Article
Evolutionary Biology
Yawako W. Kawaguchi, Yuki Tsuchikane, Keisuke Tanaka, Teruaki Taji, Yutaka Suzuki, Atsushi Toyoda, Motomi Ito, Yasuyuki Watano, Tomoaki Nishiyama, Hiroyuki Sekimoto, Takashi Tsuchimatsu
Summary: In this study, it was found that the genome size variation in the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, is heritable and mainly attributed to genome-wide copy number variation (CNV). The CNV was more frequently observed in genes with stage-specific expression and some of these genes showed dosage compensation. The nonrandom patterns in gene duplications and associated expression changes contribute to the extensive genome size variation in the C. psl. complex.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Agronomy
David G. Heckel
Summary: Gene duplication has long been known to generate evolutionary diversity, but its implications for pesticide resistance are just beginning to be understood. Transposable elements may facilitate this process, but the mechanistic details remain obscure and unpredictable. New developments in DNA sequencing technology and genome assembly offer promise for revealing more examples, but caution is needed in interpreting the results and validation through independent means is crucial.
PEST MANAGEMENT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen
Summary: This paper presents a method called "Chameleolyser" that accurately identifies variants in duplicated genomic regions. Application of this method to a large cohort of exome samples led to the identification of a significant number of rare variants, including those that resulted in direct molecular diagnoses for previously undiagnosed patients.
NATURE COMMUNICATIONS
(2023)
Article
Evolutionary Biology
Eddie K. H. Ho, Sarah Schaack
Summary: The study found that mutation rates causing structural variation vary significantly among populations and are uncorrelated across different types of mutations. This challenges prevailing theories explaining the evolution of mutation rates and highlights the importance of obtaining additional mutation rate estimates in a wider range of genotypes and species.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Eddie K. H. Ho, Sarah Schaack
Summary: The study found that mutation rates causing structural variation vary greatly among populations, are not correlated across different types of mutations, and do not occur in genic regions as expected.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Asano Ishikawa, Shun Yamanouchi, Wataru Iwasaki, Jun Kitano
Summary: The study investigates the presence of copy number variations (CNVs) associated with freshwater colonization in fishes. It identifies 23 genes whose copy number increases are related to adaptation to freshwater environments. These genes are involved in peptide receptor activity, hexosyltransferase activity, and unsaturated fatty acid metabolism. The study also reveals that certain genes involved in fatty acid metabolism, immune function, and thyroid hormone metabolism show copy number increases in freshwater populations compared to marine ancestral populations.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Agronomy
Jinlong Li, Xin Xin, Fangyao Sun, Zhenzhen Zhu, Xiangru Xu, Jiatian Yang, Xiaoming Xie, Jiazheng Yu, Xiaobo Wang, Sen Li, Shilin Tian, Baoyun Li, Chaojie Xie, Jun Ma
Summary: This study identified a dominant locus on chromosome 5AL associated with awn length in wheat. The B1 gene, which inhibits awn growth, was found to have increased copy number in awnless wheat, leading to enhanced gene expression and inhibition of awn length.
Article
Cell Biology
Mariana Andrawus, Lital Sharvit, Noga Touitou, Batia Lerrer, Haim Y. Cohen, Gil Atzmon
Summary: Copy number variations (CNV) play a significant role in genome variability and have been associated with aging and pregnancy physiology. By studying CNVs in pregnant mice, researchers have found that most of the selected CNVs showed an opposite trend during pregnancy and post-partum. Additionally, significant differential expression was observed in the nearby genes of the candidate CNVs. This study highlights the importance of using pregnancy as a model for aging and reveals the mechanisms and similarities between pregnancy and aging.
Article
Medicine, General & Internal
Guoming Chu, Pingping Li, Juan Wen, Gaoyan Zheng, Yanyan Zhao, Rong He
Summary: This study aimed to investigate the genotype-phenotype correlation of 5p deletion syndrome and redefine the relevant regions. Through studying three families and two children, different sizes of 5p deletions were detected and their pathogenicity was determined. Additionally, the potential of whole genome sequencing in identifying chromosomal breakpoints in prenatal diagnosis was demonstrated.
FRONTIERS IN MEDICINE
(2022)
Article
Pharmacology & Pharmacy
Amy J. Turner, Charity Nofziger, Bronwyn E. Ramey, Reynold C. Ly, Chad A. Bousman, Jose A. G. Agundez, Katrin Sangkuhl, Michelle Whirl-Carrillo, Simone Vanoni, Henry M. Dunnenberger, Gualberto Ruano, Martin A. Kennedy, Michael S. Phillips, Houda Hachad, Teri E. Klein, Ann M. Moyer, Andrea Gaedigk
Summary: The Pharmacogene Variation Consortium (PharmVar) provides nomenclature and a comprehensive summary for the highly polymorphic human CYP2D6 gene locus and its structural variation. Accurate prediction of a patient’s CYP2D6 phenotype requires testing for structural variants, including gene deletions, duplications, hybrid genes, and combinations thereof.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2023)
Article
Genetics & Heredity
Lydia Sagath, Vilma-Lotta Lehtokari, Katarina Pelin, Kirsi Kiiski
Summary: Intragenic segmental duplications may lead to recurrent copy number variations and potential pathogenic abnormalities. Nebulin and titin, two large sarcomeric genes, contain such duplication regions. Although the exact copy numbers of these blocks could not be determined due to method limitations, the study shows that the segmental duplication region of titin is subject to copy number variation, potentially associated with muscle disorders.
Article
Biochemistry & Molecular Biology
Sarah B. Yakimowski, Zachary Teitel, Christina M. Caruso
Summary: The study revealed a significant positive relationship between EPSPS copy number and glyphosate resistance in Amaranthus palmeri populations, with most populations exhibiting bimodality. The research also found evidence for a threshold model between copy number and resistance. Additionally, as copy number increased, the range of variation in resistance decreased, leading to a higher frequency of high phenotypic resistance individuals.
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Plant Sciences
Robin Nicole Bosman, Jessica Anne-Marie Vervalle, Danielle Lisa November, Phyllis Burger, Justin Graham Lashbrooke
Summary: Volatile organic compounds, such as terpenes, play a vital role in influencing the quality parameters of grapevine through their contribution to the flavor and aroma profile of grapes. The biosynthesis of these compounds is complex and controlled by multiple genes, many of which are unidentified. By analyzing volatile metabolic data from a grapevine mapping population, researchers identified several significant genomic regions associated with terpene modulation in grape berries. These findings provide insights into the molecular mechanisms of terpene accumulation and offer potential applications in developing grape cultivars with desired terpene profiles.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Preston Hurst, James C. Schnable, David R. Holding
Summary: Tandem duplication can lead to copy number variation and functional novelty in genes, as well as diversity between individuals in a species. In maize, the alpha-zein gene family copies show conservation in both gene sequence and gene regulation patterns between different inbreds, even though there may be differences in overall expression levels.
Article
Ecology
Jason Bertram, Joanna Masel
Article
Genetics & Heredity
Scott G. Foy, Benjamin A. Wilson, Jason Bertram, Matthew H. J. Cordes, Joanna Masel
Article
Multidisciplinary Sciences
Kun Xiong, Alex K. Lancaster, Mark L. Siegal, Joanna Masel
NATURE COMMUNICATIONS
(2019)
Article
Genetics & Heredity
Jason Bertram, Joanna Masel
Article
Evolutionary Biology
Kendra M. Meer, Paul G. Nelson, Kun Xiong, Joanna Masel
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Evolutionary Biology
Karina Zile, Christophe Dessimoz, Yannick Wurm, Joanna Masel
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biology
Kevin Gomez, Jason Bertram, Joanna Masel
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Biology
Jennifer E. James, Sara M. Willis, Paul G. Nelson, Catherine Weibel, Luke J. Kosinski, Joanna Masel
Summary: The study found that the reduction in hydrophobic clustering is universal across lineages, while only young animal domains tend to have higher structural disorder. Trends in amino acid composition among ancient domains reflect the order of recruitment into the genetic code, indicating that the composition of contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life.
Article
Genetics & Heredity
Kun Xiong, Mark Gerstein, Joanna Masel
Summary: Transcriptional regulatory networks (TRNs) exhibit certain motifs, with type 1 incoherent feed-forward loops (I1FFLs) and negative feedback loops (NFBLs) being common solutions. The evolution of these motifs is influenced by selection conditions, with I1FFLs generally evolving more frequently than NFBLs. The evolutionary accessibility and not just relative functionality shape motif evolution in TRNs, with the expression levels of specific genes playing a crucial role.
Article
Evolutionary Biology
Cuong Cao Dang, Bui Quang Minh, Hanon McShea, Joanna Masel, Jennifer Eleanor James, Le Sy Vinh, Robert Lanfear
Summary: This study introduces a new maximum likelihood method, nQMaker, that can estimate time nonreversible amino acid substitution models and rooted phylogenetic trees. The results show that the nonreversible models estimated with nQMaker are a better fit to empirical alignments than pre-existing reversible models, and the improvements in model fit scale with the size of the data set.
SYSTEMATIC BIOLOGY
(2022)
Article
Ecology
Thomas Bataillon, Thomas H. G. Ezard, Michael Kopp, Joanna Masel
Article
Evolutionary Biology
Luke J. Kosinski, Nathan R. Aviles, Kevin Gomez, Joanna Masel
Summary: Proteins, as the workhorses of the cell, can cause harm through misfolding and aggregation. However, sometimes proteins can be born from noncoding DNA without harm. By studying the fitness of different Escherichia coli lineages expressing unique random peptides, researchers found that simple amino acid frequencies, rather than the ordering of amino acids, predicted lineage fitness. Smaller amino acids that promote intrinsic structural disorder had less harmful effects on fitness. These amino acids were also enriched in young animal proteins.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jennifer E. James, Paul G. Nelson, Joanna Masel
Summary: Protein domains that emerged recently have higher disorder and clustering of hydrophobic residues. There is a hypothesis that different levels of selection affect the retention probabilities of domains with different properties. Loss rates were inferred for animal Pfam domains and were found to depend on disorder and clustering trait values. The results support the hypothesis that domain loss slowly eliminates domains with suboptimal disorder and clustering levels, affecting proteome composition.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Public, Environmental & Occupational Health
Joanna Masel, James Ian Mackie Petrie, Jason Bay, Wolfgang Ebbers, Aalekh Sharan, Scott Michael Leibrand, Andreas Gebhard, Samuel Zimmerman
Summary: Digital contact tracing and notification have not lived up to expectations in combating the COVID-19 pandemic due to multiple points of failure. Research indicates that achieving a significant reduction in transmission risk requires high success rates in technology adoption, contact detection, prompt diagnosis and notification, and behavior change. Recommendations include emphasizing user autonomy, integrating tracing/notification apps with testing, manual contact tracing, and scientific data collection.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Multidisciplinary Sciences
James Petrie, Joanna Masel
Summary: Targeted quarantine and social distancing measures should be implemented based on current disease prevalence to achieve the optimal balance between controlling transmission and minimizing total social isolation. The value of a quarantine policy increases with lower case counts, is less affected by vaccination unless exemptions are in place, and is greatly enhanced by more information on individual infectiousness risk.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)