School Of Basic And Applied Sciences
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Item Significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium(Royal Society of Chemistry, 2022-03-08T00:00:00) Kundu, Nikita; Sharm, Taniya; Kaur, Sarvpreet; Singh, Mamta; Kumar, Vinit; Sharma, Uttam; Jain, Aklank; Shankaraswamy, Jadala; Miyoshi, Daisuke; Saxena, SarikaWe selected the G-quadruplex motif located in the nuclease-hypersensitive elements (NHE) III1 region of the c-Myc promoter and for the first time performed its interaction studies with a designed peptide (QW10). Our CD results showed that the peptide bound to the c-Myc G-quadruplex and induced a significant blue shift in the positive peak of 20 nm in KCl alone or with 40wt% PEG200 or 20wt% PEG8000 in comparison to NaCl. Our Native Gel results confirmed that peptide binding destabilized the duplex and stabilized the unimolecular G-quadruplex and not binding to i-motif. UV thermal results confirmed destabilization of bimolecular structure and stabilization of unimolecular G-quadruplex. QW10 showed preferential binding towards c-MYC promoter G4 with binding constant (Kb) values of the order of 0.05 � 0.2 ?M, 0.12 � 0.1 ?M and 0.05 � 0.3 ?M for complexes in K+alone or 40wt% PEG 200 or 20wt% PEG 8000 respectively. QW10 showed preferential cytotoxicity with IC50 values of 11.10 ?M and 6.44 ?M after 72 and 96 hours' incubation on Human Breast Carcinoma MDA-MB 231 cells and was found to be non-toxic with Human Embryonic Kidney (HEK-1) cells. Interestingly, we observed reduction of c-Myc gene expression by 2.5 fold due to QW10 binding and stabilizing c-MYC G4. Our study for the first time provides an expanded overview of significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium. � 2022 Royal Society of Chemistry. All rights reserved.Item Genome-wide identification and gene expression analysis of GHMP kinase gene family in banana cv. Rasthali(Springer Science and Business Media B.V., 2023-09-20T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Thakur, Neha; Jangra, Alka; Tiwari, SiddharthBackground: The GHMP kinase gene family encompasses ATP-dependent kinases, significantly involved in the biosynthesis of isoprenes, amino acids, and metabolism of carbohydrates. Banana is a staple tropical crop that is globally consumed but known for high sensitivity to salt, cold, and drought stresses. The GHMP kinases are known to play a significant role during abiotic stresses in plants. The present study emphasizes the role of GHMP kinases in various abiotic stress conditions in banana. Methods and results: We identified 12 GHMP kinase (MaGHMP kinase) genes in the banana genome database and witnessed the presence of the conserved Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala domain in their protein sequences. All genes were found to be involved in ATP-binding and carried kinase activity confronting their biological roles in the isoprene (27%) and amino acid (20%) biosyntheses. The expression analysis of genes during cold, drought, and salt stress conditions in tissue culture grown banana cultivar Rasthali plants showed a significant involvement of MaGHMP kinase genes in these stress conditions. The highest expression of MaGHMP kinase3 (8.5 fold) was noted during cold stress, while MaGHMP kinase1 (25 fold and 40.01 fold) showed maximum expression during drought and salt stress conditions in leaf tissue of Rasthali. Conclusion: Our findings suggested that MaGHMP kinase1 (MaHSK) and MaGHMP kinase3 (MaGlcAK) could be considered promising candidates for thwarting the abiotic stresses in banana. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.Item Unravelling cross priming induced heat stress, combinatorial heat and drought stress response in contrasting chickpea varieties(Elsevier Masson s.r.l., 2022-04-01T00:00:00) Yadav, Renu; Saini, Rashmi; Adhikary, Arindam; Kumar, SanjeevDrought and high temperature stress affect chickpea growth and productivity. Often these stresses occur simultaneously in the field and lead to a wide range of molecular and metabolic adaptations. Two chickpea varieties; GPF2 (heat sensitive) and PDG4 variety (heat tolerant) were exposed to 35 �C for 24 h individually and along with drought stress. Five heat responsive signalling genes and 11 structural genes were analyzed using qPCR along with untargeted metabolites analysis using GC MS. Expression of antioxidant genes (CaSOD and CaGPX, CaAPX and CaCAT), transcription factors (CaHSFB2, CaHSFB2A, CaHSFB2B, CaHSP17.5 and CaHSP22.7) and signalling genes (CaCAM, CaGAD, and CaMAPK) were upregulated in GPF2 as compared to PDG4 variety. Principal component analysis (PCA), partial least-square discriminant analysis (PLS-DA), and heat map analysis were applied to the metabolomics data to identify the differential response of metabolites in two chickpea varieties. GC-MS analysis identified 107 and 83 metabolites in PDG4 and GPF2 varieties respectively. PDG4 variety accumulated more sugars, amino acids, sugar alcohols, TCA cycle intermediates which provided heat resistance. Additionally, the differential metabolic pathways involved in heat tolerance were alanine, aspartate, and glutamate metabolism, pantothenate CoA biosynthesis, fructose and mannose metabolism and pentose phosphate pathway in PDG4 variety. There was less accumulation of metabolites in the primed plants of both varieties as compared to the non-primed plants indicating less damage due to heat stress. The present study gives an overview of the molecular changes occurring in response to heat stress in sensitive and tolerant chickpea. � 2022 Elsevier Masson SASItem Carotenoid cleavage dioxygenases (HD-CCD1A and B) contribute as strong negative regulators of ?-carotene in Indian bread wheat (cv. HD2967)(Springer Science and Business Media Deutschland GmbH, 2021-04-16T00:00:00) Thakur, Nandita; Flowerika; Thakur, Neha; Khan, Shahirina; Pandey, Ajay K.; Tiwari, SiddharthWheat (Triticum aestivum L.) is the most common cereal crop that is considered to be deficient in provitamin A carotenoids. Carotenoids are prone to degrade into apocarotenoids by the activity of carotenoid cleavage dioxygenases (CCDs). Hence, in this study, multiple CCDs were cloned from commercial Indian wheat cultivar HD2967 to understand their role in provitamin A carotenoids degradation. The homoeolog specific expression of HD-CCD1 and HD-CCD4 at different grain filling stages revealed the higher expression of transcripts arising from the A and B subgenomes of HD-CCD1. Furthermore, the grain development stages showed a strong negative correlation of HD-CCD1A (r = ? 0.969) and B (r = ? 0.970) homoeologs expression to that of ?-carotene accumulation. It suggested that they could be potentially involved in deciding the turn-over of ?-carotene in wheat grain. Three-dimensional (3D) structures for all six homoeologs of HD-CCD1 and HD-CCD4 were predicted using maize VP14 template to gain better insight into their molecular mechanism. Ramachandran plot assessment revealed that ~ 90% of residues are in the most favoured region. Docking studies with various carotenoid substrates revealed the higher affinity of HD-CCD1A and B for ?-carotene and ?-cryptoxanthin. Bacterial complementation analysis validated the functional role of all six homoeologs with HD-CCD1B showing the highest activity followed by HD-CCD1A for ?-carotene degradation. Results of this study provide valuable insights into the characteristics of HD-CCDs in wheat and thereby justifying them (HD-CCD1A and B) as the candidate genes for employing genome editing tools for developing ?-carotene enriched wheat grains. � 2021, King Abdulaziz City for Science and Technology.Item Genome-wide identification and gene expression analysis of GHMP kinase gene family in banana cv. Rasthali(Springer Science and Business Media B.V., 2023-09-20T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Thakur, Neha; Jangra, Alka; Tiwari, SiddharthBackground: The GHMP kinase gene family encompasses ATP-dependent kinases, significantly involved in the biosynthesis of isoprenes, amino acids, and metabolism of carbohydrates. Banana is a staple tropical crop that is globally consumed but known for high sensitivity to salt, cold, and drought stresses. The GHMP kinases are known to play a significant role during abiotic stresses in plants. The present study emphasizes the role of GHMP kinases in various abiotic stress conditions in banana. Methods and results: We identified 12 GHMP kinase (MaGHMP kinase) genes in the banana genome database and witnessed the presence of the conserved Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala domain in their protein sequences. All genes were found to be involved in ATP-binding and carried kinase activity confronting their biological roles in the isoprene (27%) and amino acid (20%) biosyntheses. The expression analysis of genes during cold, drought, and salt stress conditions in tissue culture grown banana cultivar Rasthali plants showed a significant involvement of MaGHMP kinase genes in these stress conditions. The highest expression of MaGHMP kinase3 (8.5 fold) was noted during cold stress, while MaGHMP kinase1 (25 fold and 40.01 fold) showed maximum expression during drought and salt stress conditions in leaf tissue of Rasthali. Conclusion: Our findings suggested that MaGHMP kinase1 (MaHSK) and MaGHMP kinase3 (MaGlcAK) could be considered promising candidates for thwarting the abiotic stresses in banana. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.Item Unravelling cross priming induced heat stress, combinatorial heat and drought stress response in contrasting chickpea varieties(Elsevier Masson s.r.l., 2022-04-01T00:00:00) Yadav, Renu; Saini, Rashmi; Adhikary, Arindam; Kumar, SanjeevDrought and high temperature stress affect chickpea growth and productivity. Often these stresses occur simultaneously in the field and lead to a wide range of molecular and metabolic adaptations. Two chickpea varieties; GPF2 (heat sensitive) and PDG4 variety (heat tolerant) were exposed to 35 �C for 24 h individually and along with drought stress. Five heat responsive signalling genes and 11 structural genes were analyzed using qPCR along with untargeted metabolites analysis using GC MS. Expression of antioxidant genes (CaSOD and CaGPX, CaAPX and CaCAT), transcription factors (CaHSFB2, CaHSFB2A, CaHSFB2B, CaHSP17.5 and CaHSP22.7) and signalling genes (CaCAM, CaGAD, and CaMAPK) were upregulated in GPF2 as compared to PDG4 variety. Principal component analysis (PCA), partial least-square discriminant analysis (PLS-DA), and heat map analysis were applied to the metabolomics data to identify the differential response of metabolites in two chickpea varieties. GC-MS analysis identified 107 and 83 metabolites in PDG4 and GPF2 varieties respectively. PDG4 variety accumulated more sugars, amino acids, sugar alcohols, TCA cycle intermediates which provided heat resistance. Additionally, the differential metabolic pathways involved in heat tolerance were alanine, aspartate, and glutamate metabolism, pantothenate CoA biosynthesis, fructose and mannose metabolism and pentose phosphate pathway in PDG4 variety. There was less accumulation of metabolites in the primed plants of both varieties as compared to the non-primed plants indicating less damage due to heat stress. The present study gives an overview of the molecular changes occurring in response to heat stress in sensitive and tolerant chickpea. � 2022 Elsevier Masson SASItem Carotenoid cleavage dioxygenases (HD-CCD1A and B) contribute as strong negative regulators of ?-carotene in Indian bread wheat (cv. HD2967)(Springer Science and Business Media Deutschland GmbH, 2021-04-16T00:00:00) Thakur, Nandita; Flowerika; Thakur, Neha; Khan, Shahirina; Pandey, Ajay K.; Tiwari, SiddharthWheat (Triticum aestivum L.) is the most common cereal crop that is considered to be deficient in provitamin A carotenoids. Carotenoids are prone to degrade into apocarotenoids by the activity of carotenoid cleavage dioxygenases (CCDs). Hence, in this study, multiple CCDs were cloned from commercial Indian wheat cultivar HD2967 to understand their role in provitamin A carotenoids degradation. The homoeolog specific expression of HD-CCD1 and HD-CCD4 at different grain filling stages revealed the higher expression of transcripts arising from the A and B subgenomes of HD-CCD1. Furthermore, the grain development stages showed a strong negative correlation of HD-CCD1A (r = ? 0.969) and B (r = ? 0.970) homoeologs expression to that of ?-carotene accumulation. It suggested that they could be potentially involved in deciding the turn-over of ?-carotene in wheat grain. Three-dimensional (3D) structures for all six homoeologs of HD-CCD1 and HD-CCD4 were predicted using maize VP14 template to gain better insight into their molecular mechanism. Ramachandran plot assessment revealed that ~ 90% of residues are in the most favoured region. Docking studies with various carotenoid substrates revealed the higher affinity of HD-CCD1A and B for ?-carotene and ?-cryptoxanthin. Bacterial complementation analysis validated the functional role of all six homoeologs with HD-CCD1B showing the highest activity followed by HD-CCD1A for ?-carotene degradation. Results of this study provide valuable insights into the characteristics of HD-CCDs in wheat and thereby justifying them (HD-CCD1A and B) as the candidate genes for employing genome editing tools for developing ?-carotene enriched wheat grains. � 2021, King Abdulaziz City for Science and Technology.Item Expression Study of Long non-coding RNA SCAL1 and GAS6-AS1 in Lung cancer Cell line A549 Compared to IMR-90(Central University of Punjab, 2018) Pp, Arifa; Jain, AklankLung cancer is the fatal type of cancer owing to maximum number death worldwide. Despite the advances in clinical and experimental setup lung cancer still is the deadliest type of cancer wherein survival rate is as low as 15% five-yearly. The reason being the lack of proper candidate molecule for prognosis and diagnosis prior to invasion and metastasis. But usually, cancers are detected at later stages. The past cancer studies and investigations and investigations about tumorigenesis mechanism mostly focused on protein-coding gene considering them as principal regulators of cancer and diseases. But evidence from numerous high throughput genomic platform indicates that 98% of the eukaryotic genome is transcribed to non-coding RNA. The non-coding RNAs are significant in the regulation of many major biological processes that impact vi development, differentiation, and metabolism through different pathways. Non-coding RNA also plays a major role in cancer development and progression by influencing different cellular processes like proliferation, cell cycle progression, cell growth, and apoptosis. They also influence post-transcriptional gene regulation through controlling process like transport, splicing, transcriptional gene silencing, epigenetic gene expression, cell structure integrity etc. So we can assure that the long non-coding RNA and its altered expression play an important role in cancer etiology. In this project, we studied the expression of SCAL1 and GAS6-AS1 using qRT-PCR. The expression analysis shows that the long non-coding RNA is up-regulated (approximate 5-folds, P=0.000464) and GAS6-AS1 is down-regulated (approximate 4-folds, P=0.00378) in lung cancer cell line compared to control cell line. The melt curve analysis shows only one sharp peak for both SCAL1 and GAS6-AS1 and thereby indicates that there is only one specific primer binding and the primer dimer is not formed.Item Maps for when the living gets tough: Maneuvering through a hostile energy landscape(Elsevier B.V., 2016) Mondeel, T.D.G.A.; Rehman, S.; Zhang, Y.; Verma, M.; D?rre, P.; Barberis, M.; Westerhoff, H.V.With genome sequencing of thousands of organisms, a scaffold has become available for data integration: molecular information can now be organized by attaching it to the genes and their gene-expression products. It is however, the genome that is selfish not the gene, making it necessary to organize the information into maps that enable functional interpretation of the fitness of the genome. Using flux balance analysis one can calculate the theoretical capabilities of the living organism. Here we examine whether according to this genome organized information, organisms such as the ones present when life on Earth began, are able to assimilate the Gibbs energy and carbon that life needs for its reproduction and maintenance, from a relatively poor Gibbs-energy environment. We shall address how Clostridium ljungdahlii may use at least two special features and one special pathway to this end: gear-shifting, electron bifurcation and the Wood-Ljungdahl pathway. Additionally, we examined whether the C. ljungdahlii map can also help solve the problem of waste management. We find that there is a definite effect of the choices of redox equivalents in the Wood-Ljungdahl pathway and the hydrogenase on the yield of interesting products like hydroxybutyrate. We provide a drawing of a subset of the metabolic network that may be utilized to project flux distributions onto by the community in future works. Furthermore, we make all the code leading to the results discussed here publicly available for the benefit of future work. ? 2017Item Chromosomal location of non-hypersensitive leaf rust resistance genes in bread wheat cultivar PBW65 using microsatellite markers(2012) Khan, M.A.; Kamaluddin, Saini, R.G.Microsatellite or simple sequence repeat (SSRs) markers have been powerful tool for genetic mapping in wheat. Indian bread wheat (Triticum aestivum L.) cultivar PBW65 has shown significant level of resistance to most virulent race 77-5 of leaf rust (Puccinia triticina). It has been indicated that PBW65 expresses non-hypersensitive type of resistance against race 77-5. F2 and F3 crossing of PBW65 with WL711, a leaf rust susceptible wheat cultivar, and allelic tests with such already known genes (present in cultivars RL 6058 and HD 2009) revealed that cultivar PBW65 could be a potential source of novel nonhypersensitive leaf rust resistance genes. So far, only non-hypersensitive leaf rust resistance gene Lr34 was found to be effective under Indian conditions. Attempts to locate such durable leaf rust resistance genes in PBW65 through microsatellite markers showed 2B, 2D and 3D as critical chromosomes for PBW65. The primer Xgwm341 (3D) was found located 41.5 cM away from gene LrPBW1 in PBW65.