Article
Biochemistry & Molecular Biology
Feiliang Zhong, Tingting Chen, Bo Li
Summary: Gene expression is regulated by MYBL2, a transcription factor involved in cell cycle progression, which promotes tumor development by regulating genes in the Ras and ErbB signaling pathways.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Guanjue Xiang, Yuchun Guo, David Bumcrot, Alla Sigova
Summary: This article introduces a new method, JMnorm, which can simultaneously normalize multiple epigenetic features, better preserving feature correlations and improving data consistency, as well as enhancing the performance of downstream analyses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li, Jing Li, Jinjian Yang
Summary: Understanding the epigenomic landscape of human tissues, particularly the prostate, plays a key role in investigating disease mechanisms. The comprehensive epigenome map of normal prostate tissue serves as a valuable resource for studying prostate-related diseases, offering detailed insights into regulatory regions and genetic variations associated with prostate health.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Natalie Stewart, Simon Wisnovsky
Summary: Carbohydrate molecules called glycans coat living cells and play crucial roles in cell behavior and disease. Recent advancements in functional genomics technologies have allowed for a better understanding of how glycosylation is regulated and altered in various cell types. These technologies also present opportunities for further research in cellular glycobiology.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhan C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen Gordon, David E. MacHugh
Summary: This study analyzed host gene expression data from bovine alveolar macrophages infected with M. bovis, identifying core infection response pathways and gene modules at the transcriptome level. Integrating this data with GWAS datasets enhanced the detection of genomic variants associated with susceptibility/resistance to M. bovis infection. The results showed that network-based integration of transcriptomics data can provide additional information from GWAS datasets, with significant differences among breeds in SNP discovery for bTB resilience traits.
Article
Oncology
Peng Huang, Mengxiang Xu, Haijun Han, Xinyi Zhao, Ming D. Li, Zhongli Yang
Summary: DNA methylation plays a crucial role in regulating gene expression in hepatocellular carcinoma (HCC). This study identified a large number of differentially methylated CpG sites in HCC and highlighted the activation of cell cycle-related pathways and repression of metabolic pathways.
FRONTIERS IN ONCOLOGY
(2021)
Article
Genetics & Heredity
Xujun Wang, Zhengtao Zhang, Weny Qiu, Shiyi Liu, Cong Liu, Georgi Z. Genchev, Lijian Hui, Hongyu Zhao, Hui Lu
Summary: RePhine is a regression-based pharmacogenomic and ChIP-seq data integration method that infers the impact of transcriptional regulators on drug response. Evaluation on simulation and pharmacogenomic data showed improved performance of RePhine in identifying drug response-related transcriptional regulators.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Cell Biology
Nicolas Eugenie, Yvan Zivanovic, Gaelle Lelandais, Genevieve Coste, Claire Bouthier de la Tour, Esma Bentchikou, Pascale Servant, Fabrice Confalonieri
Summary: Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation, where DdrO and IrrE proteins play a significant role in gene regulation. DdrO acts as a transcriptional repressor under normal growth conditions, while IrrE cleaves DdrO to relieve gene repression after exposure to genotoxic agents. ChIP-seq analysis and RNA-seq experiments have revealed the number of genes regulated by DdrO, paving the way for better understanding of radioresistance pathways in Deinococcus species.
Article
Biology
Eva K. Fischer, Mark E. Hauber, Alison M. Bell
Summary: Driven by the genomic revolution, broadscale RNA expression surveys are replacing studies targeting individual genes to understand behavior. However, RNA-sequencing experiments and neural gene activation dynamics cannot facilitate real-time switches between behavioral states. The complexity of the brain further complicates inference on gene-behavior relationships. Explicit consideration, exploration, and discussion of factors such as environmental influences, timing, and feedback from behavior are crucial for a better understanding of the relationships between genes, environments, brain gene expression, and behavior over developmental and evolutionary timescales.
Article
Biochemistry & Molecular Biology
Haoyang Zhou, Viorel Simion, Jacob B. Pierce, Stefan Haemmig, Alex F. Chen, Mark W. Feinberg
Summary: Chronic vascular inflammation in atherosclerosis is influenced by a novel long non-coding RNA, lncRNA-MAP3K4, which regulates inflammation through the p38 MAPK signaling pathway. The expression of lncRNA-MAP3K4 is modulated during chronic and acute inflammatory conditions, and knockdown of this lncRNA can reduce inflammatory factor expression in various vascular cells. Cooperation between lncRNA-MAP3K4 and MAP3K4 in reducing inflammation in endothelial cells has also been demonstrated.
Article
Chemistry, Multidisciplinary
Federica Gamberoni, Marina Borgese, Christina Pagiatakis, Ilaria Armenia, Valeria Grazu, Rosalba Gornati, Simone Serio, Roberto Papait, Giovanni Bernardini
Summary: Despite the progress in nanotoxicology, the cellular mechanisms of nanoparticles' adverse effects and the role of epigenetics in nanotoxicity remain unclear. This study investigated changes in histone modifications and transcriptome after exposing NIH3T3 cells to iron-based magnetic NPs. The results suggest that alterations in the epigenetic landscape play a key role in defining gene expression changes and nanotoxicity.
Article
Cell Biology
Chitvan Mittal, Olivia Lang, William K. M. Lai, B. Franklin Pugh
Summary: In this study, researchers found that specific sequence transcription factors and their cofactors are bound to promoters prior to induction, rather than recruited upon induction. Induction recruits the preinitiation complex to DNA. This suggests that inducible systems are integrated with constitutive systems.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Juan Manuel Marti, Angel Garcia-Diaz, Daniel Delgado-Bellido, Francisco O'Valle, Ariannys Gonzalez-Flores, Onintza Carlevaris, Jose Manuel Rodriguez-Vargas, Jean Christophe Ame, Francoise Dantzer, George L. King, Klaudia Dziedzic, Edurne Berra, E. de Alava, A. T. Amaral, Ester M. Hammond, F. Javier Oliver
Summary: The study reveals a strong association between PARP-1 and HIF-1α expression in human melanoma, showing that the regulation of HIF-1α by PARP-1 can impact cell adaptation to hypoxia and potentially affect cancer treatment outcomes.
Article
Microbiology
Ioana M. Marian, Peter Jan Vonk, Ivan D. Valdes, Kerrie Barry, Benedict Bostock, Akiko Carver, Chris Daum, Harry Lerner, Anna Lipzen, Hongjae Park, Margo B. P. Schuller, Martin Tegelaar, Andrew Tritt, Jeremy Schmutz, Jane Grimwood, Luis G. Lugones, In-Geol Choi, Han A. B. Wosten, Igor Grigoriev, Robin A. Ohm
Summary: Wood-degrading fungi play a crucial role in nutrient recycling by breaking down all components of wood. The transcription factor Roc1 has been identified as a key regulator of cellulose degradation in the wood-decaying fungus Schizophyllum commune. This discovery provides important insights into the metabolic mechanism of wood-decaying fungi.
Article
Oncology
Quang Ong, Shingo Sakashita, Emi Hanawa, Naomi Kaneko, Masayuki Noguchi, Masafumi Muratani
Summary: The study conducted RNA-Seq and ChIP-Seq integrative analysis of clinical lung tissue samples to capture transcriptomic profiles and identify somatically altered regions marked by H3K4me3 in lung cancer. Differential expressions of cancer-related genes and enhancer activity annotations of cancer regulatory genes were observed near the altered H3K4me3 regions. The study demonstrated a practical workflow of using LMD on clinical samples for integrative analyses, improving the understanding of genetic and epigenetic dysregulation in malignancy.
Article
Plant Sciences
Arijit Panda, Diya Sen, Arup Ghosh, Akash Gupta, Mathu C. Malar, Gyan Prakash Mishra, Deeksha Singh, Wenwu Ye, Brett M. Tyler, Sucheta Tripathy
MOLECULAR PLANT PATHOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Marco Antonio Pires-Lapa, Marianna Mainardi Koga, Ildefonso Alves da Silva, Luciano Ribeiro Filgueiras, Sonia Jancar
PROSTAGLANDINS & OTHER LIPID MEDIATORS
(2019)
Article
Genetics & Heredity
Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil Kumar Raghav
FRONTIERS IN GENETICS
(2020)
Article
Cell Biology
Shweta Khanna, Prasanta Padhan, Kumar S. Jaiswal, Ankit P. Jain, Arup Ghosh, Archana Tripathy, Harsha Gowda, Sunil K. Raghav, Bhawna Gupta
Article
Immunology
Kumar Sagar Jaiswal, Shweta Khanna, Arup Ghosh, Prasanta Padhan, Sunil Kumar Raghav, Bhawna Gupta
Summary: The study revealed altered mtDNA sequence in immune cells of rheumatoid arthritis (RA) patients, indicating a potential role of mitochondrial genome in RA development and progression.
Article
Infectious Diseases
Pujarini Dash, Jyotirmayee Turuk, Santosh K. Behera, Subrata Kumar Palo, Sunil K. Raghav, Arup Ghosh, Jyotsnamayee Sabat, Sonalika Rath, Subhra Subhadra, Khokan Rana, Debdutta Bhattacharya, Srikanta Kanungo, Jaya Singh Kshatri, Bijaya Kumar Mishra, Saroj Dash, Ajay Parida, Sanghamitra Pati
Summary: This study analyzed the spike protein receptor-binding domain (RBD) sequence of SARS-CoV-2 isolates from COVID-19-positive patients in Odisha, India, and found a specific mutation leading to stronger binding affinity with human ACE2. The RBDs of all Indian isolates showed affinity for ACE2 of different species, suggesting potential wide infectivity and natural reservoirs for the virus.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Microbiology
Sunil Raghav, Arup Ghosh, Jyotirmayee Turuk, Sugandh Kumar, Atimukta Jha, Swati Madhulika, Manasi Priyadarshini, Viplov K. Biswas, P. Sushree Shyamli, Bharati Singh, Neha Singh, Deepika Singh, Ankita Datey, Kiran Avula, Shuchi Smita, Jyotsnamayee Sabat, Debdutta Bhattacharya, Jaya Singh Kshatri, Dileep Vasudevan, Amol Suryawanshi, Rupesh Dash, Shantibhushan Senapati, Tushar K. Beuria, Rajeeb Swain, Soma Chattopadhyay, Gulam Hussain Syed, Anshuman Dixit, Punit Prasad, Sanghamitra Pati, Ajay Parida
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Medicine, Research & Experimental
Pallavi Mohapatra, Omprakash Shriwas, Sibasish Mohanty, Arup Ghosh, Shuchi Smita, Sandeep Rai Kaushik, Rakesh Arya, Rachna Rath, Saroj Kumar Das Majumdar, Dillip Kumar Muduly, Sunil K. Raghav, Ranjan K. Nanda, Rupesh Dash
Summary: CMTM6, a top upregulated protein in chemoresistant oral squamous cell carcinoma, is associated with chemotherapy nonresponse and poorer prognosis. Its role in promoting cell apoptosis, restoring platinum drug sensitivity, and modulating the Wnt signaling pathway is crucial in overcoming therapy resistance.
Article
Immunology
Shuchi Smita, Arup Ghosh, Viplov Kumar Biswas, Abdul Ahad, Sreeparna Podder, Atimukta Jha, Kaushik Sen, Hans Acha-Orbea, Sunil K. Raghav
Summary: Zbtb10 is crucial for the immunogenic function of cDC1 and its knockdown affects cytokine and co-stimulatory gene expression, leading to alterations in CD4(+) T cell responses. Additionally, Zbtb10 KD enhances the expression of T cell anergic markers, potentially influencing T cell tolerance.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Voddu Suresh, Varshasnata Mohanty, Kiran Avula, Arup Ghosh, Bharati Singh, Rajendra Kumar Reddy, Deepti Parida, Amol Ratnakar Suryawanshi, Sunil Kumar Raghav, Soma Chattopadhyay, Punit Prasad, Rajeeb Kumar Swain, Rupesh Dash, Ajay Parida, Gulam Hussain Syed, Shantibhusan Senapati
Summary: This study confirmed the infectivity of a local SARS-CoV-2 isolate in a hamster model, showing similar lung pathology to COVID-19 patients and other hamsters. The lung-associated pathological changes were prominent on the 4th day post-infection and mostly resolved by 14 dpi. Proteomic analysis identified 68 significantly altered proteins between infected groups, with highlighted pathways including complement and coagulation cascade, platelet activation, ferroptosis, and focal adhesion. Additionally, altered expression of pulmonary surfactant-associated proteins Sftpd and Sftpb was observed, suggesting their potential role in SARS-CoV-2 pathogenesis and disease progression.
Article
Biochemistry & Molecular Biology
Ankit K. Pathak, Gyan Prakash Mishra, Bharathram Uppili, Safal Walia, Saman Fatihi, Tahseen Abbas, Sofia Banu, Arup Ghosh, Amol Kanampalliwar, Atimukta Jha, Sana Fatma, Shifu Aggarwal, Mahesh Shanker Dhar, Robin Marwal, Venkatraman Srinivasan Radhakrishnan, Kalaiarasan Ponnusamy, Sandhya Kabra, Partha Rakshit, Rahul C. Bhoyar, Abhinav Jain, Mohit Kumar Divakar, Mohamed Imran, Mohammed Faruq, Divya Tej Sowpati, Lipi Thukral, Sunil K. Raghav, Mitali Mukerji
Summary: During the COVID-19 pandemic, genome sequencing of SARS-CoV-2 has been valuable for tracking its spread and identifying variants of concern. Intra-host single nucleotide variations (iSNVs) can capture variability within a host, and some variations have been found to become fixed in the population. Mutations in the Spike protein may affect antigenicity and immune escape. Therefore, tracking and studying iSNVs in ongoing genome surveillance programs is important for early identification of potential variants of concern.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Marianna M. Koga, Alice Comberlato, Hugo J. Rodriguez-Franco, Maartje M. C. Bastings
Summary: DNA-based nanomaterials have been studied for their stability and uptake in different cell types. This research systematically analyzes the effects of surface parameters, such as charge, coating, fluorophore types, functionalization technique, and particle concentration, on the uptake of DNA-based nanoparticles in tumor cells, macrophages, and dendritic cells. The findings highlight the importance of proper engineering and assay development when using DNA-based materials in bioengineering and future nanotherapeutic agents.
Article
Infectious Diseases
Arup Ghosh, Safal Walia, Roma Rattan, Amol Kanampalliwar, Atimukta Jha, Shifu Aggarwal, Sana Fatma, Niyati Das, Nirupama Chayani, Punit Prasad, Sunil K. Raghav, Ajay Parida
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Punit Prasad, Soumendu Mahapatra, Rasmita Mishra, Krushna Chandra Murmu, Shifu Aggarwal, Manisha Sethi, Priyanka Mohapatra, Arup Ghosh, Rina Yadav, Hiren Dodia, Shamima Azma Ansari, Saikat De, Deepak Singh, Amol Suryawanshi, Rupesh Dash, Shantibhushan Senapati, Tushar K. Beuria, Soma Chattopadhyay, Gulam Hussain Syed, Rajeeb Swain, Sunil K. Raghav, Ajay Parida
Summary: This study found dysbiosis and an increase in opportunistic pathogens in the nasopharyngeal microbiome of COVID-19 patients. The enrichment of Mycobacteria and Mycoplasma in symptomatic patients was strongly correlated with chest pain and fever.