SUMO Sites Prediction in Human Transcription Factors Involved in Hypoxia induced Cardiac Illnesses

Protein SUMOylation is a reversible and well knownpost-translational modificationprocess of the cells. It may change a protein's cellular location, interactions, and possible structural shape before it develops to carry out its basic functions.Also, it decides the binding of transcription factors and DNA binding proteins tochromatin in addition to various cis and trans regulatory factors. Alterations in protein SUMOylation have been linked with a variety of disorders and developmental anomalies.Tentative approaches to identify SUMO binding sites are challenging due todynamic nature of the SUMOylation processand various critical lab experimentswhich are involved very high cost.Therefore, the computational methodologies may guide the experimental identification of SUMOylation sites and provide insights for improving comprehensionofSUMOylation mechanism in the cells.In this study, we identify the SUMO binding sites in transcription factors that are actively involved and have crucial roles in cardiac development andpathophysiology of the heart.A list of important transcription factors was preparedfrom thehuman transcription factor database.The GPS-SUMO, SUMO plot, and JASSA web serverswere used for the prediction of SUMO binding sites in cardiac transcription factors.We identified the SUMOylation of several novel, previously uncharacterized SUMO targetsthat are actively involved in thecardiovascular system.Thus, the present study may help to uncoverthe significance ofSUMO modificationin cardiac development and illnesses which creates a fresh avenue for future studies ontarget-specific SUMOylation for identification of novel therapeutic targets andmanagement strategies forhypoxia-induced cardiovascular disorders

Role of Moringa oleifera in regulation of diabetes-induced oxidative stress

AbstractObjectiveTo evaluate the antioxidant activity of aqueous extract ofMoringa oleifera (M. oleifera) young leaves by in vivo as well as in vitro assays.MethodsIn vitro study included estimation of total phenolic, total flavonol, total flavonoid and total antioxidant power (FRAP assay). In addition, in vivo study was done with the identified most effective dose of 200 mg/kg of its lyophilized powder on normal and diabetic rats. Its effect on different oxidative free radical scavenging enzymes,viz, superoxide dismutase (SOD), catalase (CAT), glutathione-S-transferase (GST), lipid peroxide (LPO) contents were measured.ResultsSignificant increase in activities of SOD, CAT, GST while, a decrease in LPO content was observed. Whereas, total phenolic, flavonoid and flavonol contents in the extract were found to be 120 mg/g of GAE, 40.5 mg/g of QE and 12.12 mg/g of QE, respectively. On the other hand, FRAP assay results ofM. oleifera leaves was (85.00±5.00)μM/g of extract powder.ConclusionsThe significant antioxidant activities ofM. oleifera leaves from both in vivo as well as in vitro studies suggests that the regular intake of its leaves through diet can protect normal as well as diabetic patients against oxidative damage

Laboratory Investigation of Indigenous Consortia TERIJ-188 for Incremental Oil Recovery

Bacterial Profile modification is an efficient process which brings the alteration in permeability of the porous media of the reservoir by selective plugging which eventually recover the residual oil. It is an advantageous and feasible method for residual oil recovery from high permeability zones of the reservoir. In this study, indigenous bacterial consortia, TERIJ-188 was developed from Gujarat oil fields. TERIJ-188 was identified as Thermoanaerobacter sp., Thermoanaerobacter brockii, Thermoanaerobacter italicus, Thermoanaerobacter mathranii, Thermoanaerobacter thermocopriae. The novelty of consortia was that it produces biomass (850 mg l-1), bio-surfactant (500 mg l-1), and volatile fatty acids (495 mg l-1) at 70°C in the span of 10 days, which are adequate to alter the permeability and sweep efficiency of high permeability zones facilitating the displacement of oil. The biosurfactant was analyzed for its functional group by FTIR and NMR techniques which indicate the presence of C-N bond, aldehydes, triacylglycerols. TERIJ-188 showed an effective reduction in permeability at residual oil saturation from 28.3 to 11.3 mD and 19.2% incremental oil recovery in a core flood assay. Pathogenicity test suggested that TERIJ-188 is non-toxic, non-virulent and safe for field implementation

sodC-Based Real-Time PCR for Detection of Neisseria meningitidis

Real-time PCR (rt-PCR) is a widely used molecular method for detection of Neisseria meningitidis (Nm). Several rt-PCR assays for Nm target the capsule transport gene, ctrA. However, over 16% of meningococcal carriage isolates lack ctrA, rendering this target gene ineffective at identification of this sub-population of meningococcal isolates. The Cu-Zn superoxide dismutase gene, sodC, is found in Nm but not in other Neisseria species. To better identify Nm, regardless of capsule genotype or expression status, a sodC-based TaqMan rt-PCR assay was developed and validated. Standard curves revealed an average lower limit of detection of 73 genomes per reaction at cycle threshold (Ct) value of 35, with 100% average reaction efficiency and an average R2 of 0.9925. 99.7% (624/626) of Nm isolates tested were sodC-positive, with a range of average Ct values from 13.0 to 29.5. The mean sodC Ct value of these Nm isolates was 17.6±2.2 (±SD). Of the 626 Nm tested, 178 were nongroupable (NG) ctrA-negative Nm isolates, and 98.9% (176/178) of these were detected by sodC rt-PCR. The assay was 100% specific, with all 244 non-Nm isolates testing negative. Of 157 clinical specimens tested, sodC detected 25/157 Nm or 4 additional specimens compared to ctrA and 24 more than culture. Among 582 carriage specimens, sodC detected Nm in 1 more than ctrA and in 4 more than culture. This sodC rt-PCR assay is a highly sensitive and specific method for detection of Nm, especially in carriage studies where many meningococcal isolates lack capsule genes

Mortality Among Adults With Cancer Undergoing Chemotherapy or Immunotherapy and Infected With COVID-19

Importance: Large cohorts of patients with active cancers and COVID-19 infection are needed to provide evidence of the association of recent cancer treatment and cancer type with COVID-19 mortality. // Objective: To evaluate whether systemic anticancer treatments (SACTs), tumor subtypes, patient demographic characteristics (age and sex), and comorbidities are associated with COVID-19 mortality. // Design, Setting, and Participants: The UK Coronavirus Cancer Monitoring Project (UKCCMP) is a prospective cohort study conducted at 69 UK cancer hospitals among adult patients (≥18 years) with an active cancer and a clinical diagnosis of COVID-19. Patients registered from March 18 to August 1, 2020, were included in this analysis. // Exposures: SACT, tumor subtype, patient demographic characteristics (eg, age, sex, body mass index, race and ethnicity, smoking history), and comorbidities were investigated. // Main Outcomes and Measures: The primary end point was all-cause mortality within the primary hospitalization. // Results: Overall, 2515 of 2786 patients registered during the study period were included; 1464 (58%) were men; and the median (IQR) age was 72 (62-80) years. The mortality rate was 38% (966 patients). The data suggest an association between higher mortality in patients with hematological malignant neoplasms irrespective of recent SACT, particularly in those with acute leukemias or myelodysplastic syndrome (OR, 2.16; 95% CI, 1.30-3.60) and myeloma or plasmacytoma (OR, 1.53; 95% CI, 1.04-2.26). Lung cancer was also significantly associated with higher COVID-19–related mortality (OR, 1.58; 95% CI, 1.11-2.25). No association between higher mortality and receiving chemotherapy in the 4 weeks before COVID-19 diagnosis was observed after correcting for the crucial confounders of age, sex, and comorbidities. An association between lower mortality and receiving immunotherapy in the 4 weeks before COVID-19 diagnosis was observed (immunotherapy vs no cancer therapy: OR, 0.52; 95% CI, 0.31-0.86). // Conclusions and Relevance: The findings of this study of patients with active cancer suggest that recent SACT is not associated with inferior outcomes from COVID-19 infection. This has relevance for the care of patients with cancer requiring treatment, particularly in countries experiencing an increase in COVID-19 case numbers. Important differences in outcomes among patients with hematological and lung cancers were observed

Efficient Algorithms for Some Important Problems in Bioinformatics

There is a huge amount of Biological data available because of the Genome Projects. It is challenging to extract meaningful information from the data, which has lead to many techniques proposed in the literature and more new ones are coming up. In this research work we consider some important problems in bioinformatics and provide elegant solutions for them. In particular, we focus on planted motif search and primer selection problems. ^ The Genome is an organism\u27s complete set of DNA. Human genome has about 3 billion DNA base pairs. Genes are inherited from parents and can be turned on or off by regulatory proteins or Transcription Factors. Every gene has a regulatory region upstream of the transcription start site. In the Regulatory region are Transcription Factor Binding Sites or Motifs, which are specific to a Transcription Factor. If a Motif is common in some genes, it means that they have some regulatory relationship. While looking for a Motif, we need to consider the fact that it might not occur exactly in all the DNA sequences due to Mutations at one or more locations. This makes finding Motifs computationally challenging, thus, efficient Motif Search techniques are critical. ^ There are three different versions of the Motif Search Problem. In this thesis we focus on two of these versions. ^ The run times of Motif Search Algorithms grow exponentially with l and d, which means even for highly efficient algorithms, solving larger (l, d) instances will require a lot of time, if at all possible. Thus, parallel computing comes to the rescue. Numerous multiprocessor architectures like Cell BE, Altix, etc. are available which have the potential to do extensive computations and can be faster than the regular computers. ^ The primer selection problem arises in the context of amplifying specific DNA segments. Primers are short synthetic oligonucleotides, with length varying from 15 to 30 bases, and perfect or close to perfect (mismatch could be tolerated) complements to the 3\u27 ends of the denatured DNA double strand. After several cycles of the PCR reaction, the targeted DNA segment is amplified exponentially in the PCR product. A special variant of PCR is the Multiplex Polymerase Chain Reaction (MPPCR) in which degenerate primers amplify several DNA sequences simultaneously. We call a PCR primer degenerate if there is more than one nucleotide allowed at any position of the primer. The degeneracy of the primer is equal to all its possible combination of unique, non-degenerate primers. In this thesis we investigate the degenerate primer selection problem.