two peptides (LFSSHMLDL and YIRSIAPAY) were noted to have the highest affinity to MHC class II that interact with 9 MHC class II alleles. The molecular Docking revealed the epitopes QTSNGGAAY and LFSSHMLDL have the high binding energy to MHC moleculesConclusion The epitope-based vaccines predicted by using immunoinformatics tools have remarkable advantages over the conventional vaccines that they are more specific, less time consuming, safe, less allergic and more antigenic. Further in vivo and in vitro experiments are needed to prove the effectiveness of the best candidates epitopes (QTSNGGAAY and LFSSHMLDL). To the best of our knowledge, this is the first study that has predicted B- and T-cells epitopes from Fba1 protein by using in silico tools in order to design an effective epitope-based vaccine against C. galabrata.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2020

Contamination of Currency Notes with Kanamycin Resistant Shigella flexneri

Shigella flexneri is the main causative agent of shigellosis commonly distributed in developing countries with high morbidity and mortality rates. This study aimed to examine the presence of Shigella species in Sudanese currency notes using both traditional and molecular techniques. One hundred thirty five currency notes were collected and their contaminants were isolated and identified conventionally and genetically using 16S rRNA gene amplification and sequencing. Eight isolates were identified as Shigella species in different notes, and 3 of them were resistant to penicillin, kanamycin and nitrofurantoin. One S. flexneri isolate has insertion mutation of guanine nucleotide at position 730 of lifes essential gene 16S rRNA which known evolutionarily to be stable gene. Banknotes are highly circulating items and therefore, appropriate measures such as regular replacement of the dirty notes with new papers are necessary to protect peoples from being infected with drug resistant pathogens.

microbiology↗

bioRxiv2019

Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two lineages of H. pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

BackgroundH. pylori is ubiquitous among humans, and one of the best studied examples of an intimate association between bacteria and humans. Under several diverse socio-demographic factors in Sudan, a continuous increase in the prevalence rate of H. pylori infection has been noticed which represents a major public health challenge. In this study, we analyzed the molecular evolution of H. pylori Strains detected from different ethnic and regions of Sudan using 16S rRNA gene and phylogenetic approach. Materials and methodsA total of 75 gastric biopsies taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was done by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was performed; then Blast these sequences with those available in the NCBI nucleotide database. The evolutionary aspects were analyzed using a MEGA7 software. ResultMolecular detection of H. pylori has shown that 28 (37.33%) of patients were positive for H. pylori. Bivariate analysis has found no significant differences exhibited across sociodemographic, endoscopy series and H. pylori infection. Nucleotide variations were found at five nucleotide positions (positions 219, 305, 578, 741 and 763-764) and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. The phylogenetic tree diverged into two lineages. ConclusionThe phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. Sex mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites. 66.67% of them were located in the central domain of 16S rRNA. Studying the effect of these mutations on the functions of 16S rRNA molecules in protein synthesis and antibiotic resistance is of great importance.

microbiology↗

bioRxiv2019

Genetic analysis of TP53 gene mutations in exon 4 and exon 8 among esophageal cancer patients in Sudan

BackgroundEsophageal carcinoma (EC) represents the 1st rank among all gastrointestinal cancers in Sudan. Despite little publications, there is a deep absence of literature about the molecular pathogenesis of EC considering TP53 gene from Sudanese population.\n\nAimsIn this study, we performed the expression analysis on p53 protein level by immunohistochemical staining and examined its overexpression with p53 mutations in exons 4 and 8 among esophageal cancer patients in Sudan.\n\nMaterial and MethodsFixed tissue with 10% buffered formalin was stained by Hematoxlin and Eosin (H&E), Alcian blue-Periodic Acid Schiff (PAS) and Immunohistochemistry stain. PCR-RFLP was used to study the frequencies of p53 codon 72 R/P polymorphism. Conventional PCR and sanger sequencing were applied for exon 4 and exon 8. Then detection and functional analysis of SNPs and mutations were performed using various in bioinformatics tools.\n\nResultNuclear accumulations for p53 protein was detected in all of the esophageal carcinomas examined while no accumulations were observed in normal control sections. Four patients with immune-positive for p53 showed no mutations in p53 gene (exon4 and exon8). The incidence of the homozygous mutant variant Pro/Pro was higher in esophageal cancerous patients comparing to healthy control subject 20(71. 4%) vs. 1(10%), respectively (p=0.0026). In exon 4, no mutation was detected other than NG_017013.2:g. 16397C>G. While in exon 8, g.18783-18784AG>TT, g.18803A>C, g.18860A>C, g.18845A>T and g.18863_ 18864 InsT were observed.\n\nConclusionwe found a significant association between the overexpression of TP53 protein and mutation in exon 4 and 8. A silent mutation P301P was detected in all of examined cases. Two patients who diagnosed with small cell sarcoma have shared the same mutations in exon8. Further studies with large sample size are required to demonstrate the usefulness of these mutations in the screening of EC especially SCCE.

cancer biology↗

bioRxiv2019

Knowledge Gaps of STIs in Africa; Systematic review

Sexually Transmitted Infections (STIs) are ambiguous burden of tremendous health, social and economic consequences, The current systematic review was conducted in order to determine awareness and knowledge of Africans of sexually transmitted infections, not only concerning HIV/AIDS, but also other STIs such as, gonorrhea, syphilis, HBV, HCV and HPV. A systematic review of the literature was conducted, studies were retrieved and selected after they fulfilled the inclusion criteria and passed the assessment procedure. related data was extracted, quantitative analysis was conducted among participants who responded to questions related to HIV, HBV, HCV, HPV or STIs knowledge, sensitivity analysis as well as subgroup analysis were also conducted. Seventy four articles addressing knowledge among 35 African countries were included and 136 questions were analyzed and synthesized. The question Using condom will reduce HIV transmission?" was answered by 1,799,374 Africans in 35 countries, 66.82% [95% Cl; 62.65, 70.98] answered yes. While the question "Is sexual contact a possible route of HBV transmission?" was answered by 7,490 participants in 5 countries; 42.58% [95% Cl; 20.45, 64.71] answered yes. The differences observed among populations are highlighting the possibility for containment and control by directing light toward specific populations or countries as well as addressing specific awareness knowledge to ensure that the general as well as the related specific preventive awareness knowledge is improved.

microbiology↗

bioRxiv2019

Molecular Genetic Analysis of RB1 gene among Sudanese children with Retinoblastoma

BACKGROUNDRetinoblastoma (RB), the commonest early childhood intraocular tumor, is most often related to mutations in the RB1 gene with an incidence of 3% of all pediatric tumors. It has good prognosis if diagnosed early but it is life-threatening when diagnosed late.\n\nOBJECTIVETo study the Molecular Genetic Analysis of Retinoblastoma (RB) in Sudanese families.\n\nMETHODSThirty one (n=31) clinically and histopathologically diagnosed cases of RB attending Makkah Eye Complex (MEC) Orbit clinic (Khartoum, Sudan) were included in this Molecular Genetic RB Analysis. Fresh blood samples extracted from seven RB patients and 15 close families for DNA extraction and PCR were sent for Genetic Sequencing and In silico approach for \"Exon 18 mutations\" which is one of the highly mutated exons worldwide.\n\nRESULTSThe majority of patients (41.9%) were below five years old. Females were 58.1%, males were 41.9%. Leukocoria was the commonest sign at presentation (41.9%). RB Unilaterality were in (77.4%) while Bilaterality in 19.4%. Both eyes were equally affected 50% each. The age at diagnosis time ranged from 0.02 to five years. Consanguinity of parents was very high (85.7%), the 1st degree cousins were less (28.6%) while the 2nd degree was high (57.1%). The patients ethnic background and geographical area were from seven different tribes; all belong to the Western Sudan. The molecular genetic study showed that exon 18 was free of mutation among the seven patients + their three relatives. The Functional Analysis and (SNPs) prediction study of exon 18 from NCBI data base showed that the various computational approaches used (SIFT, PolyPhen-2, I-mutant and Project hope) identified 16 reported mutations worldwide, three of which (rs137853292, rs375645171 and rs772068738) are major nsSNPs (non-synonymous) which might contribute to native RB1 protein malfunction and ultimately causing carcinoma.\n\nCONCLUSIONRB mainly affected children under five years and both sexes are equally affected. Unilaterality was predominant. Consanguinity plays a role in inheritance and the majority of patients were from Western Sudan. The most commonly detected deleterious mutations worldwide in exon 18 were not found in the Sudanese studies samples. Further screening for the highly reported mutations in exons 8, 10 and 14 or Next Generation Sequencing (NGS) are recommended. In silico tools are useful in studying the functional analysis of SNPs.

molecular biology↗

bioRxiv2018

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients

BackgroundTuberculosis (TB) is a bacterial disease considered as a global public health emergency by the World Health Organization (WHO) since 1993. In Sudan, MDR-TB represents a growing threat and one of the most important challenges that faced national tuberculosis program to establish a comprehensive multidrug-resistant tuberculosis management system.\n\nObjectiveTo characterize the diversity and frequency of mutations in Sudanese MDR-TB strains isolated from Wad Madani, Al-Gadarif and Khartoum using 16S rRNA and phylogeny approach.\n\nMaterial and MethodsA total of 60 MDR-TB isolates from Wad-Madani, Al-Gadarif and Khartoum were tested with molecular LPA (Genotype MTBDR plus) and GeneXpert MTB/RIF assay and Spoligotyping to confirm their resistance to RIF and INH. Sequencing and phylogenetic analysis was carried out using in silico tools.\n\nResultThis study revealed the circulation of different Sudanese MDR-TB strains isolated from Wad Madani and Al-Gadarif belonging to two distinct common ancestors. Two isolates from Wad Madani (isolate3 and isolate11) found in one main group which characterized by a novel mutation G511T in the 530 loop.\n\nConclusionThe recurrence of C217A mutation in Wad Madani (isolate11) indicates the spread of this mutation in Sudanese MDR-TB strains and the diversity of this inheritance leading to generate new G511T novel mutation. So, understanding the molecular characterization of resistance mechanisms in MD-TB can facilitate the early detection of resistance, the choice of appropriate treatment and ultimately the management of MD-TB transmission. Bioinformatics approaches provide helpful tools for analyzing molecular mechanisms of resistance in pathogens.

microbiology↗