Article
Biochemistry & Molecular Biology
Heather L. Vellers, Hye-Youn Cho, Wesley Gladwell, Kevin Gerrish, Janine H. Santos, Gaston Ofman, Laura Miller-DeGraff, T. Beth Mahler, Steven R. Kleeberger
Summary: In this study, the role of NRF2 in lung mitochondrial genomic features was investigated in mice. The findings showed that Nrf2 deficiency resulted in decreased mtDNA copies in the embryonic lungs and higher heteroplasmy frequency at E18.5. Additionally, exposure to hyperoxia led to increased expression of mitochondria-encoded genes regulating oxidative phosphorylation. These results highlight the potential importance of NRF2 in modulating mitochondrial function in response to oxidative stress.
Article
Genetics & Heredity
Rajan Kumar Jha, Chhavi Dawar, Qurratulain Hasan, Akhilesh Pujar, Gaurav Gupta, Venugopalan Y. Vishnu, Ramesh Kekunnaya, Kumarasamy Thangaraj
Summary: The study revealed that LHON cases are mainly caused by three primary variants, but there are still patients without these primary variants who carry other LHON-associated variants. Additionally, no individual haplogroups were explicitly associated with LHON, while two specific variants showed a significant association with the LHON phenotype.
Article
Genetics & Heredity
Pallavi Shukla, Srabani Mukherjee, Anushree Patil, Beena Joshi
Summary: Emerging studies have found that mitochondrial dysfunction and mtDNA variants play a role in the development of PCOS. Rare variants in mtDNA, in addition to common variants, may modify the risk of disease. High throughput sequencing techniques allow for comprehensive characterization of mtDNA variants, but rare variants in mtDNA encoding genes have not been extensively explored in women with PCOS. This study analyzed mtDNA copy number and variants in mtDNA encoded genes in PCOS patients for the first time using NGS, and identified significant reduction in mtDNA copy number and numerous prioritized variants that may contribute to mitochondrial dysfunction in PCOS. This study provides novel insights into the pathogenesis of PCOS by focusing on mitochondrial genetic defects as an underlying cause of mitochondrial dysfunction in women with PCOS.
Article
Genetics & Heredity
Dan Peng, Jiaojiao Geng, Jingyi Yang, Jiajun Liu, Nana Wang, Riga Wu, Hongyu Sun
Summary: The ForenSeq mtDNA Whole Genome Kit was used to detect the mtGenome in blood samples and hair shafts of 33 individuals, and high-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed, and 26 point heteroplasmy (PHP) and 11 length heteroplasmy (LHP) variations were evaluated. The study demonstrates the effective capability of the ForenSeq mtDNA Whole Genome Kit in generating complete mtGenome and highlights the complexity of mtDNA haplotype comparisons when considering heteroplasmy.
Article
Multidisciplinary Sciences
Pei - Tsai, Ekaterina Korotkevich, Patrick H. O'Farrell
Summary: Unknown processes lead to accumulation of mitochondrial DNA mutations, which promote heteroplasmic mitochondrial diseases and degenerative changes with aging. Purifying selection operates during development and growth, but loses effectiveness during aging. Quality control pathways and pharmacological interventions can mitigate accumulation of deleterious mutations and improve health span.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Medicine, Research & Experimental
Shanshan Guo, Kaixiang Zhou, Qing Yuan, Liping Su, Yang Liu, Xiaoying Ji, Xiwen Gu, Xu Guo, Jinliang Xing
Summary: This study evaluated key analysis procedures for mtDNA sequencing data in different sample types. It was found that trimming was essential for improving mtDNA mapping in plasma but not tissue samples, and using specific reference sequences was suggested for mutation detection in plasma. Additionally, setting 3 mismatches was deemed appropriate for mutation calling.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Multidisciplinary Sciences
Pedro Silva-Pinheiro, Pavel A. Nash, Lindsey Van Haute, Christian D. Mutti, Keira Turner, Michal Minczuk
Summary: Mutations in mitochondrial DNA can lead to clinically heterogeneous diseases. Here the authors demonstrate in vivo base editing of mouse mitochondrial DNA in a post-mitotic tissue by AAV delivery of DddA-derived cytosine base editor (DdCBE).
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kimberly Sturk-Andreaggi, Joseph D. Ring, Adam Ameur, Ulf Gyllensten, Martin Bodner, Walther Parson, Charla Marshall, Marie Allen
Summary: Whole-genome sequencing data can be utilized for genetics research, including population studies. However, the reconstruction of mitochondrial genome can be complicated by nuclear mitochondrial DNA segments. This study assessed the ability to produce authentic mitochondrial genome haplotypes from WGS data and found that a 10% variant detection threshold may be necessary to ensure reliability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Larry N. Singh, Brian Ennis, Bryn Loneragan, Noah L. Tsao, M. Isabel G. Lopez Sanchez, Jianping Li, Patrick Acheampong, Oanh Tran, Ian A. Trounce, Yuankun Zhu, Prasanth Potluri, Beverly S. Emanuel, Daniel J. Rader, Zoltan Arany, Scott M. Damrauer, Adam C. Resnick, Stewart A. Anderson, Douglas C. Wallace
Summary: The study introduces a novel software, MitoScape, which accurately extracts mitochondrial DNA sequences using machine learning to model the unique characteristics of mitochondrial genetics, showing superior performance in heteroplasmy estimation. By applying MitoScape to common disease examples, important heteroplasmy-disease associations are discovered, highlighting its importance in personalized medicine and clinical diagnostics.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Neurosciences
Amber Watts, Prabhakar Chalise, Jinxiang Hu, Dongwei Hui, Judy Pa, Shea J. Andrews, Elias K. Michaelis, Russell H. Swerdlow
Summary: This study examined the role of mitochondrial DNA (mtDNA) in cognitive decline, specifically in the domain of verbal memory. The results showed that individuals carrying the J haplogroup had lower baseline performance and slower rates of improvement in verbal memory compared to those carrying the H haplogroup. No significant differences were observed in executive function or attention. Further research is needed to investigate the underlying mechanisms by which mtDNA affects cognitive performance in different domains across haplogroups.
JOURNAL OF ALZHEIMERS DISEASE
(2022)
Article
Genetics & Heredity
Qi Liu, Muhammad Faaras Iqbal, Tahir Yaqub, Sehrish Firyal, Yiqiang Zhao, Mark Stoneking, Mingkun Li
Summary: This study analyzed the transmission of heteroplasmic variants in 16 four-generation families and found that the transmission of most variants appeared to be random and functionally neutral or mildly deleterious. Additionally, a nonsynonymous variant showed a consistent increase in frequency, indicating a potential fitness advantage. The effective bottleneck size during transmission was estimated to be 21-71.
Article
Biochemistry & Molecular Biology
Hansi Weissensteiner, Lukas Forer, Liane Fendt, Azin Kheirkhah, Antonio Salas, Florian Kronenberg, Sebastian Schoenherr
Summary: haplocheck is a tool that accurately detects sample contamination in mitochondrial studies, especially in large-scale datasets, without being affected by phylogenetic distance. It is available as a command-line tool and cloud web service for easy access to interactive reports.
Article
Medical Laboratory Technology
Ingrid Florez, Irune Pirrone, Liliana Casique, Carmen Luisa Dominguez, Antonieta Mahfoud, Tania Rodriguez, Daniel Rodriguez, Marisel De Lucca, Jose Luis Ramirez
Summary: Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is a progressive neurodegenerative mitochondrial disease caused by nucleotide changes in the mtDNA, with the m.3243A>G mutation being the most common. This study analyzed three Venezuelan patients with MELAS syndrome and found common symptoms of lactic acidosis, cerebral atrophy, and muscular system deficit. The mutation m.3243A>G was confirmed in different body samples with varying degrees of heteroplasmy, indicating independent origins for the mutation among the patients' mitochondrial haplogroups.
CLINICAL BIOCHEMISTRY
(2022)
Article
Agriculture, Dairy & Animal Science
Hang Wang, Qian Wen, Tongfei Wang, Fanrong Ran, Meng Wang, Xulei Fan, Shujun Wei, Zhonghu Li, Jiangli Tan
Summary: This study describes the mtgenomes of four wasps and provides new evidence for the two-origin hypothesis of eusociality in the Vespidae. The results contribute to the understanding of species evolution and phylogeny in the family Vespidae.
Article
Genetics & Heredity
Lirong Jiang, Jing Liu, Suyu Li, Yufeng Wen, Xinyue Zheng, Liu Qin, Yiping Hou, Zheng Wang
Summary: This study evaluated the performance of four commonly used variant callers in the heterogeneity authentication of human mtDNA and developed a python-based nanopore analytics pipeline, CmVCall. The results showed that CmVCall can accurately identify heterogeneity and reveal significant levels of individual differences. This analysis pipeline lays a solid foundation for comprehensive research on the characteristics of the mitochondrial genome.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
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
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
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
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
Chemistry, Physical
Shreyasi Banik, Pradeep Kumar, Vikas D. Ghule, Shweta Khanna, Dharmaraja Allimuthu, Srinivas Dharavath
Summary: In this study, a single-step synthesis of nitrogen-rich energetic materials with excellent properties was reported, using commercially available starting materials. These materials showed superior performance compared to benchmark explosives and demonstrated potential applications in space, civil, and military fields.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Viral Rawat, Sona Tiwari, Shweta Khanna, Umang Gupta, S. N. C. Sridhar, Dharmendra K. Yadav, Grace Kaul, Abdul Akhir, Deepanshi Saxena, Saravanan Matheshwaran, Sidharth Chopra, Dharmaraja Allimuthu
Summary: The study presents an in situ lactonization mechanism that generates a unique inhibitor, IITK2020, targeting antimicrobial resistance in S. aureus. This inhibitor shows effectiveness in inhibiting peptidoglycan biosynthesis and is active against multidrug-resistant clinical strains of S. aureus.
CHEMICAL COMMUNICATIONS
(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.