Article
Oncology
Tonje Bjornetro, Paula A. A. Bousquet, Kathrine Roe Redalen, Anne-Marie Siebke Troseid, Torben Luders, Espen Stang, Adriana M. M. Sanabria, Christin Johansen, Anniken Jorlo Fuglestad, Christian Kersten, Sebastian Meltzer, Anne Hansen Ree
Summary: Recent studies have found that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological characteristics of this cell-free mitochondrial DNA (mtDNA) are not well understood. In this study, the mtDNA derived from plasma EVs of colorectal cancer patients was compared to that of whole blood, peripheral blood mononuclear cells, and tumor tissue. The results showed that EV mtDNA had more variants and low-level heteroplasmy compared to whole blood mtDNA. The EV mtDNA variants were mainly located in the coding regions and had a higher proportion of missense mutations compared to whole blood and tumor tissue.
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.
Review
Biochemistry & Molecular Biology
Diwaker Tripathi, Delene J. Oldenburg, Arnold J. Bendich
Summary: This review focuses on oxidative damage and glycation damage to plant proteins, lipids, and DNA caused by reactive oxygen species (ROS) and reactive carbonyl groups, respectively. Recent studies have reported glycation damage to DNA in plant mitochondria and plastids. Maize is used as a model to study organellar DNA maintenance during leaf development, where immature organelles with intact DNA are found in slow-growing cells of the basal meristem, while highly-fragmented DNA is observed in mature organelles of fast-growing leaf cells. The coordination of responses to oxidation and glycation events during leaf development requires further investigation.
Article
Medical Laboratory Technology
Kaixiang Zhou, Yang Liu, Qing Yuan, Dong Lai, Shanshan Guo, Zhenni Wang, Liping Su, Huanqin Zhang, Xiangxu Wang, Wenjie Guo, Xiaoying Ji, Xiwen Gu, Qichao Huang, Xu Guo, Jinliang Xing
Summary: In this study, the researchers comprehensively analyzed the fragmentomic and mutational characteristics of cell-free mitochondrial DNA (cf-mtDNA) in urine and plasma samples. They found that urine cf-mtDNA exhibited increased copy numbers and wider spread in fragment size distributions compared to plasma cf-mtDNA. The results also showed that urine cf-mtDNA originated predominantly from local shedding and transrenal excretion. Furthermore, an enhanced fragmentation and mutation profiles of urine cf-mtDNA were observed in renal cell carcinoma (RCC) and colorectal cancer (CRC) patients, which could potentially be used for cancer diagnosis.
CLINICAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Arunas L. Radzvilavicius, Iain G. Johnston
Summary: Organelle bottlenecks can promote adaptation and evolvability of beneficial mutations.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Plant Sciences
Diwaker Tripathi, Delene J. Oldenburg, Arnold J. Bendich
Summary: During the development of maize leaves, the damage to organellar DNA caused by ribonucleotides increases by 2 to 5-fold, while the levels of the repair enzyme RNase H decline. This may contribute to the decline in organellar genome integrity during maize development.
Article
Medicine, General & Internal
Deborah Tolomeo, Daniele Orsucci, Claudia Nesti, Jacopo Baldacci, Roberta Battini, Claudio Bruno, Giorgia Bruno, Denise Cassandrini, Stefano Doccini, M. Alice Donati, Annarita Ferrari, Simona Fiori, Chiara Fiorillo, Renzo Guerrini, Francesco Mari, Martino Montomoli, Francesca Pochiero, Elena Procopio, Lucia Ruggiero, Simone Sampaolo, Federico Sicca, Chiara Ticci, Anna Rubegni, Filippo M. Santorelli
Summary: Mitochondrial diseases (MDs) are a group of genetically determined multisystem disorders characterized by diagnostic challenges and a lack of genetic studies. Neuroimaging evidence of basal ganglia (BG) involvement and psychomotor regression are important predictors for diagnosing MD.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Genetics & Heredity
Elsa Andrea Brugnoli, Alex Leonel Zilli, Florencia Marcon, Enzo Caballero, Eric Javier Martinez, Carlos Alberto Acuna
Summary: By evaluating the hybrid offspring of Paspalum notatum and Paspalum simplex, differences were observed in agronomic traits and apomixis expressivity, with some traits being superior to the controls. It was found that the apomixis expressivity in P. simplex hybrids varied from 0% to 100%, with 65% of the hybrids showing high apomixis expressivity (above 70%). This indicates that it is possible to generate hybrids with high apomixis expressivity, good agronomic performance, and offspring homogeneity in tetraploid P. notatum and P. simplex.
Article
Biochemistry & Molecular Biology
Shafi Mahmud, Suvro Biswas, Shamima Afrose, Mohasana Akter Mita, Md Robiul Hasan, Mst Sharmin Sultana Shimu, Gobindo Kumar Paul, Sanghyun Chung, Md Abu Saleh, Sultan Alshehri, Momammed M. Ghoneim, Maha Alruwaily, Bonglee Kim
Summary: Mitochondria play a major role in cellular energy production and mitochondrial disorders can cause various symptoms. Traditional diagnostic methods have limitations, while genetic sequencing offers a more accurate alternative.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Review
Medicine, General & Internal
Andrew D. King, Hany Deirawan, Paytra A. Klein, Bahar Dasgeb, Catherine I. Dumur, Darius R. Mehregan
Summary: Over the past decade, Next-Generation Sequencing (NGS) has greatly contributed to the diagnosis and management of various dermatological conditions, including genetic diseases of the skin, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma.
FRONTIERS IN MEDICINE
(2023)
Article
Plant Sciences
Sean V. Burke, William P. Wysocki, Fernando O. Zuloaga, Joseph M. Craine, J. Chris Pires, Patrick P. Edger, Dustin Mayfield-Jones, Lynn G. Clark, Scot A. Kelchner, Melvin R. Duvall
Article
Genetics & Heredity
Lauren M. Orton, Sean V. Burke, William P. Wysocki, Melvin R. Duvall
Article
Plant Sciences
Melvin R. Duvall, Amanda E. Fisher, J. Travis Columbus, Amanda L. Ingram, William P. Wysocki, Sean V. Burke, Lynn G. Clark, Scot A. Kelchner
INTERNATIONAL JOURNAL OF PLANT SCIENCES
(2016)
Correction
Multidisciplinary Sciences
William P. Wysocki, Sean V. Burke, Wesley D. Swingley, Melvin R. Duvall
Article
Ecology
Jane P. DiGiovanni, William P. Wysocki, Sean V. Burke, Melvin R. Duvall, Nicholas A. Barber
RESTORATION ECOLOGY
(2017)
Article
Plant Sciences
Sean V. Burke, Choun-Sea Lin, William P. Wysocki, Lynn G. Clark, Melvin R. Duvall
FRONTIERS IN PLANT SCIENCE
(2016)
Article
Plant Sciences
Sean V. Burke, Colin P. Grennan, Melvin R. Duvall
AMERICAN JOURNAL OF BOTANY
(2012)
Article
Plant Sciences
Sean V. Burke, Lynn G. Clark, Jimmy K. Triplett, Colin P. Grennan, Melvin R. Duvall
AMERICAN JOURNAL OF BOTANY
(2014)
Article
Plant Sciences
Samuel S. Jones, Sean V. Burke, Melvin R. Duvall
PLANT SYSTEMATICS AND EVOLUTION
(2014)
Article
Multidisciplinary Sciences
William P. Wysocki, Sean V. Burke, Wesley D. Swingley, Melvin R. Duvall
Article
Plant Sciences
William P. Wysocki, Lynn G. Clark, Scot A. Kelchner, Sean V. Burke, J. Chris Pires, Patrick P. Edger, Dustin R. Mayfield, Jimmy K. Triplett, J. Travis Columbus, Amanda L. Ingram, Melvin R. Duvall
Article
Ecology
Timothy J. Gallaher, Dean C. Adams, Lakshmi Attigala, Sean V. Burke, Joseph M. Craine, Melvin R. Duvall, Phillip C. Klahs, Emma Sherratt, William P. Wysocki, Lynn G. Clark
Article
Plant Sciences
Melvin R. Duvall, Shrirang R. Yadav, Sean V. Burke, William P. Wysocki
AMERICAN JOURNAL OF BOTANY
(2017)