Gene Reports最新文献

The study focused on isolating thermophilic bacteria from the hot springs of Madhya Pradesh, India, with the aim of identifying strains capable of producing industrially valuable enzymes. Among the 15 isolated strains, SR-7 identified as Bacillus subtilis exhibited significant enzyme activity, leading to its selection for further investigation. Genomic analysis revealed key characteristics of SR-7, including a 3,593,163 base pair chromosome with a GC content of 44.14 %. The genome was found to contain 55 tRNA genes, four rRNA clusters, and 3744 protein-coding genes. These genes encompass essential metabolic pathways and genes responsible for thermophilic adaptation, highlighting the potential for industrial applications. Further experimentation demonstrated SR-7 have the ability to produce various enzymes of industrial significance, such as amylase, lipase, cellulase, protease, lecithinase, gelatinase, and pectinase. Importantly, enzyme production was observed across a broad pH range (6.5 to 10) and temperature spectrum, indicating the versatility and adaptability of SR-7 to different environmental conditions. The findings suggest that SR-7 holds promise as a valuable resource for the pharmaceutical and industrial sectors. Its capacity to produce thermostable enzymes suitable for a range of applications underscores its potential contribution to biotechnological processes. By harnessing the enzymatic capabilities of thermophilic bacteria like SR-7, industries can pursue more sustainable and efficient production methods, reducing reliance on traditional chemical processes and enhancing overall productivity. Further research into the enzymatic properties and genetic mechanisms of SR-7 may unveil additional avenues for its utilization in various industrial processes.

Ovarian cancer is among the most commonly diagnosed cancer in women worldwide. Multiple risk factors could be attributed to the development of this disease, thus implicating variable incidence rates worldwide. Being the sixth in incidence and fourth in mortality among all cancers in women in the Arab world, ovarian cancer should be allocated a considerable interest among the other gynecologic cancers. This review aims to project the current epidemiological perspective in this part of the world while trying to consider several factors that could explain the incidence variability between the Arab countries internally, and externally compared to the world. The screening, prognostic factors and treatment modalities that are currently adopted in different Arab countries will be also presented. Close attention is additionally paid to the remarkable genetic difference that is found in the Arab countries pool, which could also be considered as a major factor that could explain the mentioned variability. In conclusion, noticeable efforts are seen in the Arab world when it comes to ovarian cancer-related research. However, further investigations for additional risk factors should be conducted to improve the early detection of this mostly asymptomatic disease and thereby enhance the quality of life and the disease prognosis.

Triple Negative Breast Cancer (TNBC) constitutes 12–17 % of breast cancers and is distinguished by the absence of hormone receptor expression, deviating from other breast cancer types. Coupled with its elevated proliferation index, TNBC develops multidrug resistance, diminishing treatment efficacy, weakening disease prognosis, and leading to an aggressive clinical course. This study aimed to assess ABCB1, ABCC1, ABCG2, and ABCC9 gene expression, which play a primary role in the development of multidrug resistance, alongside miRNAs (miR-466, miR-4539, miR-659-3p, miR-3123, miR-3133, and miR-655-3p) targeting these genes. While ABCB1 (p = 0.433), ABCC1 (p < 0.05), and ABCG2 (p < 0.05) exhibited increased expression in tumor tissues, ABCC9 (p = 0.587) did not. miR-466 (p = 0.802), miR-4539 (p = 0.732), miR-659-3p (p = 0.807), and miR-3123 (p = 0.980) were upregulated, whereas miR-3133 (p < 0.05) and miR-655-3p (p = 0.190) were downregulated. Within the scope of our study, we also evaluated the clinical parameters like tumor size, stage, and neoadjuvant treatment that significantly impacted Progression Free Survival (PFS) and Overall Survival (OS). Considering these results, we found that the metastatic status significantly influenced PFS and OS. Chemotherapeutics were found to not affect survival times. Assessing the impact of miRNAs, which we view as potential therapeutic targets, on average survival revealed that elevated miR-3133 expression was correlated with shorter PFS and OS, whereas decreased miR-655-3p expression was associated with longer PFS and OS. In summary, the relevant miRNAs could serve as predictive biomarkers for drug response and aid in developing miRNA-targeted gene therapy strategies.

Objective

This study aims to investigate the association between Renin-angiotensin aldosterone system (RAAS) and Cytochrome P450 gene polymorphisms in hypertension patients of the South Indian population using pharmacogenomics profile.

Methods

Hypertension cases (N = 147) and control subjects (n = 150) were collected from Tamil Nadu, India. A case-control association study was conducted to assess the involvement of RAAS gene polymorphisms (REN rs397514691, REN rs544315427, REN rs567667202) and CYP gene polymorphisms (CYP2D6 rs754164689, CYP2D6 rs1058172, CYP3A4 rs765598920) in essential hypertensive patients. Genotyping was performed using the PCR-RFLP method, and significant results were validated through RT-PCR analysis.

Results

The genotype and allele distribution of REN rs397514691 and rs544315427 variants significantly associated with hypertensive patients (Variant Allele Frequency (VAF) = 0.11; VAF = 0.27, respectively). CYP2D6 polymorphisms rs754164689 and rs1058172 variant alleles were significantly associated with female hypertensive patients, suggesting a potential risk allele for essential hypertension in the South Indian population. REN and CYP3A4 variants, highly connected in pharmacology action, were validated through RT-PCR amplification studies, providing new insights into their role in the development of hypertension. Association confirmation was achieved through multifactor dimensionality reduction analysis.

Conclusion

The genes associated with specific variants, particularly REN and CYP2D6, may serve as potential markers for the early diagnosis of hypertension and as new drug targets, particularly in the female population.

Background

Cytokines and matrix metalloproteinases play an important role in inflammation and metastasis in the development of cancer. Single nucleotide polymorphisms in these genes may affect gene expression and protein activity and, therefore, may be associated with cancer predisposition. The study seeks to examine the correlation between single nucleotide polymorphisms in the cytokines (Interleukin-1α and Interleukin-12β) and Matrix metalloproteinase (MMP9) gene with oral cancer. The interplay of the genetic variants, Interleukin 1α -889 C/T (rs1800587), Interleukin 12β +1188A/B (rs3212227), and MMP9 R279Q (rs17576) with tobacco chewing and smoking habits is determined in patients with oral cancer and controls. The relationship between these genetic variations with the tumor size, lymph node involvement, and metastasis in oral cancer was studied.

Method

Case-control research was implemented with a total of 150 participants, which includes 50 individuals who were diagnosed with oral cancer and 100 healthy volunteers. The study on Single Nucleotide Polymorphism (SNP) was performed using the Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) technique.

Results

Interleukin-1α -889 C/T polymorphism was significantly associated with oral cancer. The heterozygous genotype (CT) IL-1α -899 C/T was most frequent in oral cancer patients with a p value of 0.000002 in the chi-square test with no node involvement or metastasis. No interaction with the smoking or tobacco chewing habit with the genotypes of any of the genes is observed. The genotype of the mutant (TT) was also significantly different among the two groups (p = 0.01, OR = 7.63, CI- 1.5–37.5). The distribution of the mutant RR genotype of MMP9 R279Q in oral cancer patients was statistically significant in comparison with healthy controls (p = 0.005, OR = 4.46, CI- 1.52–3.04). The genotypic variants of IL-12β +1188A/B were, however, not found to be associated with oral cancer risk. IL-1α-899 (CT) and MMP9R279Q (RR) genotypes were found to be significantly associated with tumor size.

Conclusion

This finding indicates that the substitution of C to T at IL-1α-889 position and substitution of glutamine with arginine at amino acid position 279 in MMP9 due to single nucleotide polymorphism increases the risk of oral cancer. IL-12β +1188 polymorphism was not associated with oral cancer risk. Habit does not play any role in the interaction of these genes with oral cancer.

The increasing global prevalence of type 2 diabetes mellitus (T2DM) necessitates investigating its complex etiology. This study aimed to explore the relationship between exposure to toxic metals, expression of endoplasmic reticulum stress response (ERSR) genes, and various biochemical parameters, including glycated hemoglobin (HbA1c), insulin resistance (HOMA-IR)/sensitivity (QUICKI), lipid profile, and estimated glomerular filtration rate (eGFR) in T2DM patients. T2DM patients and control subjects were matched for age, gender, and lifestyle factors. Biochemical parameters, toxic metal levels, and ERSR gene expression were analyzed using inductively coupled plasma mass spectrometry (ICPMS) and quantitative reverse transcription PCR (qRT-PCR), respectively. T2DM patients exhibit dysregulated lipid profiles and significantly higher fasting blood sugar (FBS), HbA1c, and insulin levels (all p < 0.0001). The insulin sensitivity was lower in T2DM patients (0.32 ± 0.09) than in the control group (0.35 ± 0.02, p = 0.02). Insulin resistance was significantly higher in the T2DM group (5.38 ± 3.15) than in the control group (1.98 ± 0.86, p = 0.0001). Nickel (4.75 ± 2.45 ppb, p < 0.0001) and arsenic (1.85 ± 1.78 ppb, p < 0.0001) levels were significantly elevated in T2DM patients. There was significant upregulation of ER stress genes: GRP78, CHOP, IRE1, ATF4, ATF6, and XBP1 (all p < 0.0001), while PERK was significantly down regulated (0.68-fold, p < 0.0001). Nickel levels were positively correlated with HOMA-IR (r = 0.49, p < 0.0001) and HbA1c (r = 0.35, p = 0.002). Arsenic levels were correlated with insulin (r = 0.34, p < 0.0001), insulin resistance (r = 0.51,p < 0.0001), HbA1c (r = 0.53, p < 0.0001), Arsenic levels (β = 0.37, p < 0.001), XBP1 (β = 0.36, p < 0.0001) independently associated with HbA1c.This study has revealed a significant association between arsenic exposure and the upregulation of XBP1 at the onset of T2DM. The overexpression of XBP1 and high levels of arsenic were independently associated with HbA1c and insulin resistance.

Background

Triple-negative breast cancer (TNBC), an aggressive subtype with a poor prognosis, is notably difficult to treat. Emerging research highlights the significant roles of long non-coding RNAs (lncRNAs) in cancer biology. LncRNAs, such as NALT1 and CTBP1-AS1 are implicated in oncogenic processes; this study hypothesizes that NALT1 and CTBP1-AS1 are overexpressed in TNBC tissues compared to adjacent non-tumor tissues and may serve as biomarkers. Methods: One hundred pairs of tumor and adjacent non-tumor tissues were obtained from female patients with triple-negative breast cancer. After extracting RNA, cDNA synthesis was carried out for all samples. Quantitative real-time PCR (qRT-PCR) was employed to assess differential gene expression. Results: The expression of NALT1 (p-value <0.0001) and CTBP1-AS1 (p-value <0.0002) lncRNAs increased in TNBC tumor tissues in comparison to adjacent non-tumor tissues. A statistically positive correlation (ρ = 0.5844, p < 0.0001) was observed between the expression levels of NALT1 and CTBP1-AS1 in breast cancer patients. The ROC analysis indicated that NALT1 (AUC = 0.718, specificity = 61 %, sensitivity = 70 %) shows moderate potential and CTBP1-AS1 (AUC = 0.648, specificity = 65 %, sensitivity = 55 %) exhibits poor potential as a diagnostic biomarker for breast cancer. Conclusion: This study shows that NALT1 and CTBP1-AS1 lncRNAs are upregulated in TNBC tissues. Additionally, a positive correlation exists between their expression levels in breast cancer. Further research is needed to understand their mechanisms as molecular biomarkers.

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.