Insertion of a small peptide of six amino acids into the β7–β8 loop of the p51 subunit of HIV-1 reverse transcriptase perturbs the heterodimer and affects its activities

BACKGROUND: HIV-1 RT is a heterodimeric enzyme, comprising of the p66 and p51 subunits. Earlier, we have shown that the β7-β8 loop of p51 is a key structural element for RT dimerization (Pandey et al., Biochemistry 40: 9505, 2001). Deletion or alanine substitution of four amino acid residues of this loop in the p51 subunit severely impaired DNA binding and catalytic activities of the enzyme. To further examine the role of this loop in HIV-1 RT, we have increased its size such that the six amino acids loop sequences are repeated in tandem and examined its impact on the dimerization process and catalytic function of the enzyme. RESULTS: The polymerase and the RNase H activities of HIV-1 RT carrying insertion in the β7-β8 loop of both the subunits (p66(INS)/p51(INS)) were severely impaired with substantial loss of DNA binding ability. These enzymatic activities were restored when the mutant p66(INS) subunit was dimerized with the wild type p51. Glycerol gradient sedimentation analysis revealed that the mutant p51(INS) subunit was unable to form stable dimer either with the wild type p66 or mutant p66(INS). Furthermore, the p66(INS)/p66(INS) mutant sedimented as a monomeric species, suggesting its inability to form stable homodimer. CONCLUSION: The data presented herein indicates that any perturbation in the β7-β8 loop of the p51 subunit of HIV-1 RT affects the dimerization process resulting in substantial loss of DNA binding ability and catalytic function of the enzyme

Pharmacotherapeutic Options for Visceral Leishmaniasis—Current Scenario

Visceral leishmaniasis (VL) or Kala-azar is a protozoal disease, which was previously regarded as one of the most neglected tropical diseases. Management of this disease is quite difficult, because it is said to affect the poorest of the poor. Previously Sodium Stibogluconate (SSG) was regarded as the gold standard treatment for VL. But due to the increasing unresponsiveness, to this drug various other drugs were tried and are still being tried. Pentamidine is very toxic and has been discarded of late. Amphotericin B and its lipid formulations are very effective but require hospital admission and monitoring. Oral drugs like Miltefosine have already been launched. An amino glycoside Paromomycin and another oral drug Sitamaquine are in the pipe line. Interferon gamma has been used with discouraging results

Unexpected origins of the enhanced pairing affinity of 2 \u27-fluoro-modified RNA

Various chemical modifications are currently being evaluated for improving the efficacy of short interfering RNA (siRNA) duplexes as antisense agents for gene silencing in vivo. Among the 2\u27-ribose modifications assessed to date, 2\u27deoxy-2\u27-fluoro-RNA (2\u27-F-RNA) has unique properties for RNA interference (RNAi) applications. Thus, 2\u27-F-modified nucleotides are well tolerated in the guide (antisense) and passenger (sense) siRNA strands and the corresponding duplexes lack immunostimulatory effects, enhance nuclease resistance and display improved efficacy in vitro and in vivo compared with unmodified siRNAs. To identify potential origins of the distinct behaviors of RNA and 2\u27-F-RNA we carried out thermodynamic and X-ray crystallographic analyses of fully and partially 2\u27-F-modified RNAs. Surprisingly, we found that the increased pairing affinity of 2\u27-F-RNA relative to RNA is not, as commonly assumed, the result of a favorable entropic contribution (\u27conformational preorganization\u27), but instead primarily based on enthalpy. Crystal structures at high resolution and osmotic stress demonstrate that the 2\u27-F-RNA duplex is less hydrated than the RNA duplex. The enthalpy-driven, higher stability of the former hints at the possibility that the 2\u27-substituent, in addition to its important function in sculpting RNA conformation, plays an underappreciated role in modulating Watson-Crick base pairing strength and potentially pi-pi stacking interactions

Simple and Effective Multi-Paragraph Reading Comprehension

We consider the problem of adapting neural paragraph-level question answering models to the case where entire documents are given as input. Our proposed solution trains models to produce well calibrated confidence scores for their results on individual paragraphs. We sample multiple paragraphs from the documents during training, and use a shared-normalization training objective that encourages the model to produce globally correct output. We combine this method with a state-of-the-art pipeline for training models on document QA data. Experiments demonstrate strong performance on several document QA datasets. Overall, we are able to achieve a score of 71.3 F1 on the web portion of TriviaQA, a large improvement from the 56.7 F1 of the previous best system.Comment: 11 pages, updated a referenc

Tuberous sclerosis with visceral leishmaniasis: a case report

<p>Abstract</p> <p>Introduction</p> <p>Visceral leishmaniasis, a tropical infectious disease, is a major public health problem in India. Tuberous sclerosis, a congenital neuro-ectodermosis, is an uncommon disease which requires life long treatment.</p> <p>Case presentation</p> <p>A 15-year-old Indian patient, presented to the outpatient department of our institute with a high-grade fever for two months, splenomegaly and a history of generalized tonic-clonic convulsions since childhood. The clinical and laboratory findings suggested visceral leishmaniasis with tuberous sclerosis. The patient was treated with miltefosine and antiepileptics.</p> <p>Conclusion</p> <p>The patient responded well and in a follow up six months after presentation, she was found free of visceral leishmaniasis and seizures. Diagnosis and treatment of this rare combination of diseases is difficult.</p

Microbial beta glucosidase enzymes: recent advances in biomass conversation for biofuels application

The biomass to biofuels production process is green, sustainable, and an advanced technique to resolve the current environmental issues generated from fossil fuels. The production of biofuels from biomass is an enzyme mediated process, wherein β-glucosidase (BGL) enzymes play a key role in biomass hydrolysis by producing monomeric sugars from cellulose-based oligosaccharides. However, the production and availability of these enzymes realize their major role to increase the overall production cost of biomass to biofuels production technology. Therefore, the present review is focused on evaluating the production and efficiency of β-glucosidase enzymes in the bioconversion of cellulosic biomass for biofuel production at an industrial scale, providing its mechanism and classification. The application of BGL enzymes in the biomass conversion process has been discussed along with the recent developments and existing issues. Moreover, the production and development of microbial BGL enzymes have been explained in detail, along with the recent advancements made in the field. Finally, current hurdles and future suggestions have been provided for the future developments. This review is likely to set a benchmark in the area of cost effective BGL enzyme production, specifically in the biorefinery area

Visceral leishmaniasis and HIV co-infection in Bihar, India: long-term effectiveness and treatment outcomes with liposomal amphotericin B (AmBisome).

BACKGROUND: Visceral Leishmaniasis (VL; also known as kala-azar) is an ultimately fatal disease endemic in the Indian state of Bihar, while HIV/AIDS is an emerging disease in this region. A 2011 observational cohort study conducted in Bihar involving 55 VL/HIV co-infected patients treated with 20-25 mg/kg intravenous liposomal amphotericin B (AmBisome) estimated an 85.5% probability of survival and a 26.5% probability of VL relapse within 2 years. Here we report the long-term field outcomes of a larger cohort of co-infected patients treated with this regimen between 2007 and 2012. METHODS AND PRINCIPAL FINDINGS: Intravenous AmBisome (20-25 mg/kg) was administered to 159 VL/HIV co-infected patients (both primary infections and relapses) in four or five doses of 5 mg/kg over 4-10 days. Initial cure of VL at discharge was defined as improved symptoms, cessation of fever, improvement of appetite and recession of spleen enlargement. Test of cure was not routinely performed. Antiretroviral treatment (ART) was initiated in 23 (14.5%), 39 (24.5%) and 61 (38.4%) before, during and after admission respectively. Initial cure was achieved in all discharged patients. A total of 36 patients died during follow-up, including six who died shortly after admission. Death occurred at a median of 11 weeks (IQR 4-51) after starting VL treatment. Estimated mortality risk was 14.3% at six months, 22.4% at two years and 29.7% at four years after treatment. Among the 153 patients discharged from the hospital, 26 cases of VL relapse were diagnosed during follow-up, occurring at a median of 10 months (IQR 7-14) after discharge. After accounting for competing risks, the estimated risk of relapse was 16.1% at one year, 20.4% at two years and 25.9% at four years. Low hemoglobin level and concurrent infection with tuberculosis were independent risk factors for mortality, while ART initiated shortly after admission for VL treatment was associated with a 64-66% reduced risk of mortality and 75% reduced risk of relapse. SIGNIFICANCE: This is the largest cohort of HIV-VL co-infected patients reported from the Indian subcontinent. Even after initial cure following treatment with AmBisome, these patients appear to have much higher rates of VL relapse and mortality than patients not known to be HIV-positive, although relapse rates appear to stabilize after 2 years. These results extend the earlier findings that co-infected patients are at increased risk of death and require a multidisciplinary approach for long-term management

Molecular profiling of ETS and non‐ETS aberrations in prostate cancer patients from northern India

BACKGROUNDMolecular stratification of prostate cancer (PCa) based on genetic aberrations including ETS or RAF gene‐rearrangements, PTEN deletion, and SPINK1 over‐expression show clear prognostic and diagnostic utility. Gene rearrangements involving ETS transcription factors are frequent pathogenetic somatic events observed in PCa. Incidence of ETS rearrangements in Caucasian PCa patients has been reported, however, occurrence in Indian population is largely unknown. The aim of this study was to determine the prevalence of the ETS and RAF kinase gene rearrangements, SPINK1 over‐expression, and PTEN deletion in this cohort.METHODSIn this multi‐center study, formalin‐fixed paraffin embedded (FFPE) PCa specimens (n = 121) were procured from four major medical institutions in India. The tissues were sectioned and molecular profiling was done using immunohistochemistry (IHC), RNA in situ hybridization (RNA‐ISH) and/or fluorescence in situ hybridization (FISH).RESULTSERG over‐expression was detected in 48.9% (46/94) PCa specimens by IHC, which was confirmed in a subset of cases by FISH. Among other ETS family members, while ETV1 transcript was detected in one case by RNA‐ISH, no alteration in ETV4 was observed. SPINK1 over‐expression was observed in 12.5% (12/96) and PTEN deletion in 21.52% (17/79) of the total PCa cases. Interestingly, PTEN deletion was found in 30% of the ERG‐positive cases (P = 0.017) but in only one case with SPINK1 over‐expression (P = 0.67). BRAF and RAF1 gene rearrangements were detected in ∼1% and ∼4.5% of the PCa cases, respectively.CONCLUSIONSThis is the first report on comprehensive molecular profiling of the major spectrum of the causal aberrations in Indian men with PCa. Our findings suggest that ETS gene rearrangement and SPINK1 over‐expression patterns in North Indian population largely resembled those observed in Caucasian population but differed from Japanese and Chinese PCa patients. The molecular profiling data presented in this study could help in clinical decision‐making for the pursuit of surgery, diagnosis, and in selection of therapeutic intervention. Prostate 75:1051–1062, 2015. © 2015 The Authors. The Prostate, published by Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111808/1/pros22989.pd

Evaluating air quality and criteria pollutants prediction disparities by data mining along a stretch of urban-rural agglomeration includes coal-mine belts and thermal power plants

Air pollution has become a threat to human life around the world since researchers have demonstrated several effects of air pollution to the environment, climate, and society. The proposed research was organized in terms of National Air Quality Index (NAQI) and air pollutants prediction using data mining algorithms for particular timeframe dataset (01 January 2019, to 01 June 2021) in the industrial eastern coastal state of India. Over half of the study period, concentrations of PM2.5, PM10 and CO were several times higher than the NAQI standard limit. NAQI, in terms of consistency and frequency analysis, revealed that moderate level (ranges 101–200) has the maximum frequency of occurrence (26–158 days), and consistency was 36%–73% throughout the study period. The satisfactory level NAQI (ranges 51–100) frequency occurrence was 4–43 days with a consistency of 13%–67%. Poor to very poor level of air quality was found 13–50 days of the year, with a consistency of 9%–25%. Random Forest (RF), Support Vector Machine (SVM), Bagged Multivariate Adaptive Regression Splines (MARS) and Bayesian Regularized Neural Networks (BRNN) are the data mining algorithms, that showed higher efficiency for the prediction of PM2.5, PM10, NO2 and SO2 except for CO and O3 at Talcher and CO at Brajrajnagar. The Root Mean Square Error (RMSE) between observed and predicted values of PM2.5 (ranges 12.40–17.90) and correlation coefficient (r) (ranges 0.83–0.92) for training and testing data indicate about slightly better prediction of PM2.5 by RF, SVM, bagged MARS, and BRNN models at Talcher in comparison to PM2.5 RMSE (ranges 13.06–21.66) and r (ranges 0.64–0.91) at Brajrajnagar. However, PM10 (RMSE: 25.80–43.41; r: 0.57–0.90), NO2 (RMSE: 3.00–4.95; r: 0.42–0.88) and SO2 (RMSE: 2.78–5.46; r: 0.31–0.88) at Brajrajnagar are better than PM10 (RMSE: 35.40–55.33; r: 0.68–0.91), NO2 (RMSE: 4.99–9.11; r: 0.48–0.92), and SO2 (RMSE: 4.91–9.47; r: 0.20–0.93) between observed and predicted values of training and testing data at Talcher using RF, SVM, bagged MARS and BRNN models, respectively. Taylor plots demonstrated that these algorithms showed promising accuracy for predicting air quality. The findings will help scientific community and policymakers to understand the distribution of air pollutants to strategize reduction in air pollution and enhance air quality in the study region

Identification of Clinical Immunological Determinants in Asymptomatic VL and Post Kala-azar Dermal Leishmaniasis Patients

Background: Visceral Leishmaniasis (VL) caused by protozoa belonging to the genus Leishmania, usually have anthroponotic mode of transmission and is issue of great public health importance in Indian subcontinent. Asymptomatic cases of VL and PKDL are subject of keen interest to find their role in the transmission of VL in epidemic areas. We evaluated the immunological cytokine determinants expressed in most clinical suspects of asymptomatic VL and PKDL (IL-10, IFN-γ, and TNF-α). Methods: Eighty-four participants were included at RMRIMS, Patna, India in 2016-17 out of which 64 asymptomatic individual positive for rK-39, without sign and symptoms of VL; 15 PKDL patient’s with past history of VL and 5 endemic healthy subjects were recruited from VL endemic areas. DAT and quantitative assessment of plasma cytokines was determined from the blood samples collected in a plain and sodium-EDTA vacutainer respectively from the subjects. Results: The mean level of IL-10 in DATposLOW of asymptomatic VL and PKDL was significantly higher than endemic healthy (P<0.05). The cytokine polarization index (IFN-γ versus IL-10) was significantly low in PKDL cases compared with asymptomatic VL cases in DATposLOW titre (P<0.05). This index was low again but statistically not significant in PKDL than in asymptomatic VL when TNF-α was considered against IL-10. The ratio of IFN-γ: IL-10 and TNF-α: IL-10 was observed decreased both in asymptomatic VL and PKDL cases than in healthy from endemic areas. Conclusion: Collectively we surmise from our data that asymptomatic VL can also play an important role like PKDL in transmission of VL