Review
Cardiac & Cardiovascular Systems
James H. O'Keefe, Evan L. O'Keefe, Carl J. Lavie, Loren Cordain
Summary: While vegan diets are often promoted as beneficial for cardiovascular health, eliminating animal foods from the diet can have negative health consequences. Our ancestors started consuming meat, fish, seafood, and eggs over 2 million years ago, and humans have genetically adapted to obtain nutrients from both plant and animal sources. Strict veganism can lead to predictable nutrient deficiencies and increase the risk of bone fractures, sarcopenia, anemia, and depression. A plant-forward omnivorous eating pattern that includes modest amounts of animal foods is a more balanced and logical approach to nutrition.
PROGRESS IN CARDIOVASCULAR DISEASES
(2022)
Article
Biotechnology & Applied Microbiology
Yuanhao Li, Bo Jiang, Weijun Dai
Summary: Essential genes are crucial for bacterial viability and new drug discovery, but some false positives generated by Tn-seq may result from gene deletions by bacteria themselves. Deleting genes should be considered when evaluating essentiality, as it has been underestimated in previous studies.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Infectious Diseases
Qiao Liu, Beibei Qiu, Guoli Li, Tingting Yang, Bilin Tao, Leonardo Martinez, Limei Zhu, Jianming Wang, Xuhua Mao, Wei Lu
Summary: This study in eastern China aimed to evaluate risk factors for tuberculosis recurrence and found that older age, previous tuberculosis treatment, and bilateral cavities were associated with higher risk of recurrence. Endogenous relapse was significantly more common than exogenous reinfection in the first 2 years post-treatment.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Voelundur Hafstao, Jari Hakkinen, Helena Persson
Summary: This article presents a method for validating fusion transcripts detected by RNA sequencing in matched whole-genome sequencing data. The pipeline uses discordant read pairs and soft-clipped read alignments to identify supported fusion events and determine genomic breakpoints. The method is faster and more sensitive than commonly used structural variant detection software BreakDancer and Manta.
BMC BIOINFORMATICS
(2023)
Article
Oncology
Ya-Sian Chang, Siang-Jyun Tu, Hong-Da Chen, Chin-Chun Chung, Ming-Hon Hsu, Yu-Pao Chou, Ya-Ting Lee, Ju-Chen Yen, Long-Bin Jeng, Jan-Gowth Chang
Summary: This study demonstrates the importance of comprehensive analysis in hepatocellular carcinoma (HCC). By analyzing genomic and transcriptomic alterations, they found associations between genetic changes, immune checkpoint genes, and the tumor microenvironment, providing potential insights for HCC diagnosis and treatment.
BIOMARKER RESEARCH
(2023)
Article
Endocrinology & Metabolism
Arthur Gilly, Lucija Klaric, Young-Chan Park, Grace Png, Andrei Barysenka, Joseph A. Marsh, Emmanouil Tsafantakis, Maria Karaleftheri, George Dedoussis, James F. Wilson, Eleftheria Zeggini
Summary: In this study, a gene-based meta-analysis was conducted to identify rare variant associations with cardiometabolic proteome. The results revealed significant rare variant associations that can improve the predictive accuracy of genetic factors in common complex diseases. This study demonstrates the power of gene-based meta-analyses for discovering disease-relevant associations complementing common-variant signals.
MOLECULAR METABOLISM
(2022)
Article
Plant Sciences
Soodeh Tirnaz, Naomi Miyaji, Shohei Takuno, Philipp E. Bayer, Motoki Shimizu, Mst. Arjina Akter, David Edwards, Jacqueline Batley, Ryo Fujimoto
Summary: This study investigates the DNA methylation modifications in Brassica rapa subsp. perviridis in response to white rust infection, revealing potential regulatory role of DNA methylation in defense mechanisms.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Immunology
Kamila Romanowski, Benjamin Sobkowiak, Jennifer L. Guthrie, Victoria J. Cook, Jennifer L. Gardy, James C. Johnston
Summary: By combining WGS data with patient-level information, the timing of secondary TB among contacts of active TB patients in British Columbia, Canada can be calculated.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Benjamin M. Nash, Alan Ma, Gladys Ho, Elizabeth Farnsworth, Andre E. Minoche, Mark J. Cowley, Christopher Barnett, Janine M. Smith, To Ha Loi, Karen Wong, Luke St Heaps, Dale Wright, Marcel E. Dinger, Bruce Bennetts, John R. Grigg, Robyn Jamieson
Summary: This study investigates the role of whole genome sequencing, focused assays, and functional genomics in solving unresolved cases of inherited retinal dystrophies (IRDs) to facilitate integration into a broad molecular diagnostic clinical service. The results showed that whole genome sequencing identified variants not covered by targeted capture panel-based strategies, including structural and repetitive region variants. Focused assays also aided in further molecular investigations. These findings highlight the additional benefit and clinical value of these methods in the highly heterogeneous IRDs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
D. S. Kishor, Hea-Young Lee, Hemasundar Alavilli, Chae-Rin You, Jeong-Gu Kim, Se-Young Lee, Byoung-Cheorl Kang, Kihwan Song
Summary: This study identified the orange endocarp color gene in cucumber through genetic mapping and whole-genome sequencing, revealing that a single recessive gene encodes a chaperone DnaJ protein responsible for the orange endocarp phenotype. Point mutations in the CsOr gene were found to increase beta-carotene content in the endocarp tissue, providing insights into developing beta-carotene-rich cucumber varieties.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Natalie Pluta, Arpad von Moers, Astrid Pechmann, Werner Stenzel, Hans-Hilmar Goebel, David Atlan, Beat Wolf, Indrajit Nanda, Ann-Kathrin Zaum, Simone Rost
Summary: This article presents two young girls with severe muscle weakness, muscular dystrophies, and high creatine kinase levels. Despite standard molecular diagnostics, the genetic cause of their conditions remained unknown. However, whole-genome sequencing revealed reciprocal translocations between their X chromosomes and chromosome 5 and chromosome 19, respectively. These findings underscore the importance of accurate clinical data combined with histopathological analysis in identifying genetic factors responsible for complex genetic constellations in Duchenne muscular dystrophy (DMD).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Brigitte Glanzmann, Tracey Jooste, Samira Ghoor, Richard Gordon, Rizwana Mia, Jun Mao, Hao Li, Patrick Charls, Craig Douman, Maritha J. Kotze, Armand V. Peeters, Glaudina Loots, Monika Esser, Caroline T. Tiemessen, Robert J. Wilkinson, Johan Louw, Glenda Gray, Robin M. Warren, Marlo Moeller, Craig Kinnear
Summary: The emergence of next generation sequencing has had a significant impact on genomic research, enabling South African researchers to access high quality data comparable to international standards at the South African Medical Research Council's Genomics Centre. This has enhanced the capacity of African researchers to sequence whole genomes and analyze data locally.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Judith Guitart-Matas, Narjol Gonzalez-Escalona, Meghan Maguire, Anna Vilaro, Jaime Martinez-Urtaza, Lorenzo Fraile, Lourdes Migura-Garcia
Summary: This study provides a comprehensive analysis of the genetic variability within Actinobacillus pleuropneumoniae (APP) serotypes and enhances the understanding of transmission and epidemiological patterns. The correlation between resistance and toxin profiles with the presence of specific genetic elements and serotypes is also determined.
MICROBIOLOGY SPECTRUM
(2022)