Article
Biochemistry & Molecular Biology
Jose Carlos Montanes, Marta Huertas, Xavier Messeguer, M. Mar Alba
Summary: The formation of new genes can occur through gene duplication or de novo formation from noncoding sequences. Both mechanisms show similarities in terms of low sequence constraints in the initial evolutionary stages, high turnover rates at the species level, and comparable persistence rates in deeper branches. Additionally, de novo proteins tend to have an excess of substitutions between charged amino acids, leading to rapid loss of their initial highly basic character.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Pawandeep Singh Kohli, Lekha T. Pazhamala, Balaji Mani, Jitendra Kumar Thakur, Jitender Giri
Summary: Root hairs are extensions of root epidermal cells that increase in length and density under low phosphorus availability. This study explores the genes involved in root hair development and response to low phosphorus in chickpea, an important leguminous crop. The findings reveal that genes related to root hair initiation and cellular differentiation are upregulated, and genes involved in cell wall synthesis, cytoskeleton/vesicle transport, and ethylene biosynthesis are also upregulated in root hairs. In addition, genes related to low phosphorus responses, such as lipid and/or pectin P remobilization and acid phosphatases, are induced in root hairs. The study also highlights the preferential enrichment of processes involved in symbiotic interactions in root hairs. Overall, root hairs exhibit a multifaceted response to low phosphorus, involving molecular changes in epidermal cell differentiation and root hair initiation, as well as tip growth and various low phosphorus responses in elongated root hairs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Madiha Zaynab, Yasir Sharif, Zhaoshi Xu, Sajid Fiaz, Rashid Al-Yahyai, Hamad. A. Yadikar, Najla Amin T. Al Kashgry, Sameer H. Qari, Monther Sadder, Shuangfei Li
Summary: In this study, 30 DUF668 genes were identified in the soybean genome, distributed across fifteen chromosomes. Phylogenetic analysis classified these genes into three groups. Gene structure analysis showed that some of these genes lacked introns. Subcellular localization results indicated that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane.
Article
Plant Sciences
Catherine Damerval, Carmine Claudot, Martine Le Guilloux, Natalia Conde e Silva, Veronique Brunaud, Ludivine Soubigou-Taconnat, Jose Caius, Etienne Delannoy, Sophie Nadot, Florian Jabbour, Yves Deveaux
Summary: TCP transcription factors are important in developmental processes and hormonal pathways. We studied the TCP genes in the plant species Nigella damascena and found that they are orthologs of TCP genes in Aquilegia coerulea. Phylogenetic analysis and amino acid motif identification suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. There have been independent duplications in core eudicots and Ranunculales, resulting in different numbers of paralogs within TCP gene subclasses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Raul Huertas, Ivone Torres-Jerez, Shaun J. Curtin, Wolf Scheible, Michael Udvardi
Summary: Three PHO2-like genes in Medicago truncatula were characterized for their potential roles in phosphorus and nitrogen metabolism balance and symbiotic nitrogen fixation. Among them, MtPHO2B may play a key role in the balance of phosphorus and nitrogen, while MtPHO2C has limited regulatory effects on phosphorus metabolism. Genetic analysis also revealed a connection between phosphorus allocation, plant growth, and symbiotic nitrogen fixation performance. In conclusion, MtPHO2 genes play important roles in both systemic and localized (nodules) phosphorus metabolism.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Wenxuan Du, Junfeng Yang, Qian Li, Qian Su, Dengxia Yi, Yongzhen Pang
Summary: Growth Regulatory Factors (GRF) are plant-specific transcription factors that play critical roles in plant growth and development as well as plant tolerance against stress. In this study, 16 GRF genes were identified from the genomes of Medicago truncatula and Medicago sativa, and their sequences and expression patterns were analyzed. The results showed that these GRF genes are important for plant growth and stress tolerance, particularly in response to salt and drought stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Chongnan Wang, Hui Wang, Hao Zhu, Wenkai Ji, Yaling Hou, Yingying Meng, Jiangqi Wen, Kirankumar S. Mysore, Xuesen Li, Hao Lin
Summary: In this study, the CKX gene family in Medicago truncatula was systematically analyzed, revealing their diverse roles in plant development. Different MtCKX genes showed tissue-specific expression patterns and various responses to cytokinins, indicating their unique functions in M. truncatula. Mutants of MtCKX genes did not cause morphological changes in aerial parts, suggesting functional redundancy, but disruption of specific MtCKX genes affected root development, highlighting the importance of cytokinins in regulating plant architecture.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Yixin An, Ziqi Wang, Baijian Liu, Yuwei Cao, Lin Chen
Summary: This study investigates the translation regulation of plant genes under salt stress and finds that salt stress inhibits gene translation efficiency. It also identifies various small ORFs in the genome of Medicago truncatula, which play a role in the translation regulation of genes.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Plant Sciences
Tamanna A. Jahan, Shweta Kalve, Zachery Belak, Christopher Eskiw, Bunyamin Tar'an
Summary: Chickpea is a staple food in developing countries and can help alleviate iron deficiency. This study investigated iron accumulation and gene expression in different organs of chickpea plants at various growth stages. The highest iron accumulation was found in roots, while gene expression analysis revealed the involvement of certain genes in iron uptake and metabolism. This knowledge can be applied to develop chickpea varieties with high iron content in seeds.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Wenxuan Du, Junfeng Yang, Qian Li, Chunfeng He, Yongzhen Pang
Summary: Nuclear factor YB (NF-YB) genes are critical regulators in plant growth, development, and stress resistance. In this study, 49 NF-YB genes were identified in Medicago, and their expression levels were found to be induced by drought and salt treatments. The study provides valuable information for functional characterization and application of NF-YB genes in alfalfa breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Nandita Pasari, Rajesh Kumar Gazara, Jawahar Singh, Praveen Kumar Verma
Summary: This study identified the expression changes of SWEET genes in leguminous crop Cicerarietinum during interaction with symbiotic fungus Serendipita indica. The regulatory factor miR156 targeting CaSWEET12 was identified. This research provides insights into the regulation mechanism of these genes in plant-fungus symbiosis.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Uday Chand Jha, Harsh Nayyar, Ramesh Palakurthi, Rintu Jha, Vinod Valluri, Prasad Bajaj, Annapurna Chitikineni, Narendra P. Singh, Rajeev K. Varshney, Mahendar Thudi
Summary: This study identified key QTLs related to heat stress tolerance in chickpea through genomic region identification and evaluation under heat stress conditions. Candidate genes associated with heat tolerance were also identified, providing valuable information for further molecular breeding efforts.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Madiha Zaynab, Hamed A. Ghramh, Yasir Sharif, Sajid Fiaz, Rashid Al-Yahyai, Maryam A. Alahdal, Sameer H. Qari, Kamel Hessini, Xiazi Huang, Shuangfei Li
Summary: The present study conducted a comprehensive analysis of DUF599 genes in potato, revealing their significant roles in plant growth and stress response. The study found that these genes are important in coping with abiotic stresses and can enhance plant tolerance by regulating developmental processes and hormone responses.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Jose Luis Blanco-Pastor, Isabel M. Liberal, Muhammet Sakiroglu, Yanling Wei, E. Charles Brummer, Rose L. Andrew, Bernard E. Pfeil
Summary: By analyzing polymorphic loci from the perennial crop Medicago sativa and the annual legume model species M. truncatula, a set of candidate genes associated with adaptation to environmental gradients were identified. These shared genes explained a high proportion of variance for certain phenotypic traits associated with adaptation, dominated by genes with highly conserved functions. This suggests the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions, in line with the omnigenic model of complex traits.
Article
Biochemistry & Molecular Biology
Wenxuan Du, Junfeng Yang, Lin Ma, Qian Su, Yongzhen Pang
Summary: This study identified 23 CBL and 58 CIPK genes in Medicago sativa and Medicago truncatula, and classified them into different groups through phylogenetic analysis. The research revealed distinct expression patterns of these genes under various stress conditions, especially in response to drought, salt, and abscisic acid treatments. The findings suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Sangeeta Yadav, Gautam Anand, Vinay K. Singh, Dinesh Yadav
Summary: The study aimed to clone and analyze PNL genes from different strains of Fusarium, revealing structural characteristics through bioinformatics analysis. Sequence alignment and phylogenetic analysis showed similarity of PNL proteins from different Fusarium strains, while docking studies provided insights into the interaction mechanisms between PNL protein and ligands. The research indicated the structural and biochemical similarity of PNL proteins from diverse Fusarium species, with docking studies highlighting the compatibility of substrates for catalysis.
CURRENT PROTEOMICS
(2021)
Article
Plant Sciences
Mohd Aamir, Pradip Karmakar, Vinay Kumar Singh, Sarvesh Pratap Kashyap, Sudhakar Pandey, Binod Kumar Singh, Prabhakar Mohan Singh, Jagdish Singh
Summary: Melon is an important model plant for studying sex determination, with complex gene networks regulating sex expression. Recent research has identified differentially expressed genes and molecular mechanisms controlling sex expression in melons, offering insights into transcriptional and epigenetic regulation.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Pharmacology & Pharmacy
Yugal Goel, Saveg Yadav, Shrish Kumar Pandey, Mithlesh Kumar Temre, Vinay Kumar Singh, Ajay Kumar, Sukh Mahendra Singh
Summary: Methyl jasmonate shows anti-tumor potential by inducing apoptosis and necrosis in tumor cells through various pathways. The study also reveals its chemosensitizing effect with decreased expression of MDR1 in T-cell lymphoma.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rajesh Kumar, Ashutosh Rai, Avinash Chandra Rai, Vinay Kumar Singh, Major Singh, Prabhakar Mohan Singh, Jagdish Singh
Summary: Transcriptome analysis revealed differential gene expression between resistant and susceptible chilli genotypes, identifying key candidate genes in pathogen-responsive pathways. These results provide a valuable resource for studying plant-pathogen interactions and identifying markers for resistance breeding programs.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jitendra Kumar Yadav, Priyanka Yadav, Vinay Kumar Singh, Alka Agarwal
Summary: The study investigated the interaction of three potent antifilarial compounds with filarial proteins using molecular docking and DFT studies. Compound 3F was identified as the most bioactive molecule, with the lowest HOMO-LUMO energy gap. The study provides structural information and docking studies that could aid in screening and designing new antifilarial drugs for chemotherapy against filariasis.
STRUCTURAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Vipin Kumar, Ayushi Mishra, Vinay Kumar Singh, Anchal Singh
Summary: This study shows that natural compounds Diosgenin, Catharanthine, and Ginkgolide A have comparable binding energy and stability with HIV-1 Tat protein and the human P-TEFb Tat protein complex, potentially serving as potential inhibitors for HIV-1 treatment.
LETTERS IN DRUG DESIGN & DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Amit Gupta, Niharika Sahu, Ashish P. Singh, Vinay Kumar Singh, Suresh C. Singh, Vijay J. Upadhye, Alen T. Mathew, Rajnish Kumar, Rajeshwar P. Sinha
Summary: This study identified potential inhibitors against the main protease (Mpro) of SARS-CoV-2 through virtual screening and molecular docking. Among the identified hits, usnic acid showed stability and effectiveness in inhibiting SARS-CoV-2 Mpro. Therefore, usnic acid, variolaric acid, and gyrophoric acid could serve as lead compounds for the development of antiviral drugs targeting SARS-CoV-2.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kumud Tiwari, Aditi Gangopadhyay, Gajender Singh, Samarendra Kumar Singh
Summary: This study successfully constructed the complete structure of human TTF1 protein using molecular modelling approaches and identified two key residue clusters that are essential for maintaining its structural stability. These findings provide important structural insights for further research, including cancer biology.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Materials Science, Ceramics
Vaibhav Pandey, Mayank Kumar Yadav, Ashutosh Gupta, Kalyani Mohanta, S. K. Panda, V. K. Singh
Summary: This study utilizes a low-cost thermo-foaming technique to convert a sucrose-ceramic mixture into a porous ceramic scaffold. By controlling the experimental conditions, silica foams with high porosity and low thermal conductivity are successfully fabricated. These materials hold potential for insulation applications.
JOURNAL OF THE EUROPEAN CERAMIC SOCIETY
(2022)
Article
Biotechnology & Applied Microbiology
Kanchan Yadav, Shruti Dwivedi, Supriya Gupta, Amit K. Dubey, Vinay K. Singh, Aiman Tanveer, Sangeeta Yadav, Dinesh Yadav
Summary: In this study, 52 pectin lyase genes were predicted and characterized in six species of Fusarium. The protein sequences showed variability in terms of amino acid residues, molecular weight, and pI. Multiple sequence alignment and phylogenetic analysis revealed conserved residues and distinct groups. Three-dimensional structure prediction and analysis showed diverse structural motifs. The study provides important insights into the diversity and potential applications of pectin lyase enzymes.
Article
Biochemistry & Molecular Biology
Mithlesh Kumar Temre, Bharti Devi, Vinay Kumar Singh, Yugal Goel, Saveg Yadav, Shrish Kumar Pandey, Rajnish Kumar, Ajay Kumar, Sukh Mahendra Singh
Summary: This study reveals the molecular mechanism of the binding of glutor to GLUT1 and GLUT3, and suggests its potential in antineoplastic therapeutic applications.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Virology
Amit Gupta, Ashish P. Singh, Vinay K. Singh, Rajeshwar P. Sinha
Summary: Since the outbreak of the COVID-19 pandemic, the virus has been evolving and mutating, leading to increased transmissibility and successive waves of cases. The scientific community has developed vaccines and antiviral agents, but the emergence of new variants has impacted their efficacy. This review provides insights into the appearance and attributes of SARS-CoV-2 variants for future drug design.
Article
Microbiology
Neha Saini, Mohd Aamir, Vinay Kumar Singh, Bansal Deepak, Sharma Mona
Summary: In this research, the microbial diversity in Sohna hot spring, India was examined using shotgun metagenome sequencing. The results showed the presence of 57 phyla, 931 genera, and 2068 species. Functional annotation revealed the predominance of genes associated with primary and secondary metabolism, as well as environmental and genetic signals.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lav Kumar Jaiswal, Rakesh Kumar Singh, Tanmayee Nayak, Vinay Kumar Singh, Ankush Gupta
Summary: Rapid adaptations to environmental changes are crucial for bacterial cell survival, and this process is mediated through transcription initiation and RNA degradation/processing. Ribonuclease E (RNase E) is an essential endoribonuclease gene in Mycobacterium species and plays a key role in various RNA metabolism reactions, making it an important drug target.
IRANIAN JOURNAL OF SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
M. K. Gond, Shivendra Kumar Pandey, R. Singh, Manoj K. Bharty, Partha Pratim Manna, V. K. Singh, B. Maiti, L. B. Prasad, R. J. Butcher
Summary: In this study, three new metal complexes based on a specific ligand were synthesized and showed significant anti-tumor potential against cancer cells. These complexes exhibited stronger anti-tumor effects compared to metal salts or free ligands. Molecular docking studies also revealed favorable binding interactions between these complexes and target proteins.
NEW JOURNAL OF CHEMISTRY
(2022)