Genome-wide identification and comparative in-silico characterization of ß-galactosidase (GH-35) in ascomycetes and its role in germ tube development of Aspergillus fumigatus via RNA-seq analysis.

ß-galactosidase (Lactase), an enzyme belonging to the glycoside hydrolase family causing the hydrolysis and trans-glycosylation of ß-D-galactosides, has a vital role in dairy industries. The current investigation emphasizes on in-silico identification and comparative analysis of different fungal lactases present in Aspergillus fumigatus, Aspergillus oryzae, Botrytis cinerea, and Fusarium fujikuroi. Prediction of motifs and domains, chromosomal positioning, gene structure, gene ontology, sub-cellular localization and protein modeling were performed using different bioinformatics tools to have an insight into the structural and functional characteristics of ß-galactosidases. Evolutionary and homology relationships were established by phylogenetic and synteny analyses. A total of 14 ß-gal genes (GH-35) were identified in these species. Identified lactases, having 5 domains, were predicted to be stable, acidic, non-polar and extracellularly localized with roles in polysaccharide catabolic process. Results showed variable exonic/intronic ratios of the gene structures which were randomly positioned on chromosomes. Moreover, synteny blocks and close evolutionary relationships were observed between Aspergillus fumigatus and Aspergillus oryzae. Structural insights allowed the prediction of best protein models based on the higher ERRAT and Q-MEAN values. And RNA-sequencing analysis, performed on A. fumigatus, elucidated the role of ß-gal in germ tube development. This study would pave the way for efficient fungal lactase production as it identified ß-gal genes and predicted their various features and also it would provide a road-way to further the understanding of A. fumigatus pathogenicity via the expression insights of ß-gal in germ tube development.

Serum Vitamin D status and VDR (FokI) polymorphism association study in Pakistani females with breast cancer.

Background: Breast cancer is most common in Pakistani women at young age compared to West where it is most common after 60 years of age. Variations in genes controlling vitamin D activity would play a role in determining the risk of breast cancer in women at early age. Purpose: To determine the association of vitamin D receptors (VDR) gene polymorphisms (FokI) with breast cancer risk in Pakistani women. Methods: FokI polymorphisms were studied through the polymerase chain reaction-restriction fragment length polymorphism technique on blood samples of 300 breast cancer and 300 healthy women. Results: This study found that circulating level of 25(OH)D3 was significantly lower among breast cancer patients as well as healthy subjects. Patients with large tumor size had significantly lower vitamin D levels. VDR FokI genotypes were significantly distributed (P ≤ 0.00001) in Pakistani women with newly diagnosed breast cancer. A significant association between different FokI genotypes and circulating levels of 25(OH)D3 was found. Patients with FF genotype was significantly (P < 0.0001) associated with higher risk of breast cancer (OR 8.9, 95% CI 0.17-0.45) compared to Ff and ff genotype. Conclusion: VDR gene FokI polymorphism was associated with plasma vitamin D level and significant differences found in mean serum vitamin D levels between genotype groups of FokI. The study concluded that FokI might be one of the contributors to increase relative risk of breast cancer in Pakistani women.

MTHFR A1298C polymorphism: a predictor of reduced risk of preeclampsia in Punjab, Pakistan.

OBJECTIVES: This study aimed to investigate the genetic association between MTHFR (A1298C) SNP and preeclampsia (PE) in Punjab, Pakistan. METHODS: A sample of 80 pregnant women (40 healthy pregnant women and 40 with PE) was pooled for genotyping MTHFR A1298C polymorphism by using the tetra-primer amplification refractory mutation system (ARMS) PCR. The Genotypic and allelic assessments were performed using various statistical techniques. RESULTS: The AC genotype and C allele of MTHFR A1298C were found to be associated with decreased risk of PE (odds ratio [OR]: 0.31, risk ratio [RR]: 0.58, p = 0.01), and (odds ratio [OR]: 0.49, risk ratio [RR]: 0.61, p = 0.04), respectively. CONCLUSION: In conclusion, genetic polymorphism A1298C in MTHFR may pose a protective effect in the studied population.

A narrative review on the role of folate-mediated one-carbon metabolism and its associated gene polymorphisms in posing risk to preeclampsia.

Preeclampsia (PE) presents a major obstetrical problem for mother and fetus which is characterized by the onset of hypertension and proteinuria in formerly normotensive women. Altered folate-mediated one-carbon metabolism is one of the factors for PE development either due to nutritional insufficiencies such as folate deficiency or polymorphisms in genes that code for the key enzymes of the cycle. Commonly, there are four genes in the cycle whose polymorphisms have been described in relation to PE. These factors could cause elevation of homocysteine; the toxic metabolite, which subsequently leads to the development of PE. Sufficient levels of folate have been considered important during pregnancy and may reduce the risk of development of PE. This review aims at discussing genetic polymorphisms and nutritional deficiencies as probable predisposing factors and suggests considering fetal genotypes, varied ethnicities, and interaction of various other factors involved to render better conclusiveness to the present studies.

Structure-Function Mutational Analysis and Prediction of the Potential Impact of High Risk Non-Synonymous Single-Nucleotide Polymorphism on Poliovirus 2A Protease Stability Using Comprehensive Informatics Approaches.

Polio viral proteinase 2A performs several essential functions in genome replication. Its inhibition prevents viral replication, thus making it an excellent substrate for drug development. In this study, the three-dimensional structure of 2A protease was determined and optimized by homology modelling. To predict the molecular basis of the interaction of small molecular agonists, docking simulations were performed on a structurally diverse dataset of poliovirus 2A protease (PV2Apr°) inhibitors. Docking results were employed to identify high risk missense mutations that are highly damaging to the structure, as well as the function, of the protease. Intrinsic disorder regions (IDRs), drug binding sites (DBS), and protein stability changes upon mutations were also identified among them. Our results demonstrated dominant roles for Lys 15, His 20, Cys 55, Cys 57, Cys 64, Asp 108, Cys 109 and Gly 110, indicating the presence of various important drug binding sites of the protein. Upon subjecting these sites to single-nucleotide polymorphism (SNP) analysis, we observed that out of 155 high risk SNPs, 139 residues decrease the protein stability. We conclude that these missense mutations can affect the functionality of the 2A protease, and that identified protein binding sites can be directed for the attachment and inhibition of the target proteins.

Treatment for sleep apnea by continuous positive airway pressure improves levels of inflammatory markers - a meta-analysis.

BACKGROUND: Obstructive sleep apnea (OSA) is associated with coronary artery disease (CAD). Intermittent hypoxia associated with OSA increases sympathetic activity and may cause systemic inflammation, which may contribute to CAD in patients with OSA. Treatment with continuous positive airway pressure (CPAP) has been shown to change levels of inflammatory markers. We analyzed data from published studies by a systematic meta-analysis. OBJECTIVE: To asses if treatment for sleep apnea by CPAP will affect levels of inflammatory markers. DATA RESOURCES: PubMed, Embase and Cochrane library. METHODS: Study eligibility criteria full text English studies of adult, human subjects, addressing values of at least one of the inflammatory markers before and after CPAP treatment. We used the definition of OSA as an apnea-hypopnea index (AHI) of ≥ 5/h, reported values in mean and standard deviation or median with range. PARTICIPANTS: Adult, human. INTERVENTIONS: CPAP treatment for OSA. STUDY APPRAISAL AND SYNTHESIS METHOD: A total of 3835 studies were reviewed for inclusion, while 23 studies pooled for analysis. A total of 14 studies with 771 patients were pooled for C-reactive protein (CRP); 9 studies with 209 patients were pooled for tumor necrosis factor-alpha (TNF-α); and 8 studies with 165 patients were pooled for interleukin-6 (IL-6). ENDPOINT DEFINITIONS: THE FOLLOWING INFLAMMATORY MARKERS WERE CHOSEN: CRP, TNF-α, and IL-6. RESULTS: C-reactive protein: Study level means ranged from 0.18 to 0.85 mg/dl before CPAP treatment and 0.10 to 0.72 mg/dl after CPAP treatment. Mean differences, at a study level, ranged from -0.05 to 0.50. The pooled mean difference was 0.14 [95% confidence interval 0.08 to 0.20, p < 0.00001]. There was heterogeneity in this endpoint (df = 13, p < 0.00001, I(2) = 95%). Tumor necrosis factor-α: Study level means ranged from 1.40 to 50.24 pg/ml before CPAP treatment and 1.80 to 28.63 pg/ml after CPAP treatment. Mean differences, at a study level, ranged from -1.23 to 21.61. The pooled mean difference was 1.14 [95% confidence interval 0.12 to 2.15, p = 0.03]. There was heterogeneity in this endpoint (df = 8, p < 0.00001, I2 = 89%). Interleukin-6: Study level means ranged from 1.2 to 131.66 pg/ml before CPAP treatment and 0.45 to 66.04 pg/ml after CPAP treatment. Mean differences, at a study level, ranged from -0.40 to 65.62. The pooled mean difference was 1.01 [95% confidence interval -0.00 to 2.03, p = 0.05]. There was heterogeneity in this endpoint (df = 7, p < 0.00001, I(2) = 95%). LIMITATIONS: Only published data. Studies pooled were mainly small, non-randomized trials. CONCLUSION: Sleep apnea treatment with CPAP improves levels of inflammatory markers.