Article
Biochemical Research Methods
Huan Du, Zhicheng Jiao, Junjie Liu, Wei Huang, Liangfa Ge
Summary: A new strategy using deep-coverage whole-genome sequencing, polymorphism calling, and customized filtering was developed to sensitively identify mutation sites for fast neutron bombardment (FNB) mutants. This method demonstrated robustness in identifying causative genes for white nodule and yellow leaves mutants in Medicago truncatula, showing potential for efficient mutation site identification in FNB mutants.
Article
Medical Laboratory Technology
Lisa A. Lansdon, Maxime Cadieux-Dion, John C. Herriges, Jeffrey Johnston, Byunggil Yoo, Joseph T. Alaimo, Isabelle Thiffault, Neil Miller, Ana S. A. Cohen, Elena A. Repnikova, Lei Zhang, Midhat S. Farooqi, Emily G. Farrow, Carol J. Saunders
Summary: The study validated the clinical effectiveness of the laboratory's migration from GRCh37 to GRCh38, and identified some important differences between the two genome versions, including discrepancies leading to protein coding sequence variants and discrepancies resolved in coding regions.
CLINICAL CHEMISTRY
(2022)
Article
Immunology
Fuxiao Liu, Jiahui Lin, Qianqian Wang, Youming Zhang, Hu Shan
Summary: Canine distemper and canine parvoviral enteritis are two common infectious diseases in dogs, caused by canine distemper virus and canine parvovirus type 2, respectively. Researchers successfully generated a recombinant CDV expressing VP2 protein, but a nonsense mutation occurred in VP2 ORF during passage and became predominant. Next-generation sequencing identified multiple single-nucleotide variations, including nonsense and missense mutations.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Huiyan Luan, Lei Zhang, Sijin Zhang, Meng Zhang
Summary: This case report presents a Chinese girl diagnosed with familial hemiplegic migraine type 1 through genetic and clinical assessment. Prophylactic therapy with flunarizine did not show improvement in the intensity of attacks in this patient.
Review
Biochemistry & Molecular Biology
Jogender Singh
Summary: Forward genetics is a powerful tool for unraveling molecular mechanisms of biological processes, with C. elegans being a favored model due to ease of genetic manipulation and availability of tools. Recent advancements have accelerated mutation identification, making forward genetic screens the method of choice for understanding biological functions.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Oncology
Min Ruan, Lipeng Liu, Benquan Qi, Xiaoyan Chen, Lixian Chang, Aoli Zhang, Fang Liu, Shuchun Wang, Xiaoming Liu, Xiaojuan Chen, Li Zhang, Ye Guo, Yao Zou, Yingchi Zhang, Yumei Chen, LiXia Liu, Shanbo Cao, Feng Lou, Chengcheng Wang, Xiaofan Zhu
Summary: This study validates the diagnostic role of circulating tumor DNA in pediatric AML based on next-generation sequencing, showing that ctDNA can mirror genomic information from bone marrow and detect mutations exclusively. Monitoring ctDNA with NGS-based assays provides valuable information for precision treatment in pediatric AML.
FRONTIERS IN ONCOLOGY
(2021)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Materials Science, Multidisciplinary
Xiang Fu, Jianbin Kang, Ge Tang, Feiliang Chen, Qian Li, Mo Li, Biao Wei
Summary: AlGaN-based deep ultraviolet (DUV) light emitting diodes (LEDs) exhibit significant enhancement of output power under neutron irradiation, but performance degradation occurs as neutron fluence increases. The study identifies two competitive mechanisms of neutron radiation effect on DUV LEDs, where increased carrier efficiency in irradiated multi-quantum wells contributes to output power enhancement, while neutron irradiation-induced nitrogen vacancies in the electron blocking layer lead to current leakage and device degradation. These findings not only enrich the degradation mechanism of neutron-irradiated DUV LEDs, but also offer new insights to improve their luminous characteristics.
RESULTS IN PHYSICS
(2021)
Article
Plant Sciences
Samuel Daniel Lup, Carla Navarro-Quiles, Jose Luis Micol
Summary: Mapping-by-sequencing combines NGS with classical genetic mapping to establish gene-to-phenotype relationships. Easymap v.2 is a versatile tool that automates mapping of mutations and DNA insertions, and includes workflows for QTL-seq and variant density mapping analyses.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Materials Science, Ceramics
Zhixue Qu, Chuanjin Yu, Yitong Wei, Xiping Su, Aibing Du
Summary: This study quantitatively evaluated the contributions of various irradiation-induced defects in boron carbide and proposed a theoretical model without adjustable parameters based on phonon scattering theory. The model was validated using experimental data to predict the thermal conductivity variation under irradiation. Results suggest that substitutional defects and Frenkel defect pairs, rather than helium bubbles, play determining roles in the abrupt degradation of thermal conductivity during burnup.
JOURNAL OF ADVANCED CERAMICS
(2022)
Review
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Plant Sciences
Miriam Szurman-Zubrzycka, Marzena Kurowska, Bradley J. Till, Iwona Szarejko
Summary: Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Hematology
Naranie Shanmuganathan, Susan Branford
Summary: This review explores the methodologies of mass spectrometry and next-generation sequencing in leukemia MRD detection, highlighting their respective advantages and limitations, citing evidence and instances of their use, and proposing future detection strategies.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Review
Biology
Hui Sun, Xiao-Rong Shen, Zi-Bing Fang, Zong-Zhi Jiang, Xiao-Jing Wei, Zi-Yi Wang, Xue-Fan Yu
Summary: NGS technology has advanced understanding of the genetic causes of neurological diseases, with whole-exome and whole-genome sequencing suitable for finding new mutations and gene panels suitable for exploring specific gene roles. Proper genetic test selection based on cost-effectiveness, coverage area, and sequencing range can enhance diagnosis, treatments, and prevention.
Article
Microbiology
Beom Kyu Kim, Won-Suk Choi, Ju Hwan Jeong, Sol Oh, Ji-Hyun Park, Yu Soo Yun, Seong Cheol Min, Da Hyeon Kang, Eung-Gook Kim, Hojin Ryu, Hye Kwon Kim, Yun Hee Baek, Young Ki Choi, Min-Suk Song
Summary: The emergence of SARS-CoV-2 variants in late 2020 has raised global public health concerns. In this study, a method using circular polymerase extension cloning (CPEC) is demonstrated to efficiently generate full-length clones of SARS-CoV-2 variants. This method is valuable for studying the molecular characteristics of emerging variants and for the development and testing of vaccines and antivirals.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Ruchi Bansal, Surbhi Kumawat, Pallavi Dhiman, Sreeja Sudhakaran, Nitika Rana, Rajdeep Jaswal, Akshay Singh, Humira Sonah, Tilak Raj Sharma, Rupesh Deshmukh
Summary: In this study, we identified eight BAG genes in the rice genome and 78 BAG homologs in nine other Oryza species. We predicted the haplotype diversity and functional effect of variations in BAG genes based on whole genome resequencing data. Transcriptomic analyses revealed the multifunctional roles of BAG genes in both developmental and defense response in rice.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Yogesh Sharma, Praveen Soni, Gaurav Raturi, Rushil Mandlik, Vinay Kumar Rachappanavar, Manish Kumar, Prafull Salvi, Durgesh Kumar Tripathi, Hasthi Ram, Rupesh Deshmukh
Summary: Metalloids are elements with properties similar to both metals and non-metals, and their impact on plant growth can be both beneficial and hazardous. This article discusses the specific role and molecular mechanism involved in the uptake and transport of different metalloids in various plant tissues. The efforts to engineer metalloid transport, such as improving the uptake of beneficial metalloids and reducing the presence of hazardous ones, are also described. Understanding the molecular insights into metalloid transport and detoxification mechanisms will aid in utilizing the benefits of metalloids for crop improvement and ensuring food safety.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Cell Biology
Virender Kumar, Vinod Goyal, Rushil Mandlik, Surbhi Kumawat, Sreeja Sudhakaran, Gunashri Padalkar, Nitika Rana, Rupesh Deshmukh, Joy Roy, Tilak Raj Sharma, Humira Sonah
Summary: In this study, a meta-analysis incorporating QTL information, region-specific association, and transcriptomic analysis was performed. The results identified 14 meta-QTLs for oil and 16 meta-QTLs for protein content in soybean. Further analysis using whole genome re-sequenced data revealed a haplotypic association of certain genes with oil and protein content. The transcriptomic analysis provided insights into the tissue-specific expression of candidate genes. This study provides valuable information for map-based cloning of regulatory genes and marker-assisted breeding in soybean.
Review
Plant Sciences
Deepmala Sehgal, Priyanka Dhakate, Heena Ambreen, Khasim Hussain Baji Shaik, Nagenahalli Dharmegowda Rathan, Nayanahalli Munireddy Anusha, Rupesh Deshmukh, Prashant Vikram
Summary: Plant omics has played a crucial role in discovering new genes and biomolecules that can improve crops, and has made significant progress in wheat research on both qualitative and quantitative traits. Combining various omics approaches has led to advances in gene discovery, pathway investigation, and understanding stress responses and yields. The development of a Wheat Omics database further aids functional genomics studies in wheat.
Article
Chemistry, Applied
Gunashri Padalkar, Rushil Mandlik, Sreeja Sudhakaran, Sanskriti Vats, Surbhi Kumawat, Virender Kumar, Vineet Kumar, Anita Rani, Milind B. Ratnaparkhe, Pravin Jadhav, Javaid Akhter Bhat, Rupesh Deshmukh, Tilak Raj Sharma, Humira Sonah
Summary: Soybean is an important crop globally, known for its nutritional value and industrial uses. However, the presence of anti-nutritional factors and off-flavor-producing compounds limits its acceptance as a staple food. Developing anti-nutrient free soybean could help address global malnutrition.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Rajdeep Jaswal, Sivasubramanian Rajarammohan, Himanshu Dubey, Kanti Kiran, Hukam Rawal, Humira Sonah, Rupesh Deshmukh, Tilak Raj Sharma
Summary: A novel effector protein family similar to Kiwellin proteins has been discovered in rust fungi, demonstrating a classical example of effector evolution at the structural level.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Sanskriti Vats, S. M. Shivaraj, Humira Sonah, Gunvant Patil, Joy Roy, Tilak Raj Sharma, Rupesh Deshmukh
Summary: In this study, a highly efficient protocol for tomato transformation was developed and optimized. Different factors affecting regeneration and transformation were evaluated, and the best conditions were determined. This standardized protocol can be applied to transform any tomato variety.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Review
Environmental Sciences
Gaurav Raturi, Anchal Chaudhary, Varnika Rana, Rushil Mandlik, Yogesh Sharma, Vitthal Barvkar, Prafull Salvi, Durgesh Kumar Tripathi, Jagdeep Kaur, Rupesh Deshmukh, Hena Dhar
Summary: Arsenic contamination is a serious environmental issue in aquatic and terrestrial ecosystems. Microbial approaches, such as oxidation of arsenite, methylation of arsenic, biosorption, bioprecipitation, and bioaccumulation, are promising strategies for arsenic remediation. Genetic engineering of bacteria also plays a significant role in bioremediation strategies.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Genetics & Heredity
Sanskriti Vats, Virender Kumar, Rushil Mandlik, Gunvant Patil, Humira Sonah, Joy Roy, Tilak Raj Sharma, Rupesh Deshmukh
Summary: We reported a reference-guided genome assembly of the superior tomato cultivar Solanum lycopersicum cv. Pusa Ruby (PR), which covers 97.6% of the single-copy genes in the solanales order. The PR genome contains 34,075 genes and 423,288 variants, with 127,131 intragenic variants and 1232 high impact variants. PR shows the lowest affinity towards Fla.8924 among the compared tomato varieties. The high regeneration rate (45.51%) of PR was analyzed and only AGAMOUS-LIKE15 was found to have a null mutation.
Article
Genetics & Heredity
Payal Kapoor, Saloni Sharma, Apoorv Tiwari, Satveer Kaur, Anita Kumari, Humira Sonah, Ajay Goyal, Meena Krishania, Monika Garg
Summary: Research has identified eight putative structural genes involved in anthocyanin biosynthesis in colored wheat. These genes have unique functions and also play a role in defense responses. The information can guide targeted anthocyanin production in wheat seed endosperm.
Article
Biochemistry & Molecular Biology
Prasanta K. Dash, Rhitu Rai, Sharat Kumar Pradhan, Sheelavanta Matha Shivaraj, Rupesh Deshmukh, Rohini Sreevathsa, Nagendra K. Singh
Summary: Flax is a crop grown for its oil, bast fiber, and industrial solvent, but it is affected by climate changes, such as high temperature and drought, which hinder its growth and productivity. In this study, gene expression profiling was conducted to analyze the effects of drought-induced oxidative stress on flax, and a stable reference gene for normalization of qRT-PCR data was identified. The results suggest that EF1a alone or in combination with ETIF5A is suitable for real-time visualization of the cellular impact of drought and oxidative stress on flax.
Article
Plant Sciences
Vandana Thakral, Yogesh Sharma, Rushil Mandlik, Surbhi Kumawat, Gunvant Patil, Humira Sonah, Paul Isenring, Richard Belanger, Tilak Raj Sharma, Rupesh Deshmukh
Summary: In this study, VrNIP2-1 was identified as a metalloid transporter in mungbean through a comprehensive evaluation of AQPs in the mungbean genome. Molecular dynamics simulation revealed the pore-morphology of VrNIP2-1. The study also found that VrNIP2-1 has a unique aromatic/arginine selectivity filter, different from other metalloid transporters in higher plants. The metalloid transport activity of VrNIP2-1 with its unique structural features provides insights into the solute specificity of NIP2s in mungbean and related pulses.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Hemant B. Kardile, Suhas Gorakh Karkute, Clarissa Challam, Nirmal Kant Sharma, Rahul Mahadev Shelake, Prashant Govindrao Kawar, Virupaksh U. Patil, Rupesh Deshmukh, Vinay Bhardwaj, Kumar Nishant Chourasia, Srikar Duttasai Valluri
Summary: This study identified and characterized 37 putative SWEET genes in potato and investigated their response to the late blight disease caused by Phytophthora infestans. Nine transporter genes were found to be responsive to P. infestans, with their expression levels correlating with the life cycle of the pathogen.