Extrapolation of significant genes and transcriptional regulatory networks involved in Zea mays in response in UV-B stress

Saurabh Gupta,Vikas Gupta,Vishal Singh,Pritish Kumar Varadwaj 한국유전학회 2018 Genes & Genomics Vol.40 No.9

A wide range of plant species growth influenced when they exposed to solar UV-B radiation. Leaves of the plant are highly affected by UV-B radiation lead to the reduction in the growth of the plant. Current work demonstrates the comparative transcriptional changes and visible symptoms occurred in the maize leaf growth zone (GZ). Primary objective of this study was to identify differentially expressed genes (DEGs) responsible for leaf growth and their association in the transcriptional regulatory network under UV-B stress. Whole transcriptomic data was analysed and the quality check was tested for each sample and further genome-wide mapping and DEGs were performed. Gene Ontology (GO) based functional annotation, associated transcriptional networks and molecular pathways were annotated. Reduction in cell production due to UV-B stress causes a decrease in leaf’s length and size was observed. Further, the specific role of the DEGs, in UV-B signalling pathways and other molecular functions responsible for leaf cell death was discovered. Results also infer that the major changes occurred in the cell cycle, transcriptional regulation, post-transcriptional modification, phytohormones, flavonoids biosynthesis, and chromatin remodeling. UV-B signalling pathways and the transcriptional regulatory networks infer the different molecular steps along with downstream transcriptional and post-transcriptional control of metabolic enzymes used in long-term memory adoption and attainment resistance to UV-B stress identified. Effects of UV-B radiation on leaf growth was noted in this study. UV-B stress response genes and associated transcriptional regulatory networks were identified, can be used in developing the marker assist UB-B stress tolerant genotypes of the maize.

Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress

Saurabh Gupta,Vinod Kumar Mishra,Sunita Kumari,Raavi,Ramesh Chand,Pritish Kumar Varadwaj 한국유전학회 2019 Genes & Genomics Vol.41 No.1

WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress. Some earlier studies done by individual researchers reported different wheat WRKY TFs. Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs. Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation. The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed. Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation. The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences. Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites. Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress. Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress. These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development.

Change detection of landscape connectivity arisen by forest transformation in Hazaribagh wildlife sanctuary, Jharkhand (India)

Gupta Saurabh Kumar,Pandey Arvind Chandra 대한공간정보학회 2020 Spatial Information Research Vol.28 No.4

Forest land conversion is the primary driver of biodiversity decline worldwide. Hazaribagh wildlife sanctuary is a region of rich biodiversity in which forests and wildlife are deteriorating fast. The prime reasons for forest degradation and wildlife loss are the landscape connectivity weakening and forest transformation. In the present work, landscape connectivity and forest transformation relationships were analyzed in a spatio-temporal domain. The forest patches as a group of spectral abundance were extracted using the endmember retrieval technique. The connectivity analysis was performed by using a connectivity index in the extracted forest patches. Forest transformation is calculated using a post-classification change detection strategy for five types of forest cover during the four phases of the year (1992–2005, 2005–2010, 2010–2017 and 1992–2017). The forest cover was measured using a forest canopy density model using spectral indices. The landscape connectivity of 80–100% exhibit a rapid increase of 38% in 2005 from 1992 contrary to a 13% decrease in 2010 and 2017. The 23% loss of forest cover from 2005 to 2010 and a 17% loss in 2010–2017 phase of forest transformation weakened the forest connectivity. Forest cover, having a density higher than 40% was more vulnerable to degradation and landscape connectivity loss. The result shows that such declines of forest cover and landscape connectivity will reduce the genetic diversity in the forest, especially the mammalian population.

Experimental Investigations on Spray Characteristics of Potential Fuels for Advance Low Temperature Combustion Engines

( Saurabh Kumar Gupta ),( M. Murugesa Pandian ),( Anand Krishnasamy ) 한국액체미립화학회 2017 한국액체미립화학회 학술강연회 논문집 Vol.2017 No.-

Advanced low temperature combustion (LTC) strategies including Premixed Charge Compression Ignition (PCCI), Reactivity Controlled Compression Ignition (RCCI), Stratified Charge Compression Ignition (SCCI) and High Efficiency Clean Combustion (HECC) are proposed to simultaneously reduce oxides of nitrogen (NOx) and particulate matter (PM) emissions to near zero levels along with higher thermal efficiencies. However, precise control of ignition timings is difficult to achieve in these LTC strategies as it is primarily controlled by the molecular composition of fuel by altering physical and chemical delay period and creating reactivity stratification. Fuel spray characteristics plays a vital role in varying the rate of fuel-air mixing and physical delay period. The potential fuels for advanced LTC modes include fuels with optimal reactivity and better volatility. The effects of physical properties and its impact on spray behavior of potential fuels for LTC are sparsely available. The present work intends to study the effects of changes in properties and injection pressures on the macroscopic spray behavior of potential fuels for advanced LTC engines. The experiments are carried out in a constant volume spray chamber with different potential fuels for advanced combustion engines, viz. Diesel with 10%,20% and 30% gasoline (DG10, DG20 and DG30) and Diesel with 10%,20% and 30% kerosene (DK10, DK20 and DK30). The fuel injection pressures and the injection strategies have been chosen as representative of direct injection diesel engine working conditions. The spray characteristics such as spray tip penetration distance, spray cone angle are obtained by using a high resolution spray visualization system for the different fuel blends. The obtained results show that the changes in physical properties of the fuel blends affect the macroscopic fuel spray behavior. Further, as compared to that of conventional diesel, all the fuel blends show a significant difference in the macroscopic spray characteristics.

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.

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.

Vascular Injuries during Cholecystectomy; Incidence, Management and Long Term Outcomes: A 20-year Tertiary Center Experience!!!

Saurabh Galodha,Anu Behari,Rajneesh K Singh,Ashok Kumar Gupta,V K Kapoor,Rajan Saxena 대한외과학회 2020 대한외과학회 학술대회 초록집 Vol.2020 No.11

Parameters Involved in Autophosphorylation in Chronic Myeloid Leukemia: a Systems Biology Approach

Kumar, Himansu,Tichkule, Swapnil,Raj, Utkarsh,Gupta, Saurabh,Srivastava, Swati,Varadwaj, Pritish Kumar Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.13

Background: Chronic myeloid leukemia (CML) is a stem cell disorder characterized by the fusion of two oncogenes namely BCR and ABL with their aberrant expression. Autophosphorylation of BCR-ABL oncogenes results in proliferation of CML. The study deals with estimation of rate constant involved in each step of the cellular autophosphorylation process, which are consequently playing important roles in the proliferation of cancerous cells. Materials and Methods: A mathematical model was proposed for autophosphorylation of BCR-ABL oncogenes utilizing ordinary differential equations to enumerate the rate of change of each responsible system component. The major difficulty to model this process is the lack of experimental data, which are needed to estimate unknown model parameters. Initial concentration data of each substrate and product for BCR-ABL systems were collected from the reported literature. All parameters were optimized through time interval simulation using the fminsearch algorithm. Results: The rate of change versus time was estimated to indicate the role of each state variable that are crucial for the systems. The time wise change in concentration of substrate shows the convergence of each parameter in autophosphorylation process. Conclusions: The role of each constituent parameter and their relative time dependent variations in autophosphorylation process could be inferred.

Portal Hypertension and Secondary Biliary Cirrhosis in Post Cholecystectomy Benign Biliary Strictures: Factors Responsible, Surgical Implications and Outcomes

( Saurabh Galodha ),( Rajneesh K Singh ),( Anu Behari ),( Ashok Kumar Gupta ),( V K Kapoor ),( Rajan Saxena ) 대한간학회 2017 춘·추계 학술대회 (KASL) Vol.2017 No.1

Aims: Portal hypertension (PHT) and secondary biliary cirrhosis (SBC) are found in 7-20% patients of postcholecystectomy benign biliary strictures (BBS), which can lead to significant morbidity and mortality. This study was done to look for factors associated with PHT and SBC in BBS and its effect on perioperative morbidity and final outcomes. Methods: A retrospective analysis of 613 patients of BBS managed between January 1989 and December 2012 was done. Preoperative and intraoperative parameters and perioperative morbidity were registered. Outcomes were analyzed with McDonald grading with grades A and B considered as success. Results: A retrospective analysis of 613 patients of BBS managed between January 1989 and December 2012 was done. Preoperative and intraoperative parameters and perioperative morbidity were registered. Outcomes were analyzed with McDonald grading with grades A and B considered as success. Nineteen patients of BBS with PHT were operated. PHT was seen more commonly in BBS grade III and above (n=12,63%). The median time to repair in patients with PHT was more than 4 times that of patients without PHT (826 days vs. 210 days). Two patients with PHT had strictured previous primary repair in the form of Roux-en Y hepaticojejunostomy (RYHJ). In all patients RYHJ with liver biopsy was performed. None of the patients required prior portosystemic shunting. In patients with PHT mean operating time (4.6 ± 2.8 vs. 3.5 ± 2 hours) as well as median blood loss (400 ml vs. 200 ml) was increased but there was no significant increase in perioperative morbidity. Median follow up for these patients was 54 months. Success rate for RYHJ was 89% and only 1 patient required a revision RYHJ due to stricture and recurrent cholangitis. Conclusions: Delayed repair, higher grade of BBS and failed primary repair are factors associated with development of PHT in BBS. RYHJ is feasible without need of portosystemic shunting in all these patients with minimal morbidity and good long-term results.

Efficacy of Bacillus Calmette-Guérin in Cancer Prevention and Its Putative Mechanisms

Sakshi Gupta,Pawan Kumar,Saurabh Yadav 대한암예방학회 2024 Journal of cancer prevention Vol.29 No.1

Bacillus Calmette-Guérin (BCG) is an attenuated strain of Mycobacterium bovis. Although it was developed as a prophylactic vaccine against tuberculosis (TB), researchers have also evaluated it for preventing cancer development or progression. These studies were inspired by the available data regarding the protective effects of microbial infection against cancers and an inverse relationship between TB and cancer mortality. Initial studies demonstrated the efficacy of BCG in preventing leukemia, melanoma and a few other cancers. However, mixed results were observed in later studies. Importantly, these studies have led to the successful use of BCG in the tertiary prevention of non-muscle invasive bladder cancer, wherein BCG therapy has been found to be more effective than chemotherapy. Moreover, in a recently published 60-year follow-up study, childhood BCG vaccination has been found to significantly prevent lung cancer development. In the present manuscript, we reviewed the studies evaluating the efficacy of BCG in cancer prevention and discussed its putative mechanisms. Also, we sought to explain the mixed results of BCG efficacy in preventing different cancers.