Proteomic Analysis of Global Changes in Protein Expression During Exposure of Gamma Radiation in Bacillus sp. HKG 112 Isolated from Saline Soil

( Gupta Anil Kumar ),( Rajiv Pathak ),( Bharat Singh ),( Hemlata Gautam ),( Ram Kumar ),( Raj Kumar ),( Rajesh Arora ),( Hemant K. Gautam ) 한국미생물 · 생명공학회 2011 Journal of microbiology and biotechnology Vol.21 No.6

A Gram-positive bacterium was isolated from the saline soils of Jangpura (U.P.), India, and showed high-level of radiation-resistant property and survived upto 12.5 kGy dose of gamma radiation. The 16S rDNA sequence of this strain was examined, identified as Bacillus sp. strain HKG 112, and was submitted to the NCBI GenBank (Accession No. GQ925432). The mechanism of radiation resistance and gene level expression were examined by proteomic analysis of whole-cell extract. Two proteins, 38 kDa and 86.5 kDa excised from SDS-PAGE, which showed more significant changes after radiation exposure, were identified by MALDI-TOF as being flagellin and S-layer protein, respectively. Twenty selected 2-DE protein spots from the crude extracts of Bacillus sp. HKG 112, excised from 2- DE, were identified by liquid chromatography mass spectrometry (LC-MS) out of which 16 spots showed significant changes after radiation exposure and might be responsible for the radiation resistance property. Our results suggest that the different responses of some genes under radiation for the expression of radiation-dependent proteins could contribute to a physiological advantage and would be a significant initial step towards a fullsystem understanding of the radiation stress protection mechanisms of bacteria in different environments.

Service Users’ Confidence in Accessing Public Services in Nepal: What Makes Differences?

Anil Kumar Gupta,Anup Bhurtel,Prakash C. Bhattarai 서울대학교행정대학원 2023 The Korean Journal of Policy Studies Vol.38 No.1

This paper presents the factors associated with service users’ confidence in receiving public services in Nepal. The factors were taken from National Governance Survey 2017/ 18 (N=7334). The survey respondents were randomly selected from 43 of 77 districts of Nepal by using four-stage multiple cluster sampling from the service users who received public services in a year duration. The result showed that service users’ confidence in receiving public services differs by their locale, education level, caste/ethnicity, not having close contact (Afno Manchhe), and presence of intermediaries. Education, not having a person in close contact (Afno manchhe) and the presence of intermediaries have a negative effect, whereas locale (rural) and caste/ethnicity (Brahman/Chettri) have positive effects on service users’ confidence in accessing public services. Consideration of these factors boosts the confidence of the service users, which, in turn, promotes effective service delivery.

Identification of Biomarker for Determining Genotypic Potential of Nitrogen-Use-Efficiency and Optimization of the Nitrogen Inputs in Crop Plants

Kumar, Anil,Gupta, Nidhi,Gupta, Atul Kumar,Gaur, Vikram Singh 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.4

Worldwide, the nitrogen use efficiency (NUE) for crop plants is of great concern. The burgeoning world population needs crop genotypes that respond to higher nitrogen and show a direct relationship to yield with use of nitrogen inputs, i.e. high nitrogen-responsive genotypes. However, for fulfilling the high global demand of organic produce, it requires the low nitrogen responsive genotypes with greater NUE and grain yields. The lack of knowledge about precise regulatory mechanisms to explain NUE in crop plants hampers the goal of agricultural productivity. Understanding the molecular basis of NUE will enable to provide handle for crop improvement through biotechnological means. With the advent of modern genomics and proteomics approaches such as subtractive hybridization, differential display, and microarray techniques are revolutionizing to identify the candidate genes which play a pivotal role in the regulation of NUE. Beside it, quantitative real-time polymerase chain reaction technology is also being used to establish marker-trait association for NUE. The identification of potential candidate genes/proteins in the regulation of NUE will serve as biomarker(s) for screening genotypes for their nitrogen responsiveness for optimization of nitrogen input in agriculture. This paper describes the molecular basis of NUE with respect to nitrogen metabolism and its intimate relationship with carbon metabolism, use of molecular-physiological-genetics approaches for understanding the role of various genes/proteins, and their validation to use as biomarker(s) for determining genotypic potential for NUE. Since NUE in plants is a complex trait which not only involves the primary process of nitrogen uptake and assimilatory pathways but also a series of events, including metabolite partitioning, secondary remobilization, C-N interactions, as well as molecular signalling pathways and regulatory control outside the metabolic cascades. Therefore, identification of novel nitrogen responsive genes and their cis- and trans-acting gene elements is essential. Thus, fishing out a single gene, biomarker or a master regulator controlling complex trait of NUE could serve as an appropriate strategy for nitrogen management in agriculture.

Identification of Biomarker for Determining Genotypic Potential of Nitrogen-Use-Efficiency and Optimization of the Nitrogen Inputs in Crop Plants

Anil Kumar,Nidhi Gupta,Atul Kumar Gupta,Vikram Singh Gaur 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.4

Worldwide, the nitrogen use efficiency (NUE) for crop plants is of great concern. The burgeoning world population needs crop genotypes that respond to higher nitrogen and show a direct relationship to yield with use of nitrogen inputs, i.e. high nitrogenresponsive genotypes. However, for fulfilling the high global demand of organic produce, it requires the low nitrogen responsive genotypes with greater NUE and grain yields. The lack of knowledge about precise regulatory mechanisms to explain NUE in crop plants hampers the goal of agricultural productivity. Understanding the molecular basis of NUE will enable to provide handle for crop improvement through biotechnological means. With the advent of modern genomics and proteomics approaches such as subtractive hybridization, differential display, and microarray techniques are revolutionizing to identify the candidate genes which play a pivotal role in the regulation of NUE. Beside it, quantitative real-time polymerase chain reaction technology is also being used to establish marker-trait association for NUE. The identification of potential candidate genes/proteins in the regulation of NUE will serve as biomarker(s) for screening genotypes for their nitrogen responsiveness for optimization of nitrogen input in agriculture. This paper describes the molecular basis of NUE with respect to nitrogen metabolism and its intimate relationship with carbon metabolism, use of molecular-physiological-genetics approaches for understanding the role of various genes/proteins, and their validation to use as biomarker(s) for determining genotypic potential for NUE. Since NUE in plants is a complex trait which not only involves the primary process of nitrogen uptake and assimilatory pathways but also a series of events, including metabolite partitioning, secondary remobilization, C-N interactions, as well as molecular signalling pathways and regulatory control outside the metabolic cascades. Therefore, identification of novel nitrogen responsive genes and their cis- and trans-acting gene elements is essential. Thus, fishing out a single gene, biomarker or a master regulator controlling complex trait of NUE could serve as an appropriate strategy for nitrogen management in agriculture. Worldwide, the nitrogen use efficiency (NUE) for crop plants is of great concern. The burgeoning world population needs crop genotypes that respond to higher nitrogen and show a direct relationship to yield with use of nitrogen inputs, i.e. high nitrogenresponsive genotypes. However, for fulfilling the high global demand of organic produce, it requires the low nitrogen responsive genotypes with greater NUE and grain yields. The lack of knowledge about precise regulatory mechanisms to explain NUE in crop plants hampers the goal of agricultural productivity. Understanding the molecular basis of NUE will enable to provide handle for crop improvement through biotechnological means. With the advent of modern genomics and proteomics approaches such as subtractive hybridization, differential display, and microarray techniques are revolutionizing to identify the candidate genes which play a pivotal role in the regulation of NUE. Beside it, quantitative real-time polymerase chain reaction technology is also being used to establish marker-trait association for NUE. The identification of potential candidate genes/proteins in the regulation of NUE will serve as biomarker(s) for screening genotypes for their nitrogen responsiveness for optimization of nitrogen input in agriculture. This paper describes the molecular basis of NUE with respect to nitrogen metabolism and its intimate relationship with carbon metabolism, use of molecular-physiological-genetics approaches for understanding the role of various genes/proteins, and their validation to use as biomarker(s) for determining genotypic potential for NUE. Since NUE in plants is a complex trait which not only involves the primary process of nitrogen uptake and assimilatory pathways but also a series of events, including metabolite partitioning, secondary remobilization, C-N interactions, as well as molecular signalling pathways and regulatory control outside the metabolic cascades. Therefore, identification of novel nitrogen responsive genes and their cis- and trans-acting gene elements is essential. Thus, fishing out a single gene, biomarker or a master regulator controlling complex trait of NUE could serve as an appropriate strategy for nitrogen management in agriculture.

Interleukin-1B (IL-1B-31 and IL-1B-511) and interleukin-1 receptor antagonist (IL-1Ra) gene polymorphisms in primary immune thrombocytopenia

Deependra Kumar Yadav,Anil Kumar Tripathi,Divya Gupta,Saurabh Shukla,Aloukick Kumar Singh,Ashutosh Kumar,Jyotsna Agarwal,K. N. Prasad 대한혈액학회 2017 Blood Research Vol.52 No.4

Background: Immune thrombocytopenia (ITP) is an immune-mediated disease caused by autoanti-bodies against platelets membrane glycoproteins GPIIb/IIIa and GPIb/IX. The etiology of ITP remains unclear. This study evaluated the association of polymorphisms in interleukin (IL)-1B-31, IL-1B-511, and IL-1Ra with ITP. Methods: Genotyping of IL-1B-31, IL-1B-511, and IL-1Ra was performed in 118 ITP patients and 100 controls by polymerase chain reaction restriction fragment length polymorphism and detection of variable number tandem repeats. Results: Genotype differences in IL-1B-31 and IL-1Ra were significantly associated with ITP. Patients showed a higher frequency of the IL-1B-31 variant allele (T) and a 1.52-fold greater risk of susceptibility to ITP (odds ratio [OR]=1.52, 95% confidence interval [CI]=1.04‒2.22, P=0.034). The frequencies of both homozygous and heterozygous variant geno-types of IL-1B-31 were higher (OR=2.33, 95% CI=1.069‒5.09, P=0.033 and OR=2.044, 95% CI=1.068‒39, P=0.034) among patients and were significantly associated with ITP susceptibility. Both homozygous and heterozygous variant genotypes of IL-1Ra were also more frequent (OR=4.48, 95% CI=1.17‒17.05, P=0.0230 and OR=1.80, 95% CI=1.03‒3.14, P=0.0494) among patients and were associated with ITP risk. IL-1B-31 and IL-1Ra also showed significant association with severe ITP. However, IL-1B-511 was not asso-ciated with ITP. Conclusion: IL-1B-31 and IL-1Ra polymorphisms may significantly impact ITP risk, and they could be associated with disease severity, which may contribute to the pathogenesis of ITP.

Residual gall bladder: An emerging disease after safe cholecystectomy

Vikas Gupta,Anil Kumar Sharma,Pradeep Kumar,Mantavya Gupta,Ajay Gulati,Saroj Kant Sinha,Rakesh Kochhar 한국간담췌외과학회 2019 Annals of hepato-biliary-pancreatic surgery Vol.23 No.4

Backgrounds/Aims: Residual gallbladder mucosa left after subtotal/partial cholecystectomy is prone to develop recurrent lithiasis and become symptomatic, which mandates surgical removal. Methods: we retrospectively evaluated the patients with residual gallbladder referred to us from January 2011 to December 2017. Based on MRCP we classified calot’s anatomy to – type I where cystic duct was seen and type II where sessile GB stump was seen. Results: 21 patients with median age 38 years and M:F::1:9.5, had undergone cholecystectomy (3 months-20 years) prior, presented with recurrent biliary pain. 3 had jaundice (CBD stone, Mirizzi and biliary stricture), 1 had pancreatitis and one had malignancy of the GB. Imaging revealed type I anatomy in 14 (67%) and type II in 7 (33%). All underwent completion cholecystectomy – open in 18 and laparoscopic in 3 (one converted to open). Additional procedure was required in 5 patients – CBD exploration in 2 (10%) and one each Hepatico-jejunostomy, extended cholecystectomy and splenectomy. Median hospital stay was 1 day. There was no mortality and 10% morbidity. One patient with malignancy died at 2 years, two died of unrelated cause, one developed incisional hernia and the remaining were well at a median follow up of 29 months. Conclusions: Residual GB lithiasis should be suspected if there are recurrent symptoms after cholecystectomy. MRCP based proposed classification can guide the management strategy. Completion cholecystectomy is curative.

Interleukin-1B (IL-1B-31 and IL-1B-511) and interleukin-1 receptor antagonist (IL-1Ra) gene polymorphisms in primary immune thrombocytopenia

Deependra Kumar Yadav,Anil Kumar Tripathi,Divya Gupta,Saurabh Shukla,Aloukick Kumar Singh,Ashutosh Kumar,Jyotsna Agarwal,K. N. Prasad 대한혈액학회 2017 Blood Research Vol.51 No.4

Background: Immune thrombocytopenia (ITP) is an immune-mediated disease caused by autoanti-bodies against platelets membrane glycoproteins GPIIb/IIIa and GPIb/IX. The etiology of ITP remains unclear. This study evaluated the association of polymorphisms in interleukin (IL)-1B-31, IL-1B-511, and IL-1Ra with ITP. Methods: Genotyping of IL-1B-31, IL-1B-511, and IL-1Ra was performed in 118 ITP patients and 100 controls by polymerase chain reaction restriction fragment length polymorphism and detection of variable number tandem repeats. Results: Genotype differences in IL-1B-31 and IL-1Ra were significantly associated with ITP. Patients showed a higher frequency of the IL-1B-31 variant allele (T) and a 1.52-fold greater risk of susceptibility to ITP (odds ratio [OR]=1.52, 95% confidence interval [CI]=1.04‒2.22, P=0.034). The frequencies of both homozygous and heterozygous variant geno-types of IL-1B-31 were higher (OR=2.33, 95% CI=1.069‒5.09, P=0.033 and OR=2.044, 95% CI=1.068‒39, P=0.034) among patients and were significantly associated with ITP susceptibility. Both homozygous and heterozygous variant genotypes of IL-1Ra were also more frequent (OR=4.48, 95% CI=1.17‒17.05, P=0.0230 and OR=1.80, 95% CI=1.03‒3.14, P=0.0494) among patients and were associated with ITP risk. IL-1B-31 and IL-1Ra also showed significant association with severe ITP. However, IL-1B-511 was not asso-ciated with ITP. Conclusion: IL-1B-31 and IL-1Ra polymorphisms may significantly impact ITP risk, and they could be associated with disease severity, which may contribute to the pathogenesis of ITP.

Estimation of glacial retreat and mass loss in Baspa basin, Western Himalaya

Vinay Kumar Gaddam,Anil V. Kulkarni,Anil Kumar Gupta 대한공간정보학회 2016 Spatial Information Research Vol.24 No.3

Glaciers are one of the valuable natural resources in Indian Himalaya. A large number of people depend on glacier melt for social and industrial activities. Therefore, monitoring the glacial changes becomes crucial. In the present study, retreat and mass balance of 19 glaciers in Baspa basin were analysed. An overall de-glaciation of 24 % (41.1 ± 8.37 km2) was observed between 1962 and 2014. Mass balance was estimated by Accumulation Area Ratio and Equilibrium Line Altitude (ELA) methods. The mean ELA estimate varies between 5147 ± 178 and 5405 ± 173 m. Negative mass balance was observed and the estimated mass loss is 3.6 mega tonne (3.6 9 106 m3), for a period of 9 years between 1998 and 2014. In addition, temperature and precipitation data obtained at Rackham observatory (3050 m) were analysed for a period of 29 years, between 1984 and 2013. The analysis showed an increasing trend in annual mean temperature, decreasing trend in precipitation and a higher rise in minimum temperatures of both summer and winter. Thus, the overall observations suggest continuous loss of glacier area and mass, which may influence the glacier’s health and run-off in Baspa basin.

CYP1A1 Gene Polymorphisms: Modulator of Genetic Damage in Coal-Tar Workers

Giri, Shiv Kumar,Yadav, Anita,Kumar, Anil,Dev, Kapil,Gulati, Sachin,Gupta, Ranjan,Aggarwal, Neeraj,Gautam, Sanjeev Kumar Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.7

Aim: It is well known that polycyclic aromatic hydrocarbons (PAHs) such as benzo (a) pyrene have carcinogenic properties and may cause many types of cancers in human populations. Genetic susceptibility might be due to variation in genes encoding for carcinogen metabolizing enzymes, such as cytochrome P-450 (CYP450). Our study aimed to investigate the effect of genetic polymorphisms of CYP1A1 (m1 and m2) on genetic damage in 115 coal-tar workers exposed to PAHs at their work place. Methods: Genetic polymorphisms of CYP1A1 were determined by the PCR-RFLP method. Comet and buccal micronucleus assays were used to evaluate genetic damage among 115 coal tar workers and 105 control subjects. Results: Both CYP1A1 m1 and CYP1A1 m2 heterozygous and homozygous (wt/mt+mt/mt) variants individually as well as synergistically showed significant association (P<0.05) with genetic damage as measured by tail moment (TM) and buccal micronuclei (BMN) frequencies in control and exposed subjects. Conclusion: In our study we found significant association of CYP1A1 m1 and m2 heterozygous (wt/mt)+homozygous (mt/mt) variants with genetic damage suggesting that these polymorphisms may modulate the effects of PAH exposure in occupational settings.

Alteration of Genetic Make-up in Karnal Bunt Pathogen (Tilletia indica) of Wheat in Presence of Host Determinants

Gupta, Atul K.,Seneviratne, J.M.,Bala, Ritu,Jaiswal, J.P.,Kumar, Anil The Korean Society of Plant Pathology 2015 Plant Pathology Journal Vol.31 No.2

Alteration of genetic make-up of the isolates and mono-sporidial strains of Tilletia indica causing Karnal bunt (KB) disease in wheat was analyzed using DNA markers and SDS-PAGE. The generation of new variation with different growth characteristics is not a generalized feature and is not only dependant on the original genetic make up of the base isolate/monosporidial strains but also on interaction with host. Host determinant(s) plays a significant role in the generation of variability and the effect is much pronounced in monosporidial strains with narrow genetic base as compared to broad genetic base. The most plausible explanation of genetic variation in presence of host determinant(s) are the recombination of genetic material from two different mycelial/sporidia through sexual mating as well as through parasexual means. The morphological and development dependent variability further suggests that the variation in T. indica strains predominantly derived through the genetic rearrangements.