Article
Multidisciplinary Sciences
Theodore A. Chavkin, Loc-Duyen Pham, Aleksandar Kostic
Summary: The study found that oral probiotics EcN can reduce postprandial glycemic response in mice, but not through direct glucose uptake. Further exploration is needed to understand the potential indirect mechanisms of EcN on host glucose metabolism.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Multidisciplinary
Xin Zhao, Zhangjiang He, Yifei Gao, Yanze Kan, Yufei Jiao, Yunxia Liu, Shuaishuai Huang, Zhibing Luo, Yongjun Zhang
Summary: In the insect fungal pathogen, Beauveria bassiana, BbSre1 regulates oxidative stress response, peroxisome division, and redox homeostasis. Gene disruption inhibits peroxisome division, affects redox homeostasis, and impairs lipid/fatty acid metabolism and sterol biosynthesis. These findings broaden our understanding of the role of Sre1 in regulating oxidative stress and lipid metabolism.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Tingwen Xiang, Zihan Deng, Chuan Yang, Jiulin Tan, Ce Dou, Fei Luo, Yueqi Chen
Summary: This review summarizes the important roles of bile acids in the gut-bone axis and highlights their regulation of osteoblast and osteoclast activity, as well as their potential to reduce articular cartilage degradation and facilitate bone repair. It also demonstrates the bidirectional effects of bile acid signaling networks in coordinating bone matrix balance and suggests their promising effects in the development or treatment of pathological bone diseases.
PHARMACOLOGICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Hui Wang, Mei Ma, Yuying Li, Jinxin Liu, Chao Sun, Shengnan Liu, Yiruo Ma, Ying Yan, Zhili Tang, Siyi Shen, Jing Yu, Yuting Wu, Jingjing Jiang, Li Wang, Zi-Bing Jin, Hao Ying, Yan Li
Summary: miR-183 and miR-96 have been demonstrated as master coordinators of fuel selection and metabolic homeostasis by modulating glucose utilization and fat catabolism in skeletal muscle. Their loss enhances oxidative phenotype and alters substrate utilization in mice, potentially offering therapeutic targets for obesity and glucose metabolism induced by high-fat diet.
Article
Biochemistry & Molecular Biology
Sebastian Grunberg, Baptiste Coxam, Tien-Hao Chen, Nan Dai, Lana Saleh, Ivan R. Correa, Nicole M. Nichols, Erbay Yigit
Summary: Escherichia coli RNase I has been found to have a strong calcium-dependent activity on double-stranded RNA (dsRNA) and a novel hybridase activity dependent on calcium, while not affecting single-stranded RNA (ssRNA). Mutations in a previously overlooked calcium binding site on RNase I resulted in a gain-of-function enzyme highly active on dsRNA and no longer responsive to metal stimulation. In summary, native RNase I contains a calcium ion binding site, allowing it to target both single- and double-stranded RNAs, indicating a broader substrate specificity than initially proposed.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Immunology
Xiaoxue Deng, Lingxia Wang, Yunze Zhai, Qiuyue Liu, Fengxue Du, Yu Zhang, Wenxing Zhao, Tingtao Wu, Yiwen Tao, Jie Deng, Yongbing Cao, Pei Hao, Jiazi Ren, Yunli Shen, Zuoren Yu, Yuejuan Zheng, Haibing Zhang, Haikun Wang
Summary: Regulatory T (T-reg) cells are important for maintaining immune balance, and RIPK1 plays a critical role in regulating T-reg cell survival and homeostasis by controlling both apoptosis and necroptosis mechanisms.
CELLULAR & MOLECULAR IMMUNOLOGY
(2023)
Review
Cell Biology
Binyue Xu, Lu Chen, Yu Zhan, Karl Nelson S. Marquez, Lvjia Zhuo, Shasha Qi, Jinyu Zhu, Ying He, Xudong Chen, Hao Zhang, Yingying Shen, Gongxing Chen, Jianzhong Gu, Yong Guo, Shuiping Liu, Tian Xie
Summary: This review summarizes the recent advances in the research of FABP5, highlighting its crucial role in modulating cellular processes and participating in the pathogenesis of various diseases. Furthermore, the potential of using FABP5 as a diagnostic biomarker and therapeutic target is discussed, shedding light on future research challenges.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Julien Pujo, Camille Petitfils, Pauline Le Faouder, Venessa Eeckhaut, Gaelle Payros, Sarah Maurel, Teresa Perez--Berezo, Matthias Van Hul, Frederick Barreau, Catherine Blanpied, Stephane Chavanas, Filip Van Immerseel, Justine Bertrand--Michel, Eric Oswald, Claude Knauf, Gilles Dietrich, Patrice D. Cani, Nicolas Cenac
Summary: In this study, it was found that a probiotic strain contained increased levels of 3-hydroxyoctadecaenoic acid (C18-3OH), which was shown to decrease colitis in mice and was associated with anti-inflammatory properties of prebiotic fructooligosaccharides (FOS). The concentration of C18-3OH was correlated with an increase in specific bacterial genera in the microbiota. This suggests that C18-3OH production by bacteria could play a role in the anti-inflammatory properties of probiotics and in microbiota/host interactions.
Article
Oncology
Kun-Chi Chen, I-Hsin Hsiao, Yu-Nan Huang, Yu-Tung Chou, Yi-Chun Lin, Ju-Yi Hsieh, Yung-Lung Chang, Kang-Hsi Wu, Guang-Yaw Liu, Hui-Chih Hung
Summary: Acute myeloid leukemia (AML) is a fast-growing and fatal blood cancer, and targeting the human mitochondrial NAD(P)(+)-dependent malic enzyme (ME2) shows promise in AML treatment. ME2 inhibition through silencing or using its allosteric inhibitor Na(2)EA decreases pyruvate, NADH, and NADPH levels, leading to reduced ATP production, increased reactive oxygen species (ROS), and cellular apoptosis. ME2 inhibition also impairs pyruvate metabolism and the biosynthetic pathway, inhibiting the growth of AML cells. Overall, ME2 plays a crucial role in AML energy metabolism, and its inhibition provides a potential approach for AML treatment.
Article
Plant Sciences
Andrew P. Sayer, Marcel Llavero-Pasquina, Katrin Geisler, Andre Holzer, Freddy Bunbury, Gonzalo Mendoza-Ochoa, Andrew D. Lawrence, Martin J. Warren, Payam Mehrshahi, Alison G. Smith
Summary: Microalgae are important in global ecosystems and require vitamin B-12 for growth. This study identifies a protein, CBA1, that is essential for B-12 uptake in microalgae. Through targeted knockouts and mutagenesis, the researchers demonstrate that CBA1 is necessary for B-12 uptake in two different microalgae species. The study also shows that CBA1 is present in other eukaryotes, indicating its conserved role in the biological kingdom.
Article
Biochemistry & Molecular Biology
Baylee J. Russell, Steven D. Brown, Nicole Siguenza, Irene Mai, Anand R. Saran, Amulya Lingaraju, Erica S. Maissy, Ana C. Dantas Machado, Antonio F. M. Pinto, Concepcion Sanchez, Leigh-Ana Rossitto, Yukiko Miyamoto, R. Alexander Richter, Samuel B. Ho, Lars Eckmann, Jeff Hasty, David J. Gonzalez, Alan Saghatelian, Rob Knight, Amir Zarrinpar
Summary: This study demonstrates the potential of using native bacteria as chassis for transgene delivery to manipulate the gut microbiome and reverse pathology in conventionally raised hosts.
Article
Chemistry, Medicinal
Ebru Cetin, Tandac F. Guclu, Isik Kantarcioglu, Ilona K. Gaszek, Erdal Toprak, Ali Rana Atilgan, Burcu Dedeoglu, Canan Atilgan
Summary: In this study, the researchers investigated the interaction and inhibition mechanisms of a newly proposed DHFR inhibitor, 4´-deoxy methyl trimethoprim (4´-DTMP). They found that the kinetic differences in the inhibitory effects between 4´-DTMP and trimethoprim (TMP) can be attributed to the polar modification in 4´-DTMP, which induces additional interactions with the enzyme. These changes propagate through the hydrogen bond networks in the whole enzyme. The study also highlighted the importance of avoiding segmentation of the loop domain in inhibitor-bound DHFR.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Julien Hurbain, Quentin Thommen, Francois Anquez, Benjamin Pfeuty
Summary: Living cells utilize signaling and regulatory mechanisms to adapt to environmental stresses, including oxidative stress. Research on adaptation to oxidative stress has shown that carbon flux rerouting into the pentose phosphate pathway involves the upregulation of G6PD activity, a decreased NADPH/NADP(+) ratio, and differential control of glycolytic fluxes. These regulatory feedback mechanisms promote efficient detoxification and homeostasis response.
Article
Food Science & Technology
Lanlin Yu, Su Zhang, Yuanyuan Xu, Xiaoyu Mi, Tong Xing, Jiaolong Li, Lin Zhang, Feng Gao, Yun Jiang
Summary: Shiga toxin-producing Escherichia coli (STEC) strains, classified as important foodborne pathogens, exhibited inhibited growth in lactic acid-supplemented medium. Transcriptomic analysis revealed similar responses in acid resistance mechanisms of strains O157 and O26, with O157 showing stronger acid resistance capability and enhanced cysteine biosynthesis playing a crucial role in long-term acid treatment. This study sheds light on deciphering the acid resistance mechanisms of microbes over time and provides insights for better control of microbial-induced food contamination.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Biochemical Research Methods
Adil Alsiyabi, Ariadna Gonzalez Solis, Edgar B. Cahoon, Rajib Saha
Summary: This study reconstructed a metabolic network of the sphingolipid pathway in plants and used ensemble modeling to investigate the regulatory mechanisms. The results suggest a repressive effect of ORMs on SPT and a potential activating role of ORM proteins on ceramide synthases, modulated by the concentration of free ceramides. These predictions pave the way for future guided experiments and have implications in engineering crops with higher biotic stress tolerance.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Environmental Sciences
Janani Ravichandran, Bagavathy Shanmugam Karthikeyan, Palak Singla, S. R. Aparna, Areejit Samal
Summary: This study established the first dedicated knowledgebase, NeurotoxKb 1.0, focusing on environmental neurotoxicants specific to mammals, compiling detailed information on 475 potential neurotoxicants. Through analyzing global chemical regulations and human biospecimens, potential neurotoxicants were identified in external exposomes and detected in human samples, providing insights into human exposure risks associated with these neurotoxicants. The construction of a chemical similarity network revealed the diversity of toxicological space among the 475 potential neurotoxicants.
Article
Biochemistry & Molecular Biology
R. P. Vivek-Ananth, Sankaran Krishnaswamy, Areejit Samal
Summary: The study identified potential natural product inhibitors targeting the ATP-binding site of the SARS-CoV-2 helicase Nsp13 through molecular docking and molecular dynamics simulations. A library of over 14,000 phytochemicals from Indian medicinal plants was used for virtual screening, resulting in 368 phytochemicals identified as potential inhibitors.
MOLECULAR DIVERSITY
(2022)
Article
Chemistry, Multidisciplinary
R. P. Vivek-Ananth, Ajaya Kumar Sahoo, Ashutosh Srivastava, Areejit Samal
Summary: In this study, molecular docking and molecular dynamics simulations were used to virtually screen phytochemicals from Indian medicinal plants as potential inhibitors of SFTSV L polymerase endoN domain. Five potential phytochemical inhibitors were identified and may serve as lead molecules in the development of antiviral drugs against SFTSV.
Article
Multidisciplinary Sciences
Yasharth Yadav, Areejit Samal, Emil Saucan
Summary: This paper presents a method to represent hypergraphs as partially ordered sets and proposes a geometric framework based on posets to compute the Forman-Ricci curvature of vertices and hyperedges in hypergraphs. The empirical study shows a high correlation between Forman-Ricci curvature and standard hypergraph measures.
Article
Biology
Ajay Subbaroyan, Olivier C. Martin, Areejit Samal
Summary: Boolean modelling is a powerful framework for understanding biological networks, and this study focuses on the importance of link operator functions (LOFs) in these networks. The research shows that among all Boolean functions, LOFs form a small subset that is abundant in reconstructed biological networks. By applying steady-state constraints and selecting LOFs that satisfy these constraints, the space of acceptable models can be narrowed down. Furthermore, LOFs are found to drive biological network dynamics towards criticality.
JOURNAL OF BIOSCIENCES
(2022)
Article
Environmental Sciences
Janani Ravichandran, Bagavathy Shanmugam Karthikeyan, Areejit Samal
Summary: An adverse outcome pathway (AOP) is a representation of mechanistic information on adverse effects caused by environmental exposure. This study focuses on the construction and analysis of an endocrine-relevant AOP (ED-AOP) network. The connectivity analysis and graph-theoretic analyses of the network revealed important events and system-level perturbations caused by endocrine disruption, providing insights for risk assessment and the development of new endpoints or assays.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Ajaya Kumar Sahoo, Priya Dharshini Augusthian, Ishwarya Muralitharan, R. P. Vivek-Ananth, Kishan Kumar, Gaurav Kumar, Geetha Ranganathan, Areejit Samal
Summary: A computational drug repurposing study was conducted to identify potential inhibitors for monkeypox virus proteins. Four drugs, Tipranavir, Cefiderocol, Doxorubicin, and Dolutegravir, were identified as candidates for repurposing against monkeypox virus.
MOLECULAR DIVERSITY
(2023)
Article
Chemistry, Multidisciplinary
R. P. Vivek-Ananth, Ajaya Kumar Sahoo, Shanmuga Priya Baskaran, Areejit Samal
Summary: Based on a cheminformatics-based investigation, this study reveals that the secondary metabolite space of medicinal fungi has similar or higher scaffold diversity compared to other natural product libraries. Moreover, the secondary metabolites of medicinal fungi have minimal overlap with approved drugs in terms of chemical space visualization. These findings highlight the potential of medicinal fungi as a valuable resource for natural product-based drug discovery.
Article
Biochemical Research Methods
Ajay Subbaroyan, Priyotosh Sil, Olivier C. Martin, Areejit Samal
Summary: Boolean models are a well-established framework for modeling developmental gene regulatory networks (DGRNs) in cell identity acquisition. This study proposes a method for model selection of Boolean DGRNs by leveraging the developmental landscape and using the relative stability of attractors. The novelty of the methodology is rated at 8 out of 10.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Ananya Natarajan, Nikhil Chivukula, Gokul Balaji Dhanakoti, Ajaya Kumar Sahoo, Janani Ravichandran, Areejit Samal
Summary: Ectopic Pregnancy Expression Knowledgebase (EPEK) is the first and only dedicated resource on the expression profile of ectopic pregnancy (EP) in humans. It includes information on 314 differentially expressed genes, 17 metabolites, and 3 SNPs associated with EP, as well as computational analyses suggesting the involvement of cellular signaling processes in EP and the potential use of exosome markers in EP diagnosis.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
R. P. Vivek-Ananth, Karthikeyan Mohanraj, Ajaya Kumar Sahoo, Areejit Samal
Summary: IMPPAT 2.0 is an enhanced and expanded database that compiles manually curated information on 4010 Indian medicinal plants, 17,967 phytochemicals, and 1095 therapeutic uses. It also provides a nonredundant in silico stereo-aware library of 17,967 phytochemicals from Indian medicinal plants.
Article
Biochemistry & Molecular Biology
Ishwarya Muralitharan, Ajaya Kumar Sahoo, Priya Dharshini Augusthian, Areejit Samal
Summary: Rift Valley fever is a zoonotic disease with potential for a future epidemic. In this study, we use virtual screening to identify 5 potential phytochemical inhibitors from Indian medicinal plants for the cap-binding domain of the Rift Valley fever virus. These inhibitors show promise as drug lead molecules for further experimental validation against RVFV infection.
MOLECULAR DIVERSITY
(2023)
Article
Chemistry, Multidisciplinary
Ajaya Kumar Sahoo, Shanmuga Priya Baskaran, Nikhil Chivukula, Kishan Kumar, Areejit Samal
Summary: The thyroid stimulating hormone receptor (TSHR) plays a crucial role in thyroid hormone production and dysregulation in its activation can have adverse health effects. Animal studies suggest that chemicals binding to TSHR can lead to developmental toxicity. The ToxCast project has screened several such chemicals for their adverse effects in human cells, but the predictive ability of toxicity models can be limited due to variations in structure-activity relationships. This study systematically investigates the heterogeneity in structure-activity and structure-mechanism relationships of TSHR binding chemicals and provides insights for the development of better predictive toxicity models.
Article
Chemistry, Multidisciplinary
R. P. Vivek-Ananth, Ajaya Kumar Sahoo, Shanmuga Priya Baskaran, Areejit Samal
Summary: In this study, the scaffold and structural diversity of the secondary metabolite space of medicinal fungi were investigated using cheminformatics. The results showed that medicinal fungi have similar or higher scaffold diversity compared to other natural product libraries. Moreover, the secondary metabolites of medicinal fungi were found to be structurally different from approved drugs but shared similar molecular properties. These findings highlight the importance of the secondary metabolite space of medicinal fungi for natural product-based drug discovery.
Article
Multidisciplinary Sciences
Ajay Subbaroyan, Olivier C. Martin, Areejit Samal
Summary: This study focuses on biologically meaningful types of Boolean functions and their prevalence in published models. The analysis reveals that most of the functions have an odd bias, producing an odd number of output combinations for inputs. Furthermore, read-once functions and nested canalyzing functions exhibit minimum Boolean complexity and average sensitivity. These results highlight the importance of minimum complexity in the regulatory logic of biological networks.