Article
Biochemistry & Molecular Biology
Janet Pinero, Pablo S. Rodriguez Fraga, Jordi Valls-Margarit, Francesco Ronzano, Pablo Accuosto, Ricard Lambea Jane, Ferran Sanz, Laura I. Furlong
Summary: The use of molecular biomarkers in disease diagnosis, monitoring, and drug treatment has increased significantly in recent decades. However, information on the biomarkers being used and their relevance is not readily accessible, posing challenges in finding and analyzing them. We propose a text mining strategy to identify and classify proteomic and genomic biomarkers used in clinical trials. Analysis of the data reveals patterns of use across therapeutic areas over time. This data is made available through the Clinical Biomarker App, a valuable and timely resource for biomarker discovery and development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Tania Lima, Rita Ferreira, Marina Freitas, Rui Henrique, Rui Vitorino, Margarida Fardilha
Summary: Prostate cancer is the most common noncutaneous cancer among men, and there is a need for new noninvasive biomarkers. This study used text-mining and bioinformatic analysis to identify key entities associated with prostate cancer, and confirmed the consistency between gene and protein expression levels of certain proteins. The findings suggest potential biomarkers and demonstrate the applicability of the proposed pipeline.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Plant Sciences
Chloe P. Drummond, Tanya Renner
Summary: Plant trait evolution is influenced by mechanisms of genome evolution, and comparative studies using genome sequencing have shed light on the evolution of plant chemical defense. Chemical defense in plants is achieved through defensive compounds, which play important roles in plant physiology.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
Keqiang Yan, Zhanlong Mei, Jingjing Zhao, Md Aminul Islam Prodhan, Detlef Obal, Kartik Katragadda, Benjamin Doelling, David Hoetker, Dheeraj Kumar Posa, Liqing He, Xinmin Yin, Jasmit Shah, Jianmin Pan, Shesh Rai, Pawel Konrad Lorkiewicz, Xiang Zhang, Siqi Liu, Aruni Bhatnagar, Shahid P. Baba
Summary: This study reveals the central role of histidyl dipeptides in coordinated regulation of myocardial structure, function, and energetics through integrated triomics approach. Higher levels of histidyl dipeptides in the heart were associated with extensive changes in microRNAs targeting contractile proteins, beta-fatty acid oxidation, and citric acid cycle enzymes. The overexpression of carnosine synthesizing enzyme in mice led to enrichment in the expression of contractile proteins, beta-fatty acid oxidation enzymes, and the TCA in the heart. Integration of multiple data sets suggested that beta-fatty acid oxidation and TCA pathways exhibit correlative changes in the Carns transgenic hearts.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2022)
Article
Biochemical Research Methods
Benjamin C. Orsburn
Summary: Mutations in the KRAS gene are common drivers of cancer in humans. This study discovered a promising compound, MRTX1133, that inhibits the activity of KRAS(G12D) mutant proteins in pancreatic cancer cells. Through proteomics and metabolomics analysis, it was found that after 48 hours of treatment, the compound showed different levels of effectiveness in reducing the abundance of KRAS protein in different cell populations.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Katherine F. Steward, Mohammed Refai, William E. Dyer, Valerie Copie, Jennifer Lachowiec, Brian Bothner
Summary: This study demonstrates that physiological stress leads to a reduction in variation and an increase in phenotypic similarity in metabolomes and proteomes. The Replicate Variation Analysis (RVA) approach provides a foundation for understanding omics level shifts in response to cellular stress.
BMC BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Adrianna Radulska, Iwona Pelikant-Malecka, Kamila Jendernalik, Iwona T. Dobrucki, Leszek Kalinowski
Summary: Skin diseases such as psoriasis and psoriatic arthritis are immune-mediated inflammatory diseases. Proteomics and metabolomics have been extensively studied to identify proteins and small molecules involved in the pathogenesis and development of these diseases, aiming to discover biomarkers and targets for biological drugs. This review discusses the utility of proteomics and metabolomics strategies in both research and clinical practice, summarizing studies from animal models to clinical trials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Yuehan Yang, Mara Grace C. Kessler, Maria Raquel Marchan-Rivadeneira, Yong Han
Summary: Constantly evolving drug-resistant superbugs have created a pressing need for new antimicrobial agents. Advances in technology, such as genome mining and bioinformatic algorithms, have revitalized natural product research and allowed for more targeted discovery of potential antimicrobial candidates. Synthetic biology and advanced analytical instruments also enable the rapid identification of novel antibiotics with distinct structures. This review highlights noteworthy examples of antimicrobial agents discovered through various methodologies and emphasizes their potent effectiveness against antimicrobial-resistant pathogens.
Article
Oncology
Argun Akcakanat, Xiaofeng Zheng, Christian X. Cruz Pico, Tae-Beom Kim, Ken Chen, Anil Korkut, Aysegul Sahin, Vijaykumar Holla, Emily Tarco, Gopal Singh, Senthil Damodaran, Gordon B. Mills, Ana Maria Gonzalez-Angulo, Funda Meric-Bernstam
Summary: Molecular profiling in metastatic breast cancer patients revealed common and less frequent but potentially actionable alterations, demonstrating intertumoral heterogeneity and potential evolution of actionable targets with tumor progression. Further optimization of testing and integrated analysis for treatment selection is needed.
CLINICAL CANCER RESEARCH
(2021)
Article
Microbiology
Peng Hou, Vincent V. Nowak, Chanel J. Taylor, Mark J. Calcott, Allison Knight, Jeremy G. Owen
Summary: In this study, 322 actinomycetes were isolated and their genome sequences were obtained from New Zealand lichens. By enumerating biosynthetic gene clusters (BGCs) and comparing to reference collections, it was found that actinomycetes from New Zealand lichens have the genetic capacity to produce large numbers of natural products, which are expected to be different from those identified in previous soil-based studies. This study sheds light on the actinomycete assemblage in New Zealand lichens and highlights the potential of lichen-sourced actinobacteria for discovering new secondary metabolites.
Review
Oncology
Dana C. Borcherding, Kevin He, Neha Amin, Angela C. Hirbe
Summary: This review highlights the role of TYK2 in cancer and metastases, as well as the potential of TYK2 inhibitors as effective cancer therapies. Recent studies have identified TYK2 as an oncogene that is frequently mutated or overexpressed in many types of cancer and metastases. Personalized medicine approaches aid in the more targeted treatment of tumors by detecting specific gene mutations, overexpression, or activity.
Article
Chemistry, Medicinal
Xu Hu, Yuqi Tang, Yuanyuan Liu, Xinwei Pei, Ziwei Huang, Fuhang Song, Huawei Zhang
Summary: By combining different sequencing technologies, the genome and plasmid of the Chrysomycin A-producing strain 891 were successfully assembled. The strain was identified as belonging to the Streptomyces genus, and key biosynthetic gene clusters for Chrysomycin were identified. These findings provide insights for further research on increasing the production of Chrysomycin A using genetic engineering and combinatorial biology approaches.
Article
Clinical Neurology
Dominique F. Leitner, Yik Siu, Aryeh Korman, Ziyan Lin, Evgeny Kanshin, Daniel Friedman, Sasha Devore, Beatrix Ueberheide, Aristotelis Tsirigos, Drew R. Jones, Thomas Wisniewski, Orrin Devinsky
Summary: High-fat and low-carbohydrate diets, such as the modified Atkins diet (MAD), can reduce seizure frequency in treatment-resistant epilepsy patients. These diets mimic fasting and induce high levels of ketone bodies, potentially shifting brain energy production and impacting neuronal and astrocyte metabolism.
Review
Cardiac & Cardiovascular Systems
Alex N. Smith, Raffaele Altara, Ghadir Amin, Nada J. Habeichi, Daniel G. Thomas, Seungho Jun, Abdullah Kaplan, George W. Booz, Fouad A. Zouein
Summary: Heart failure with preserved ejection fraction (HFpEF) is a medical anomaly with undefined metabolic and molecular alterations. Various animal models and genomic approaches have been used to better understand the pathophysiological and metabolic developments in HFpEF, providing insights into potential pharmacotherapy options.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2022)
Article
Biotechnology & Applied Microbiology
Haiyu Zhang, Lu Wang, Dechun Yin, Qi Zhou, Lin Lv, Zengxiang Dong, Yuanqi Shi
Summary: This study integrates proteomics and metabolomics analyses to explore the dysregulated proteins and metabolites in AF patients with and without HF. Several significant pathways and potential biomarkers were identified, and a subclassification of HF based on metabolomics was conducted. This study provides novel insights into the mechanisms of AF-induced HF progression and identifies potential biomarkers for prognosis of AF with HF.
Article
Plant Sciences
Nishi Mishra, Manoj Kumar Tripathi, Sushma Tiwari, Niraj Tripathi, Swapnil Sapre, Ashok Ahuja, Sharad Tiwari
Summary: This experiment explored somaclonal variation as a method to increase drought tolerance in soybean. By treating calli/cell clumps/embryoids, drought-tolerant plantlets were successfully regenerated, confirming the presence of variability through random decamer primers.
Article
Agronomy
Rahul Patidar, Shivam Vajpayee, Sumit Kakade, Moni Thomas, Niraj Tripathi, Anubha Upadhyay, Brajesh Kumar Namdev, Anil Kurmi, H. L. Sharma, P. S. Kulhare
Summary: This study evaluated a low input technology that can improve the yield and quality of pigeonpea under resource-constrained conditions by using different combinations of soil microbes. The results showed that by using this technology, growers can double their income and improve household nutrition and soil nutrient status.
Article
Plant Sciences
Sushmita Mandloi, M. K. Tripathi, Sushma Tiwari, Niraj Tripathi
Summary: This study investigated the genetic variability among different groundnut germplasm using morphological characters and SSR markers. Highly polymorphic markers were identified, and resistant genotypes for foliar diseases were grouped together. These findings can be further utilized for molecular diversity analysis and crop improvement.
ISRAEL JOURNAL OF PLANT SCIENCES
(2022)
Review
Plant Sciences
Niraj Tripathi, Manoj Kumar Tripathi, Sushma Tiwari, Devendra K. Payasi
Summary: This article summarizes the genetic aspects of various diseases caused by pathogens in soybean and the molecular breeding research work conducted to date.
Article
Plant Sciences
Ravindra Singh Solanki, Anita Babbar, Niraj Tripathi
Summary: Genetic diversity of fifty indigenous and exotic kabuli chickpea lines was assessed using 20 SSR markers, with similar clustering patterns found between quantitative traits and molecular analysis, indicating an association between molecular markers and targeted quantitative traits in the study.
BANGLADESH JOURNAL OF BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Satish Kachare, Sharad Tiwari, Niraj Tripathi
Summary: This study investigated the biochemical, physiological, and expression changes of genes related to dehydration response in soybean under water-restricted and well-watered conditions. The results showed significant alterations in growth and proline accumulation of soybean under water restriction. Additionally, the antioxidant enzyme activities varied among different soybean cultivars under water-restricted conditions. This study provides valuable information for selecting osmotic stress-tolerant soybean genotypes and improving the cultivation of this important crop.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2023)
Article
Agronomy
Purnima Singh, Sushma Tiwari, Prerana Parihar, Reeti Singh, Niraj Tripathi, R. K. Pandya, M. K. Tripathi
Summary: A fast method for extracting genomic DNA from the resting structure (sclerotia) of S. rolfsii without proteinase K supplementation has been developed, yielding high quality and quantity of DNA.
Review
Biology
Ruchi Asati, Manoj Kumar Tripathi, Sushma Tiwari, Rakesh Kumar Yadav, Niraj Tripathi
Summary: Chickpea, the third largest pulse crop, has natural abilities to combat drought stress through breeding methods like hybridization and genomics, where root characteristics play a crucial role in improving crop breeding efficiency.
Article
Pharmacology & Pharmacy
Moni Thomas, Kailash C. Meena, Atul Shrivastava, Niraj Tripathi
Summary: Guggul, a resin with immense medicinal properties, has shown cytotoxicity against L929 cells, indicating its potential applications.
ANNALS OF PHYTOMEDICINE-AN INTERNATIONAL JOURNAL
(2022)
Review
Biology
Rakesh Kumar Yadav, Manoj Kumar Tripathi, Sushma Tiwari, Niraj Tripathi, Ruchi Asati, Vinod Patel, R. S. Sikarwar, Devendra K. Payasi
Summary: Chickpea is an important crop with potential for protein provision and soil nitrogen improvement. Fusarium wilt, a major fungal disease, significantly reduces its productivity. Traditional breeding methods are time-consuming and environment-dependent, while modern technologies can enhance conventional approaches to overcome these constraints.
Article
Biology
Prakash N. Tiwari, Sharad Tiwari, Swapnil Sapre, Anita Babbar, Niraj Tripathi, Sushma Tiwari, Manoj Kumar Tripathi
Summary: The drought-tolerant response of forty desi chickpea genotypes was screened through various physio-biochemical selection indices and yield-attributing traits. Genotypes with higher physiological and biochemical traits were identified as tolerant. Among them, genotypes with higher yield per plant and pod numbers were selected. These drought-tolerant genotypes can be further utilized in climate-smart breeding programs for sustainable production under changing climate.
Article
Agronomy
Rahul Sharde, Manoj Kumar Tripathi, Deepa Bhatt, Sushma Tiwari, Mohini Sharma, Yashi Singh Tomar, Niraj Tripathi
Summary: Potato is the third most important crop in the world and it produces more yield, nutrients, and high-quality protein compared to wheat, maize, and rice. However, there are challenges in the production and supply of quality planting materials for potatoes. Therefore, it is crucial to develop a systematic protocol for large-scale production of planting materials.
Review
Biology
Rakesh Kumar Yadav, Manoj Kumar Tripathi, Sushma Tiwari, Niraj Tripathi, Ruchi Asati, Shailja Chauhan, Prakash Narayan Tiwari, Devendra K. Payasi
Summary: Genome editing aims to revolutionize plant breeding and safeguard the global food supply. Mega nucleases were the first tools used for genome editing, followed by zinc finger nucleases (ZFNs) which are more effective due to their ability to create double-stranded breaks. Clustered regularly interspaced short palindromic repeats (CRISPR) are utilized to improve genetics, biomass production, nutrient usage efficiency, and disease resistance. Genome editing technologies can modify plant genomes effectively without introducing foreign DNA, leading to precise breeding methods. Genome-edited crops hold promise for improving the sustainability and climate resilience of food systems and enhancing resistance to abiotic stressors.
Article
Agronomy
Shraddha Tomar, Stuti Sharma, Niraj Tripathi, Sunny Thakur, Nidhi Pathak, Radhyeshyam Sharma, Priya Tiwari
Summary: This study used microsatellite markers to analyze the genetic diversity among 37 lentil genotypes. The results showed abundant genetic diversity and the highly informative polymorphic markers can be used for further polymorphism analysis.
Article
Agronomy
Shikha Upadhyay, A. K. Singh, M. K. Tripathi, Sushma Tiwari, Niraj Tripathi, R. P. Patel
Summary: Soybean is a vital oilseed crop, but it suffers from significant yield loss due to charcoal rot caused by the fungus Macrophomina phaseolina. Researchers used callus and cell suspension cultures from susceptible soybean cultivars to study the impact of toxic culture filtrate generated by the fungus. Continuous exposure to the toxin resulted in high mortality rates, while discontinuous exposure allowed the calli to recover their regeneration capability. Several resistant lines were identified for further study.
Article
Plant Sciences
Vinayak Nayak, Sushmita Patra, Shrushti Rout, Atala Bihari Jena, Rohit Sharma, Kali Prasad Pattanaik, Jay Singh, Shyam S. Pandey, Ravindra Pratap Singh, Sanatan Majhi, Kshitij R. B. Singh, Rout George Kerry
Summary: This study introduces a customized engineering and designing approach for novel nanotherapeutics, which involves the use of polymeric nanoparticles loaded with specific phytocompounds and coated with an antibody targeting the transferrin receptor. This approach aims to effectively tackle AD-related neuroinflammation by crossing the Blood-Brain Barrier and interacting with target molecules within the brain.
Article
Plant Sciences
Zhi Shang, Yating Gao, Yan Xue, Congcong Zhang, Jiahao Qiu, Yihan Qian, Miao Fang, Xin Zhang, Xuehua Sun, Xiaoni Kong, Yueqiu Gao
Summary: This study investigated the mechanism of Shenge Formula (SGF) in the treatment of nonalcoholic fatty liver disease (NAFLD) using proteomics strategy. The results revealed that SGF could regulate the lipid metabolism and energy consumption process of hepatocytes to treat NAFLD.
Article
Plant Sciences
Long You, Ting Shen, Weicheng Hu, Jae Youl Cho
Summary: By activating growth factor receptors such as EGFR and HER2, protopanaxatriol (PPT) can regulate skin moisturizing factors and multiple signaling pathways, thereby protecting and moisturizing the skin.
Article
Plant Sciences
Lingmei Li, Lei Li, Ce Cao, Fan Guo, Aoao Wang, Li Lin, Zixin Liu, Hongxu Meng, Peng Zhang, Gaojie Xin, Jianxun Liu, Junguo Ren, Jianhua Fu
Summary: The study found that Shuangshen Ningxin Capsule (SSNX) has a protective effect against myocardial ischemia-reperfusion injury. It works by correcting abnormal myocardial energy metabolism, changing the levels and distribution patterns of phospholipids, and stabilizing the structure of the myocardial cell membrane. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) can be used to detect the spatial distribution of small molecule metabolites in the myocardium.
Article
Plant Sciences
Nidhi Sharma, Ramakrishna Sistla, Sai Balaji Andugulapati
Summary: The study investigates the anti-fibrotic activity of Yohimbine hydrochloride (YHC) in chronic liver injury. The results show that YHC can reduce inflammation and fibrosis, potentially making it a potential lead compound for liver fibrosis treatment.
Article
Plant Sciences
Tao-tao Wang, Cheng-yong Yang, Li Peng, Li Li, Nan-ting Chen, Xue Feng, Jing Xie, Ting-chun Wu, Tao Xu, Yun-zhi Chen
Summary: QSYQ has been found to have an anti-atherosclerotic effect by targeting TTC39B-LXR mediated reverse cholesterol transport in the liver. QSYQ not only promotes reverse cholesterol transport, but also improves fatty liver and protects liver function.
Article
Plant Sciences
Zhuo Liu, Yuli Geng, Yanjing Huang, Runan Hu, Fan Li, Jiahui Ding, Wenwen Ma, Haoxu Dong, Kunkun Song, Xiaohu Xu, Xiao Wu, Yufan Song, Mingmin Zhang
Summary: This study investigated the therapeutic efficacy of the Bushen Antai recipe (BAR) in abortion-prone mice and explored its potential mechanisms related to myeloid-derived suppressor cells (MDSCs). The results showed that BAR improved embryo absorption rate and increased the number of MDSCs, promoting normal pregnancy processes.
Article
Plant Sciences
Xue-Ping Yang, Jia-Hua Huang, Fan-Long Ye, Qing-Yun Yv, Sheng Chen, Wen-Wei Li, Min Zhu
Summary: This study found that ECH exerts neuroprotective effects on Parkinson's disease (PD) by regulating the expression of the TLR2/NF-kappa B/NLRP3 axis and reducing the expression of alpha-syn.
Article
Plant Sciences
Lihui Qian, Sirui Huang, Xiaoli Liu, Yongxia Jiang, Yongqu Jiang, Yue Hu, Zhou Yang
Summary: This study highlights the potential use of morroniside in treating post-stroke depression (PSD) by activating the MiR-409-3p-mediated BDNF/TrkB signaling pathway.
Article
Plant Sciences
Jiahui Wu, Hoi Lam Zhang, Suisui Guo, Xin Li, Tingxia Dong, Yue Zhu, Karl Wah Keung Tsim
Summary: This study revealed the significant MDR-preventing effects of Acori Tatarinowii Rhizoma (ATR) in fluoxetine-induced Escherichia coli (E. coli). ATR reduced the accumulation of fluoxetine in bacteria and reversed the fluoxetine-induced membrane damage and superoxide response. The polysaccharide fraction of ATR exhibited the most significant anti-MDR activity.
Article
Plant Sciences
Chao-Sheng Lu, Chen-Yu Wu, Yi-Hong Wang, Qing-Qing Hu, Rong-Yue Sun, Min-Jie Pan, Xin-Yu Lu, Ting Zhu, Shuang Luo, Hong-Jing Yang, Dan Wang, Hong-Wei Wang
Summary: This study demonstrates the potential of icariin in alleviating testicular dysfunction induced by T1D, with the involvement of AMPK-mediated Nrf2 activation and NF-kappa B p65 inhibition.
Article
Plant Sciences
Hongkang Zhu, Fanglin Shen, Xiaochen Wang, He Qian, Yu Liu
Summary: This study explores the therapeutic effect and underlying mechanism of chlorogenic acid (CGA) in alleviating sleep deprivation-induced cognitive deficits and neuroinflammation. By interacting with the gut microbiota, CGA improves intestinal barrier, regulates immune function, and enhances hippocampal-dependent spatial memory via Nrf2/PPAR signaling pathways. This research provides important insights into the clinical application of CGA in sleep-related disorders.
Article
Plant Sciences
Meng Liu, Pengli Guo, Mengnan Zeng, Yuhan Zhang, Jufang Jia, Yanling Liu, Xu Chen, Haixue Kuang, Weisheng Feng, Xiaoke Zheng
Summary: This study found that Fre D and Reh C improved S-AKI through the ER-TLR4-IL-1β pathway, and ERα and ERβ may have direct or indirect interactions with TLR4.
Review
Plant Sciences
Puja Ghosh, Niloy Patari, Chennu Manisha, Duraiswamy Basavan, Velammal Petchiappan, Antony Justin
Summary: This article reviews the possible mechanisms of alternative treatment using lectins for cancer, particularly MDRC cancer. Lectins have the ability to reverse drug resistance mechanisms and show synergistic effects when combined with complementary medicine. They can also serve as nano drug carriers for targeted delivery.
Article
Plant Sciences
Tian Lan, Xiao-juan Geng, Si-jia Zhang, Xi-xi Zeng, Jun-jie Ying, Yi Xu, Shi-yu Liu, Ping Li, Yu-hua Tong, Wen Wang, Zhu-jun Mao, Si-wei Wang
Summary: This study investigates the impact of SNS on MAFLD in mice and explores its underlying molecular mechanisms. The results show that SNS effectively reduces lipid accumulation and improves MAFLD through the activation of AMPK and the modulation of lipid metabolism-related proteins.
