Article
Biochemistry & Molecular Biology
Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang
Summary: Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation and disease occurrence and progression. HUSCH is a large-scale database that integrates high-quality single-cell transcriptomic datasets from different tissues, providing comprehensive visualization and analysis of gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Zhibin Zhang, Mao Chai, Zhaoen Yang, Zuoren Yang, Liqiang Fan
Summary: This study constructs a Gossypium Resource And Network Database (GRAND) that integrates a wide range of cotton genome and transcriptome data. It provides various tools for exploration and mining of these data, which can potentially accelerate the progress of cotton breeding.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Baosheng Liao, Haoyu Hu, Shuiming Xiao, Guanru Zhou, Wei Sun, Yang Chu, Xiangxiao Meng, Jianhe Wei, Han Zhang, Jiang Xu, Shilin Chen
Summary: The Global Pharmacopoeia Genome Database (GPGD) contains a vast amount of genomic data from 903 herb species from eight global pharmacopoeias, serving as a valuable resource for herbal medicine research. Through uniform formatting and arrangement, GPGD plays an important role in species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Entomology
Lizhen Guo, Min Tang, Shiqi Luo, Xin Zhou
Summary: In this study, a class of antimicrobial peptides (AMPs) called Cecropin was identified from insect transcriptomes using bioinformatics. The identified Cecropin genes were found in several insects and their antimicrobial activity against bacteria was validated. This study provides a reliable analytical method for the discovery of AMPs, which have promising applications in diverse fields.
Article
Biology
Mukesh Jain, Juhi Bansal, Mohan Singh Rajkumar, Rohini Garg
Summary: A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Rajdeep Das, Martin Sjostrom, Raunak Shrestha, Christopher Yogodzinski, Emily A. Egusa, Lisa N. Chesner, William S. Chen, Jonathan Chou, Donna K. Dang, Jason T. Swinderman, Alex Ge, Junjie T. Hua, Shaheen Kabir, David A. Quigley, Eric J. Small, Alan Ashworth, Felix Y. Feng, Luke A. Gilbert
Summary: The study integrates clinical and functional genomics data, identifying potential driver genes KIF4A and WDR62 for metastatic prostate cancer. These genes are shown to drive aggressive prostate cancer phenotypes in multiple models, regardless of AR status, and are associated with poor patient outcomes.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin, Shu-Hwa Chen
Summary: Motivation: Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. In this study, we merged widely used 16S rRNA sequence databases and a collection of novel sequences into an integrated resource named MetaSquare version 1.0. The database contains over 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods.
Article
Gastroenterology & Hepatology
Chrissy Bolton, Christopher S. Smillie, Sumeet Pandey, Rasa Elmentaite, Gabrielle Wei, Carmen Argmann, Dominik Aschenbrenner, Kylie R. James, Dermot P. B. McGovern, Marina Macchi, Judy Cho, Dror S. Shouval, Jochen Kammermeier, Sibylle Koletzko, Krithika Bagalopal, Melania Capitani, Athena Cavounidis, Elisabete Pires, Carl Weidinger, James McCullagh, Peter D. Arkwright, Wolfram Haller, Britta Siegmund, Lauren Peters, Luke Jostins, Simon P. L. Travis, Carl A. Anderson, Scott Snapper, Christoph Klein, Eric Schadt, Matthias Zilbauer, Ramnik Xavier, Sarah Teichmann, Aleixo M. Muise, Aviv Regev, Holm H. Uhlig
Summary: Our study establishes a quantitative integrated taxonomy that defines the cellular landscape of monogenic IBD gene expression across 102 genes with high and moderate penetrance. We illustrate distinct cellular networks, highlight expression profiles across understudied cell types, and define genotype phenotype associations. The taxonomy integrates genetic, clinical, and multi-omic data, providing a basis for genomic diagnostics and testable hypotheses for disease functions and treatment responses.
Article
Multidisciplinary Sciences
Apoorv Gupta, Sandhya Pathak, Rajeev Varshney, Yasmin Ahmad, Pankaj Khurana
Summary: HighAltitudeOmicsDB is a unique resource that provides detailed information on genes/proteins, protein-protein interactions, and gene ontology semantic similarities related to high altitude conditions, aiming to facilitate research and analysis on the complex mechanisms of high altitude acclimatization.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Long-Fei Zhao, Jin-Ge Zhang, Feng-Yu Qi, Wei-Yan Hou, Yin-Rui Li, Dan-Dan Shen, Li-Juan Zhao, Lin Qi, Hong-Min Liu, Yi-Chao Zheng
Summary: This study developed the first web-based public database called Sex Differences in Cancer (SDC) to analyze the impact of sex differences in cancer by integrating resources from multiple databases. SDC contains various types of cancer, molecular data, donors, and cancer cell lines, providing different modules for users to study the effects of sex differences.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Plant Sciences
Yong Wang, Jialei Ji, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv
Summary: The Brassica oleracea Genome Database (BoGDB) is a platform that integrates multi-omics data for comprehensive research on B. oleracea.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yuwei Zhang, Dechao Bu, Peipei Huo, Zhihao Wang, Hao Rong, Yanguo Li, Jingjia Liu, Meng Ye, Yang Wu, Zheng Jiang, Qi Liao, Yi Zhao
Summary: ncFANs v2.0 is an online platform that offers multiple computational methods for ncRNA functional annotation, including functional modules for different networks. It provides convenience for biological researchers to unravel the regulatory mechanisms of ncRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Min Sun, Haidong Yan, Aling Zhang, Yarong Jin, Chuang Lin, Lin Luo, Bingchao Wu, Yuhang Fan, Shilin Tian, Xiaofang Cao, Zan Wang, Jinchan Luo, Yuchen Yang, Jiyuan Jia, Puding Zhou, Qianzi Tang, Chris Stephen Jones, Rajeev K. K. Varshney, Rakesh K. K. Srivastava, Min He, Zheni Xie, Xiaoshan Wang, Guangyan Feng, Gang Nie, Dejun Huang, Xinquan Zhang, Fangjie Zhu, Linkai Huang
Summary: A free, web-accessible, user-friendly millets multi-omics database platform (Milletdb) has been developed, which contains six millets and their one related species genomes, as well as stress-related multi-omics data. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools and can effectively serve researchers in the mining of key genes, genome editing, and molecular breeding of millets.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Angelika Buczynska, Iwona Sidorkiewicz, Anna Trochimiuk, Slawomir Lawicki, Adam Jacek Kretowski, Monika Zbucka-Kretowska
Summary: Research suggests that evaluating novel prenatal screening biomarkers using advanced technology may improve the diagnostic accuracy of biochemical prenatal screening for Trisomy 21, while potentially uncovering new potential medical targets.
Article
Plant Sciences
Manish Roorkiwal, Aditi Bhandari, Rutwik Barmukh, Prasad Bajaj, Vinod Kumar Valluri, Annapurna Chitikineni, Sarita Pandey, Bharadwaj Chellapilla, Kadambot H. M. Siddique, Rajeev K. Varshney
Summary: Micronutrient malnutrition is a global concern, and this study focused on enhancing the nutrient content of chickpea. By evaluating a diverse set of chickpea germplasm, the study identified significant variations in nutritional traits and conducted genome-wide association studies to identify marker-trait associations. The study also explored the effect of heterozygosity on trait detection. Seven promising accessions were identified as potential donors for developing nutrient-rich, high-yielding chickpea varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Kunchapu Chennakesavulu, Harshita Singh, Prabodh Kumar Trivedi, Mukesh Jain, Shri Ram Yadav
Summary: The review highlights the principles and functional importance of CRISPR-Cas9 in plant genome editing, emphasizing recent advancements like CRISPR-Cpf1, base editing, and prime editing. These technologies have the potential to improve stress tolerance in crops, essential for enhancing food security and agricultural practices globally.
PLANT CELL REPORTS
(2022)
Review
Biotechnology & Applied Microbiology
Vikram Singh, Mukesh Jain
Summary: CRISPR-based imaging methods play a crucial role in studying the localization, interaction, and coordinated regulation of chromatin, genomic loci, RNAs, and proteins. These methods, utilizing various tools and technologies, have significantly improved the efficiency and clarity of imaging, offering insights into chromatin organization and dynamics, RNA visualization, and protein imaging for genome biology research.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Summary: Drought stress affects plant growth and yield in chickpea. Genome diversity and selective alleles in different genotypes of crop plants may influence agronomic traits, including drought stress response. DNA polymorphisms were found in genes related to stress response, highlighting their importance in engineering drought tolerance in chickpea.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Developmental Biology
Tushar Garg, Zeenu Singh, Kunchapu Chennakesavulu, Khrang Khrang Khunggur Mushahary, Anuj Kumar Dwivedi, Vijina Varapparambathu, Harshita Singh, Raj Suryan Singh, Debabrata Sircar, Divya Chandran, Kalika Prasad, Mukesh Jain, Shri Ram Yadav
Summary: In this study, the researchers investigated the molecular mechanisms controlling the development of shoot-borne adventitious/crown roots in rice. They identified transcription factors from the WUSCHEL-RELATED HOMEOBOX and PLETHORA gene families that play non-redundant and species-specific roles in determining root architecture. The study also revealed the involvement of PLT genes in promoting crown root development through the activation of local auxin biosynthesis genes. Interestingly, the PLT genes from rice were able to rescue lateral root primordia outgrowth defects in Arabidopsis mutants, indicating their conserved role in root primordia outgrowth regardless of their developmental origin. This research provides a molecular framework for understanding the tissue transdifferentiation during root primordia establishment and the evolution of transcription regulation in acquiring species-specific function.
Article
Biotechnology & Applied Microbiology
Mukesh Jain, Juhi Bansal, Mohan Singh Rajkumar, Naveen Sharma, Jitendra P. Khurana, Paramjit Khurana
Summary: In this study, a high-quality genome sequence of a cultivated Indian mulberry was obtained using multiple technologies. It identified repetitive DNA and a large number of protein-coding genes supported by transcript evidence. Comparative analysis with other plant genomes revealed species-specific genes in the mulberry genome. Transcriptome profiling showed tissue-specific and differential expression of these genes across different accessions and implicated in various biological processes.
Article
Plant Sciences
Nidhi Kandhol, Mukesh Jain, Durgesh Kumar Tripathi
Summary: This review discusses the role and mechanisms of nanoparticles in helping plants cope with drought, highlighting their importance in addressing global water scarcity issues in agriculture.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Niraj Khemka, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Summary: Integrated transcriptome data analysis identified candidate long non-coding RNAs (lncRNAs) associated with QTLs and involved in miRNA-mediated seed size/weight determination in chickpea seed development. The study provides a comprehensive resource and identifies potential lncRNAs that play important roles in chickpea seed development and seed size/weight determination.
Article
Medicine, General & Internal
Al Ozonoff, Joanna Schaenman, Naresh Doni Jayavelu, Carly E. Milliren, Carolyn S. Calfee, Charles B. Cairns, Monica Kraft, Lindsey R. Baden, Albert C. Shaw, Florian Krammer, Harm van Bakel, Denise A. Esserman, Shanshan Liu, Ana Fernandez Sesma, Viviana Simon, David A. Hafler, Ruth R. Montgomery, Steven H. Kleinstein, Ofer Levy, Christian Bime, Elias K. Haddad, David J. Erle, Bali Pulendran, Kari C. Nadeau, Mark M. Davis, Catherine L. Hough, William B. Messer, Nelson I. Agudelo Higuita, Jordan P. Metcalf, Mark A. Atkinson, Scott C. Brakenridge, David Corry, Farrah Kheradmand, Lauren I. R. Ehrlich, Esther Melamed, Grace A. McComsey, Rafick Sekaly, Joann Diray-Arce, Bjoern Peters, Alison D. Augustine, Elaine F. Reed, Matthew C. Altman, Patrice M. Becker, Nadine Rouphael, IMPACC Study Grp
Summary: This study aims to better understand the association between characteristics of COVID-19 patients and their outcomes. It found that risk factors such as age, Hispanic ethnicity, elevated baseline creatinine or troponin levels, baseline lymphopenia, presence of infiltrate by chest imaging, and high SARS-CoV2 viral load were associated with prolonged hospitalization or death. Female sex was the only risk factor associated with post-acute sequalae of COVID-19 (PASC). The findings provide important insights for patient management and prognosis improvement.
Editorial Material
Plant Sciences
Rohini Garg, Prasanta K. K. Subudhi, Rajeev K. K. Varshney, Mukesh Jain
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Rama Shankar, Anuj Kumar Dwivedi, Vikram Singh, Mukesh Jain
Summary: Drought stress is a significant threat to rice productivity. This study analyzed the genetic variations between drought-tolerant and drought-sensitive rice cultivars and identified millions of single nucleotide polymorphisms and insertions/deletions. The genetic variations were unevenly distributed throughout the rice genome, with a higher frequency near the transcription start and stop sites. The study also identified cis-regulatory motifs and differentially expressed genes associated with stress-related transcription factors, providing valuable insights into candidate genes for drought stress tolerance in rice.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Plant Sciences
Anuj Kumar Dwivedi, Vikram Singh, Khalid Anwar, Ashwani Pareek, Mukesh Jain
Summary: Drought is a serious threat to rice production caused by climate change. Comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars identified the molecular mechanisms involved in drought tolerance/response. This study characterized the global transcriptome, proteome, and metabolome profiles and integrated them to reveal the role of transporters, translational machinery, aromatic amino acids, soluble sugars, and auxiliary carbohydrate metabolism in drought tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Reetu Singh, Monika Mahajan, Sheetal Das, Vinay Kumar
Summary: Post-translational modification, such as the small ubiquitin-like modification (SUMOylation), plays a crucial role in various cellular signaling events and environmental stress responses in plants. SUMOylation has been shown to regulate plant growth and development, as well as defense against pathogens. This review provides insight into the SUMO conjugation machinery and its isoforms, and their potential roles in cellular processes and stress conditions in plants. Understanding SUMOylation mechanisms can contribute to the development of stress tolerance and resistance mechanisms.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Biotechnology & Applied Microbiology
Reetu Singh, Rama Shankar, Sudesh Kumar Yadav, Vinay Kumar
Summary: In this study, comparative transcriptome analysis was conducted on pre- and post-fertilization stages of chickpea ovules to identify key regulatory transcripts. The analysis revealed 3399 differentially expressed genes after fertilization, including upregulated genes involved in the accumulation of carbohydrates and proteins. This research provides insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules and contributes to a comprehensive understanding of the developmental events in chickpea seeds after fertilization.
Article
Biochemistry & Molecular Biology
Shalini Tiwari, Mukesh Jain, Sneh Lata Singla-Pareek, Prem L. Bhalla, Mohan B. Singh, Ashwani Pareek
Summary: The study found that the salt-tolerant rice genotype Pokkali plays a crucial role in stress response through the regulation of long non-coding RNA (lncRNA). These lncRNAs modulate various cellular processes, including transcriptional regulation, ion homeostasis, and secondary metabolite production. Furthermore, lncRNAs are predicted to bind to stress-responsive transcription factors. Additionally, some lncRNAs are also regulated under other abiotic stresses and phytohormone treatments, indicating possible cross-talk and further functional characterization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Elise Marsan, Dmitry Velmeshev, Arren Ramsey, Ravi K. Patel, Jiasheng Zhang, Mark Koontz, Madeline G. Andrews, Martina de Majo, Cristina Mora, Jessica Blumenfeld, Alissa N. Li, Salvatore Spina, Lea T. Grinberg, William W. Seeley, Bruce L. Miller, Erik M. Ullian, Matthew F. Krummel, Arnold R. Kriegstein, Eric J. Huang
Summary: Mutations in the GRN gene are a major cause of FTLD. Comparative single-cell transcriptomics in mice and FTLD-GRN patients revealed a conserved astroglial pathology characterized by upregulated GJA1, AQP4, and APOE, and downregulated SLC1A2, leading to synaptic degeneration. This astroglial toxicity was confirmed in cell cultures and cortical organoids, suggesting its potential role in neurodegeneration in FTLD-GRN.
JOURNAL OF CLINICAL INVESTIGATION
(2023)