National Center For Biotechnology Information Research Articles

Weighted Gene Co-expression Network Analysis (WGCNA) of Wnt Signaling Related to Periodontal Ligament Formation: A Bioinformatics-Based Analysis.

Introduction The Wnt signaling pathway is crucial for tooth development, odontoblast differentiation, and dentin formation. It interacts with epithelial cadherin (E-cadherin) and beta-catenin in tooth development and periodontal ligament (PDL) formation. Dysregulation of Wnt signaling is linked to periodontal diseases, requiring an understanding of therapeutic interventions. Weighted gene co-expression network analysis (WGCNA) can identify co-expressed gene modules. Our study aims to identify hub genes in WGCNA analysis of Wnt signaling-based PDL formation. Methods The study used a microarray datasetGSE201313 from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus to analyze the impact of DMP1 expression on XLH dental pulp cell differentiation and PDL formation. The standardized dataset was used for WGCNA analysis, which generated a co-expression network by calculating pairwise correlations between genes and constructing an adjacency matrix. The topological overlap matrix (TOM) was transformed into a hierarchical clustering tree and then cut into modules or clusters of highly interconnected genes. The module eigengene (ME) was calculated for each module, and the genes within this module were identified as hub genes. Gene ontology (GO) and KEGG pathway enrichment analysis were performed to gain insights into the biological functions of the hub genes. The integrated Differential Expression and Pathway analysis (iDEP) tool (http://bioinformatics.sdstate.edu/idep/; South Dakota State University, Brookings, USA) was used for WGCNA analysis. Results The study used the WGCNA package to analyze 1,000 differentially expressed genes, constructing a gene co-expression network and generating a hierarchical clustering tree and TOM. The analysis reveals a scale-free topology fitting index R2 and mean connectivity for various soft threshold powers, with an R2 value of 5. COL6A1, MMP3, BGN, COL1A2, and FBN2 are hub genes implicated in PDL development. Conclusion The study identified key hub genes, including COL6A1, MMP3, BGN, and FBN2, crucial for PDL formation, tissue remodeling, and cell-matrix interactions, guiding future therapeutic strategies.

In Silico Comparative Analysis of Different vacA Genes of Helicobacter pylori

Helicobacter pylori is a class I carcinogen responsible for 90% of gastrointestinal and gastroduodenaldisorders, including gastric cancer and peptic ulcer disease. The virulence and pathogenicity peculiar to H. pylorihave been associated with several genes, including cytotoxin associated gene (cagA), vacuolating cytotoxin A(vacA), outer inflammatory protein A (oipA), and duodenal ulcer promoting (dupA). This study explored therelationship between African-generated vacA genes with genes from other regions with high gastrointestinaldisorder prevalence. Nucleotide sequences of 228 vacA genes of H. pylori were retrieved from the NationalCentre for Biotechnology Information (NCBI). Pairwise and multiple sequence alignment was carried out on228 vacA nucleotide sequences using MEGA 10.2.4 software to identify regions of similarities. Phylogeneticanalysis, also using MEGA software, was carried out to establish the evolutionary relationships between allextracted sequences. Analysis for conserved domain was also performed on the NCBI Conserved DomainDatabase to better understand each geographical data's properties. After the evolutionary analysis, it wasobserved that South African vacA genes were more closely related to genes from Mexico, Italy, Spain, andGermany—with Italy having the highest occurring relationship. Conserved domain analysis showed 2 highlyconserved superfamilies, cl20029 and cl22877, and 2 protein family models, pfam02691 and pfam03797.The results demonstrate relatedness of vacA genes from the African region to the European region; Italy,Mexico, and Spain. The study shows the biogeographical diversity among vacA genes and emphasizes thedegree of domain conservation across each gene. It also shows the need for a holistic assessment of thevirulent genes in H. pylori.

Global epidemiology of severe fever with thrombocytopenia syndrome virus in human and animals: a systematic review and meta-analysis

Since the initial identification of the Severe Fever with Thrombocytopenia Syndrome (SFTS) in ticks in rural areas of China in 2009, the virus has been increasingly isolated from a diverse array of hosts globally, exhibiting a rising trend in incidence. This study aims to conduct a systematic analysis of the temporal and spatial distribution of SFTS cases, alongside an examination of the infection rates across various hosts, with the objective of addressing public concerns regarding the spread and impact of the disease. In this systematic review and meta-analysis, an exhaustive search was conducted across multiple databases, including PubMed, Web of Science, Embase, and Medline, CNKI, WanFang, and CQVIP. The literature search was confined to publications released between January 1, 2009, and May 29, 2023. The study focused on collating data pertaining to animal infections under natural conditions and human infection cases reported. Additionally, species names were unified using the National Center for Biotechnology Information (NCBI) database. The notification rate, notification death rate, case fatality rate, and infection rates (or MIR) were assessed for each study with available data. The proportions were pooled using a generalized linear mixed-effects model (GLMM). Meta-regressions were conducted for subgroup analysis. This research has been duly registered with PROSPERO, bearing the registration number CRD42023431010. We identified 5492 studies from database searches and assessed 238 full-text studies for eligibility, of which 234 studies were included in the meta-analysis. For human infection data, the overall pooled notification rate was 18.93 (95% CI 17.02-21.05) per ten million people, the overall pooled notification deaths rate was 3.49 (95% CI 2.97-4.10) per ten million people, and the overall pooled case fatality rate was 7.80% (95% CI 7.01%-8.69%). There was an increasing trend in notification rate and deaths rate, while the case fatality rate showed a significant decrease globally. Regarding animal infection data, among 94 species tested, 48 species were found to carry positive nucleic acid or antibodies. Out of these, 14 species were classified under Arthropoda, while 34 species fell under Chordata, comprising 27 Mammalia and 7 Aves. This systematic review and meta-analysis present the latest global report on SFTS. In terms of human infections, notification rates and notification deaths rates are on the rise, while the case fatality rate has significantly decreased. More SFTSV animal hosts have been discovered than before, particularly among birds, indicating a potentially broader transmission range for SFTSV. These findings provide crucial insights for the prevention and control of SFTS on a global scale. None.

Genetic analyses of the structural protein E2 bovine viral diarrhea virus isolated from dairy cattle in Yogyakarta, Indonesia.

Bovine viral diarrhea (BVD), a highly pathogenic ribonucleic acid (RNA) virus, causes devastating financial losses and reproductive deaths among dairy cattle in Yogyakarta and globally. This study aimed to identify point mutations within the E2 structural protein of the acquired BVD virus (BVDV) isolates using genetic analysis. The study period shows that we performed the research in 2023. We collected 118 serum samples from 2019 to 2023, among which only 10 BVDV positive were used and 108 were negative lacking the BVDV antigen. An anti-Erns monoclonal antibody-coated protein was used in indirect antigen capture enzyme-linked immunosorbent assay (I-ACE) to detect the BVD antigen present in positive BVDV serum specimens. In the initial step of the two-step reverse transcription polymerase chain reaction, the enzyme (superscript III reverse transcriptase) and the primer (random hexamer) were used to convert the RNA of the BVDV into complementary deoxyribonucleic acid (cDNA) during the process of reverse transcription. The final step involved the amplification of the E2 gene of the resultant BVDV cDNA through gene-specific primers (E2_fwd: 5'-TGGTGGCCTTATGAGAC-3' and P7_rev: 5'-CCCATCATCACTATTTCACC-3') and enzyme (platinum taq DNA polymerase high fidelity). For conducting Sanger sequencing, those 3 BVDV-1-positive isolates (about 2.6% of all isolates) were selected as a typical specimen for each site and year between 2019 and 2023 using a proportional computation. Therefore, only two BVDV isolates with complete genomes were chosen to perform their homological and genetic analysis based on the E2 gene by means of Blast and MEGA Version 11 in addition to the Bioedit 7.2.5 program. By applying phylogenetic analysis relying on the E2 gene, a sum of 1011 nucleotides of the BVDV-1 isolates derived from each of the two BVDV-1 Indonesian isolates (n = 2) and its 23 reference BVDV strains were acquired from the National Center for Biotechnology Information (NCBI) database. The findings of the genetic analysis inside the phylogenetic tree revealed that the two BVDV Indonesian isolates were clustered into BVDV-1a subgenotype, while the reference BVDV strains were clustered into the five BVDV subgenotype, BVDV-1a (n = 6), BVDV-1b (n = 3), BVDV-1c (n = 11), BVDV-1m (n = 1), and BVDV-1n (n = 2). The branch exists in phylogenetic tree located before the division of our two BVDV isolates was divided into two branches with the same maximum bootstrap values of 99%, indicating a high degree of confidence, was seen. Next, we observed the branch near our study samples, which displayed the bootstrap value of 100, indicating that our 02 isolates were identical. In both isolates, V11 BVDV1/Indonesia/Yogyakarta/2023 and V16 BVDV1/Indonesia/Yogyakarta/2023 with GenBank accession numbers PP836388 and PP836389, respectively, conserved D7E residues were mutated as well as cysteine changed/altered into serine (S) was identified at amino acid position 201. We identified two isolates of BVDV belonging to the BVDV-1a subgenotype. Our findings indicate that the conserved D7E residues of isolates V11 BVDV1/Indonesia/Yogyakarta/2023 and V16 BVDV1/Indonesia/Yogyakarta/2023 were altered. The Indonesian BVDV isolates exhibited a cysteine to serine mutation at amino acid position 201, leads to vaccination failure, range of animal's host will increase, and diagnostic kit will not be effective.

Development of a nucleic acid detection method based on the CRISPR-Cas13 for point-of-care testing of bovine viral diarrhea virus-1b.

Bovine viral diarrhea (BVD) is a single-stranded, positive-sense ribonucleic acid (RNA) virus belonging to the genus Pestivirus of the Flaviviridae family. BVD frequently causes economic losses to farmers. Among bovine viral diarrhea virus (BVDV) strains, BVDV-1b is predominant and widespread in Hanwoo calves. Reverse-transcription polymerase chain reaction (RT-PCR) is an essential method for diagnosing BVDV-1b and has become the gold standard for diagnosis in the Republic of Korea. However, this diagnostic method is time-consuming and requires expensive equipment. Therefore, Clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems have been used for point-of-care (POC) testing of viruses. Developing a sensitive and specific method for POC testing of BVDV-1b would be advantageous for controlling the spread of infection. Thus, this study aimed to develop a novel nucleic acid detection method using the CRISPR-Cas13 system for POC testing of BVDV-1b. The sequence of the BVD virus was extracted from National Center for Biotechnology Information (NC_001461.1), and the 5' untranslated region, commonly used for detection, was selected. CRISPR RNA (crRNA) was designed using the Cas13 design program and optimized for the expression and purification of the LwCas13a protein. Madin Darby bovine kidney (MDBK) cells were infected with BVDV-1b, incubated, and the viral RNA was extracted. To enable POC viral detection, the compatibility of the CRISPR-Cas13 system was verified with a paper-based strip through collateral cleavage activity. Finally, a colorimetric assay was used to evaluate the detection of BVDV-1b by combining the previously obtained crRNA and Cas13a protein on a paper strip. In conclusion, the CRISPR-Cas13 system is highly sensitive, specific, and capable of nucleic acid detection, making it an optimal system for the early point-of-care testing of BVDV-1b.

DNA barcoding is currently unreliable for species identification in most crayfishes.

DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.

UNVEILING THE GENETIC BASIS OF BACTERIOCIN PRODUCTION FROM Enterococcus faecium ATCC 19434

The prevalence of resistance to traditional antimicrobials is increasing rapidly, leading to a significant rise in annual deaths from antibiotic-resistant illnesses. In 2020, the global death toll from such diseases was approximately 500,000. If current trends continue, this figure could exceed 10 million by 2050, with associated economic damages surpassing 100 trillion USD. These alarming statistics highlight the urgent need for alternative antimicrobials. Bacteriocins are considered among the most promising options. Enterococcus faecium ATCC 19434 is known to produce a potent bacteriocin effective against Listeria monocytogenes and Staphylococcus aureus, though its specific bacteriocin and genetic properties have not been fully explored. This study aimed to identify the gene responsible for bacteriocin production in Enterococcus faecium ATCC 19434. DNA was extracted from the bacterium, and polymerase chain reaction (PCR) was conducted. The PCR products were analyzed through agarose gel electrophoresis, sequenced, and subjected to homology searches using the BLASTN and BLASTX tools from the National Center for Biotechnology Information (NCBI). Results revealed that Enterococcus faecium ATCC 19434 contains a gene encoding enterocin B. Additionally, it was found to harbor the gene for enterocin A immunity protein production. This discovery paves the way for future genetic modification of Enterococcus faecium ATCC 19434 to enhance enterocin B synthesis, facilitating its commercial application.

Molecular Detection and Identification of Begomovirus Infecting Cucumber (Cucumis sativus) in Terengganu, Malaysia

The genus Begomovirus from the family Geminiviridae is responsible for causing significant economic losses to many important horticultural crops, including cucumber (Cucumis sativus L.). Begomovirus infection during the early stages of plant growth can lead to complete yield loss. Hence, the identification of begomovirus species is important to design a precise resistant breeding strategy. This study aims to detect the presence of begomovirus in typical symptomatic cucumber leaves, identify the species of begomovirus present, and investigate the evolutionary relationships with other reported begomoviruses using phylogenetic analysis. Leaf samples from symptomatic cucumber plants were collected from the Green World Genetics (GWG) research station and a farm in Lembah Bidong, Rhu Tapai, Setiu, Terengganu. To detect the presence of begomovirus, PCR was carried out using universal primers targeting DNA-A, DNA-B, and betasatellite regions. DNA-A and betasatellite fragments were amplified, but not DNA-B. The amplified partial sequences of DNA-A were then analysed and compared with other begomovirus sequences in the GenBank database managed by the National Centre for Biotechnology Information (NCBI). The newly isolated DNA-A sequence from cucumber was 100% identical to the tomato leaf curl New Delhi virus (ToLCNDV). The phylogenetic tree was divided into two groups: group A, consisting of the newly isolated DNA-A sequence from cucumber, ToLCNDV, followed by squash leaf curl China virus (SLCCNV) and a monopartite begomovirus Ageratum yellow vein virus (AYVV); and group B, consisting of tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), pepper yellow leaf curl Indonesia virus (PepYLCIV), and pepper yellow leaf curl Aceh virus (PepYLCAV). For the first time in cucumber, betasatellite is reported in association with ToLCNDV, a bipartite old-world begomovirus. This study provides a basis for the selection and breeding of begomovirus-resistant cucumber varieties in the future.

Exploring the potential mechanism of WuFuYin against hypertrophic scar using network pharmacology and molecular docking

BACKGROUND Hypertrophic scar (HTS) is dermal fibroproliferative disorder, which may cause physiological and psychological problems. Currently, the potential mechanism of WuFuYin (WFY) in the treatment of HTS remained to be elucidated. AIM To explore the potential mechanism of WFY in treating HTS. METHODS Active components and corresponding targets were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. HTS-related genes were obtained from the GeneCards, DisGeNET, and National Center for Biotechnology Information. The function of targets was analyzed by performing Gene Ontology and Kyoto Encyclopaedia of Genes and Genome (KEGG) enrichment analysis. A protein + IBM-protein interaction (PPI) network was developed using STRING database and Cytoscape. To confirm the high affinity between compounds and targets, molecular docking was performed. RESULTS A total of 65 core genes, which were both related to compounds and HTS, were selected from multiple databases. PPI analysis showed that CKD2 , ABCC1 , MMP2 , MMP9 , glycogen synthase kinase 3 beta (GSK3B ), PRARG , MMP3 , and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma (PIK3CG ) were the hub targets and MOL004941, MOL004935, MOL004866, MOL004993, and MOL004989 were the key compounds of WFY against HTS. The results of KEGG enrichment analysis demonstrated that the function of most genes were enriched in the PI3K-Akt pathway. Moreover, by performing molecular docking, we confirmed that GSK3B and 8-prenylated eriodictyol shared the highest affinity. CONCLUSION The current findings showed that the GSK3B and cyclin dependent kinase 2 were the potential targets and MOL004941, MOL004989, and MOL004993 were the main compounds of WFY in HTS treatment.

Short Notes: First Report of Cucurbite Aphid-Borne Yellows Virus in Iraq

Squash (Cucurbita pepo) fields in Mosul suffered from virus-like symptoms, such as vein clearing, severe mosaic, mottling, chlorosis, necrosis, stunting and fruit discoloration. The symptoms were associated with aphids presence in the infected fields. A metatranscriptomic analysis has been applied to detect the causal agent. The result showed that 559,024 mapped reads were related to Cucurbit aphid-borne yellows virus with full coverage to produce 5,662 bp consensus sequence. The virus sequence was deposited in National Center for Biotechnology Information (NCBI) under accession number OQ865059, and the isolate named Iraq. For the first time in Iraq, the infection of the virus has been reported in squash, highlighting the impact of such virus infection that spread epidemically across the squash and other cucurbits fields.

Breast Cancer High-Penetrance Genes BRCA1 and BRCA2 Mutations Using Next-Generation Sequencing Among Iraqi Kurdish Women.

Background BRCA1andBRCA2genesare the main high-penetrance genes that are responsible for most cases of inherited breast cancer. The present study aimed to detect the frequencies of inherited breast cancer caused by BRCA1 and BRCA2 genes among Kurdish breast cancer patients, including all the exome of these two genes, using next-generation sequencing (NGS). Methodology Seventy women who were diagnosed with breast cancer and registered at Nanakali Hospital in Erbil, Iraq, were included. Blood samples were collected for molecular testing (polymerase chain reaction (PCR)) targeting all exomes of BRCA1 and BRCA2 genes. All exome regions are sequenced by NGS using the Miseq system (Illumina Inc., San Diego, CA). Obtained data were visualized using Integrative Genomics Viewer (IGV 2.3 Software, Broad Institute, Cambridge, MA). Data were interpreted based on the National Center for Biotechnology Information (NCBI), Clinically Relevant Variation (ClinVar) archives, and other databases. Results Among 70 samples, more than forty-two variants have been detected, 20 on BRCA1 and 22 on BRCA2. Regarding clinical significance, six (14.28%) variants were pathogenic, four of them on theBRCA1 gene, which were: c.3607C>T, c.3544C>T, c.68_69del, and c.224_227delAAAG, and two pathogenic variants were on BRCA2 gene: c.100G>T, and c.1813delA. Also, two (4.76%) variants were conflict interpretations of pathogenicity, one (2.38%) was a variant of uncertain significant VUS, and the rest 29 (69%) variants were benign.In addition, four new variants (three in BRCA1 and one in BRCA2 gene), never previously reported, were identified. Conclusions In conclusion, analyzing the BRCA1/2 genes provide a better prediction for the risk of developing breast cancer in the future. Variant types and frequencies differ among different populations and ethnicities, the common mutations worldwide may not be prevalent in the Kurdish population. The current research findings will be useful for future screening studies of these two genes in the Kurdish population.

Clustered Regularly Interspaced Short Palindromic Repeat-1 (CRISPR-1) Locus as a Tool for Tracing the Zoonotic History of Salmonella enterica Strains.

Background Salmonella enterica is a significant foodborne pathogen that causes considerable illness and death in humans and animals. The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system in bacteria acts as an adaptive immune defense against invasive genetic elements by incorporating short intergenic spacers (IGSs) into CRISPR loci. These loci serve as molecular records of past interactions with phages and plasmids, providing insights into the transmission and evolution of bacterial strains across different hosts. Aim This study aimed to investigate the diversity of IGSs in the CRISPR-1 locus of S. enterica isolates from humans and camels. The objective was to assess the potential of IGSs to distinguish strains, track sources, and understand patterns of zoonotic transmission. Materials and methods Genomic DNA was extracted from multiple strains of S. enterica, and the CRISPR-1 locus was polymerase chain reaction (PCR) amplified and sequenced. The sequences were compared to identify distinct patterns of IGSs and potential host-specific characteristics. Sanger sequencing and bioinformatics tools were used to classify the IGSs and determine their similarity to known sequences in the National Center for Biotechnology Information (NCBI) database. Results Sequence analysis revealed five distinct CRISPR-1 types among S. enterica isolates from humans and three among camel isolates. The presence of shared IGSs between human and camel S. entericaisolates suggested zoonotic or reverse-zoonotic transmission events. Additionally, host-specific unknown IGSs (UIGS) were identified. Importantly, camel isolates initially identified as S. enterica subspeciesenterica serovar Enteritidis based on rrnH gene sequencing were reclassified as S. enterica serovar Enteritidis based on CRISPR-1 profiling, demonstrating the higher resolution of CRISPR-based genotyping. Conclusion The diversity of IGSs in the CRISPR-1 locus effectively differentiated S. enterica strains and provided insights into their evolutionary origins and transmission dynamics. CRISPR-based genotyping proves to be a promising tool to complement traditional serotyping methods, enhancing the molecular epidemiology of salmonellosis and potentially leading to better management and control strategies for this pathogen.

Exploring the mechanisms of glycolytic genes involvement in pulmonary arterial hypertension through integrative bioinformatics analysis.

The purpose of this study was to identify the mechanisms underlying the involvement of glycolytic genes in pulmonary arterial hypertension (PAH). This study involved downloading 3 datasets from the GEO database at the National Center for Biotechnology Information. The datasets were processed to obtain expression matrices for analysis. Genes involved in glycolysis-related pathways were obtained, and genes related to glycolysis were selected based on significant differences in expression. Gene Ontology functional annotation analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and GSEA enrichment analysis were performed on the DEGs. Combining LASSO regression with SVM-RFE machine learning technology, a PAH risk prediction model based on glycolysis related gene expression was constructed, and CIBERSORTx technology was used to analyse the immune cell composition of PAH patients. Gene enrichment analysis revealed that the DEGs work synergistically across multiple biological pathways. A total of 6 key glycolysis-related genes were selected using LASSO regression and SVM. A bar plot was constructed to evaluate the weights of the key genes and predict the risk of PAH. The clinical application value and predictive accuracy of the model were assessed. Immunological feature analysis revealed significant correlations between key glycolysis-related genes and the abundances of different immune cell types. The glycolysis genes (ACSS2, ALAS2, ALDH3A1, ADOC3, NT5E, and TALDO1) identified in this study play important roles in the development of pulmonary arterial hypertension, providing new evidence for the involvement of glycolysis in PAH.

Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations.

The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. A total of 7540 complete nucleotide genomes from 51 African nations were obtained and analysed using the National Center for Biotechnology Information and Global Initiative on Sharing Influenza Data databases to examine the genetic diversity and spread dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Using various clade and lineage nomenclature schemes, we examined their diversity and used maximum parsimony inference methods to reconstruct the evolutionary hypotheses about the spread of the virus in Africa. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa three years after the COVID-19 pandemic, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya and Nigeria as key sources of viral transmission among sub-Saharan African nations. These findings provide insights into the viral strains that circulate in Africa and their evolutionary patterns.

Phylogenetic analysis on 16S rRNA of Pseudomonas Species isolated from clinical specimens in Nigeria and other Regions

This project was to study the clinical isolates of Pseudomonas organisms in Nigeria in comparison with those of other regions of the world, to understand their evolutional relationship, using phylogenetic analysis of 16SrRNA. A total of 51 sequence data files of Pseudomonas species from different countries were selected based on 16S rRNA, using the National Centre for Biotechnology Information (NCBI) webpage. Geneious software (V9.0.5) was employed for sequence alignment. Tamura- Nei was used as the genetic distant model, while the tree build method was Neighbor-Joining with a bootstrap value of 1000 and 100 numbers of replicates to indicate the revolutionary process analyzed over time. Majority of the strains from Nigeria (7) have very little or no mutations in the sequences. These strains with other strains from the other countries were clustered at the 2nd branch of the tree, with a bootstrap value of 96%. Generally, there is similarity in diversity of the Pseudomonas species across the globe. Much diversity was seen in all the strains from Saudi Arabia, as all were found on the 10th branch of the tree. Two Pseudomonas strains previously identified as belonging to other species than aeruginosa were seen to be Pseudomonas aeruginosa strains. The low diversity shown by the strain isolates from Nigeria implies high fidelity to genetic stability with regard to the ancestral origin. The high mutation observed in all the strains from Saudi-Arabia indicates high diversity from the common ancestor and this may likely result to increased virulence and multi-drug resistance.

Bioinformatics analysis of clinical isolates of Escherichia coli from Nigeria and other countries for quinolone and fluoroquinolone resistance

Quinolones were the drugs of choice for the treatment of bacterial infections, especially, infections caused by Gram negative bacteria. Unfortunately, these drugs have been resisted by the microbial agents including Escherichia coli, known to be the leading cause of Urinary Tract Infection (UTI) globally. This study therefore was aimed at detecting all the genes involved in Quinolone resistance by the E. coli pathogen isolated from Nigeria and from other geographical regions, using robust techniques. Twenty-three sequence data files of Escherichia coli from various countries of the world were retrieved from the National Centre for biotechnology Information (NCBI) database and sent for genome assembly for processing of the short reads into long reads. The outcome was config. fasta files which were comprehensively annotated and characterized for genetic functions and mechanisms. A total of 208 antibiotic resistance genes were detected, out of which 27(13.0%) were linked to quinolone resistance and 14(6.7%) to multi- drug resistance. The result of this study significantly implicated many genes in quinolone resistance; notably were the efflux pump genes and their high percentage abundance. We recommend in-depth study of the genes for their expression capabilities, also the structure and features of the efflux pump genes to enable proper redesigning of drugs by integrating anti efflux pump substances that will selectively prevent the expression of the genes for antibiotic resistance, without any harm to the host, or that can destabilize the positive regulation of the operon for antibiotic resistance.

Utilizing the Banana S-Adenosyl-L-Homocysteine Hydrolase Allergen to Identify Cross-Reactive IgE in Ryegrass-, Latex-, and Kiwifruit-Allergic Individuals.

Food allergies mediated by specific IgE (sIgE) have a significant socioeconomic impact on society. Evaluating the IgE cross-reactivity between allergens from different allergen sources can enable the better management of these potentially life-threatening adverse reactions to food proteins and enhance food safety. A novel banana fruit allergen, S-adenosyl-L-homocysteine hydrolase (SAHH), has been recently identified and its recombinant homolog was heterologously overproduced in E. coli. In this study, we performed a search in the NCBI (National Center for Biotechnology Information) for SAHH homologs in ryegrass, latex, and kiwifruit, all of which are commonly associated with pollen-latex-fruit syndrome. In addition, Western immunoblot analysis was utilized to identify the cross-reactive IgE to banana SAHH in the sera of patients with a latex allergy, kiwifruit allergy, and ryegrass allergy. ClustalOmega analysis showed more than 92% amino acid sequence identity among the banana SAHH homologs in ryegrass, latex, and kiwifruit. In addition to five B-cell epitopes, in silico analysis predicted eleven T-cell epitopes in banana SAHH, seventeen in kiwifruit SAHH, twelve in ryegrass SAHH, and eight in latex SAHH, which were related to the seven-allele HLA reference set (HLA-DRB1*03:01, HLA-DRB1*07:01, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DRB5*01:01). Four T-cell epitopes were identical in banana and kiwifruit SAHH (positions 328, 278, 142, 341), as well as banana and ryegrass SAHH (positions 278, 142, 96, and 341). All four SAHHs shared two T-cell epitopes (positions 278 and 341). In line with the high amino acid sequence identity and B-cell epitope homology among the analyzed proteins, the cross-reactive IgE to banana SAHH was detected in three of three latex-allergic patients, five of six ryegrass-allergic patients, and two of three kiwifruit-allergic patients. Although banana SAHH has only been studied in a small group of allergic individuals, it is a novel cross-reactive food allergen that should be considered when testing for pollen-latex-fruit syndrome.

Multifractal Properties of Human Chromosome Sequences

The intricacy and fractal properties of human DNA sequences are examined in this work. The core of this study is to discern whether complete DNA sequences present distinct complexity and fractal attributes compared with sequences containing exclusively exon regions. In this regard, the entire base pair sequences of DNA are extracted from the NCBI (National Center for Biotechnology Information) database. In order to create a time series representation for the base pair sequence {G,C,T,A}, we use the Chaos Game Representation (CGR) approach and a mapping rule f, which enables us to apply the metric known as the Complexity–Entropy Plane (CEP) and multifractal detrended fluctuation analysis (MF-DFA). To carry out our investigation, we divided human DNA into two groups: the first is composed of the 24 chromosomes, which comprises all the base pairs that form the DNA sequence, and another group that also includes the 24 chromosomes, but the DNA sequences rely only on the exons’ presence. The results show that both sets provide fractal patterns in their structure, as obtained by the CGR approach. Complete DNA sequences show a sharper visual fractal pattern than sequences composed only of exons. Moreover, the sequences occupy distinct areas of the complexity–entropy plane, and the complete DNA sequences lead to greater statistical complexity and lower entropy than the exon sequences. Also, we observed that different fractal parameters between chromosomes indicate diversity in genomic sequences. All these results occur in different scales for all chromosomes.

Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex.

The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.

Genome-Wide Identification, Expression Analysis and Functional Study of DELLA Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).

DELLA protein is a crucial factor which played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, little is known about the function and information of DELLA protein in Chinese cabbage. Using 5 DELLA gene sequences in Arabidopsis Thaliana as probes, 5 DELLA genes in Chinese cabbage were identified by Blast search in Chinese cabbage database (Brassica database (BRAD)). The National Center for Biotechnology Information (NCBI), ExPaSy, SWISS-MODEL, DNAMAN, MEGA 11, PlantCARE were used to identify and analyze the DELLA gene family of Chinese cabbage. Gene expression was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). The function of BraA10gRGL3 was verified by overexpression and phenotypic analysis of BraA10gRGL3 and yeast hybrid. In this study, 5 BraDELLAs homologous to Arabidopsis thaliana were identified and cloned based on the Brassica database, namely, BraA02gRGL1, BraA05gRGL2, BraA10gRGL3, BraA06gRGA and BraA09gRGA. All BraDELLAs contain the DELLA, TVHYNP, and GRAS conserved domains. Cis-element analysis revealed that the promoter regions of these 5 DELLA genes all contain light-responsive elements, TCT motif, I-box, G-box, and box 4, which are associated with GA signaling. Transcriptome analysis results proved that the expression of BraA02gRGL1, BraA05gRGL2, and BraA10gRGL3 in Y2 at different growth stages were lower than them in Y7, which is consistent with the phenotype that Y7 exhibited stronger stress tolerance than Y2. It is worth emphasizing that even through the overexpression of BraA10gRGL3-Y7 in Arabidopsis resulted in smaller leaf size and lower fresh weight compared to the wild type (WT) Arabidopsis: Columbia, a stronger response to abiotic stresses was observed in BraA10gRGL3-Y7. It indicated that BraA10gRGL3-Y7 can improve the stress resistance of plants by inhibiting their growth. Moreover, the yeast two-hybrid experiment confirmed that BraA10gRGL3-Y7 can interacted with BraA05gGID1a-Y7, BraA04gGID1b1, BraA09gGID1b3-Y2, and BraA06gGID1c, whereas BraA10gRGL3-Y2 cannot interact with any BraGID1. Collectively, BraDELLAs play important role in plant development and response to abiotic stress. The differences in amino acid sequences between BraA10gRGL3-Y2 and BraA10gRGL3-Y7 may result in variations in their protein binding sites, thus affecting their interaction with the BraGID1 family proteins. This systematic analysis lays the foundation for further study of the functional characteristics of DELLA genes of Chinese cabbage.