Differentially Expressed Genes and Their Clinical Significance in Ischaemic Stroke: An In-Silico Study.

BACKGROUND: Ischaemic stroke (IS), a multifactorial neurological disorder, is mediated by interplay between genes and the environment and, thus, blood-based IS biomarkers are of significant clinical value. Therefore, this study aimed to find global differentially expressed genes (DEGs) in-silico, to identify key enriched genes via gene set enrichment analysis (GSEA) and to determine the clinical significance of these genes in IS. METHODS: Microarray expression dataset GSE22255 was retrieved from the Gene Expression Omnibus (GEO) database. It includes messenger ribonucleic acid (mRNA) expression data for the peripheral blood mononuclear cells of 20 controls and 20 IS patients. The bioconductor-package 'affy' was used to calculate expression and a pairwise t-test was applied to screen DEGs (P < 0.01). Further, GSEA was used to determine the enrichment of DEGs specific to gene ontology (GO) annotations. RESULTS: GSEA analysis revealed 21 genes to be significantly plausible gene markers, enriched in multiple pathways among all the DEGs (n = 881). Ten gene sets were found to be core enriched in specific GO annotations. JunD, NCX3 and fibroblast growth factor receptor 4 (FGFR4) were under-represented and glycoprotein M6-B (GPM6B) was persistently over-represented. CONCLUSION: The identified genes are either associated with the pathophysiology of IS or they affect post-IS neuronal regeneration, thereby influencing clinical outcome. These genes should, therefore, be evaluated for their utility as suitable markers for predicting IS in clinical scenarios.

Multi-stimuli-responsive and dynamic color tunable security ink for multilevel anticounterfeiting.

Luminescent security features have been used for anticounterfeiting for a long time. However, constant effort is required to strengthen these security features to be ahead of counterfeiters. Here, we developed a multi-stimuli-responsive luminescent security ink containing Tb(ASA)3Phen, K2SiF6:Mn4+,and NaYF4:Yb3+/Er3+luminescent materials in PVC gold medium. Tb(ASA)3Phen complex shows a broad excitation band in the UV region; upon UV light radiation it shows strong greenish emission of Tb3+ions through the antenna effect. K2SiF6:Mn4+, on the other hand, has three excitation bands with maxima at 248, 354, and 454 nm which emit red light after excitation through these bands. NaYF4:Yb3+/Er3+is used as an upconverting nanophosphor showing green emission under 976 nm laser excitation. Thus, the multi-stimuli-responsive luminescent security ink shows greenish, red, and green emissions under 367 nm, 450 nm, and 976 nm excitations, respectively. Furthermore, the distinct lifetimes of the activators in Tb(ASA)3Phen and K2SiF6:Mn4+, i.e. 0.1708 ms and 8.165 ms, respectively, under 380 nm excitation make this ink suitable for dynamic anticounterfeiting as well. The ink shows a change in the emission color with time delay, after the removal of the 380 nm excitation source, from greenish yellow (at 0 delays) to reddish color after a delay of 7.5 ms. These unique optical features along with excellent photo-, chemical- and environmental stability make this ink useful for advanced-level anticounterfeiting.

Systematic review and meta-analysis of candidate gene association studies of benign prostate hyperplasia.

BACKGROUND: Benign prostate hyperplasia (BPH) is the most common urological problem in elderly males. Recent studies have reported polymorphism in various metabolic genes in BPH. However, their association with the susceptibility of BPH is still inconsistent. Here, we systematically reviewed and performed a meta-analysis of CYP17, VDR, and ACE genes to determine their precise association with the risk of BPH. METHODS: A comprehensive literature search for published studies on candidate gene associations involving vitamin D receptor (VDR), angiotensin-converting enzyme (ACE), and CYP17 genes with the risk of BPH was done up to April 2020 in PubMed, Scopus, Cochrane Central Register of Controlled Trials (CENTRAL), and Google Scholar databases. Fixed/random effects models were used to estimate the odd's ratio (OR) and 95% confidence intervals (CIs). Begg's funnel plot was used to assess the potential for publication bias. RESULTS: We found a total of 23 studies containing 3461 cases and 3833 controls for these gene polymorphisms. A significant association of ACE gene polymorphism was observed under the recessive (II vs. ID + DD) model for BPH susceptibility compared to control subjects (overall OR = 1.67, 95% CI = 1.03-2.73). Similar trends were observed for ACE gene polymorphism in Caucasian (OR = 6.18, 95% CI = 1.38-27.68) and Asian (OR = 1.42, 95% CI = 0.99-2.03) populations under study. No significant association was observed in VDR and CYP17 gene polymorphisms in any dominant or recessive models. CONCLUSION: Significant OR demonstrated the implication of ACE gene polymorphism in the proliferation of prostate tissue, which in turn is associated with BPH susceptibility. However, prospective studies at large scale and sample size are needed to confirm the current findings.

Differential Transcriptome Profiling Unveils Novel Deregulated Gene Signatures Involved in Pathogenesis of Alzheimer's Disease.

Alzheimer's disease (AD) is a neurodegenerative disorder that is characterized by a progressive loss of cognitive functions at a higher level than normal aging. Although the apolipoprotein (APOE) gene is a major risk factor in developing AD, other genes have also been reported to be linked with complex phenotypes. Therefore, this genome-wide expression study explored differentially expressed genes as possible novel biomarkers involved in AD. The mRNA expression dataset, GSE28146, containing 15 sample data composed of 7 AD cases from the hippocampus region with age-matched control (n = 8, >80 years), was analyzed. Using "affy" R-package, mRNA expression was calculated, while pathway enrichment analysis was performed to determine related biological processes. Of 58 differentially expressed genes, 44 downregulated and 14 upregulated genes were found to be significantly (p < 0.001) altered. The pathway enrichment analysis revealed two altered genes, i.e., dynein light chain 1 (DYNLL1) and kalirin (KLRN), associated with AD in the elderly population. The majority of genes were associated with retrograde endocannabinoid as well as vascular endothelial growth factors affecting the complex phenotypes. The DYNLL1 and KLRN genes may be involved with AD and Huntington's disease (HD) phenotypes and represent a common genetic basis of these diseases. However, the hallmark of AD is dementia, while the classic motor sign of HD includes chorea. Our data warrant further investigation to identify the role of these genes in disease pathogenesis.

Profile of Secondary Glaucoma in a Tertiary Eye Hospital of Eastern Nepal.

BACKGROUND: To determine the clinical profile and causes of various types of secondary glaucoma. MATERIALS AND METHODS: This was a hospital-based cross-sectional study conducted in a tertiary eye hospital of eastern Nepal from 1st June to 30th November, 2017. Patients who met the criteria for secondary glaucoma underwent detailed ophthalmic examination. RESULTS: Out of 7079 patients diagnosed with glaucoma or glaucoma suspects, 528 (7.4%) had secondary glaucoma. The mean age at presentation was 52 ± 17 years with male to female ratio of 1.5:1. The most common cause was lens induced 173 (32.8%) followed by neovascular 107 (20.3%), steroid induced 86 (16.3%), traumatic 76 (14.4%), post-vitrectomy 17 (3.2%), uveitic 11 (2.1%), pseudophakic 10 (1.9%), aphakic 8 (1.5%), post-keratoplasty 5 (0.9%) and miscellaneous included 35 (6.6%). Post-traumatic 31 (29.5%) was more prevalent below 41 years while lens induced glaucoma 86 (49%) above 60 years of age. At presentation, the average IOP was 40 ± 11 mmHg. 36 (6.8%) had no light perception in the presenting eye and a large number of participants 307 (58.1%) presented with visual acuity of <3/60 to perception of light. Glaucomatous optic atrophy was found in 22 (9.0%) cases. CONCLUSION: The causes of secondary glaucoma are diverse, lens induced glaucoma being most common. Most patients present late with poor vision, high IOP and even glaucomatous optic atrophy. So, early identification and treatment of the causes is important so that we can prevent the burden of blindness due to secondary glaucoma.

Genome-Wide Scanning of Potential Hotspots for Adenosine Methylation: A Potential Path to Neuronal Development.

Methylation of adenosines at N6 position (m6A) is the most frequent internal modification in mRNAs of the human genome and attributable to diverse roles in physiological development, and pathophysiological processes. However, studies on the role of m6A in neuronal development are sparse and not well-documented. The m6A detection remains challenging due to its inconsistent pattern and less sensitivity by the current detection techniques. Therefore, we applied a sliding window technique to identify the consensus site (5'-GGACT-3') n ≥ 2 and annotated all m6A hotspots in the human genome. Over 6.78 × 107 hotspots were identified and 96.4% were found to be located in the non-coding regions, suggesting that methylation occurs before splicing. Several genes, RPS6K, NRP1, NRXN, EGFR, YTHDF2, have been involved in various stages of neuron development and their functioning. However, the contribution of m6A in these genes needs further validation in the experimental model. Thus, the present study elaborates the location of m6A in the human genome and its function in neuron physiology.