Computational Identification and Comparative Genomic Analysis of Soybean Oxidative Stress-Related Genes

Sharma Arti,Bong-Gyu Mun,Byung-Wook Yun 경북대학교 농업생명과학대학 2014 Current Research on Agriculture and Life Sciences Vol.32 No.1

Reactive oxygen and nitrogen species (ROS and RNS, respectively) are messengers that carry signals to alter the redox state in order to activate plant responses and other physiological processes, such as differentiation, aging, senescence, and pathogen defense. Quite a large number of genes are involved in this signaling and lead to oxidative stress in plants. Although the role of ROS/RNS during stress conditions is well documented, a comprehensive list of genes and comparative study of these genes has not yet been completed. Accordingly, the in silico identification of oxidative stress-related genes was performed for soybeans and Arabidopsis. These genes were also studied in relation to multiple domain prediction. The presence of domains like dehydogenase and ATPase suggests that these genes are involved in various metabolic processes, as well as the transportation of ions under optimal environmental conditions. In addition to a sequence analysis, a phylogenetic analysis was also performed to identify orthologous pairs among the soybean and Arabidopsis oxidative stress-related genes based on neighbor joining. This study was also conducted with the objective of further understanding the complex molecular signaling mechanism in plants under various stress conditions.

Computational Identification and Comparative Genomic Analysis of Soybean Oxidative Stress-Related Genes

Arti, Sharma,Mun, Bong-Gyu,Yun, Byung-Wook Institute of Agricultural Science and Technology 2014 慶北大農學誌 Vol.32 No.1

Reactive oxygen and nitrogen species (ROS and RNS, respectively) are messengers that carry signals to alter the redox state in order to activate plant responses and other physiological processes, such as differentiation, aging, senescence, and pathogen defense. Quite a large number of genes are involved in this signaling and lead to oxidative stress in plants. Although the role of ROS/RNS during stress conditions is well documented, a comprehensive list of genes and comparative study of these genes has not yet been completed. Accordingly, the in silico identification of oxidative stress-related genes was performed for soybeans and Arabidopsis. These genes were also studied in relation to multiple domain prediction. The presence of domains like dehydogenase and ATPase suggests that these genes are involved in various metabolic processes, as well as the transportation of ions under optimal environmental conditions. In addition to a sequence analysis, a phylogenetic analysis was also performed to identify orthologous pairs among the soybean and Arabidopsis oxidative stress-related genes based on neighbor joining. This study was also conducted with the objective of further understanding the complex molecular signaling mechanism in plants under various stress conditions.

A Bioinformatics Approach for Identification, Evolution and Expression Analysis of Rapid Alkalization Factor Gene Family in Plant Species

Sharma Arti,Byung-Wook Yun 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Receptor mediated signal carriers play a critical role in regulation of plant defense and development. Rapid Alkalization Factor (RALF) is an important signaling family which has a role in plant growth and development. However, only few RALF polypeptides have been identified till date, mainly because of enormous efforts required for their isolation or identify their gene through mutational analysis. In this study, an extensive database search yield 39, 43, 34 and 23 potential RALF genes in Arabidopsis, rice, corn and soybeans, respectively. RALF genes are highly conserved across the plant species. A comprehensive analysis including the chromosomal location, gene structure, subcellular location, conserved motif, protein structure and promoter analysis was performed. RALF genes from four plants under study were divided in 7 groups based on phylogenetic analysis. In silico expression analysis of these genes, using microarray and EST data, reveled that these genes exhibit a variety of expression pattern. Furthermore, RALF genes showed distinct expression pattern under nitricoxide (NO) stress in Arabidopsis. This suggests a role of RALF genes in plant defense regulation. Our comprehensive analysis of RALF genes is a valuable resource that further elucidates the roles of RALF family members in plant growth and development. In addition, comparative genomics analyses deepen our understanding of the evolution of RALF gene family and will contribute to further genetics and genomics studies of other monocot and dicot plant species.

The diagnostic accuracy of ultrasonographic method over manual aspiration technique for gastric reserve volume estimation in critically ill patients

Rahul Sharma,Ravi Kant Dogra,Jyoti Pathania,Arti Sharma 대한중환자의학회 2023 Acute and Critical Care Vol.38 No.1

Background Although gastric reserve volume (GRV) is a surrogate marker of gastrointestinal dysfunction and feeding intolerance, there is ambiguity in its estimation due to problems associated with its measurement. Introduction of point-of-care ultrasound as a tool for anesthetists kindled interest in its use for GRV estimation. Methods In this prospective observational study, we recruited 57 critically ill patients and analyzed 586 samples of GRV obtained by both ultrasonography (USG) and manual aspiration. Results The analysis showed that USG-guided GRV was significantly correlated (r=0.788, P<0.001) and in positive agreement with manual aspiration based on Bland-Altman plot, with a mean difference of 8.50±14.84 (95% confidence interval, 7.389–9.798). The upper and lower limits of agreement were 37.7 and –20.5, respectively, within the ±1.96 standard deviation (P<0.001). The respective sensitivity and positive predictive value, specificity and negative predictive value, and area under the curve of USG for feeding intolerance were 66.67%, 98.15%, and 0.82%, with 96.49% diagnostic accuracy. Conclusions Ultrasonographic estimation of GRV was positively, significantly correlated and in agreement with the manual aspiration method and estimated feeding intolerance earlier. Routine use of gastric USG could avoid clinical situations where feeding status is unclear and there is high risk of aspiration and could become a standard practice of critical care.

Diagnostic accuracy of left ventricular outflow tract velocity time integral versus inferior vena cava collapsibility index in predicting post-induction hypotension during general anesthesia: an observational study

Vibhuti Sharma,Arti Sharma,Arvind Sethi,Jyoti Pathania 대한중환자의학회 2024 Acute and Critical Care Vol.39 No.1

Background: Point of care ultrasound (POCUS) is being explored for dynamic measurements like inferior vena cava collapsibility index (IVC-CI) and left ventricular outflow tract velocity time integral (LVOT-VTI) to guide anesthesiologists in predicting fluid responsiveness in the preoperative period and in treating post-induction hypotension (PIH) with varying accuracy.Methods: In this prospective, observational study on included 100 adult patients undergoing elective surgery under general anesthesia, the LVOT-VTI and IVC-CI measurements were performed in the preoperative room 15 minutes prior to surgery, and PIH was measured for 20 minutes in the post-induction period.Results: The incidence of PIH was 24%. The area under the curve, sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the two techniques at 95% confidence interval was 0.613, 30.4%, 93.3%, 58.3%, 81.4%, 73.6% for IVC-CI and 0.853, 83.3%, 80.3%, 57.1%, 93.8%, 77.4% for LVOT -VTI, respectively. In multivariate analysis, the cutoff value for IVC-CI was >51.5 and for LVOT-VTI it was ≤17.45 for predicting PIH with odd ratio [OR] of 8.491 (P=0.025) for IVCCI and OR of 17.427 (P<0.001) for LVOT. LVOT-VTI assessment was possible in all the patients, while 10% of patients were having poor window for IVC measurements.Conclusions: We recommend the use of POCUS using LVOT-VTI or IVC-CI to predict PIH, to decrease the morbidity of patients undergoing surgery. Out of these, we recommend LVOT-VTI measurements as it has showed a better diagnostic accuracy (77.4%) with no failure rate.

Cambial Meristematic Cell Specific Homologous Gene, At1G71110 May Play in R Gene Mediated Defense Signaling Pathway

Bong-Gyu Mun,Sang-Uk Lee,Arti Sharma,Byung-Wook Yun 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Cambial meristematic cells (CMCs) are innately undifferentiated cells located in the meristems of plant with function as a stem cell to renew itself or replace specialized tissues. Another interesting feature of plant stem cells is controlling the plant defense in response to various stresses. Several groups have studied for stem cell triggered immunity signaling however, the molecular basis of the stem cell triggered immunity remains unclear. We previously obtained deferentially expressed 563 stem cell specific gene profiles from transcriptome analysis between two different cell types, CMC and dedifferentiated dells (DDCs) of yew tree (Taxuscuspidate). In a line of comparative genomics approach, we have selected 30 Arabidopsis homologous immune regulator candidate genes that showed significantly enriched GO terms ; at “response to stress” and “defense response”. We obtained one of homologous knock-out (KO) Arabidopsis mutant line on the locus At1G71110 whose cognate yew homologous gene showed predominantly expressed in CMCs compared to DDCs (20 times higher). For the assessment of basal disease resistance KO mutant plants were inoculated with Pseudomonas syringae pv. tomato (Pst) DC3000 and counted pathogen isolated from inoculated leaves. Interestingly, the KO mutant plants were not compromised in basal disease resistant, however, the hypersensitive response was significantly enhanced in the mutant compared to wild type in response to PstavrB, suggesting R-gene mediated defense response involved. We also investigated there sponse to the small reactive redox molecules such as reactive oxygen species (ROS) and reactive nitrogen species (RNS) that associated significantly in plant immune response. Notably the KO mutant plants exhibited hypersensitivity specifically under nitrosative stress condition derived by S-nitrosiglutathione (GSNO), anitrioxide (NO) donor. Taken all together, putative endomembrane components At1G71110 may play a pivotal role in R gene mediated plant immune system. To further investigate its role(s) and molecular signaling network various defense gene expression profiles and functional genomics approach are ongoing for the long term aim of muti-stress tolerant crop development

Efficacy and tolerability of exclusive enteral nutrition in adult patients with complicated Crohn’s disease

( Sanchit Sharma ),( Arti Gupta ),( Saurabh Kedia ),( Samagra Agarwal ),( Namrata Singh ),( Sandeep Goyal ),( Saransh Jain ),( Vipin Gupta ),( Pabitra Sahu ),( Sudheer Kumar Vuyyuru ),( Bhaskar Kante 대한장연구학회 2021 Intestinal Research Vol.19 No.3

Background/Aims: Exclusive enteral nutrition (EEN), an established modality for pediatric Crohn’s disease (CD) is seldomly utilized in adults. The present study reports the outcome of EEN in adult CD patients at a tertiary care hospital in India. Methods: This was a retrospective analysis of CD patients who received EEN as a sole modality/adjunct to other treatment. The primary and secondary outcomes changed in Crohn’s Disease Activity Index (CDAI), and clinical response (decline in CDAI >70), respectively, at 4 and 8 weeks. Subgroup analysis evaluated response across different phenotypes, EEN formulations and prior treatment. Linear mixed effect model was created to assess the predictors of EEN response. Results: Thirty-one CD patients received EEN over median duration of 4 weeks (range, 2-6 weeks). CDAI showed a significant improvement post EEN at 4 (baseline 290 [260-320] vs. 240 [180-280], P=0.001) and 8 weeks (baseline 290 [260-320] vs. 186 [160-240], P=0.001), respectively. The cumulative clinical response rates at 4 and 8 weeks were 37.3% and 80.4% respectively. The clinical response rates at 8 weeks across B1 (n=4), B2 (n=18), and B3 (n=9) phenotypes were 50%, 78.8%, and 100% respectively (log-rank test, P=0.093). The response rates at 8 weeks with polymeric (n=8) and semi-elemental diet (n=23) were 75% and 82.6% respectively (log-rank test, P=0.49). Baseline CDAI (odds ratio, 1.008; 95% confidence interval, 1.002-1.017; P=0.046) predicted response to EEN. Conclusions: EEN was effective in inducing clinical response across different phenotypes of CD. Baseline disease activity remained the most important predictor of clinical response to EEN. (Intest Res 2021;19:291-300)

Dielectric behavior of carbon-nanotube-doped ferroelectric liquid crystal mixture

Samriti Khosla,Arti Sharma 한국정보디스플레이학회 2013 Journal of information display Vol.14 No.4

The dielectric spectra of pure and 0.1% multi-walled-carbon-nanotube-(MWCNT)-doped ferroelectric liquid crystal (FLC)mixture KCFLC10S materials were studied in the 50 Hz to 1MHz frequency range at different bias voltages. An unusual behavior-increase of ε with increasing E was observed in both samples. It was found that although the relaxation mode was not observable in the MWCNT-FLC sample, the increased effect of the bias voltage on the FLC with the addition of MWCNTs is clearly visible. A theory is presented to explain this effect of MWCNTs in the FLC material.

Dielectric behavior of carbon-nanotube-doped ferroelectric liquid crystal mixture

Khosla, Samriti,Sharma, Arti 한국정보디스플레이학회 2013 Journal of information display Vol.14 No.4

The dielectric spectra of pure and 0.1% multi-walled-carbon-nanotube-(MWCNT)-doped ferroelectric liquid crystal (FLC) mixture KCFLC10S materials were studied in the 50 Hz to 1MHz frequency range at different bias voltages. An unusual behavior-increase of ${\varepsilon}^{\prime}$ with increasing E was observed in both samples. It was found that although the relaxation mode was not observable in the MWCNT-FLC sample, the increased effect of the bias voltage on the FLC with the addition of MWCNTs is clearly visible. A theory is presented to explain this effect of MWCNTs in the FLC material.

Profile and Time-Scale Dynamics of Differentially Expressed Genes in Transcriptome of Populus davidiana Under Drought Stress

Mun, Bong-Gyu,Hussain, Adil,Park, Eung-Jun,Lee, Sang-Uk,Sharma, Arti,Imran, Qari Muhammad,Jung, Ki-Hong,Yun, Byung-Wook Springer-Verlag 2017 Plant molecular biology reporter Vol.35 No.6

<P>The genus Populus contains 25-35 species of deciduous flowering plants in the family Salicaceae. It has evolved to overcome various environmental stresses including drought stress through changes in physiological processes such a stomatal movement, photosynthesis, stress signaling, defense responses, and overall growth rate. In this study, we performed RNA-seq-based transcriptome profiling of Populus davidiana in response to drought stress induced by 10% PEG at two time points (6 and 12 h). We generated over 527 million reads by applying Populus trichocarpa as reference genome. Assembly of the reads yielded 32,650 genes and 75,820 transcripts; of these, after quantile normalization, a total of 997 genes were identified with dynamic expression over time, classifying them into nine different clusters. Among them, 550 genes responded significantly to drought stress treatment after 6 h (108 genes up-regulated and 201 genes down-regulated) and 12 h (161 up-regulated and 80 down-regulated) respectively, with at least twofold change in their expression. Based on analysis of these genes, we found several differentially expressed genes (DEGs) involved in cellular transport, transcriptional regulation, protein modification, regulation of cellular redox state, and those involved in response to other stresses. We also validated RNA-seq-mediated transcriptome data by RT-qPCR analysis of eight randomly selected DEGs. It showed significantly high correlation coefficient (0.95) suggesting high reliability of RNA-seq analysis. This study presents the first RNA-seq mediated transcriptome profile of P. davidiana in response to drought stress, providing critical information necessary for understanding the mechanisms underpinning drought stress tolerance in forest trees and other plant species.</P>