Review
Biochemistry & Molecular Biology
Qiaoyun Qi, Bichun Hu, Weiyu Jiang, Yixiong Wang, Jinjiao Yan, Fengwang Ma, Qingmei Guan, Jidi Xu
Summary: Plant epistatic regulation involves DNA methylation, non-coding RNA regulation, and histone modification to regulate gene expression and plant growth without altering the genome sequence. This review summarizes the recent progress of CRISPR/Cas9 in epigenome editing and discusses its potential applications in crop breeding and gene expression. The CRISPR/Cas9 system is known for its high editing efficiency and rapid translation of results, making it a valuable tool for plant epigenetic modification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Stefan J. Tekel, Nicholas Brookhouser, Kylie Standage-Beier, Xiao Wang, David A. Brafman
Summary: The introduction of transient reporters of editing enrichment (TREE) has enabled highly efficient single-base editing of human cells using a transient episomal fluorescent reporter, allowing for rapid generation of clonal editing efficiencies exceeding 80% in biallelic or multiplexed edited isogenic human pluripotent stem cell lines within approximately 3-4 weeks.
Review
Plant Sciences
Mohamed Abdelrahman, Zheng Wei, Jai S. S. Rohila, Kaijun Zhao
Summary: Multiplex genome-editing technologies, especially CRISPR/Cas-based tools, have revolutionized plant molecular biology by enabling precise editing of multiple loci or genes, thus advancing crop-breeding methods.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Agriculture, Dairy & Animal Science
Julia Popova, Victoria Bets, Elena Kozhevnikova
Summary: Genome editing has practical applications in farm animals, improving production traits, economic value, and disease resistance. It also has potential in biomedical research and drug production, as well as xenograft donors. Recent advancements in site-specific nucleases and embryological delivery methods have revolutionized transgenesis, providing efficient and reliable tools for genome engineering in agriculture.
Review
Biochemistry & Molecular Biology
Yulin Mu, Chengxiao Zhang, Taihua Li, Feng-Jie Jin, Yun-Ju Sung, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin
Summary: Lactobacillus, important in food production and probiotics, can benefit from CRISPR/Cas9-based genome editing to improve strain efficiency and achieve traceless genome modification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Xueli Zhang, Chaohui Zhang, Caijiao Liang, Bizhou Li, Fanmei Meng, Yuncan Ai
Summary: Bacteriophages, the most abundant organisms in the biosphere, have been sequenced extensively. However, the study of bacteriophage functional genomics has been hindered by a lack of effective research methods. This study designed a phage genome editing platform based on the CRISPR-Cas9 system, and successfully achieved gene editing in Vibrio natriegens phage TT4P2. This platform has the potential to advance research on phage gene diversity and accelerate the development of phage synthetic biology and nanotechnology.
MICROBIOLOGY SPECTRUM
(2022)
Article
Plant Sciences
Qihui Kong, Jie Li, Shoudong Wang, Xianzhong Feng, Huixia Shou
Summary: CRISPR/Cas system, a new gene-editing technology, is widely used for genome engineering. This study provides a modified protocol for generating transgenic hairy soybean roots to evaluate the efficiency of CRISPR/Cas constructs. The results demonstrated that soybean hairy root transformation could rapidly assess the efficiency of designed gRNA sequences on genome editing, making it a useful tool for functional study and pre-screening of gRNA in CRISPR/Cas gene editing.
Review
Pharmacology & Pharmacy
Siwei Chen, Deng Chen, Bin Liu, Hidde J. Haisma
Summary: CRISPR/Cas9-mediated genome engineering has extensive applications in basic biology, biotechnology, and medicine. However, the low gene modification efficiency and uncontrollable prolonged Cas9 activity hinder its further use. Researchers have explored small molecules with clinical potential to precisely modulate CRISPR/Cas9 genome editing activity.
DRUG DISCOVERY TODAY
(2022)
Review
Plant Sciences
Narayan Chandra Paul, Sung-won Park, Haifeng Liu, Sungyu Choi, Jihyeon Ma, Joshua S. MacCready, Martin Chilvers, Hyunkyu Sang
Summary: The CRISPR/Cas9 system has been utilized to enhance disease resistance among different crops against fungal and oomycete pathogens, providing a powerful approach for plant disease management.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Min Ho Lee, Jae Il Shin, Jae Won Yang, Keum Hwa Lee, Do Hyeon Cha, Jun Beom Hong, Yeoeun Park, Eugene Choi, Kalthoum Tizaoui, Ai Koyanagi, Louis Jacob, Seoyeon Park, Ji Hong Kim, Lee Smith
Summary: This review highlights the current and potential use of CRISPR-Cas9 in the management of autoimmune diseases. Several studies have shown that CRISPR-Cas9 can be utilized for immunomodulation, reducing cholesterol, and treating rare diseases. However, there is limited research on the treatment of autoimmune diseases using CRISPR-Cas9.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Kristina J. Tatiossian, Robert D. E. Clark, Chun Huang, Matthew E. Thornton, Brendan H. Grubbs, Paula M. Cannon
Summary: This study found that CRISPR-Cas9 indel signatures can be used to identify gRNAs that maximize HDR outcomes, with the frequency of deletions resulting from MMEJ repair of at least 3 base pairs better predicts HDR frequency. Existing tools can be repurposed to identify gRNAs that promote HDR.
Article
Plant Sciences
Syed Inzimam Ul Haq, Dianfeng Zheng, Naijie Feng, Xingyu Jiang, Feng Qiao, Jin-Sheng He, Quan-Sheng Qiu
Summary: This review summarizes the advances of CRISPR/Cas9 technology in plant genome editing and discusses its applications in forage breeding, as well as the potential and challenges.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Chemistry, Physical
Juhee Lee, Yoo Kyung Kang, Eonju Oh, Juhee Jeong, San Hae Im, Duk Ki Kim, Haeshin Lee, Sang-Gyu Kim, Keehoon Jung, Hyun Jung Chung
Summary: The study presents a cancer gene therapy strategy based on NanoRNP that efficiently blocks the PD-L1 immune checkpoint and induces an antitumor effect in vivo without the need for combination therapy. In vivo results demonstrate that NanoRNP can induce indels in target cells at high frequencies, significantly suppressing tumor growth.
CHEMISTRY OF MATERIALS
(2022)
Article
Multidisciplinary Sciences
Beate Rieblinger, Hicham Sid, Denise Duda, Tarik Bozoglu, Romina Klinger, Antonina Schlickenrieder, Kamila Lengyel, Krzysztof Flisikowski, Tatiana Flisikowska, Nina Simm, Alessandro Grodziecki, Carolin Perleberg, Andrea Bahr, Lucie Carrier, Mayuko Kurome, Valeri Zakhartchenko, Barbara Kessler, Eckhard Wolf, Lutz Kettler, Harald Luksch, Ibrahim T. Hagag, Daniel Wise, Jim Kaufman, Benedikt B. Kaufer, Christian Kupatt, Angelika Schnieke, Benjamin Schusser
Summary: Research on genetically modified animals has mostly focused on mice, but also includes species like pigs that are more physiologically similar to humans, and cross-species comparisons with phylogenetically distant species like chickens. CRISPR-Cas9 is a versatile genetic editing method applicable across various species. The successful generation of transgenic chickens and pigs that express Cas9 in all organs has confirmed the functionality of Cas9 across different target genes, cell types, and in vivo applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Chao Zhang, Shanhe Liu, Xuan Li, Ruixuan Zhang, Jun Li
Summary: CRISPR/Cas-based genome editing technologies have revolutionized plant science by allowing precise manipulation of plant genomes. Virus-induced genome editing (VIGE) has emerged as a powerful method for delivering CRISPR/Cas reagents into plant cells, with high editing efficiency and simplified process. This article provides an overview of CRISPR/Cas-based genome editing and focuses on the VIGE systems, types of viruses used for CRISPR/Cas9 cassette delivery, recent applications, and challenges and potential of VIGE in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Debasis Mitra, Devvret Verma, Bhaswatimayee Mahakur, Anshul Kamboj, Rakesh Srivastava, Sugam Gupta, Ajita Pandey, Bhawna Arora, Kumud Pant, P. Panneerselvam, Arabinda Ghosh, Durga P. Barik, Pradeep K. Das Mohapatra
Summary: The study utilized molecular docking to screen potential drug compounds from Vitex negundo L., with some compounds showing inhibitory activity against the papain-like protease of SARS CoV-2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Environmental Sciences
Mahapatra Smruthi Sagarika, Chidambaranathan Parameswaran, Ansuman Senapati, Jatiprasd Barala, Debasis Mitra, S. R. Prabhukarthikeyan, Anjani Kumar, Amaresh Kumar Nayak, Periyasamy Panneerselvam
Summary: Rice straw, a highly abundant ligno-cellulosic waste globally, presents challenges in efficient utilization. The discovery of a novel microbial enzyme, LPMOs, and its combination with other glycolytic enzymes shows promise in improving bioconversion efficiency. Researchers are working on exploring LPMOs producers for rapid decomposition of agricultural wastes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Pradeep Kumar Dash, Soumya Ranjan Padhy, Pratap Bhattacharyya, Ankita Pattanayak, Soumya Routray, Periyasamy Panneerselvam, Amaresh Kumar Nayak, Himanshu Pathak
Summary: This study investigated the impact of lignin decomposing microbial consortium on rice straw decomposition process. It was found that the LB 18 + LF 3 consortium decomposed rice straw faster compared to other strains/consortium and showed significant effects within 28 days, but also increased methane and carbon dioxide emissions.
WASTE AND BIOMASS VALORIZATION
(2022)
Review
Plant Sciences
Debasis Mitra, Boya Saritha, Edappayil Janeeshma, Poonam Gusain, Bahman Khoshru, Fatma A. Abo Nouh, Abo Nouh, Anju Rani, Adeyemi N. Olatunbosun, Janki Ruparelia, Aniruddh Rabari, Lyda P. Mosquera-Sanchez, Rittick Mondal, Devvret Verma, Periyasamy Panneerselvam, Pradeep K. Das Mohapatra, B. E. Guerra Sierra
Summary: Arsenic is a potentially toxic metalloid released into the environment through various activities, causing severe health issues upon long-term exposure. Plants respond to arsenic toxicity by inducing oxidative stress, while AMF may be a sustainable approach to alleviate arsenic toxicity.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Agronomy
Shweta Kumari, K. Nagendran, C. Manimurugan, K. K. Pandey, J. Singh
Summary: The study conducted in major vegetable growing areas in the eastern Indo-Gangetic plains of Uttar Pradesh over 5 years from 2015 to 2019 revealed the prevalence and distribution of tospoviruses. GBNV was found mainly in solanaceous crops, while WBNV was predominant in cucurbitaceous crops, with some weeds identified as alternative hosts. Moreover, the ill-effects of GBNV infection on cowpea seed quality were documented, showing significant reductions in various parameters compared to healthy seeds.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Agronomy
V. Venkataravanappa, M. H. Kodandaram, M. Manjunath, Neha S. Chauhan, K. Nagendran, Shailesh K. Tiwari, B. Sarkar, Govind Pratap Rao
Summary: Brinjal little leaf (BLL) is a significant disease affecting eggplant cultivation in India, leading to economic losses. Research has identified resistant eggplant varieties and wild Solanum species that show immunity or resistance to BLL, suggesting the potential for breeding resistant varieties using these materials.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Soil Science
Debasis Mitra, Rittick Mondal, Bahman Khoshru, Ansuman Senapati, T. K. Radha, Bhaswatimayee Mahakur, Navendra Uniyal, Ei Mon Myo, Hanane Boutaj, Beatriz Elena Guerra Sierra, Periyasamy Panneerselvam, Arakalagud Nanjundaiah Ganeshamurthy, Snezana Andelkovic, Tanja Vasic, Anju Rani, Subhadeep Dutta, Pradeep K. Das Mohapatra
Summary: Agricultural land is deteriorating due to population increase, urbanization, and industrialization. To increase crop production from smaller areas, high doses of inorganic fertilizers are used, damaging soil health and causing nutrient imbalance. Recent technological advances have shown the benefits of microbial inoculants such as Actinobacteria in replacing harmful chemicals and promoting sustainable farming practices. Actinobacteria have multifunctional traits that promote plant growth, control phytopathogens, solubilize nutrients, produce phytohormones, enhance organic matter decomposition, and suppress soil-borne pathogens.
Article
Genetics & Heredity
V. Kavi Sidharthan, Krishnan Nagendran, V. K. Baranwal
Summary: Transcriptome datasets in public domain are valuable for identifying novel viral genomes, and in this study, five putative novel Poleroviruses and one new Enamovirus were identified from plant transcriptomes. Phylogenetic analysis showed that Poleroviruses of apiaceous plants formed a monophyletic clade.
Article
Biotechnology & Applied Microbiology
Manjunatha T. Gowda, Bharat Raj Meena, Nagendran Krishnan, M. Manjunath, C. Sellaperumal, A. B. Rai, Arpita Singh, C. Manimurugan, Jagadeesh Patil, K. K. Pandey, J. Singh
Summary: In this study, native strains of Bacillus species were isolated and evaluated for their efficacy in controlling Meloidogyne incognita in okra. Two Bacillus spp., Bacillus marisflavi CRB2 and Bacillus subtilis CRB7, were found to be most effective against M. incognita. These strains were also found to harbor multiple antimicrobial peptide genes, which may contribute to their efficacy against M. incognita. Under laboratory, pot, and field conditions, the application of B. marisflavi CRB2 and B. subtilis CRB7 significantly reduced the incidence of M. incognita in okra and increased yield. These findings suggest that these native Bacillus strains can be used as part of an integrated nematode management strategy.
BIOLOGICAL CONTROL
(2022)
Article
Agronomy
Nagendran Krishnan, Shweta Kumari, Sudhakar Pandey, Baradwaj Dangar Ram, Tusar Kanti Behera, Karthikeyan Gandhi
Summary: This study documented the occurrence of Cucurbit yellow stunting disorder virus (CYSDV), a Crinivirus, for the first time in cucurbitaceous crops in India.
Article
Plant Sciences
Nagendran Krishnan, Shweta Kumari, Koshlendra Kumar Pandey, Sudhakar Pandey, Tusar Kanti Behera, Karthikeyan Gandhi, Lawrence Kenyon
Summary: The pathogen responsible for yellowing and downward rolling of leaves of squash and watermelon plants from Uttar Pradesh state, India, was identified probably as strains of Cucurbit aphid-borne yellows virus (CABYV) through RT-PCR and sequencing. The full-length genome sequences of these isolates were determined, and they showed closest identity with a recombinant strain reported from Taiwan infecting Luffa aegyptiaca. These sequences are likely to represent recombinant strains of CABYV and provide new information about the virus.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2022)
Review
Green & Sustainable Science & Technology
Panneerselvam Peramaiyan, Peter Craufurd, Virender Kumar, Lavanya P. Seelan, Andrew J. McDonald, Balwinder-Singh, Avinash Kishore, Sudhanshu Singh
Summary: Zinc is an essential trace element in the human diet, and its deficiency is prevalent in regions where dietary intake of rice is high. This article reviews strategies for enhancing the zinc concentration in rice through agronomic biofortification, such as timing, dose, and method of zinc fertilizer application, as well as the influence of nitrogen, phosphorus, and crop establishment methods. Data-driven zinc recommendations and targeted policies to support agronomic biofortification are proposed.
Article
Biotechnology & Applied Microbiology
Nagendran Krishnan, B. Rajasekhar Reddy, Shweta Kumari, Achuit Kumar Singh
Summary: In this study, a Begomovirus associated with golden mosaic disease on vegetable cowpea was characterized. The genomic components were cloned and sequenced, showing high similarity to mungbean yellow mosaic India virus previously reported from India. Phylogenetic analysis suggested a common ancestral relationship between the study isolate and MYMIV isolates from India, Pakistan, and Nepal. Recombination analysis indicated that this cowpea isolate likely evolved through recombination of MYMIV sequences. Additionally, Agrobacterium-based dimeric clone constructs were found to be highly infectious on cowpea host, causing typical golden mosaic symptoms.
Article
Biology
Debasis Mitra, Periyasamy Panneerselvam, Ansuman Senapati, Parameswaran Chidambaranathan, Amaresh Kumar Nayak, Pradeep Kumar Das Mohapatra
Summary: The aim of this experiment was to determine the prominent effects of arbuscular mycorrhizal fungi (AMF) on rice mycorrhizal colonization, responsiveness, P utilization, and growth-promoting traits under P-deficient conditions in aerobic rice cultivation. The data analysis showed that AMF colonization was highly correlated with soil enzymes and plant P uptake. The study also found that AMF intervention significantly increased plant P uptake, soil enzyme activities, and plant growth promotion in aerobic rice cultivation under P-deficient conditions.
Article
Agronomy
Panneerselvam Peramaiyan, Andrew J. McDonald, Virender Kumar, Peter Craufurd, Iftikar Wasim, Nabakishore Parida, Sanghamitra Pattnaik, Balwinder Singh, Ashok Yadav, Anurag Ajay, Sudhanshu Singh, Ram K. Malik
Summary: Field experiments were conducted in the rainfed plateau region of Odisha over two years to study the effects of diverse agronomic and varietal interventions on maize yield. The results showed that the combination of optimum plant population, fertilizer management, and herbicide-based weed management significantly increased maize yield compared to farmers' current practices. Furthermore, the combination of long-duration hybrids and best management practices (BMPs) led to even higher grain yields and profitability. The study highlights the importance of using hybrids and BMPs to improve the productivity and profitability of rainfed maize.
EXPERIMENTAL AGRICULTURE
(2022)