Gene Reports最新文献

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.

Azithromycin (AZM) is a primary treatment for shigellosis in children and a secondary option for adults. However, Shigella spp., has increasingly developed resistance to multiple antibiotics, including AZM. This rise in AZM-induced resistance complicates treatment, particularly with the emergence of multi-drug resistant (MDR) strains and the inappropriate and excessive use of antibiotics. Moreover, various mechanisms contribute to the decreased susceptibility to azithromycin (DSA) in Shigella spp., often involving antimicrobial resistance genes harboring on mobile genetic elements. These mechanisms hinder efforts to control the spread of DSA-Shigella strains. Therefore, this review aims to discuss the mechanisms of AZM resistance in Shigella infections and shed light on the important mechanisms underlying DSA in Shigella.

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is responsible for causing the coronavirus disease 2019 (COVID-19) pandemic that brought the world to a standstill in 2019, enters human cells by angiotensin-converting enzyme 2 (ACE2) receptors. The virus binds to ACE2 using the spike-like protein on its surface. ACE2 receptors also play an essential role in promoting the proliferation and invasion of oral squamous cell carcinoma (OSCC) cells by converting Angiotensin I, which binds to its type 1 or type 2 receptor inducing anti-apoptotic and anti-oxidative stress phenotypes. This study aimed to assess the long-term effects of SARS-CoV-2 by determining its effect on cell cycle regulatory proteins p53, cyclin D1, cyclin-dependent kinase 4 (CDK 4) and protein carbonylation in saliva.

Objective

To estimate and correlate the levels of p53, cyclin D1, CDK 4 and protein carbonylation measured at baseline and 6 months follow-up among post COVID-19 cohort.

Method

The study was conducted among 40 outpatients who were diagnosed with SARS-CoV-2 between January 2022 and February 2022. The study commenced after Institutional Ethics Committee clearance. The study comprised 40 post-COVID patients who were tested positive for COVID-19. Unstimulated whole saliva samples were collected from study participants by spitting method at baseline and 6 months. p53, cyclin D1, CDK 4 and protein carbonylation expression were assessed using ELISA. The obtained data were subjected to statistical analysis.

Results

The levels of proteins p53, cyclin D1, CDK 4 and protein carbonylation measured at baseline and six months were (687.02 ± 88.15 and 801.59 ± 82.72), (36.27 ± 5.04 and 45.71 ± 4.78), (9.25 ± 1.92 9.71 ± 0.98) and (864.76 ± 171.29 and 960.15 ± 82.03) respectively. There was a significant increase in levels of p53 (p < 0.05), cyclin D1 (p < 0.05), and protein carbonylation (p < 0.05) from baseline to 6 months.

Conclusion

An increase in salivary levels of p53, cyclin D1, CDK 4 and protein carbonylation suggests that there may be long-term effects of SARS-CoV-2 on cell cycle regulatory proteins. Over-expression of these markers does not signify that these patients are likely to get OSCC in the future instead, there may be some retained long-term effects of the virus whose mechanism yet needs to be understood. Further, transcriptomic profiling of tumor suppressor proteins may give us interesting results on the long-term effects of SARS-CoV-2.