Article
Agricultural Engineering
Kajal Kumari, Sanjeev Kumar, Prashant, Amrit Kumar Jha, Nitish Kumar
Summary: This review paper discusses the application of biotechnological techniques for enhancing the production of secondary metabolites in O. sanctum. By using modern technology, the pharmaceutical yield of this plant can be improved, and studies on gene transfer and genome structure have been conducted.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Immunology
Kamila Romanowski, Benjamin Sobkowiak, Jennifer L. Guthrie, Victoria J. Cook, Jennifer L. Gardy, James C. Johnston
Summary: By combining WGS data with patient-level information, the timing of secondary TB among contacts of active TB patients in British Columbia, Canada can be calculated.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Plant Sciences
Hisashi Udagawa, Hiroyuki Ichida, Takanori Takeuchi, Tomoko Abe, Yoshimitsu Takakura
Summary: In this study, a whole-exome sequencing (WES) procedure was developed in tobacco to characterize EMS-induced mutations in a test population, revealing a high number of single nucleotide variants. The amount of mutations detected by WES was 93.5% of those detected by whole-genome sequencing, while requiring significantly less sequencing data, making it a cost-effective tool for high-throughput mutation identification in tobacco.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Mukund R. Shukla, Annaliese Kibler, Christina E. Turi, Lauren A. E. Erland, J. Alan Sullivan, Susan J. Murch, Praveen K. Saxena
Summary: Tulsi, a sacred plant in many cultures, is known for its medicinal and spiritual significance with antioxidant phytochemicals. This study screened a large seed population to select lines with high antioxidant potential and standardized protocols for phytochemically consistent crop production. The integrated approach of in vitro selection and propagation shows potential for developing safe, effective, and novel natural health products.
Article
Plant Sciences
Salvador Guzman-Diaz, Fabian Augusto Aldaba Nunez, Emily Veltjen, Pieter Asselman, Isabel Larridon, Marie-Stephanie Samain
Summary: Chloroplast genomes in Magnoliaceae are considered highly conserved but intergenic regions show significant nucleotide diversity, contributing to phylogenetically informative data. The gene content is consistent across species, with a length of about 160kb, and differences between genera are greater than within genera. Phylogenetic analyses confirm that the current infrageneric classification in Magnolia does not reflect natural relationships.
Review
Biochemistry & Molecular Biology
Mohammad Raghibul Hasan, Bader Saud Alotaibi, Ziyad Mohammed Althafar, Ahmed Hussain Mujamammi, Jafar Jameela
Summary: In most cases, cancer develops due to abnormal cell growth and subsequent tumour formation. Because of limitations in current treatment options, natural compounds are being investigated as potential alternatives. Around 30 natural compounds are currently in clinical trials for cancer treatment. Tulsi, or Holy Basil, is an inexpensive and widely available medicinal plant with significant religious and medicinal importance in India. The essential oil of Tulsi contains bioactive compounds such as camphor, eucalyptol, eugenol, alpha-bisabolene, beta-bisabolene, and beta-caryophyllene, which are proposed to contribute to its antimicrobial properties. Tulsi leaves, rich in eugenol, have shown anticancer properties and are being evaluated in ongoing clinical trials.
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Plant Sciences
Abhisek Chakraborty, Shruti Mahajan, Manohar S. Bisht, Vineet K. Sharma
Summary: This study sequenced the genome and transcriptome of Syzygium cumini, also known as jambolan or jamun. The genome analysis revealed the tetraploid and highly heterozygous nature of S. cumini, as well as the adaptive evolution of genes involved in secondary metabolism pathways and stress tolerance mechanisms. These findings provide insights into the medicinal properties of S. cumini.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
James Friel, Aureliano Bombarely, Carmen Dorca Fornell, Francisco Luque, Ana Maria Fernandez-Ocana
Summary: Olive, a tree species of great economic and cultural importance in the Mediterranean region, has numerous cultivars that can be characterized using different genetic methods. Both whole-genome sequencing (WGS) and genotype by sequencing (GBS) yield similar results in olive genotyping, with GBS being a cost-effective option for characterizing genetic relationships between different accessions. The study also suggests that variants from GBS and WGS datasets can be combined, enabling the reuse of publicly available data.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Matheus Fernandes Gyorfy, Emma R. Miller, Justin L. Conover, Corrinne E. Grover, Jonathan F. Wendel, Daniel B. Sloan, Joel Sharbrough
Summary: The study reveals that in plant whole genome duplication events, the imbalance in copy numbers between nuclear and organellar genomes can trigger an immediate cellular response, with polyploids maintaining an elevated organellar genome copy number trend despite changes in nuclear genome copy number. Maintenance of cytonuclear stoichiometry is identified as a crucial component in the establishment of polyploid lineages.
Article
Plant Sciences
Wentao Sheng, Jianlan Deng, Chao Wang, Quan Kuang
Summary: In this study, the whole mitochondrial genome of garden asparagus was sequenced, annotated and assembled using a combination of Illumina and PacBio data. The circular mitochondrial genome of garden asparagus was found to be 492,062 bp with a GC value of 45.9%. It contained 36 protein-coding genes, 17 tRNA genes, and 6 rRNA genes, along with several SSRs and sequence fragments that had migrated from the chloroplast genome. Phylogenetic analysis revealed a close genetic relationship between garden asparagus and onion within the Liliaceae family. The study provides valuable insights into gene exchange between organelle genomes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Sergey Gulyaev, Xin-Jie Cai, Fei-Yi Guo, Satoshi Kikuchi, Wendy L. Applequist, Zhi-Xiang Zhang, Elvira Horandl, Li He
Summary: This study used whole genome re-sequencing data to reconstruct the phylogenetic relationships of willows. The results revealed differences between clade Salix and clade Vetrix, with multiple subclades identified within each clade. The chloroplast genomes provided better resolution for distinguishing these two clades. The findings highlight the importance of whole genome re-sequencing for phylogenomic studies of willows.
Review
Biotechnology & Applied Microbiology
Shanshan Zhang, Wenzhong Yang, Jian Chen, Chuanguang Zhang, Siqi Zhang, Lanjing Gao
Summary: Scleroderma yunnanense is a popular edible mushroom in Yunnan Province, China, with significant ecological and economic implications. This study presents the first genome assembly and annotation of S. yunnanense, identifying functional genes involved in secondary metabolite and carbohydrate production pathways.
Article
Plant Sciences
Chenxin Li, Chaonan Cai, Yutian Tao, Zhongshuai Sun, Ming Jiang, Luxi Chen, Junmin Li
Summary: The study sequenced 27 complete chloroplast genomes of 11 wild Fragaria species and analyzed the variation among them, revealing higher variability in non-coding regions compared to coding regions. Five variable loci suitable for DNA barcoding of Fragaria species were identified. Phylogenetic analyses based on the whole cp genomes supported the clustering of species into two groups, with different geographic distributions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
R. K. Srivastava, A. K. Singh, R. P. Bansal, A. Pal, P. Khare, R. S. Sharma, S. Kumar, A. Kalra
Summary: Several Asian countries have the tradition of offering flowers, leaves, and fragrant smoke to the Gods and Goddesses at places of worship. However, the improper disposal of flower waste and burning of incense sticks cause air, soil, and water pollution. To tackle this issue, the Council of Scientific and Industrial Research-Central Institute Medicinal and Aromatic Plants (CSIR-CIMAP) in India has developed a technology to make incense sticks and fragrant cones using offered flowers and leaves, reducing environmental pollution.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anagha S. Setlur, K. Chandrashekar, Ritwija Bhattacharjee, Jitendra Kumar, Vidya Niranjan
Summary: The study aimed to decipher the mechanism of interaction between selected natural actives and larval proteins of A. aegypti to identify potential natural alternative larvicides. The structures of larval proteins were modeled and validated, and the ligand properties and toxicities of natural actives were predicted. Molecular docking and simulation studies revealed the robustness of docking and molecular mechanisms of interactions. Evolutionary studies and protein-protein interaction network analysis demonstrated the potential of these natural compounds as larvicides. Therefore, this study provides computational insights into the molecular interaction of naturals against larval proteins.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Anagha S. Setlur, Chandrashekar Karunakaran, Shruti Pandey, Manas Sarkar, Vidya Niranjan
Summary: This study explores the structural and molecular binding properties of natural alternative thymol against the principal vector Aedes aegypti. Thymol was found to form stable complexes with glutathione-S-transferase, octopamine receptor, and glutamate-gated chloride channels.
MOLECULAR SIMULATION
(2023)
Article
Biochemistry & Molecular Biology
Vidya Niranjan, Sanjana Jayaprasad, Akshay Uttarkar, Raviraj Kusanur, Jitendra Kumar
Summary: Breast cancer is a heterogeneous disease and the second leading cause of cancer-related deaths among women. Plant-based derivatives and their derivatives are safer than synthetic compounds in combating chemoresistance. In this study, a template-based design of a coumarin derivative was developed to target the ADP-sugar pyrophosphatase protein. Molecular docking, molecular dynamics simulation, and metadynamics studies were performed, demonstrating the stable interaction and potential anticancer activity of the designed coumarin derivative. In vitro validation using a cytotoxicity assay confirmed its effectiveness.
Article
Biochemistry & Molecular Biology
Sinosh Skariyachan, Prinith Kaveramma Uluvangada Praveen, Akshay Uttarkar, Vidya Niranjan
Summary: This study screened potential molecular targets and natural lead candidates for BCC using computational modeling, molecular docking, and MD simulation. The 3D structures of the targets were predicted computationally and the drug-likeness and pharmacokinetic properties of 70 natural compounds were assessed. The best lead molecules were identified through molecular docking and their stability was validated by MD simulation. Honokiol showed effective binding with the targets and ideal drug-likeness and pharmacokinetic features, making it a potential lead molecule against BCC.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Satyamvada Maurya, Amita Jain, Md Tabish Rehman, Ali Hakamy, Farkad Bantun, Mohamed F. AlAjmi, Vineeta Singh, Aafreen Zehra, Feroz Khan, Shafiul Haque, Bhartendu Nath Mishra
Summary: This study aimed to identify potential new drug targets/candidates for multi-drug-resistant Mycobacterium tuberculosis (Mtb) through computational techniques. The protein structure of ribonuclease VapC2 of Mtb H37Rv was analyzed, and docking studies were performed with 22 anti-TB drugs. Rifampicin showed the best binding energy and was selected as the parent molecule for designing derivatives. One of the derivatives, RIF-155841, showed activity in inhibiting VapC2. Molecular dynamics simulations confirmed the stability of the VapC2-RIF155841 complex, and a chemical synthesis scheme was designed for future validation.
Article
Biotechnology & Applied Microbiology
D. Sujitha, H. G. Jalendra Kumar, Garima Thapliayal, Garima Pal, P. A. Vanitha, Akshay Uttarkar, Mahesh Patil, B. H. Rajashekar Reddy, Vidya Niranjan, Usha Rayalcheruvu, Geetha Govind, M. Udayakumar, Ramu S. Vemanna
Summary: Through microarray analysis, we identified 52 differentially expressed transcription factors (TFs) that induce gene expression in resistant or sensitive genotypes under oxidative stress. These TFs have reactive oxygen species binding elements (ROSE) in their promoters. Promoter analysis of stress-responsive genes revealed different expression patterns in contrasting rice genotypes. The transcript levels of TFs correlate with the expression of stress-responsive genes involved in various pathways. Functional validation of HSF-C1a confirmed its role as a transcriptional regulator of oxidative stress tolerance. These TFs can serve as markers and potential candidates for improving stress tolerance in plants.
PLANT BIOTECHNOLOGY REPORTS
(2023)
Article
Microbiology
N. Kavya, M. K. Prasannakumar, Gopal Venkateshbabu, Vidya Niranjan, Akshay Uttarkar, P. Buela Parivallal, Sahana N. Banakar, H. B. Mahesh, Pramesh Devanna, K. G. Manasa, Tagginahalli N. Shivakumara
Summary: In this study, seven novel effectors in Rhizoctonia solani were identified and their functions, reactivity, and stability were evaluated. Target proteins involved in the regulation of rice defense mechanisms were also identified. These findings have implications for the management of sheath blight in rice.
Article
Mathematical & Computational Biology
Piyush Bhanu, Anagha S. Setlur, K. Chandrashekar, Vidya Niranjan, Nisha Hemandhar Kumar, Sakshi Buchke, Jitendra Kumar, Anita Rani, Sushil M. Tiwari, Vachaspati Mishra
Summary: We conducted docking and molecular docking simulation (MDS) analyses on fifty-one drugs known for their potential disease treatment roles and identified five compounds with promising features as potential repurposing candidates for COVID-19. These compounds, namely boswellic acid, pimecrolimus, GYY-4137, BMS-345541, and triamcinolone hexacetonide, interacted with the chosen receptors 1R42, 4G3D, 6VW1, 6VXX, and 7MEQ, respectively, with binding energies of -9.2 kcal/mol, -9.1 kcal/mol, -10.3 kcal/mol, -10.1 kcal/mol, and -8.7 kcal/mol. MDS studies revealed the importance of the chosen receptor, human NF-kappa B transcription factor, as a crucial drug target in COVID-19-based drug development strategies.
Article
Biochemistry & Molecular Biology
Sumeer Ahmed, Ajmal R. Bhat, Aziz Kalilur Rahiman, Rajendra S. Dongre, Aso Hameed Hasan, Vidya Niranjan, C. Lavanya, S. A. Sheikh, Joazaizulfazli Jamalis, Malika Berredjem, Sarkar M. A. Kawsar
Summary: In this study, a series of thiazolidine-2,4-dione derivatives were synthesized and evaluated for their antibacterial and antifungal activities. The results showed that these derivatives exhibited strong antimicrobial effects against a broad range of microorganisms, and molecular docking study revealed their strong interaction with the target enzyme. Pharmacokinetic studies also indicated the drug-like properties and non-toxic nature of these compounds.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Vidya Niranjan, Anagha S. Setlur, K. Chandrashekar, Sneha Kumkum, Sanjana Dasgupta, Varsha Singh, Vrushali Desai, Jitendra Kumar
Summary: This study proposes a synergistic approach to combat breast cancer by blocking AP2A2 factor, making cancer cells more sensitive to anti-cancer drugs. The results show that certain natural molecules can stably block AP2A2 and act in synergy with anti-cancer drugs on breast cancer cells.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Vidya Niranjan, Akshay Uttarkar, Ananya Ramakrishnan, Anagha Muralidharan, Abhay Shashidhara, Anushri Acharya, Avila Tarani, Jitendra Kumar
Summary: The drug discovery and research for an anti-COVID-19 drug is still ongoing despite the availability of repurposed drugs in the market. Machine Learning (ML) plays a critical role in the search for novel drug compounds targeting the spike protein of SARS-CoV-2.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Oncology
C. Lavanya, S. Pooja, Abhay H. Kashyap, Abdur Rahaman, Swarna Niranjan, Vidya Niranjan
Summary: Lung cancer is the most common and deadliest cancer type, with two main subtypes: small cell lung cancer and non-small cell lung cancer. RNA-Seq has aided in understanding gene expression in lung cancer diagnostics, but discovering biomarkers remains challenging. Machine learning models can classify biomarkers based on gene expression levels, and the Random Forest classifier showed the best performance in predicting NSCLC and SCLC biomarkers.
CANCER INFORMATICS
(2023)
Article
Ecology
A. Kumar, A. C. Jnanesha, V. M. Kumar, R. K. Lal
Summary: This study investigated the stability of economic traits in five ashwagandha genotypes in south India and found significant differences among different genotypes. Choosing one trait had a beneficial impact on its associated attributes, and genotypes nearest the ideal variety were more desirable. Two genotypes, W.S.3 and W.S.5, showed highly stable dry root yield with high-quality alkaloids and are recommended for further cultivation in south India.
ACTA ECOLOGICA SINICA
(2023)
Article
Ecology
R. K. Lal, C. S. Chanotiya, V. R. Singh, P. Gupta, A. Mishra, S. Srivastava, A. Dwivedi
Summary: The goal of this study was to investigate the impact of genetic and environmental factors on the yield and content of patchouli essential oil and alcohol in India. The study found significant differences in most of the traits and identified stable and high-yielding genotypes. Additionally, a novel compound called ar-curcumene was discovered in certain genotypes. This research provides valuable insights for cultivating patchouli in India.
ACTA ECOLOGICA SINICA
(2023)
