Integrative analysis of complex genomic and epigenomic maps

Modern healthcare research demands collaboration across disciplines to build preventive measures and innovate predictive capabilities for curing diseases. Along with the emergence of cutting-edge computational and statistical methodologies, data generation and analysis has become cheaper in the last ten years. However, the complexity of big data due to its variety, volume, and velocity creates new challenges for biologists, physicians, bioinformaticians, statisticians, and computer scientists. Combining data from complex multiple profiles is useful to better understand cellular functions and pathways that regulates cell function to provide insights that could not have been obtained using the individual profiles alone. However, current normalization and artifact correction methods are platform and data type specific, and may require both the training and test sets for any application (e.g. biomarker development). This often leads to over-fitting and reduces the reproducibility of genomic findings across studies. In addition, many bias correction and integration approaches require renormalization or reanalysis if additional samples are later introduced. The motivation behind this research was to develop and evaluate strategies for addressing data integration issues across data types and profiling platforms, which should improve healthcare-informatics research and its application in personalized medicine. We have demonstrated a comprehensive and coordinated framework for data standardization across tissue types and profiling platforms. This allows easy integration of data from multiple data generating consortiums. The main goal of this research was to identify regions of genetic-epigenetic co-ordination that are independent of tissue type and consistent across epigenomics profiling data platforms. We developed multi-‘omic’ therapeutic biomarkers for epigenetic drug efficacy by combining our biomarker regions with drug perturbation data generated in our previous studies. We used an adaptive Bayesian factor analysis approach to develop biomarkers for multiple HDACs simultaneously, allowing for predictions of comparative efficacy between the drugs. We showed that this approach leads to different predictions across breast cancer subtypes compared to profiling the drugs separately. We extended this approach on patient samples from multiple public data resources containing epigenetic profiling data from cancer and normal tissues (The Cancer Genome Atlas, TCGA; NIH Roadmap epigenomics data)

IN SILICO IDENTIFICATION AND CHARACTERIZATION OF MUTUAL EPITOPE-BASED SUBUNIT VACCINE AGAINST EBOLA VIRUS AND MARBURG VIRUS

Objective: The objective of the study was to analyze the mutual epitope-based vaccine that can evoke immune response against hemorrhagic fever caused by Ebola virus (EBOV) and Marburg virus (MARV). Methodology: VP40, VP24, VP35, VP30, and NP proteins of Ebola and MARV were recovered from the protein database and subjected to many bioinformatics tools to predict the best B- and T-cell epitopes. And finally, the selected proteins were subjected to molecular docking human leukocyte antigen (HLA)-DR (major histocompatibility complex [MHC] Class I and II) to confirm their antigenicity in silico. Results: The epitopes from EBOV were stable while were unstable from MARV. Further, molecular docking simulation using most significant MHC Class II and Class I molecules demonstrated that their epitopes may bind within HLA-binding affinity to evoke an immune response. Conclusions: In this study, the data revealed the epitopes from VP40 protein could be the specific target for peptide-based vaccine design against Ebola and MARV

Prevalence of sexually transmitted infections among pregnant women with known HIV status and their perinatal outcome- a retrospective single centre analysis

Background: The objective of this study was to determine the prevalence of sexually transmitted infections (STIs) and other reproductive tract infections (RTIs) among pregnant women and their perinatal outcome.Methods: Pregnant women in their 3rd trimester (N=1000) from September 2009 and august 2010 were included. Information related to demographic profile, obstetrics complications, previous genital infections and gynecological diseases were taken. All pregnant women were followed up for their 4-week perinatal outcome.Results: The prevalence of sexually transmitted infection was 25.2% in pregnant women. The prevalence of HIV, Hepatitis B, HSV2 and HPV infection was 2.3%, 4.2%, 0.6%, 0.1% respectively. Prevalence of infection with C. trachomatis, G. vaginalis, T. vaginalis and C. albicans was 5.8%, 10.2%, 5.2%, 9.5% respectively. The prevalence of infection with N. gonorrhea and T. pallidum was found to be 0.Conclusions: Rates of STIs and RTIs are still high among pregnant women. A declining trend for curable STIs/RTIs (syphilis and gonorrhea) was noted. Perinatal outcome was affected adversely in pregnant women with STIs/RTIs

Novel Coronavirus 2019: A Recent Update

Since last year of December 2019, a virus has been identifying in china’s city of Wuhan, virus name Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2). 2019 Novel Coronavirus (COVID-19) Disease is a very scary Disease. This disease is a challenge for Human for cure.  These virus are effected all over the world’s country like America, Brazil, Turkey, China, Italy, Iran, India, Canada Russia etc., this virus first time reported in relation to the Huainan Seafood Wholesale Market (South China Seafood City Food Market) in Wuhan, China. This market gained media attention after being identified as a point of origin of the 2019–20 coronavirus pandemic. This virus have the common sign & symptoms like pneumonia and show symptoms of  fever, headache, joint pain, Common cold, chills, shortness of breath, cough severe pneumonia, dyspnea, renal insufficiency. The detection of 2019- SCoV-like viruses in tiny size, live wild mammals in a market indicates a route of inters species spreading, although the natural loch is not known. This theory assembles a study of the molecular biology fundamental of these infectious agents, with particular prominence on the nature and identify of viral receptors, viral RNA synthesis, and the molecular interactions governing viral assembly

THE STUDY OF ANTIOXIDANTS TO EVALUATE THE HEALING EFFECTS OF PUNICA GRANATUM PEEL ON ACETIC ACID-INDUCED COLITIS IN CHARLES-FOSTER ALBINO RATS

Objective: The study aims to analyze the effect of 50% ethanolic extract of the dried Punica granatum peel (PGE) on the healing of acetic- acid-induced colitis in rats. Methods: Colitis was induced in rats using 50% acetic acid and then PGE extract was administered by oral route daily for 14 days to those rats. Optimal healing was observed by the administration of a 100 mg/kg dose of PGE extract. Effectiveness of the above-mentioned dosage of PGE, biochemical parameters namely- antioxidants-superoxide dismutase and reduced glutathione were studied on 18 h fasting rats on the 15th day of the experiment. Results: The results were suggestive of the healing properties of PGE extract by reduction of the inflammation and mucosal damage in the colon of those rats. The effect was established by the levels of antioxidants that indicate healing of the mucosal damage. The safety of extract was established by the effective administration of 10 times the therapeutic dose, that is, 1000 mg/kg dosage of the PGE extract with no noticeable adverse effects or side effects related to autonomic nervous system or central nervous system. Conclusion: PGE extract was found to be effective in healing mucosal damage due to colitis by controlling the infection and reducing the inflammation

Plant Metabolomics: An Emerging Technology for Crop Improvement

The astounding ability of plants to make smart decisions in response to environment is evident. As they have evolved a long list of complex and unique processes that involve photosynthesis, totipotency, long-distance signaling, and ability to restore structural and metabolic memory, recognition, and communication via emission of the selected class of volatiles. In recent years, use of metabolite profiling techniques in detection, unambiguous identification, quantification, and rapid analysis of the minute quantity of cellular micromolecules has increased considerably. Metabolomics is key to understand the chemical footprints during different phases of growth and development of plants. To feed the ever-increasing population with limited inputs and in a rapidly changing environment is the biggest challenges that the world agriculture faces today. To achieve the project genetic gains, the breeding strategies employing marker-assisted selection for high-yielding varieties and identifying germplasm resistant to abiotic and biotic stresses are already in vogue. Henceforth, new approaches are needed to discover and deploy agronomically important gene/s that can help crops better withstand weather extremes and growing pest prevalence worldwide. In this context, metabolic engineering technology looks viable option, with immense potential to deliver the future crops

Tomato 26S Proteasome subunit RPT4a regulates ToLCNDV transcription and activates hypersensitive response in tomato

Involvement of 26S proteasomal subunits in plant pathogen-interactions, and the roles of each subunit in independently modulating the activity of many intra- and inter-cellular regulators controlling physiological and defense responses of a plant were well reported. In this regard, we aimed to functionally characterize a Solanum lycopersicum 26S proteasomal subunit RPT4a (SlRPT4) gene, which was differentially expressed after Tomato leaf curl New Delhi virus (ToLCNDV) infection in tolerant cultivar H-88-78-1. Molecular analysis revealed that SlRPT4 protein has an active ATPase activity. SlRPT4 could specifically bind to the stem-loop structure of intergenic region (IR), present in both DNA-A and DNA-B molecule of the bipartite viral genome. Lack of secondary structure in replication-associated gene fragment prevented formation of DNA-protein complex suggesting that binding of SlRPT4 with DNA is secondary structure specific. Interestingly, binding of SlRPT4 to IR inhibited the function of RNA Pol-II and subsequently reduced the bi-directional transcription of ToLCNDV genome. Virus-induced gene silencing of SlRPT4 gene incited conversion of tolerant attributes of cultivar H-88-78-1 into susceptibility. Furthermore, transient overexpression of SlRPT4 resulted in activation of programmed cell death and antioxidant enzymes system. Overall, present study highlights non-proteolytic function of SlRPT4 and their participation in defense pathway against virus infection in tomato

A Study on Evaluation of Various Tongue Patterns in North Indian Population and a Working Classification System for These Tongue Print Patterns

INTRODUCTION: Tongue is a vital internal organ enclosed within the oral cavity and is well protected from the external environment. The color, shape, and surface features are characteristic of every individual, and this serves as a tool for identification. The search for a new personal identification method secure has led to the use of the tongue print as a method of biometric verification.AIM AND OBJECTIVE: To analyze the shape, margins, texture of tongue prints and compare these between males and females. Also, formulate a working classification system for these tongue prints.MATERIAL AND METHODS: Subjects were asked to protrude tongue in relaxed position. After this tongue images were captured using Nikon digital camera to evaluate the shape, texture, margins, and papillations of tongue patterns.RESULT: The most common pattern seen in males and females was Patternless, with majority of subjects showing scalloped lateral margins, prominent papillations with short and broad tongue. Mostly female patients had pointed tip of tongue. Also, we in this paper have formulated a working classification system for easily categorizing the tongue print patterns in individuals.CONCLUSION: The human tongue is unique and delivers relevant information about shape, size, color, texture, margins and is suitable for forensic case identification