National Center For Biotechnology Information Research Articles

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.

Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis

Hepatitis is a major public health issue, affecting 10–17 million people worldwide, with its prevalence continuously increasing. The Hepatitis C virus (HCV) is responsible for liver related diseases, which include liver cirrhosis, hepatocellular carcinoma, and chronic hepatitis. Pakistan is experiencing a serious rise in HCV cases. This study aimed to assess the prevalence and distribution of HCV genotypes in Sindh, Pakistan. Serum samples from HCV-positive patients were collected from various local hospitals in Sindh. These samples were first screened for HCV antibodies using ELISA. Samples that tested positive for HCV RNA underwent further genotyping through sequencing using the standard Sanger method. The genotypes were identified by comparing the sequences with those available in the National Center for Biotechnology Information (NCBI) database, and a phylogenetic tree was constructed. The phylogenetic analysis showed that all isolates in this study were clustered with genotypes 3a and 3b, except for one sequence that was clustered with genotype 1a. No isolates were found to be clustered with reference genomes of genotypes 2, 4, 5, 6, and 7 suggesting that genotype 3a is endemic in this region. The analyzed sequences demonstrated a 98% similarity with reference and isolated sequences. In summary, sequencing of the HCV 5′ UTR essential for identifying the predominant genotype of HCV RNA in the Sindh region Further research on the distribution of HCV genotypes in other regions of Pakistan could aid in improving screening processes, identifying more effective treatment options, and developing suitable prevention strategies.

The State of Knowledge of CCA Diversity in the Caribbean Coral Reefs

Crustose coralline algae (CCA) are a diverse and ecologically important species found in most of the world’s oceans. The current lack of taxonomic knowledge and relative abundance compromises our ability to predict species diversity numbers and, thus, their ecological roles and impacts on coral reefs. To gather a better understanding of the state of knowledge of crustose coralline algae taxonomy in the Caribbean, 107 different research papers, and other primary and secondary literature were studied; any source with taxonomical information, species identification, or genetic markers for identification was recorded. All Genebank codes were collected and sorted by supposed species marker and then ran through the National Center of Biotechnology Information. The location these genetic markers were gathered from was compared to the natural habitat range of the species, based on the Algaebank habitat description. Of the supposed 83 described species of crustose algae in the Caribbean, based on morphological characteristics, only 24 total were confirmed by DNA markers. This leaves at least 59 species of CCA to be confirmed in the Caribbean Sea with molecular markers. This indicates the importance of DNA barcode survey studies to assess the accurate diversity of this group in the region. With this limited knowledge apparent, it should be seen that a CCAs phylogenetic and taxonomical review must be done. An in-depth assessment should be conducted on CCA collections to identify the Caribbean species correctly and thus know their biodiversity in local habitats.

Total Transanal Endorectal Pull-through Versus Laparoscopic-Assisted Approach in Children with Rectosigmoid Hirschsprung's Disease: A Systematic Review and Meta-Analysis.

Objective: To compare the clinical outcomes between total transanal endorectal pull-through (TTEPT) and laparoscopic-assisted transanal endorectal pull-through (LTEPT) in children with rectosigmoid Hirschsprung's disease. Methods: A retrospective study was conducted to compare patients with rectosigmoid Hirschsprung's disease who underwent TTEPT or LTEPT at Beijing Children's Hospital between January 2016 and June 2021. Clinical details were collected from medical records. Patients' parents completed the Krickenbeck questionnaire to evaluate the long-term bowel function (age >4 years) by telephone. A literature search was conducted by using the National Center for Biotechnology Information (NCBI) PubMed database. We combined data from our data with eligible articles and performed a meta-analysis. Result: From our data, there was no difference in the incidence of postoperative complications or long-term bowel function between the patients undergoing TTEPT and LTEPT. A meta-analysis, including five published articles and our data, was performed with a total of 414 patients (n = 236 with TTEPT and n = 178 with LTEPT). For postoperative complications, there were no significant differences between TTEPT and LTEPT for the incidence of HAEC (odds ratio [OR], 0.90; 95% confidence interval [CI], 0.45-1.80; P = .77) or anastomotic leak (OR, 2.52; 95% CI, 0.40-15.80; P = .32). Regarding bowel function outcomes, the incidence of soiling (OR, 1.77; 95% CI, 0.84-3.71; P = .13) and constipation (OR, 1.20; 95% CI, 0.54-2.64; P = .66) were also similar for the two approaches. Conclusion: There was no significant difference in postoperative complications and bowel functional outcomes in patients with rectosigmoid HD undergoing TTEPT or LTEPT. Levels of Evidence: III.

HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants

Background: Human papillomavirus (HPV) is the main risk factor for the development of squamous cell cervical cancer, and E6 oncoprotein and E7 oncoprotein are important components of the viral genome and its oncogenic potential. It is known that different viral variants of HPV16 have different pathology and impact on the development of neoplasia, although few studies have been performed on South American variants. Objective: Therefore, the present study aimed to analyze in silico the genomic diversity of HPV16 in 20 complete genome variants of South America in the National Center for Biotechnology Information (NCBI) database. Methods: We performed a descriptive study to characterize the polymorphic regions of the E6 and E7 genes in HPV16 variants, using software for genomic data and single nucleotide polymorphism (SNP) analysis and others for phylogenetic analysis. Results: The variants analyzed included six SNPs linked to cancer (A131G, G145T, C335T, T350G, C712A, and T732C) and significant variation (798 nucleotide substitutions). Despite this, the variants showed low genetic diversity. Eighteen variants of unclear significance (VUS) were identified, 10 of which were in the coding E6 regions and 8 in the coding E7 regions. The prevalence of lineage D variants is of concern due to their pathology in cervical cancer and requires more research and epidemiological vigilance regarding their prevalence in the population. Conclusion: study may contribute to future research on South American variants of HPV16, their pathogenicity, and the development of treatments.

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments.

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

Association between Mir-17-92 gene promoter polymorphisms and depression in a Chinese population

BackgroundDepression is a common chronic debilitating disease with a heavy social burden. single nucleotide polymorphisms (SNPs) can affect the function of microRNAs (miRNAs), which is in turn associated with neurological diseases. However, the association between SNPs located in the promoter region of miR-17-92 and the risk of depression remains unclear. Therefore, we investigated the association between rs982873, rs9588884 and rs1813389 polymorphisms in the promoter region of miR-17-92 and the incidence of depression in a Chinese population.Methodswe used GWAS (Genome-wide association study) and NCBI (National Center for Biotechnology Information) to screen three SNPs in the miR-17-92 cluster binding sites. A case-control study (including 555 cases and 541 controls) was conducted to investigate the relationship between the SNPs and risk of depression in different regions of China. The gene sequencing ii was used to genotype the collected blood samples.Resultsthe following genotypes were significantly associated with a reduced risk of depression: rs982873 TC (TC vs. TT: OR = 0.72, 95% CI, 0.54–0.96, P = 0.024; TC/CC vs. TT: OR = 0.74, 95% Cl, 0.56–0.96, P = 0.025); CG genotype of rs9588884 (CG vs. CC: OR = 0.74, 95% CI, 0.55–0.98, P = 0.033; CG/GG vs. CC: OR = 0.75, 95% Cl, 0.57–0.98, P = 0.036); and AG genotype of rs1813389 (AG vs. AA: OR = 0.75, 95% CI, 0.57-1.00, P = 0.049; AG/GG vs. AA: OR = 0.76, 95% Cl, 0.59-1.00, P = 0.047). Stratified analysis showed that there was no significant correlation between the three SNPS and variables such as family history of suicidal tendency (P > 0.05).Conclusionsour findings suggest that rs982873, rs9588884, and rs1813389 polymorphisms may be associated with protective factors for depression.

Immune Responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccines: Updated Insights

Background: Using a multidisciplinary approach, this review explores and investigates the relationship between immune responses, effectiveness, and results of various vaccination strategies among a range of demographics. Moreover, this review aims to aid healthcare professionals in understanding the intricacies of immune responses and their implications for future vaccine development.Methodology: In this systematic review, we employed an electronic online database platform including the National Centre for Biotechnology Information (NCBI), the National Institute for Health and Clinical Excellence (NICE), and the World Health Organization (WHO) for evidence-based material, utilizing the keywords throughout this literature review.Results: This review provides a detailed framework regarding immune responses to the COVID- 19 vaccine, based on demographics, age, sex, types of immunity, and immunization strategies. Such research can provide important academic support for the development of not only COVID- 19 vaccines but also other vaccines.Conclusions: Overall, immune responses tended to dwindle a few months after vaccine administration. This is because B cells block SARS-CoV-2 from infecting cells via antibodies and T cells destroy infected cells. The most efficient tool for providing long-lasting protection against SARS-CoV-2 is vaccination. Humans have developed immunity to SARS-CoV-2, particularly antibody-mediated humoral immunity. The development of vaccines across the whole family of coronaviruses that target antibody epitopes (antigenic determinants) prevents the emergence of mutant strains.

TPMGD: A genomic database for the traditional medicines in Pakistan

ObjectiveIn Pakistan, traditional medicines are an important component of the medical system, with numerous varieties and great demands. However, due to the scattered resources and the lack of systematic collection and collation, adulteration of traditional Pakistani medicine (TPM) is common, which severely affects the safety of their medicinal use and the import and export trades. Therefore, it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of TPM. MethodsWe collected and organized the information on 128 TPMs with regard to their medicinal parts, efficacy, usage, and genetic material, based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine: Pharmaceutical Codex. The genetic information of TPM is summarized from national center for biotechnology information (NCBI) and global pharmacopoeia genome database (GPGD). Furthermore, we utilized bioinformatics technology to supplement the chloroplast genome (cp-genome) data of 12 TPMs. To build the web server, we used the Linux+Apache+MySQL+PHP (LAMP) system and constructed the webpage on a PHP: Hypertext Preprocessor (PHP) model view controller (MVC) framework. ResultsWe constructed a new genomic database, the traditional Pakistani medicine genomic database (TPMGD). This database comprises five entries, namely homepage, medicinal species, species identification, basic local alignment search tool (BLAST), and download. Currently, TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs, including 140 cytochrome c oxidase subunit I (COI) sequences and 119 mitochondrial genome sequences from Bombyx mori, 1 396 internal transcribed spacer 2 (ITS2) sequences and 1 074 intergenic region (psbA-trnH) sequences specific to 92 and 83 plant species, respectively. Additionally, TPMGD includes 199 cp-genome sequences of 82 TPMs. ConclusionTPMGD is a multifunctional database that integrates species description, functional information inquiry, genetic information storage, molecular identification of TPM, etc. The database not only provides convenience for TPM information queries but also establishes the scientific basis for the medication safety, species identification, and resource protection of TPM.

EVALUATION OF PROPHAGES AND ANTI MICROBIAL RESISTANCE PROFILE OF BACILLUS SUBTILIS USING IN SILICO APPROACH

The main objective of this study was to identify the prophages and antimicrobial resistance profile of Bacillus subtilis using computational methods. Prophages are potential therapeutic antimicrobial agents against antibiotic- resistant pathogens. The potential of prophage to induce antimicrobial resistance and increase pathogenicity in bacterial genomes resulted in renewed interest in the identification of prophage sequences and their associated antimicrobial resistant genes in bacterial genomes. Sequences of Bacillus subtilis retrieved from the sequence raw archive (SRA) of the National Centre for Biotechnology Information was submitted to bacterial viral bioinformatics resource centre for genome assembly. Prophage sequences were identified using the PHASTER server. The region length, region position and GC percentage of nucleotides of prophage sequences were identified. The antimicrobial resistance gene family, drug class, resistance mechanism and length of reference sequences were identified using the resistance gene identifier protocol of the comprehensive antimicrobial resistance database. It can be concluded that the Bacillus subtilis strain evaluated contained prophage sequences associated with antimicrobial resistance genes, there is, therefore, the need to assess the safety of bacteriophages before they are utilized as alternative to antibiotics.

Integrating Bulk RNA and Single-Cell Sequencing Data Unveils Efferocytosis Patterns and ceRNA Network in Ischemic Stroke.

Excessive inflammatory response following ischemic stroke (IS) injury is a key factor affecting the functional recovery of patients. The efferocytic clearance of apoptotic cells within ischemic brain tissue is a critical mechanism for mitigating inflammation, presenting a promising avenue for the treatment of ischemic stroke. However, the cellular and molecular mechanisms underlying efferocytosis in the brain after IS and its impact on brain injury and recovery are poorly understood. This study explored the roles of inflammation and efferocytosis in IS with bioinformatics. Three Gene Expression Omnibus Series (GSE) (GSE137482-3m, GSE137482-18m, and GSE30655) were obtained from NCBI (National Center for Biotechnology Information) and GEO (Gene Expression Omnibus). Differentially expressed genes (DEGs) were processed for GSEA (Gene Set Enrichment Analysis), GO (Gene Ontology Functional Enrichment Analysis), and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses. Efferocytosis-related genes were identified from the existing literature, following which the relationship between Differentially Expressed Genes (DEGs) and efferocytosis-related genes was examined. The single-cell dataset GSE174574 was employed to investigate the distinct expression profiles of efferocytosis-related genes. The identified hub genes were verified using the dataset of human brain and peripheral blood sample datasets GSE56267 and GSE122709. The dataset GSE215212 was used to predict competing endogenous RNA (ceRNA) network, and GSE231431 was applied to verify the expression of differential miRNAs. At last, the middle cerebral artery (MCAO) model was established to validate the efferocytosis process and the expression of hub genes. DEGs in two datasets were significantly enriched in pathways involved in inflammatory response and immunoregulation. Based on the least absolute shrinkage and selection operator (LASSO) analyses, we identified hub efferocytosis-related genes (Abca1, C1qc, Ptx3, Irf5, and Pros1) and key transcription factors (Stat5). The scRNA-seq analysis showed that these hub genes were mainly expressed in microglia and macrophages which are the main cells with efferocytosis function in the brain. We then identified miR-125b-5p as a therapeutic target of IS based on the ceRNA network. Finally, we validated the phagocytosis and clearance of dead cells by efferocytosis and the expression of hub gene Abca1 in MCAO mice models.

Molecular identification of the bacterium acute conjunctivitis by the method of sequensing gen 16S rRNA

Conjunctivitis is the most common eye disease, characterized by contextual inflammation, which can be caused by bacteria. The diagnosis of conjunctivitis is established based various factors, including the patients’s medical history, onset of eye symptoms, non-ocular symptoms, previous disease history, family medical history, allergies, and physical examination of the eyes, which may include assessments of visual acuity and vision field. Some cases of conjunctivitis require laboratory examinations to confirm the diagnosis. These may include cytological examination with Giemsa staining, Chlamydia Diagnostic Test, Nucleic acid amplification tests (NAATs) or Polymerase chain reaction (PCR), and microbiological tests. Microbiological examination helps identify the bacteria responsible for conjunctivitis and aids in treatment by prescribing antibiotics to suppress the growth of the infecting bacteria. While identification tests are not routinely performed, researchers often seek to determine the specific type of bacteria causing conjunctivitis infections, which may require several laboratory tests. Bacterial virulence plays a significant role, with genetic mutations potentially leading to severe infections of varying severity. Virulence genes encode proteins that express pathogenic properties. The species responsible for conjunctivitis can be definitively identified definitively through microbiological examination, utilizing methods such as the 16S Ribosomal RNA Sequencing (rRNA) technique, known for its accuracy and speed. This study aims to analyze the results of rRNA sequencing in cases of acute bacterial conjunctivitis caused by 16S rRNA genotyping. The research employed an exploratory metholodolot, with the results analyzed using the The Basic Local Alignment Search Tool (BLAST) tracking program database on the National Center for Biotechnology Information (NCBI) website. The findings revealed that Sphingomonas paucimobilis encoded the 16S rRNA using Universal Primary 27 F and 1492 R, obtained in a sequence size of 1351bp. The isolate demonstrated similarities to Sphingomonas paucimobilis.

Two putative calcium-dependent protein kinases are involved in the regulation of sugarcane defense genes

Sugarcane is a primary sugar crop and an important source of bioenergy. Pathogens are the major factors affecting sugarcane yield and sugar content. However, the mechanisms of sugarcane defense regulation remain largely unknown, and research on prospective genetic targets for modification is scarce. As the main class of calcium sensors, calcium-dependent protein kinases (CDPKs/CPKs) play a crucial role in the immune regulatory network. Using sugarcane genomic data, we identified 229 putative ScCDPKs in primordial specie Saccharum officinarum. Searching the putative CDPKs in sugarcane cultivars from National Center for Biotechnology Information (NCBI), 12 putative ScCDPKs in cultivars were identified. Phylogenetic analysis revealed evolutionary relationships among these CDPKs in sugarcane cultivars and those in S. officinarum, Arabidopsis thaliana, and rice. Truncation mutants of ScCDPKs were introduced into the reporter system and examined for activity in inducing Sugarcane Pathogenesis Related Protein 1 (ScPR1). The results showed that truncated ScCDPK1 and ScCDPK8 induce higher expression of ScPR1 than full-length ScCDPK1 and ScCDPK8. Additionally, transient expression of truncated ScCDPK1 and ScCDPK8 exhibit stronger activity in sugarcane protoplasts for activation of ScPR1 and sugarcane Serine Protease Inhibitor (ScSPI). These results demonstrate that ScCDPK1 and ScCDPK8 possess auto-inhibitory activity. The findings of this study provide a basis for an in-depth study of the sugarcane CDPK gene family and lay the foundation for further genetic improvement.

Sequence Analysis of some species in the genus Amaranthus L. using Ribulose-1.5 - bisphosphate carboxylase/oxygenase (rbcL) genes

Bioinformatics is a novel method to investigate evolutionary relationships and genetic diversity among species. This study assessed the evolutionary patterns and genetic diversity of Amaranthus species using ribulose-1.5-bisphosphate carboxylase/oxygenase (rbcL gene). A total of 20 full FASTA-format rbcL gene sequences for accessions of Amaranthus tricolor, A. dubius, A. cruentus, A. viridis, and A. spinosus from different regions were retrieved from the National Center for Biotechnology Information. Multiple sequence alignment was used to determine genetic variations. A phylogenetic tree was constructed using neighbor-joining clustering method while a distant matrix was created using Tamura-Nei genetic distance model. From position 1 to 22 in nucleotide alignment, only accession KX082771.1 from USA, aligns. The exclusive alignment in this region suggests an exceptionally conserved sequence among species, implying a common genetic origin. However, from position 23 to 50, nine different accessions namely MN192576.1, MN204800.1, EF590496.1, GQ248546.1, OQ737000.1, MG246937.1, MN104855.1, MN104858.1, and MN04859.1 align. The phylogenetic tree representing the evolutionary relationships offers insights into the genetic diversity and relatedness of these species within specific regions. The genetic distance matrix shows that sequences within the same region share relatively high similarity scores, indicating a genetic connection likely influenced by their geographic proximity. However, sequences from different regions, exhibit moderate genetic differences, emphasizing the genetic diversity across geographically distinct regions. The observed genetic diversity and evolutionary relationships among accessions of Amaranthus revealed by rbcL genes highlight the unique genetic features of these species in different regions, and therefore should be explored for their genetic improvement and conservation purposes.

Network pharmacology prediction and experiment validation of anti liver cancer activity of curcumae rhizoma and hedyotis diffusa willd

Objective: This study aims to elucidate anti liver cancer components and potential mechanisms of Curcumae Rhizoma and Hedyotis diffusa Willd (CR-HDW). Methods: Effective components and targets of CR-HDW were identified from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Liver cancer-related genes were collected from GeneCards, Gene-Disease Association (DisGeNET), and National Center for Biotechnology Information (NCBI). Protein-protein interaction networks, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were conducted to analyze the identified genes. Molecular docking was used to simulate binding of the active components and their target proteins. Cell activity assay, Western blot, and Senescence-associated β-galactosidase (SA-β-gal) experiments were conducted to validate core targets identified from molecular docking. Results: Ten active compounds of CR-HDW were identified including quercetin, 3-epioleanic acid and hederagenin. The primary core proteins comprised Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Protein Kinase B（AKT1）, etc. The pathways for Phosphoinositide 3-kinase (PI3K)/ AKT, cellular senescence, Fork head boxO (FOXO) were revealed as important for anti-cancer activity of CR-HDW. Molecular docking demonstrated strong binding between liver cancer target proteins and major active components of CR-HDW. In vitro experiments confirmed that hederagenin and 3-epioleolic acid inhibited HuH-7 cell growth, reduced expression of PI3K, AKT, and mechanistic target of rapamycin (mTOR) proteins. Hederagenin also induced HuH-7 senescence. Conclusion: In summary, our results suggest that the CR-HDW component (Hederagenin, 3-epoxy-olanolic acid) can inhibit the proliferation of HuH-7 cells by decreasing PI3K, AKT, and mTOR. Hederagenin also induced HuH-7 senescence.

Evaluation of Antifungal Effect of Allium jesdianum Bacterial Endophytes on Rhizopus stolonifer, Penicillium, Cladosporium, and Trichophyton mentagrophytes

: Antimicrobial resistance (AMR) is the ability of microbes to survive and grow in the presence of antimicrobial drugs. Bacterial endophytes, which reside within plants, can promote plant growth and other essential activities. Endophytes have the potential to produce novel and unique products for use in modern medicine, agriculture, and industry. They may hold the key to combating drug-resistant strains by providing new antimicrobial compounds, potentially leading to the development of new medications. In this study, bacterial endophytes of Allium jesdianum were extracted and characterized. The antifungal effect of these endophytes on Rhizopus stolonifer, Penicillium, Cladosporium, and Trichophyton mentagrophytes was evaluated. Various parts of the plant were used to isolate ten bacterial endophytes to assess their antifungal properties. Universal eubacterial primers were used to amplify a 1500 bp region of the 16S rRNA gene. The resulting partial nucleotide sequences were compared with sequences available from the National Center for Biotechnology Information (NCBI) and EzBioCloud Database. Subsequent comparisons determined their similarity. Each isolated endophyte was cultured with equal amounts of R. stolonifer, Penicillium, Cladosporium, and T. mentagrophytes. This study measured the level of antagonism by assessing the extent of potential interactions. Ten bacterial endophytes, primarily cocci and bacilli, were extracted from different parts of A. jesdianum. The isolates were identified as Staphylococcus warneri AJB1, Staphylococcus succinus AJB2, Pseudomonas thivervalensis AJB3, Bacillus subtilis AJB4, Acinetobacter lwoffii AJB5, and Pantoea brenneri AJB6. AJB1 and AJB3 showed no antagonistic activity. AJB2, AJB5, and AJB6 displayed antagonistic action against R. stolonifer. Only AJB4 showed strong antagonistic activity against Penicillium. Further research is necessary to determine whether these endophytes possess antibiotic activity and can be used for food preservation.

Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation.

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.

A hybrid stacking classifier with feature selection for handling imbalanced data

Nowadays, cancer has become more alarming. This paper discusses the most significant Ovarian Cancer, Epithelial Ovarian Cancer (EOC), due to the low survival rate. The proposed algorithm for this work is a ‘Multi classifier ShapRFECV based EOC’ (MSRFECV-EOC) subtype analysis technique that utilized the EOC data from the National Centre for Biotechnology Information and Cancer Cell Line Encyclopedia websites for early identification of EOC using Machine Learning Techniques. This approach increases the data size, balances different classes of the data, and cuts down the enormous number of features unrelated to the disease of interest to prevent overfitting. To incorporate these functionalities, in the data preprocessing stage, OC-related gene names were taken from the Cancermine database and other OC-related works. Moreover, OC datasets were merged based on OC genes, and missing values of EOC subtypes were identified and imputed using Iterative Logistic Imputation. Synthetic Minority Oversampling Technique with an Edited Nearest Neighbors approach is applied to the imputed dataset. Next, in the Feature Selection phase, the most significant features for subtypes of EOC were identified by applying the Shapley Additive Explanations based on the Recursive Feature Elimination Cross-Validation (ShapRFECV) algorithm, preserving predefined features while selecting new EOC features. Eventually, an accuracy of 97% was achieved with Optuna-optimized Random Forest, which outperformed the existing models. SHAP plotted the most prominent features behind the classification. The Pickle tool saves much training time by preserving hidden parameter values of the model. In the final phase, by using the Stratified K Fold Stacking Classifier, the accuracy was improved to 98.9%.

The Effect of Honey on Bacteria Isolated from Urinary Tract Infections among Patients Attending Ruhengeri Referral Hospital

Background: Urinary tract infections (UTIs) occur when bacteria enter the urethra from the skin or rectum and infect the bladder, causing symptoms. UTIs are becoming increasingly multidrug-resistant, with some drugs no longer effective in treatment. According to the National Center for Biotechnology Information (NCBI), honey has been shown to have high osmotic pressure and high acidity that prevent the multiplication of bacteria. This study aimed to evaluate the effect of honey on bacteria isolated from urine samples collected from patients with UTI’s attending Ruhengeri Referral Hospital.
 Methodology: Urine samples were collected in sterile containers at Ruhengeri Referral Hospital and transported to the microbiology laboratory at the Ruhengeri Institute of Higher Education (INES Ruhengeri). Two types of honey, raw and processed were used as antimicrobial agents on bacteria isolated from UTIs. Various methods were used to isolate and identify bacterial isolates, including culture on solid medium, gram staining, and biochemical tests.
 Results: The most commonly isolated bacterium was S. aureus (33.3%) which is in the second group of bacteria susceptible to honey, followed by P. aeruginosa (13.8%) and CoNS (13.8%). E. coli, K. pneumonia, and Streptococcus spp. each accounted for 11.2%. The former and the latter were the most susceptible bacteria to natural honey honey (mIZ = 36 ±2.83; ±4.24 mm, respectively), while E. aerogenes was the least isolated bacterium at 5.5% and the least susceptible to honey.
 Conclusion: Honey was showed to exhibit an antimicrobial effect against all bacteria isolated from the UTI, suggesting natural honey as a remedy in controlling urinary tract bacterial infection. Further studies are needed to evaluate its capacity compared to classical antibiotics currently used to treat bacteria in UTIs. The practical way to use honey to get targeted area is also an interested point that need to be investigated.
 Keywords: Urinary tract infection; honey; bacteria.