Gene Reports最新文献

The increasing prevalence in antibiotic resistance has driven the search for novel bioactive compounds in previously unexplored marine habitats. Seaweed-associated symbionts have emerged as significant sources of novel antibacterials against nosocomial pathogens. Herein, eighty-one bacterial isolates were obtained through culture-dependent isolation of seaweed symbionts from the southern coast of India. Bacillus velezensis SK54 represented the largest share (54 %), followed by Bacillus siamensis SK53 (33 %), Bacillus subtilis SK20 (8 %), and Bacillus filamentous SK55 (5 %). B. siamensis SK53 and B. velezensis SK54, which were separated from seaweeds Turbinaria conoides and Dictyota cervicornis, respectively, demonstrated clearance zones over 25 mm on spot-over-lawn assay against multiple clinical pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Staphylococcus aureus (VRSA). Selected isolates were sensitive to commercially available antibiotics, and no pathogenicity was observed. The isolates did not amplify pore-forming non-haemolytic haemolysin BL (hbl) and enterotoxin (nhe) genes, and haemolysis on blood agar confirmed their non-pathogenic nature. The bacterial extracts exhibited significant antibacterial activity against the tested pathogens, including MRSA and VRSA, with a minimum inhibitory concentration (MIC) range of 6.25–12.5 μg/mL. The 700 bp type-I polyketide synthase (pks) genes (OQ657454, OQ706631, OQ737799, and OQ834957) were amplified from the heterotrophic B. siamensis SK53 and B. velezensis SK54, with a 99 % identity in the BLAST search. The substantial antibacterial potential against drug-resistant bacteria, along with the presence of genes encoding bioactive lead molecules, suggests that these marine symbiotic bacteria, B. siamensis SK53 and B. velezensis SK54, could be effective in combating emerging antibiotic resistance.

Striped murrel (Channa striata) is highly valued in the Indian subcontinent and Southeast Asia for its nutritional and medicinal benefits. However, the limited availability of high-quality seeds of murrel and the asynchronous maturation of brooders, particularly during peak spawning seasons creates problems in aquaculture. Beta-hydroxysteroid dehydrogenases (β-HSDs) are steroidogenic enzymes involved in the biosynthesis of active steroids in gametogenesis and steroidogenesis. This study aimed to clone and characterize the full-length cDNA sequences of two crucial enzymes, 3-beta hydroxysteroid dehydrogenase (Hsd3β) and 17-beta hydroxysteroid dehydrogenase (Hsd17β). It resulted in full-length cDNA sequences for Hsd3β and Hsd17β with 1101 bp and 771 bp length, respectively, encoding 366 and 256 amino acids. Signal peptide analysis indicated that both proteins are secretory, and hydropathy profiles suggested their hydrophilic nature. Notably, Rossmann-fold NAD(P)(+)-binding domains characteristic of Short-chain dehydrogenases/reductases (SDR) family genes were identified in Hsd3β (between 9-355 aa) and in Hsd17β (between 10-254 aa). Gene expression analyses were performed in testes and ovaries using qPCR at three key stages: preparatory, mature, and 16 h post human chorionic gonadotropin (hCG) injection (16 hpi). Results demonstrated a significant 2-fold upregulation of Hsd17β in mature and 16 hpi testes, while Hsd3β showed a significant 10-fold upregulation in mature testes compared to premature and 16 hpi stages. Ovarian expression of Hsd3β and Hsd17β showed minimal expression upon hCG injection (P < 0.05). These findings contribute to our understanding of Beta-hydroxysteroid dehydrogenases (β-HSDs), providing insights into regulating sex steroid hormone synthesis during the gonadal development of striped murrel.

In the current study, we report whole genome sequencing (WGS) data on EAEC strains from India to identify lineages and different sequence types (STs) in our geographical regions across North India. We performed WGS comparative genomics characterization to examine the diversity of 122 EAEC strains collected from a large geographic area from clinical (Human sources) and non-clinical sources (animal and environmental sources). M-PCR for 21 virulence genes was performed. A triplex PCR detected phylogenetic groups A, B1, B2, and D was done. All strains were genome-sequenced, and bioinformatics analysis was performed. EAEC isolates belonged to 29 sequence types, further clustered into 11 clonal complexes, among which CC38 was the largest, containing 38 isolates mainly belonging to two ST types (ST38 and ST315). CC10 was the most diverse group, comprising 8 STs (ST43, ST2706, ST1286, ST 10, ST167, ST34, ST227, and ST4305). The most frequently detected virulence gene among the 96 clinical EAEC isolates was astA (87.5%), followed by ORF3 (62.5%), and aap (54.1 %). ST131, known for multidrug resistance and causing various diseases, was detected in acute diarrhea cases and animal sources, underscoring its clinical significance. These findings indicate the high diversity of EAEC and different sources of unique ST types of EAEC. The study reinforces the One Health approach, highlighting the interconnection between human health, animal reservoirs, and environmental sources in EAEC transmission dynamics. The identification of EAEC strains in animals suggests the zoonotic potential of these pathogens, necessitating comprehensive surveillance and control measures. The study emphasizes the need for continued surveillance and a One Health approach to address the complex transmission dynamics of EAEC.

Background

Mitochondria are vital subcellular organelles that orchestrate the intricate process of oxidative phosphorylation (OXPHOS), generating adenosine triphosphate (ATP) as the primary energy molecule fueling cellular activities. During our research on mitochondrial mutations in breast cancer patients, we identified two notable single nucleotide polymorphisms (SNPs) present in both cancer patients and control individuals from the Pakistani population.

Materials and methods

DNA was extracted from the blood samples of 30 individuals, and MT-ATP8 and MT-ATP6 were amplified using PCR with specific primers. Purified PCR products were sequenced and analyzed for mutations using SnapGene and BioEdit. Bioinformatics tools, Consurf and PolyPhen-2, were used to analyze the genetic variants and their impact on protein function and stability.

Results

The analysis revealed two significant mutations in MT-ATP6 gene i.e., m.8860A>G (found in all 30 out of 30 samples) which results in the variant p.(Thr112Ala) and m.8701A>G (found in 13 out of 30 samples) which results in the variant p.(Thr59Ala). PolyPhen-2 analysis reveals the benign nature of both mutations, suggesting that the sequence variants are unlikely to cause any adverse effects on protein structure and function.

Background

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. Genetic variations, particularly gene polymorphisms, have been closely linked to increased susceptibility to ALL. One of those genes is Forkhead box O3 (FOXO3), which is considered a potential tumor suppressor gene.

Aim

This study intended to examine the potential significance of the FOXO3 (rs17069665) single nucleotide polymorphism (SNP) as a risk factor for childhood ALL, in addition to its effect on the laboratory results, clinical manifestations and the clinical outcome after induction of chemotherapy.

Subjects and methods

Sixty-six newly diagnosed ALL children and 70 healthy children of matched age and sex as controls were recruited. FOXO3 (rs17069665) polymorphism was detected using TaqMan real time PCR.

Results

Higher frequencies of the (AG) genotype and G-allele of FOXO3 (rs17069665) variant were present in ALL patients in comparing with the controls (16.7 % vs. 4.3 %, p = 0.017 and 11.4 % vs. 2.1 %, p = 0.003, respectively). The frequencies of the FOXO3 (rs17069665) SNP reflected a noticeably higher risk of ALL under diverse genetic models, including the co-dominant model (AG vs. AA, OR = 2.55), dominant (AG + GG vs. AA, OR = 2.81), and allelic (G-allele vs. A-allele, OR = 2.9) models. The single case of c-MYC mutation was observed with the (GG) genotype. No significant association between FOXO3 (rs17069665) SNP polymorphism and response to chemotherapy was found.

Conclusion

Our findings showed that the FOXO3 (rs17069665) polymorphism was associated with a greater incidence of ALL in Egyptian children, which might be a potential biomarker for ALL susceptibility.

The emergence of multidrug-resistant (MDR) Acinetobacter baumannii poses an escalating threat to the healthcare system worldwide. A significant factor contributing to increasing resistance is the overexpression of chromosomally encoded efflux pumps, which expel antibiotics from bacterial cells, thereby rendering treatments less effective. The efflux pumps not only mediate resistance to antibiotics through drug efflux but also work synergistically with other resistance mechanisms, thereby doubling the resistance. Despite their crucial role in antibiotic resistance, understanding of the structure, function, mechanisms of action, and regulation of efflux pumps remains limited, which is necessary for devising effective strategies to restore drug susceptibility and to combat MDR isolates. In this context, the present study evaluated the prevalence of efflux pump overexpression in clinical A. baumannii isolates using phenotypic and genotypic methods and identified potential therapeutic targets employing a network-based approach. A total of 172 A. baumannii isolates were collected and subjected to antibiotic susceptibility tests using the Kirby-Bauer disk diffusion method. All the isolates were found to be MDR, with 94.76 % showing resistance to carbapenems. Efflux pump overexpression was detected in 54.65 % of isolates using the Ethidium-Bromide Agar Cartwheel method, and efflux pump inhibitory activity was observed in 68.71 % of isolates using cyanide m-chlorophenylhydrazone (CCCP). A total of thirteen efflux pump genes were detected in the tested isolates using diagnostic PCR, which were considered for interaction network analysis using STRING. Clustering analysis of the merged network identified two highly interconnected clusters, each comprising functional partners crucial for efflux pump function and regulation. Key hub genes, including AdeB, AdeJ, AdeK, AdeC, macB, tolC, AIL80285.1, AdeR, and AdeS, were identified as primary targets due to their significant influence on the network. Additionally, 24 clustered genes were pinpointed as potential drug targets for developing novel therapeutics to combat the formidable challenge of efflux pump-mediated MDR in A. baumannii.

This study focuses on identifying functional single nucleotide polymorphisms (SNPs) within the gonadotropin-releasing hormone receptor (GNRHR) gene and conducting subsequent in-silico analysis of their effects on protein structure and function in two distinct South Indian goat breeds, namely Attapady Black (n = 120) and Malabari goats (n = 180), known for their divergent prolificacy traits. Utilizing a DNA pool sequencing assay, ten SNPs were uncovered in the study population: c.-1129T>G, c.-1069A>G, c.-978A>C, c.-605A>G, c.-33A>G, c.-29T>G, c.48G>A, c.75G>A, c.209T>G, and c.*212A>G. Notably, two polymorphisms, c.-1129T>G and c.-33A>G, were novel. Additionally, two polymorphisms, c.-33A>G and c.-978A>C, were exclusive to Malabari goats. Analysis of upstream variants revealed modifications to transcription factor and micro-RNA (miRNA) binding sites, suggesting potential alterations in GNRHR expression. Of particular significance was the non-synonymous exonic variant at c.209T>G locus, resulting in methionine to arginine substitution at the 70^th position within the first intracellular loop of the receptor protein. This amino acid change may have implications for the functional dynamics of the receptor as GnRHR intracellular loops are involved in G protein coupling thereby facilitation of downstream signalling pathways. The identified SNPs and their in-silico impact analysis contribute to our understanding of the molecular mechanisms underlying reproductive traits in these goat populations, with implications for future breeding strategies and genomic selection programs.

Ralstonia solanacearum is one of the most destructive soil-borne pathogen, causing bacterial wilt to the solanaceae vegetables. Streptomyces sp. UP1A-1 isolated from healthy solanaceae rhizosphere soil, exhibited the lowest disease incidence and increased fruit yield of solanaceae vegetables. However, the genomic and functional properties of UP1A-1 are unclear. Therefore, we conducted the present study to elucidate the genomic characteristics of UP1A-1 by whole genome sequencing. The results indicate that the genome of Streptomyces sp. UP1A-1 consists of 8,252,902 bp and contains 72.42 % G + C. We identified the genes that confer plant growth promoting (PGP) function, which include those involved in siderophore production, indole-3-acetic acid biosynthesis, phosphate solubilization, nitrogen metabolism, and potassium metabolism. We also identified several other genes, such as chitinase, peroxidase, superoxide dismutase, catalase, proline biosynthesis, and glucose dehydrogenase, which are believed to be involved in the control of wilt disease. These genes revealed that the strain UP1A-1 has physiologically adapted to varied environmental conditions and could potentially control both abiotic and biotic stresses.

Nigerian laughing doves (Streptopelia senegalensis) are small birds with long tail and living in bushes of the Sub-Saharan regions of African continent, the middle East and Asia, especially India. They are used for food, medicinal and religious purposes in Nigeria. Despite their usage, there is a lack of information on the genetic diversity of laughing doves in Nigeria. This study investigates taxonomic order and diversity of Nigerian laughing doves based on the mitochondrial cytochrome oxidase subunit I (COI) and cytochrome B (CYTB). The results showed 20 haplotypes within the 28 Nigerian coupled with Global Streptopelia genus using concatenated sequences. The Nigerian laughing dove constitute 16 distinct haplotypes. The haplotype diversity was 0.743 ± 0.070, and nucleotide diversity 0.154 ± 0.101 within Nigerian population using COI sequences. Phylogenetic tree showed that Nigerian laughing doves were in the same monophyletic clade with other Streptopela orientalis, S. decocto and S. chinensis; and this confirmed that Nigerian laughing doves might have shared descendant. The median-joining network further grouped Nigerian laughing doves into two: the first group consisting of Nigerian populations only, while the second group are with Saudi Arabian and Djiboutian populations. Population expansion was revealed in Nigerian dove individuals. This study revealed 16 unique haplotypes among Nigerian laughing dove population using concatenated sequences. Interestingly, CYTB showed clustering in African laughing doves (For instance, Nigerian individuals shared haplotypes with Sao Tome and Principe, an island country in the Gulf of Guinea, the western equatorial coast of Central Africa). The current data is the first report on genetic diversity of Nigerian laughing dove using mitochondrial COI and CYTB genes.

Background

Cirrhosis is defined as diffuse liver fibrosis (LF) caused by various chronic liver diseases and characterized by excessive deposition of extracellular matrix in liver tissue. However, the molecular mechanism of cirrhosis has not been well understood. This study aimed to identify significant gene expression profiles that participate in cirrhosis pathogenesis using bioinformatics and to discover novel biomarkers.

Methods

Two LF datasets (GSE14323 and GSE139602), both consisted of cirrhosis patients and healthy individuals, were obtained from the Gene Expression Omnibus (GEO) database and used for further analysis. Firstly, differential expression analyses were conducted to discover overlapping differentially expressed genes (DEGs) using the limma package. Next, the clusterProfiler function was adopted to carry out the Gene Ontology (GO) and Kyoto Encyclopedia of Genes as well as Genomes (KEGG) enrichment analyses. Furthermore, protein-protein interaction (PPI) network of the DEGs was constructed in the STRING database. In addition, hub genes were extracted through the cytoHubba plug-in. To verify the results we observed from the bioinformatics analysis, mouse models were established by receiving Carbon tetrachloride (CCl₄) injections or 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet.

Results

A total of 81 upregulated and 21 downregulated overlapping DEGs were identified in cirrhosis tissues compared to healthy controls. 9 hub genes included SPP1, SOX9, THBS2, LUM, LAMA2, PECAM1, VIM, COL1A2, and COL3A1 were identified by the PPI analysis from the 81 upregulated overlapping DEGs. RT-PCR of the fibrotic liver tissues from the mouse model showed that the mRNA levels of Spp1, Sox9, Col1a2 and Col3a1 were up-regulated in mice treated with CCl₄, while Spp1, Thbs2, Lum, Pecam1, Vim, Col1a2, and Col3a1 were up-regulated in mice treated with DDC. Predictive analyses provided drug compounds that are associated with LF.

Conclusion

The present study identified hub genes that were associated with the occurrence of LF may provide reference for future studies to better explore the pathogenesis of cirrhosis, and play a possible role for developing drugs for LF.