42 results on '"Singh, Alla"'
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2. Fungal Secretomes of Aspergillus terreus Repertoires Cultivated on Native and acid/alkali Treated Paddy Straw for Cellulase and Xylanase Production
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Kaur, Gurkanwal, Taggar, Monica Sachdeva, Kalia, Anu, Krishania, Meena, and Singh, Alla
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- 2024
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3. Cloning, characterization and evaluation of toxicity of newly identified Vip3Aa proteins from Bacillus thuringiensis recovered from diverse environments for biological control of Helicoverpa armigera
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Gupta, Mamta, Kumar, Harish, Kalia, Vinay K., Singh, Satnam, Singh, Alla, Debbarma, Ashika, and Kaur, Sarvjeet
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- 2024
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4. Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India
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Choudhary, Mukesh, Singh, Alla, Das, MM, Kumar, Pardeep, Naliath, Ritu, Singh, Vishal, Kumar, Bhupender, and Rakshit, Sujay
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- 2023
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5. Beyond colors: The health benefits of maize anthocyanins
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Bhushan, Bharat, Kumar, Satish, Kaur, Charanjeet, Devi, Veena, Chaudhary, Dharam Paul, Singh, Alla, Dagla, Manesh Chander, Karjagi, Chikkappa Gangadhar, Saleena, Lejaniya Abdul Kalam, Chandran, Deepak, and Kumar, Manoj
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- 2024
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6. Surveying the genomic landscape of silage-quality traits in maize (Zea mays L.)
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Sharma, Jatin, Sharma, Shubham, Sai Karnatam, Krishna, Prakash Raigar, Om, Lahkar, Chayanika, Kumar Saini, Dinesh, Kumar, Sushil, Singh, Alla, Kumar Das, Abhijit, Sharma, Priti, and Kumar, Ramesh
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- 2023
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7. FTIR spectra, antioxidant capacity and degradation kinetics of maize anthocyanin extract under variable process conditions
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Bhushan, Bharat, Bibwe, Bhushan, Pal, Ajay, Mahawar, Manoj Kumar, Dagla, Manesh Chander, KR, Yathish, Jat, Bahadur Singh, Kumar, Pardeep, Aggarwal, Sumit Kumar, Singh, Alla, and Chaudhary, Dharam Paul
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- 2023
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8. A Rapid Single Kernel Screening Method for Preliminary Estimation of Amylose in Maize
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Dhir, Akanksha, Kaur, Charanjeet, Devi, Veena, Singh, Alla, Das, Abhijit K., Rakshit, Sujay, and Chaudhary, Dharam Paul
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- 2022
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9. Characterization and evaluation of extracellular hydrolytic proteins from rhizobacterial antagonists isolated from Fusarium oxysporum f. sp. ciceris infected chickpea fields
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Kumari, Suman, Khanna, Veena, and Singh, Alla
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- 2022
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10. A comparative evaluation of the effects of seed invigoration treatments with precursor zinc salt and nano-sized zinc oxide (ZnO) particles on vegetative growth, grain yield, and quality characteristics of Zea mays
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Tondey, Manisha, Kalia, Anu, Singh, Alla, Abd-Elsalam, Kamel, Hassan, Montaser M., and Dheri, Gurmeet Singh
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- 2022
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11. Pretreatment and saccharification of corn cobs using partially purified fungal ligninozymes.
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Reddy, Kandukuri Thanuja, Kocher, Gurvinder Singh, and Singh, Alla
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CORNCOBS ,CELLULASE ,LIGNOCELLULOSE ,ION exchange chromatography ,MANGANESE peroxidase ,EXTRACELLULAR enzymes ,PHANEROCHAETE chrysosporium - Abstract
Corn cobs consist primarily of a lignocellulosic material comprising hemicellulose, cellulose, and lignin in a crystalline state, which is resistant to microbial saccharification. Bioethanol production from corn cobs has rarely been attempted, especially using chemical pretreatment methods. The present study deals with the production and purification of fungal (Phanerochaete chrysosporium MTCC 787 and Pleurotus florida PAU 22‐01) extracellular ligninolytic enzymes – lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac) – followed by their utilization for the biological pretreatment of corn cobs along with saccharification using commercial cellulase. Crude LiP, MnP, and Lac demonstrated specific activity of 2.23, 2.1, and 2.63 U/mg, respectively. The one‐step purification of crude enzyme using diethyl amino ethyl (DEAE) cellulose ion exchange chromatography resulted in 11.3, 10.1 and 8.62‐fold purification of LiP, MnP and Lac activity, respectively, with corresponding specific activity of 25.1 U/mg (LiP), 21.2 U/mg (MnP) and 22.7 U/mg (Lac) in the partially purified ligninozymes. Using the latter, biological pretreatment of 2.5 g corn cobs in a reaction volume of 30 mL containing approximately 200 units of Lac, Lip and MnP enzymes (in phosphate buffer, pH 6) resulted in a maximum of 78.4% delignification with a saccharification efficiency of 97.1% using commercial cellulases. [ABSTRACT FROM AUTHOR]
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- 2024
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12. Meta-QTL analysis for mining of candidate genes and constitutive gene network development for fungal disease resistance in maize (Zea mays L.)
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Gupta, Mamta, Choudhary, Mukesh, Singh, Alla, Sheoran, Seema, Singla, Deepak, and Rakshit, Sujay
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- 2022
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13. Introgression of the low phytic acid locus (lpa2) into elite maize (Zea mays L.) inbreds through marker-assisted backcross breeding (MABB)
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Yathish, K. R., Karjagi, Chikkappa Gangadhar, Gangoliya, Shivraj Singh, Kumar, A., Preeti, J., Yadav, Hemant Kumar, Srivastava, Shraddha, Kumar, Santosh, Swamy, H. K. M., Singh, Alla, Phagna, Ramesh Kumar, Das, Abhijit Kumar, Sekhar, Javaji Chandra, Hossain, Firoz, Rakshit, Sujay, and Gadag, Ravindra N.
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- 2022
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14. Genetically modified crops : current status and future prospects
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Kumar, Krishan, Gambhir, Geetika, Dass, Abhishek, Tripathi, Amit Kumar, Singh, Alla, Jha, Abhishek Kumar, Yadava, Pranjal, Choudhary, Mukesh, and Rakshit, Sujay
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- 2020
15. Unraveling the role of δ‐zeins in methionine bio‐fortification of maize.
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Devi, Veena, Sethi, Mehak, Singh, Alla, and Chaudhary, Dharam P.
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Background and Objectives: Maize is a major ingredient of animal feed. However, its nutritional quality is poor due to the deficiency of essential amino acid methionine. The animal feed, prepared as a corn–legume mixture to balance the nutritional quality, remains deficient in methionine. Therefore, the bio‐fortification of maize for methionine is the best option to make nutritionally balanced animal and poultry feed. The present study was designed to evaluate the profile of zeins and the expression profile of methionine‐associated target genes in high‐ and low‐methionine maize. Findings: Results of sodium dodecyl sulfate‐polyacrylamide gel electrophoresis revealed that the 10‐kDa zein was accumulated during kernel development, and its accumulation was higher in high methionine lines. Gene expression analysis through real‐time polymerase chain reaction revealed that higher expression of 10‐ and 18‐kDa zeins is associated with higher methionine accumulation. Conclusions: The above results indicate that 10‐ and 18‐kDa genes are the potential targets for the methionine bio‐fortification in maize, which is required for animal and poultry feed. Significance and Novelty: The present study suggests that 10‐ and 18‐kDa genes are the major source of methionine, and the regulation of these genes is crucial to enhancing the methionine content in maize. The results indicate that these genes are potential targets for genetic engineering in maize to enhance methionine accumulation. [ABSTRACT FROM AUTHOR]
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- 2024
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16. Expression profile of protein fractions in the developing kernel of normal, Opaque-2 and quality protein maize
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Sethi, Mehak, Singh, Alla, Kaur, Harmanjot, Phagna, Ramesh Kumar, Rakshit, Sujay, and Chaudhary, Dharam Paul
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- 2021
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17. Temporal profiling of essential amino acids in developing maize kernel of normal, opaque-2 and QPM germplasm
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Sethi, Mehak, Kumar, Sanjeev, Singh, Alla, and Chaudhary, Dharam Paul
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- 2020
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18. Elucidation of zein isoforms associated with high protein quality traits for targeted improvement in maize‐based nutrition.
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Sethi, Mehak, Singh, Alla, Garg, Monika, Chunduri, Venkatesh, Kumar, Parminder, Devi, Veena, Hossain, Firoz, Phagna, Ramesh K., Gupta, Mamta, and Chaudhary, Dharam P.
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Background and Objectives: Zein proteins of maize endosperm are nutritionally poor, but important for vitreous kernel texture. The Opaque‐2 mutation enhances the protein quality but downregulates zein expression, distorting the kernel texture. Quality protein maize (QPM) is nutritionally improved, hard endosperm maize developed by introgression of endosperm modifiers under an opaque‐2 background. The present study aims to analyze the variability in zein expression patterns in normal, opaque‐2, and QPM lines through sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and two‐dimensional gel electrophoresis analyses. Findings: Results revealed that the total number of zein isoforms is almost similar in opaque‐2, normal, and QPM lines. Overall, in this study, it is concluded that the opaque‐2 mutation specifically affects the expression of high‐molecular‐weight zeins, which are being counterbalanced by the expression of low‐molecular‐weight zein isoforms and nonzein proteins. Conclusion: Genomic data retrieval studies revealed the possible presence of multiple 27 kDa isoforms with varied isoelectric points (pI), which is a subject for further investigation. The differential expression of 15 kDa zein in QPM emerged as a novel player in endosperm modification. Significance and Novelty: The present study provides insight into the diversified expression of zeins in different maize types. The variable isoform expression has the potential to generate stable QPM lines by targeting effective isoforms, ensuring endosperm modification without hampering the nutritional quality. [ABSTRACT FROM AUTHOR]
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- 2024
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19. Minimally altering a critical kinase for low-phytate maize
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Singh, Alla, Karjagi, Chikkappa, and Rakshit, Sujay
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- 2020
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20. Unravelling the genetic framework associated with grain quality and yield-related traits in maize (Zea mays L.).
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Sethi, Mehak, Saini, Dinesh Kumar, Devi, Veena, Kaur, Charanjeet, Singh, Mohini Prabha, Singh, Jasneet, Pruthi, Gomsie, Kaur, Amanpreet, Singh, Alla, and Chaudhary, Dharam Paul
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CORN ,RICE ,LOCUS (Genetics) ,WHEAT ,GENOME-wide association studies ,GENETIC engineering ,GENOME editing - Abstract
Maize serves as a crucial nutrient reservoir for a significant portion of the global population. However, to effectively address the growing world population’s hidden hunger, it is essential to focus on two key aspects: biofortification of maize and improving its yield potential through advanced breeding techniques. Moreover, the coordination of multiple targets within a single breeding program poses a complex challenge. This study compiled mapping studies conducted over the past decade, identifying quantitative trait loci associated with grain quality and yield related traits in maize. Meta-QTL analysis of 2,974 QTLs for 169 component traits (associated with quality and yield related traits) revealed 68 MQTLs across different genetic backgrounds and environments. Most of these MQTLs were further validated using the data from genome-wide association studies (GWAS). Further, ten MQTLs, referred to as breeding-friendly MQTLs (BF-MQTLs), with a significant phenotypic variation explained over 10% and confidence interval less than 2 Mb, were shortlisted. BF-MQTLs were further used to identify potential candidate genes, including 59 genes encoding important proteins/products involved in essential metabolic pathways. Five BF-MQTLs associated with both quality and yield traits were also recommended to be utilized in future breeding programs. Synteny analysis with wheat and rice genomes revealed conserved regions across the genomes, indicating these hotspot regions as validated targets for developing biofortified, high-yielding maize varieties in future breeding programs. After validation, the identified candidate genes can also be utilized to effectively model the plant architecture and enhance desirable quality traits through various approaches such as marker-assisted breeding, genetic engineering, and genome editing. [ABSTRACT FROM AUTHOR]
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- 2023
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21. Genetic and molecular understanding for the development of methionine-rich maize: a holistic approach.
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Devi, Veena, Bhushan, Bharat, Gupta, Mamta, Sethi, Mehak, Kaur, Charanjeet, Singh, Alla, Singh, Vishal, Kumar, Ramesh, Rakshit, Sujay, and Chaudhary, Dharam P.
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ESSENTIAL amino acids ,LOCUS (Genetics) ,SYNTHETIC genes ,NATURAL selection ,SEED proteins ,CORN ,SEED storage - Abstract
Maize (Zea mays) is the most important coarse cereal utilized as a major energy source for animal feed and humans. However, maize grains are deficient in methionine, an essential amino acid required for proper growth and development. Synthetic methionine has been used in animal feed, which is costlier and leads to adverse health effects on end-users. Bio-fortification of maize for methionine is, therefore, the most sustainable and environmental friendly approach. The zein proteins are responsible for methionine deposition in the form of d-zein, which are major seed storage proteins of maize kernel. The present review summarizes various aspects of methionine including its importance and requirement for different subjects, its role in animal growth and performance, regulation of methionine content in maize and its utilization in human food. This review gives insight into improvement strategies including the selection of natural high-methionine mutants, molecular modulation of maize seed storage proteins and target key enzymes for sulphur metabolism and its flux towards the methionine synthesis, expression of synthetic genes, modifying gene codon and promoters employing genetic engineering approaches to enhance its expression. The compiled information on methionine and essential amino acids linked Quantitative Trait Loci in maize and orthologs cereals will give insight into the hotspot-linked genomic regions across the diverse range of maize germplasm through meta-QTL studies. The detailed information about candidate genes will provide the opportunity to target specific regions for gene editing to enhance methionine content in maize. Overall, this review will be helpful for researchers to design appropriate strategies to develop highmethionine maize. [ABSTRACT FROM AUTHOR]
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- 2023
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22. Development of low-phytate maize inbred lines through marker-assisted introgression of lpa1.
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Yathish, K. R., Karjagi, Chikkappa G., Gangoliya, Shivraj S., Gadag, Raveendra N., Mallikarjuna, M. G., Sekhar, Javaji C., Das, Abhijit K., Lakshmi Soujanya, P., Kumar, Ramesh, Singh, Alla, Singh, Shyam Bir, and Rakshit, Sujay
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CORN breeding ,PHYTIC acid ,SINGLE nucleotide polymorphisms ,CORN ,MICROSATELLITE repeats ,INBREEDING ,ALIMENTARY canal - Abstract
Context: Phytic acid is the major storage form of phosphorus in cereals and is considered an anti-nutritional factor because it chelates major mineral micronutrient cations, resulting in micronutrient malnutrition in humans. For monogastric animals fed maize (Zea mays L.) grains, the stored phosphorus does not release into the digestive tract, leading to phosphorus deficiency and environmental pollution. Aims: The aim of the study was to develop maize lines with a lower level of phytic acid that might substantially enhance the nutritional value of maize. Methods: The lpa1 mutant allele conferring low phytic acid was transferred into the parental lines of popular maize hybrid DMH 121 (i.e. BML 6 and BML 45) through marker-assisted backcross breeding. Foreground selection was performed using a co-dominant single nucleotide polymorphism marker through a high-resolution melting approach, and background selection was undertaken using 50–55 polymorphic sequence-tagged microsatellite site markers. Key results: Near-isogeneic lines were produced with >90% recurrent parental genome and reduction of phytic acid content by up to 44–56% compared with the original lines. Conclusions: The near-isogeneic lines carrying lpa1 can be used to reconstitute DHM 121 with low phytate content. Implications: The low-phytate maize hybrids produced can be useful in reducing micronutrient malnutrition in humans, as well as environmental pollution. Phytic acid is an anti-nutritional factor that chelates major mineral micronutrient cations, resulting in micronutrient malnutrition in humans. In this study, the lpa1 mutant allele was transferred into the parental lines of DMH 121 (i.e BML 6, and BML 45) through marker-assisted backcross breeding. Near-isogeneic lines were produced with 44–56% reduction of phytic acid content relative to the original lines. [ABSTRACT FROM AUTHOR]
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- 2023
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23. Chapter 16 - Role of phospholipase D in abiotic stress tolerance
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Bhushan, Bharat, Jat, Bahadur Singh, Kumar, Satish, Pal, Ajay, Dagla, Manesh Chander, Kumar, Pardeep, Singh, Alla, Aggarwal, Sumit Kumar, and Chaudhary, Dharam Paul
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- 2023
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24. 21 - Posttranslational modifications and metal stress tolerance in plants
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Singh, Alla, Gupta, Mamta, Kumar, Sunil, Chawla, Hiroshi, Mehra, Mathanki, Kumar, Krishan, Jat, Bahadur Singh, and Bhushan, Bharat
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- 2023
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25. Meta-QTL analysis for mining of candidate genes and constitutive gene network development for fungal disease resistance in maize (Zea mays L.).
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Gupta, Mamta, Choudhary, Mamta, Singh, Alla, Sheoran, Seema, Singla, Deepak, and Rakshit, Sujay
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CORN yields ,CORN genetics ,FUNGAL diseases of plants ,PLANT germplasm ,COMPUTER algorithms - Abstract
The development of resistant maize cultivars is the most effective and sustainable approach to combat fungal diseases. Over the last three decades, many quantitative trait loci (QTL) mapping studies reported numerous QTL for fungal disease resistance (FDR) in maize. However, different genetic backgrounds of germplasm and differing QTL analysis algorithms limit the use of identified QTL for comparative studies. The meta-QTL (MQTL) analysis is the meta-analysis of multiple QTL experiments, which entails broader allelic coverage and helps in the combined analysis of diverse QTL mapping studies revealing common genomic regions for target traits. In the present study, 128 (33.59%) out of 381 reported QTL (from 82 studies) for FDR could be projected on the maize genome through MQTL analysis. It revealed 38 MQTL for FDR (12 diseases) on all chromosomes except chromosome 10. Five MQTL namely 1_4, 2_4, 3_2, 3_4, and 5_4 were linked with multiple FDR. Total of 1910 candidate genes were identified for all the MQTL regions, with protein kinase gene families, TFs, pathogenesis-related, and disease-responsive proteins directly or indirectly associated with FDR. The comparison of physical positions of marker-traits association (MTAs) from genome-wide association studies with genes underlying MQTL interval verified the presence of QTL/candidate genes for particular diseases. The linked markers to MQTL and putative candidate genes underlying identified MQTL can be further validated in the germplasm through marker screening and expression studies. The study also attempted to unravel the underlying mechanism for FDR resistance by analyzing the constitutive gene network, which will be a useful resource to understand the molecular mechanism of defense-response of a particular disease and multiple FDR in maize. [ABSTRACT FROM AUTHOR]
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- 2023
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26. Characterization of phi112, a Molecular Marker Tightly Linked to the o2 Gene of Maize, and Its Utilization in Multiplex PCR for Differentiating Normal Maize from QPM.
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Singh, Alla, Karjagi, Chikkappa, Kaur, Sehgeet, Jeet, Gagan, Bhamare, Deepak, Gupta, Sonu, Kumar, Sunil, Das, Abhijit, Gupta, Mamta, Chaudhary, D. P., Bhushan, Bharat, Jat, B. S., Kumar, Ramesh, Dagla, M. C., and Kumar, Manoj
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ESSENTIAL amino acids , *MOLECULAR interactions , *TRANSCRIPTION factors , *CORN diseases , *CORN , *PROTEIN synthesis , *POLYMERASE chain reaction - Abstract
Quality Protein Maize (QPM) contains higher amounts of essential amino acids lysine and tryptophan. The QPM phenotype is based on regulating zein protein synthesis by opaque2 transcription factor. Many gene modifiers act to optimize the amino acid content and agronomic performance. An SSR marker, phi112, is present upstream of the opaque2 DNA gene. Its analysis has shown the presence of transcription factor activity. The functional associations of opaque2 have been determined. The putative transcription factor binding at phi112 marked DNA was identified through computational analysis. The present study is a step towards understanding the intricate network of molecular interactions that fine-tune the QPM genotype to influence maize protein quality. In addition, a multiplex PCR assay for differentiation of QPM from normal maize is shown, which can be used for Quality Control at various stages of the QPM value chain. [ABSTRACT FROM AUTHOR]
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- 2023
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27. Potential use of random and linked SSR markers in establishing the true heterotic pattern in maize (Zea mays).
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Kumar, Sumit, Das, Abhijit Kumar, Naliath, Ritu, Kumar, Ramesh, Karjagi, Chikkappa G., Sekhar, Javaji C., Vayas, Mukesh, Yathish, K. R., Singh, Alla, Mukri, Ganapati, and Rakshit, Sujay
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CORN breeding ,GENOTYPE-environment interaction ,MICROSATELLITE repeats ,GENETIC distance ,GENETIC variation ,CORN - Abstract
Context: Establishment of true heterotic pattern in maize germplasm can increase the efficiency of hybrid breeding. Heterosis is dependent on the genetic diversity of parents and the extent of dominance at different loci. Estimation of genetic diversity through use of molecular markers is routine practice in maize breeding. Aims: The present study was designed to test whether simple sequence repeat (SSR) markers linked to yield-contributing traits are more reliable for heterotic grouping than random SSRs. Methods: Diallel crosses developed among 19 inbred lines were evaluated at multi-locations. The genotypes were also grouped using polymorphic random (50) and linked (47) SSRs. Key results: The crosses generated with lines belonging to different heterotic groups of linked SSR markers did not reveal any superiority over the crosses of the diallel set. By contrast, mean performance of inter-heterotic group crosses generated on the basis of random markers was superior to that of intra-heterotic crosses. Specific combining ability effects did not reveal any significant association with genetic distance of random or linked markers. Conclusions: The lack of improved efficiency of linked markers over random markers can be attributed to factors including the quantitative nature of the trait, genotype × environment interactions, genetic background of germplasm in which the markers are expressed, and multiple alleles. Implications: Markers linked to yield-contributing traits are no more reliable for heterotic grouping than random markers. Establishment of true heterotic pattern in maize germplasm can increase the efficiency of hybrid breeding, and therefore, it is useful to compare efficiency of SSRs linked to yield-related traits with that of random SSRs for heterotic grouping. Mean performance of inter-heterotic group crosses generated on the basis of random markers was superior to that of intra-heterotic crosses. Specific combining ability effects did not reveal significant association with genetic distance of random or linked markers. [ABSTRACT FROM AUTHOR]
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- 2022
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28. SEQUENTIAL FERMENTATION OF ORGANOSOLV PRETREATED CORN STOVER FOR IMPROVED CELLULOSE HYDROLYSIS AND BIOETHANOL YIELD.
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Gill, Mandeep Kaur, Kocher, Gurvinder Singh, and Singh, Alla
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CORN stover ,ETHANOL as fuel ,FERMENTATION ,CELLULOSE ,ETHANOL ,HYDROLYSIS ,ACETIC acid - Abstract
In this study, organosolv pretreatment of corn stover using 40% acetic acid was investigated for its amenability for enzymatic saccharification and bioethanol production. The pretreated corn stover resulted in 63.4±1.7% solids, 46.4±2.5% hemicellulose and 53.7±2.1% cellulose recoveries with 84.6% delignification. The reducing sugars of 0.107g/gds (107/Kg) released during pretreatment can be fermented to produce 0.125ml/gds (125ml/Kg) bioethanol. The saccharification of pretreated biomass under optimized conditions released 0.395g/gds reducing sugars, which upon subsequent fermentation by Saccharomyces cerevisiae and Pachysolen tannophilus produced 0.112g/gds (140ml/Kg) ethanol, with 66.54% fermentation efficiency and 33.9% ethanol yield (YPS), under separate hydrolysis and fermentation (SHF) conditions. The net price for the bioconversion of 1Kg corn stover for bioethanol (265 ml) production was calculated to be Rs. 144.3/L of ethanol. This price is high being calculated on laboratory scale (1Kg) and will decrease substantially upon upscaling. [ABSTRACT FROM AUTHOR]
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- 2022
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29. Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives.
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Aggarwal, Sumit Kumar, Singh, Alla, Choudhary, Mukesh, Kumar, Aundy, Rakshit, Sujay, Kumar, Pardeep, Bohra, Abhishek, and Varshney, Rajeev K.
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WHOLE genome sequencing , *GENE mapping , *GENETIC variation , *GENE targeting , *PLANT diversity - Abstract
Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems. [ABSTRACT FROM AUTHOR]
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- 2022
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30. Contributors
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Abbas Bukhari, Syed Nasir, Abhilash, M., Abinaya, K., Adefegha, Stephen A., Adeleke, Oluwakemi V., Aggarwal, Sumit Kumar, Arni, Raghuvir Krishnaswamy, Azam, Mohammad, Baldissera, Antonielle, Bano, Sarika, Bedir, Ipek, Bhatt, Lokesh Kumar, Bhushan, Bharat, Binu, P., Castelli, María Eugenia, Cerminati, Sebastián, Chakraborti, Sajal, Chakraborti, Tapati, Chaudhary, Dharam Paul, Chaurasiya, Shivendra K., Clarke, Christopher J., Correa, Fernando, Dagla, Manesh Chander, De Laurentiis, Andrea, de Oliveira Leite, Isabel, Devadasan, Velmurugan, Dey, Sanjay Kumar, Dhalla, Naranjan S., Ejike, Uju Dorathy Iliemene, Etcheverry, Tomás, Farina, Mariana, Fujita, Masaaki, Ghandour, Botheina, Ghumman, Shazia Akram, Gismene, Carolina, Gonzalez, Jorge Enrique Hernandez, Gremski, Luiza Helena, Hails, Guillermo, Hannun, Yusuf A., Hasan, Sara, Ijaz, Bushra, Jain, Kripa, Jat, Bahadur Singh, Jiang, Xian-Cheng, Jiménez, Jaime Andrés Pereañez, Kumar, Pardeep, Kumar, Satish, Lacava, Franco Emanuel, Liman, Mubarak Labaran, Lo Vasco, Vincenza Rita, Marchisio, Fiorela, Mariutti, Ricardo Barros, Mathew, Bijina J., Matsubara, Fernando Hitomi, Menzella, Hugo Gabriel, Mohammed, Samia, Molehin, Olorunfemi R., Mondal, Kausik, Murakami, Makoto, Muthezhilan, R., Nair, R. Harikumaran, Naz, Anjum, Nezir, Ayca Ece, Noreen, Sobia, Olonishuwa, Paul T., Onal, Meltem Selen, Ozturk, Kaan, Pal, Ajay, Pandey, Amit Kumar, Paoletti, Luciana, Polli, Nayanne Louise Costacurta, Puviarasan, K., Rai, Rupal, Raman, Pachaiappan, Ren, Jihui, Ruwali, Munindra, Senff-Ribeiro, Andrea, Sengupta, Sayan, Singh, Alla, Singh, Amarjeet, Singh, Vinayak, Sonkar, Kamankshi, Takada, Yoko K., Takada, Yoshikazu, Taketomi, Yoshitaka, Tan, Choo Hock, Tan, Kae Yi, Tappia, Paramjit S., Telci, Dilek, Vadak, Namrata, Val, Diego S., Varghese, Mathews V., and Veiga, Silvio Sanches
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- 2023
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31. List of contributors
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Aamir, Mohd, Aftab, Tariq, Agarwala, Niraj, Ahmad, Imran, Aqeel, Umra, Arora, Bhumika, Barman, Ramen, Benavides, María Patricia, Bhardwaj, Renu, Bhola, Latika, Bhushan, Bharat, Bilias, Fotis, Bokolia, Muskan, Cabrera, Andrea Viviana, Carillo, Petronia, Chauhan, Nar Singh, Chávez-Martínez, Ana Isabel, Chawla, Hiroshi, Deepa, Dogra, Neha, Farouk, Saad, Garg, Tashima, Gasparatos, Dionisios, Giannakopoulou, Foteini, Gill, Ritu, Gill, Sarvajeet Singh, Giri, Shiv Kumar, Goel, Sonia, Grewal, Sapna, Groppa, María Daniela, Guerrero-González, María de la Luz, Gupta, Mamta, Hasan, Mahmodol, Hossain, Anwar, Ipsilantis, Ioannis, Islam, S.M. Shahinul, Itoh, Kimiko, Jat, Bahadur Singh, Jiménez-Bremont, Juan Francisco, Joshi, Anjali, Kalderis, Dimitrios, Kalwan, Gopal, Kashyap, Sampurna, Kaur, Gurvarinder, Kaur, Harpreet, Kaur, Simranjeet, Kaushik, Shruti, Khan, Nafees A., Koutsougera, Dimitra, Kumar, Adarsh, Kumar, Anil, Kumar, Avneesh, Kumar, Krishan, Kumar, Manoj, Kumar, Sunil, Kumar, Vinay, Kumari, Santosh, Kundu, Punam, Kushwaha, Aparna Singh, Madaan, Isha, Maman, Shalma, Maury, Jayhind, Mehra, Mathanki, Mishra, Pallavi, Naeem, M., Nath, Manabendra, Neha, Nehra, Ashima, Ortega-Amaro, Maria Azucena, Papa, Stefania, Priya, Kanu, Rana, Varnika, Recalde, Laura, Rodríguez-Kessler, Margarita, Rouphael, Youssef, Saini, Neha, Sharaya, Ritu, Sharma, Bhaskar, Sharma, Pinki, Sharma, Sandeep, Shilpa, Shukla, Jagriti, Sidhu, Anmol, Singh, Alla, Singh, Gulab, Singh, Kulwinder, Singh, Pooja, Singh, Rajesh Kumar, Singh, Reetu, Singh, Shruti, Sirhindi, Geetika, Soni, Udit, Tuteja, Narendra, Tyagi, Aditya, Tyagi, Swati, Verma, Neha, Walia, Aniket, and Zafeiriou, Ioannis
- Published
- 2023
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32. Coping with low moisture stress: Remembering and responding.
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Choudhary, Mukesh, Singh, Alla, and Rakshit, Sujay
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- *
DROUGHTS , *PSYCHOLOGICAL adaptation , *DROUGHT tolerance , *MOISTURE , *ARID regions , *MEMORY - Abstract
Low-moisture stress, also referred to as drought, is one of the major factors that negatively impact the agricultural yield. The present scenario of climate change is expected to aggravate it further. Considering the extended time required to develop resistant crops, it is important to prioritize research efforts for coping with low moisture, prevalent in arid and semi-arid regions of the world. While agricultural yield is a tradeoff between many choices, tolerance to biotic and abiotic stresses comes with yield penalties. To balance the tradeoffs and maximize productivity, the use of region-specific cultivars and/or introgression of precise genetic proportions in an elite variety may prove useful. Stress memory is an emerging approach that helps plants to record and respond to repeated stress in an effective manner. In this context, we discuss the role of "stress memory" in imparting drought tolerance in plants. Future research efforts for its effective deployment for "drought hardening" in agricultural settings, along with a discussion on the yield tradeoff involved, is implicated. [ABSTRACT FROM AUTHOR]
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- 2021
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33. Heterosis in Genomic Era: Advances in the Molecular Understanding and Techniques for Rapid Exploitation.
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Das, Abhijit Kumar, Choudhary, Mukesh, Kumar, Pardeep, Karjagi, Chikkappa G, KR, Yathish, Kumar, Ramesh, Singh, Alla, Kumar, Santosh, and Rakshit, Sujay
- Subjects
COMPLEMENTATION (Genetics) ,HETEROSIS ,CLOCK genes ,MOLECULAR clock ,REGULATOR genes ,CORN ,HETEROSIS in plants - Abstract
Heterosis has been widely exploited in plants and animals, and also revolutionized agriculture by improving important agronomic traits. However, the molecular mechanism is still remaining elusive. Though different classical models, viz., dominance, overdominance and epistasis still holds true, the recent studies on epigenomics, transcriptomic, proteomic, metabolomics and circadian model have provided new insights. Multigene models have been proposed as the basis of complementation of allelic and gene expression variation, which is a major probable contributor to heterosis. The evolving epigenetic and genomic field put forward the role of interaction of alleles from different parental genomes in reprogramming the genes involved in stress tolerance, fitness and growth of hybrids. In the majority of the studies, transcriptomic, proteomic and metabolomic studies have found many complex regulatory network changes in genetic, epigenetic, regulatory and biochemical levels and only a few patterns could be established. Thus, heterosis is the outcome of the series of interactions in the genomes. Furthermore, epigenetic modifications of the circadian clock genes and their reciprocal regulators were reported to regulate the expression of downstream genes and pathways leading to more product accumulation in hybrids. Moreover, the majority of the epigenetic studies are limited to Arabidopsis thaliana and Zea mays, however, such studies on different crops may further bring more insights on the role of epigenetic mechanisms in determining heterosis. Further, none of the models is capable to explain heterosis alone which reflects the limitations of the individual model. The present review critically assesses different theories from different fields and also unravels the existing rapid methods to exploit them. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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34. Enabling technologies for utilization of maize as a bioenergy feedstock.
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Choudhary, Mukesh, Singh, Alla, Gupta, Mamta, and Rakshit, Sujay
- Subjects
- *
RESEARCH & development , *ALTERNATIVE fuels , *CORN , *SWITCHGRASS , *FOSSIL fuels , *CORN stover , *CORN breeding , *FOOD security - Abstract
Limited supplies of fossil fuels have led to a search for alternative sources of fuel to drive economic growth. Maize, and especially the grain portion, has been utilized to a large extent for biofuel production while the abundant lignocellulosic portion has remained underexplored owing to its recalcitrant nature. The diversion of grain for bioethanol production has consequences for food security. However, the lignocellulosic portion can easily be directed for ethanol production without any consequences for food security. Maize has emerged as the leading crop in the last decade and hence provides a vast amount of grain and biomass. Biomass quantity and its digestibility are the two key traits for efficient biofuel production. Significant variation has been reported for these traits in maize. The brown midrib mutants (bm) of maize, with reduced lignin content, can be exploited for the development of cultivars with better digestibility. Recent advances in genetics and genomics revealed key genomic regions associated with biomass‐contributing traits. The molecular markers associated with the identified genomic regions can be utilized for marker‐aided development of cultivars with high biomass and better digestibility. Advances in phenomics have also facilitated bioethanol‐targeted breeding in maize. Biorefining uses feedstock as input and processes it into biofuel. In this review, the improvement of maize as a feedstock and biological conversion strategies of lignocellulosic biomass are assessed. Research and development platforms to enable improvements in feedstock and biological processing are also discussed. © 2019 Society of Chemical Industry and John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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35. Analysis of granule-associated Starch branching enzyme IIb, involved in amylose extender mutation of maize.
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Singh, Alla, Chaudhary, D. P., Kumar, Ramesh, and Rakshit, Sujay
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- *
STARCH , *AMYLOSE , *PULLULANASE , *CORNSTARCH , *CORN , *SIGNAL recognition particle receptor , *ENZYMES - Abstract
Maize starch is an important industrial commodity. Starch synthase, phosphorylase, branching and debranching enzymes act in concert and results in a particular starch architecture. Starch branching enzymes play an important role in defining the overall starch structure. In maize endosperm, Starch branching enzyme IIb is predominant. The computational structure of Starch branching enzyme IIb has been determined. The putative substrate binding site and active site pore channel have been elucidated. As the enzyme is known to prefer amylopectin as substrate, the disachharide melibiose containing α- 1,6 glycosidic bond was docked on the modelled protein. The substrate binding site and active site channel has been discussed. Understanding of starch structure is essential for its modification and processing in forms, that are desirable for specific end-use applications. Generation of feedstock specific for a particular starch modification would result in environmentally-friendly starch production system by minimizing the requirement of chemicals for starch modifications. This is also necessary for allele mining to direct further breeding goals in this area. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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36. Insight into the functional role of unique determinants in RNA component of RNase P of Mycobacterium tuberculosis.
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Singh, Alla and Batra, Janendra K.
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- *
RNA , *MYCOBACTERIUM tuberculosis - Abstract
Abstract RNase P, an essential ribonucleoprotein enzyme is involved in processing 5′ end of pre-tRNA molecules. All bacterial RNase P holoenzymes, including that of Mycobacterim tuberculosis , an important human pathogen contain a catalytically active RNA subunit and a protein subunit. However, the mycobacterial RNA is larger than typical bacterial RNase P RNAs. It contains the essential core structure and many unique features in the peripheral elements. In the current study, an extensive mutational analysis was performed to analyze the function of the unique features in P12, P15.A, P18 and P19 helices in the mycobacterial RNase P RNA. The study demonstrates that P12 interacts with monovalent and divalent ions and is important for the function of mycobacterial holoenzyme. The helices, P15.A and P18 appear to interact with ammonium and magnesium ions, respectively. P19 is involved in the thermostability of the RNA component as well as interaction with ammonium ions. A homology model of M. tuberculosis RNase P RNA indicates many new inter- and intra-helical interactions. The significance of the unique interactions paves way towards understanding the differential functioning of M. tuberculosis RNase P RNA, for exploring specific inhibition of the same in the pathogen to contain infection. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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37. Functional role of putative critical residues in Mycobacterium tuberculosis RNase P protein.
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Singh, Alla, Ubaid-ullah, Shah, and Batra, Janendra K.
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- *
MYCOBACTERIUM tuberculosis , *RIBONUCLEASE P , *TRANSFER RNA , *BACTERIAL proteins , *CATALYTIC activity - Abstract
RNase P is involved in processing the 5′ end of pre-tRNA molecules. Bacterial RNase P contains a catalytic RNA subunit and a protein subunit. In this study, we have analyzed the residues in RNase P protein of M. tuberculosis that differ from the residues generally conserved in other bacterial RNase Ps. The residues investigated in the current study include the unique residues, Val27, Ala70, Arg72, Ala77, and Asp124, and also Phe23 and Arg93 which have been found to be important in the function of RNase P protein components of other bacteria. The selected residues were individually mutated either to those present in other bacterial RNase P protein components at respective positions or in some cases to alanine. The wild type and mutant M. tuberculosis RNase P proteins were expressed in E. coli , purified, used to reconstitute holoenzymes with wild type RNA component in vitro , and functionally characterized. The Phe23Ala and Arg93Ala mutants showed very poor catalytic activity when reconstituted with the RNA component. The catalytic activity of holoenzyme with Val27Phe, Ala70Lys, Arg72Leu and Arg72Ala was also significantly reduced, whereas with Ala77Phe and Asp124Ser the activity of holoenzyme was similar to that with the wild type protein. Although the mutants did not suffer from any binding defects, Val27Phe, Ala70Lys, Arg72Ala and Asp124Ser were less tolerant towards higher temperatures as compared to the wild type protein. The K m of Val27Phe, Ala70Lys, Arg72Ala and Ala77Phe were >2-fold higher than that of the wild type, indicating the substituted residues to be involved in substrate interaction. The study demonstrates that residues Phe23, Val27 and Ala70 are involved in substrate interaction, while Arg72 and Arg93 interact with other residues within the protein to provide it a functional conformation. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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38. Influence of Conformation of M. tuberculosis RNase P Protein Subunit on Its Function.
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Singh, Alla, Ubaid-ullah, Shah, Ramteke, Anup K., and Batra, Janendra K
- Subjects
- *
MYCOBACTERIUM tuberculosis , *RIBONUCLEASE P , *PROTEIN conformation , *NUCLEOTIDE sequence , *TRANSFER RNA , *CATALYTIC activity - Abstract
RNase P is an essential enzyme that processes 5' end leader sequence of pre-tRNA to generate mature tRNA. The bacterial RNase Ps contain a RNA subunit and one protein subunit, where the RNA subunit contains the catalytic activity. The protein subunit which lacks any catalytic activity, relaxes the ionic requirements for holoenzyme reaction and is indispensable for pre-tRNA cleavage in vivo. In the current study, we reconstituted the M. tuberculosis RNase P holoenzyme in vitro. We prepared the RNase P protein through two different strategies that differ in the conditions under which the recombinant M. tuberculosis protein, expressed in E. coli was purified. The mycobacterial RNase P protein which was purified under native conditions subsequent to isolation from inclusion bodies and in vitro renaturation, was capable of cleaving pre-tRNA specifically without the requirement of RNase P RNA. However, the preparation that was purified under denaturing conditions and refolded subsequently lacked any inherent pre-tRNA processing activity and cleaved the substrate only as a component of the holoenzyme with the RNA subunit. We found that the two RNase P protein preparations attained alternative conformations and differed with respect to their stability as well. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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39. Insight into the role of histidine in RNR motif of protein component of RNase P of M. tuberculosis in catalysis.
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Singh, Alla, Ramteke, Anup K., Afroz, Tariq, and Batra, Janendra K.
- Subjects
- *
HISTIDINE , *NUCLEOPROTEINS , *RIBONUCLEASES , *INTRONS , *MYCOBACTERIA - Abstract
RNase P, a ribonucleoprotein endoribonuclease, is involved in the 5′ end processing of pre-tRNAs, with its RNA component being the catalytic subunit. It is an essential enzyme. All bacterial RNase Ps have one RNA and one protein component. A conserved RNR motif in bacterial RNase P protein components is involved in their interaction with the RNA component. In this work, we have reconstituted the RNase P of M. tuberculosis in vitro and investigated the role of a histidine in the RNR motif in its catalysis. We expressed the protein and RNA components of mycobacterial RNase P in E. coli, purified them, and reconstituted the holoenzyme in vitro. The histidine in RNR motif was mutated to alanine and asparagine by site-directed mutagenesis. The RNA component alone showed activity on pre-tRNAala substrate at high magnesium concentrations. The RNA and protein components associated together to manifest catalytic activity at low magnesium concentrations. The histidine 67 in the RNR motif of M. tuberculosis RNase P protein component was found to be important for the catalytic activity and stability of the enzyme. Generally, the RNase P of M. tuberculosis functions like other bacterial enzymes. The histidine in the RNR motif of M. tuberculosis appears to be able to substitute optimally for asparagine found in the majority of the protein components of other bacterial RNase P enzymes. © 2016 IUBMB Life, 68(3):178-189, 2016 [ABSTRACT FROM AUTHOR]
- Published
- 2016
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40. Seed Priming and Coating by Nano-Scale Zinc Oxide Particles Improved Vegetative Growth, Yield and Quality of Fodder Maize (Zea mays).
- Author
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Tondey, Manisha, Kalia, Anu, Singh, Alla, Dheri, Gurmeet Singh, Taggar, Monica Sachdeva, Nepovimova, Eugenie, Krejcar, Ondrej, and Kuca, Kamil
- Subjects
CORN ,ANIMAL feeds ,PLANT biomass ,ZINC coating ,ZINC oxide ,CORN stover ,CORN seeds ,FODDER crops - Abstract
Nano-fertilizers of essential plant nutrients, including micronutrients, have the potential to improve nutrient use efficiency and productivity of field crops in deficient soils. The present study reports the comparative influence of zinc oxide nanoparticles (ZnONPs) and bulk Zn salt (ZnSO
4 ) on the growth, yield, and quality of fodder maize (Zea mays) (var. J-1006) cultivated under field conditions in the year 2019. Three levels (0, 20, and 40 mg L−1 ) of Zn fertilizers were used for seed priming and coating in triplicate following the randomized complete block design model. An increase in vegetative and yield parameters (number of plants, plant height, stover yield, plant biomass), acid detergent fiber (ADF%), and hemicellulose contents and shoot zinc (Zn) content on treatment of seeds with ZnONPs (20 mg L−1 ) concentration as compared to bulk ZnSO4 and control treatments was observed. The application of ZnONPs (40 mg L−1 ) significantly enhanced the total chlorophyll content, available soil nitrogen and phosphorus, neutral detergent fiber (NDF%), and cellulose contents and improved the total soil microbial counts and soil enzyme activities (dehydrogenase, acid and alkaline phosphatase enzyme activities), whereas a significant increase in available soil potassium and zinc contents was recorded under ZnONPs (20 mg L−1 ) treatments. These findings suggest an encouraging effect on the growth and yield attributing characteristics of fodder maize after ZnONPs seed coating at low concentration. Furthermore, ZnONPs seed coating can also be considered an effective tool for the delivery of Zn micronutrient to fodder maize crop. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
41. Corrigendum: Unravelling the genetic framework associated with grain quality and yield-related traits in maize (Zea mays L.).
- Author
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Sethi M, Saini DK, Devi V, Kaur C, Singh MP, Singh J, Pruthi G, Kaur A, Singh A, and Chaudhary DP
- Abstract
[This corrects the article DOI: 10.3389/fgene.2023.1248697.]., (Copyright © 2023 Sethi, Saini, Devi, Kaur, Singh, Singh, Pruthi, Kaur, Singh and Chaudhary.)
- Published
- 2023
- Full Text
- View/download PDF
42. Improvement in nutritional quality of traditional unleavened flat bread using Quality Protein Maize.
- Author
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Kaur N, Kumar R, Singh A, Shobha D, Das AK, Chaudhary D, Kaur Y, Kumar P, Sharma P, and Singh B
- Abstract
Maize grains are consumed majorly in the form of unleavened flat bread ( chapatti ) in the South East Asian region. The landraces are better accepted for their chapatti -making attributes such as grain color and good organoleptic properties. However, these cultivars are low in essential amino acids, particularly lysine and tryptophan content. Hence, an investigation was performed to identify maize genotypes with high nutritional value coupled with good chapatti -making qualities. Seven genotypes, comprising two Quality Protein Maize (QPM) hybrids, two normal maize hybrids, and three normal white maize landraces were assessed for their physical characteristics, proximate composition, and chapatti -making quality. Landrace 593 showed the highest protein and ash content. Flours obtained from different genotypes were significantly different ( p ≤ 0.001) in terms of protein content, color value, textural, as well as mineral content. PMH 10 and IQMH 203 exhibited the highest and lowest hydration index, respectively. Two QPM hybrids showed significantly higher lysine and tryptophan content as compared to other genotypes. QPM hybrids were identified as the promising material with improved nutritional quality with respect to chapatti making. In combination with mustard greens, maize chapatti constitutes an important traditional delicacy in north India. The enhanced nutritional quality of QPM chapattis is an added advantage. We show the differentiation of chapattis made from QPM and normal maize using a rapid protocol developed previously. This is expected to enable the development and quality control of commercial enterprises based on high protein quality QPM., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kaur, Kumar, Singh, Shobha, Das, Chaudhary, Kaur, Kumar, Sharma and Singh.)
- Published
- 2022
- Full Text
- View/download PDF
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