Review
Soil Science
Nicolas Romillac, Lucia Santorufo
Summary: The paper discusses the growing interest and difficulties in using functional trait approaches to study soil bacterial communities. The authors propose to identify functional traits based on bacterial fitness rather than their relationship to ecosystem functions, and suggest a framework including growth rate, survival, and dispersion as components of bacterial fitness.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Environmental Sciences
Jianlin Lou, Shoukai Yu, Lingfang Feng, Xinnian Guo, Meng Wang, Alan T. Branco, Tao Li, Bernardo Lemos
Summary: Exposure to hexavalent chromium induces instability in the rDNA of human cells, leading to rapid amplification and contraction of the array. Environmental exposure and drinking habits, but not age, influence the natural variation in rDNA copy number in human populations exposed to Cr (VI).
ENVIRONMENT INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Su-Jung Kim, Chrystelle Maric, Lina-Marie Briu, Fabien Fauchereau, Giuseppe Baldacci, Michelle Debatisse, Stephane Koundrioukoff, Jean-Charles Cadoret
Summary: Over the past ten years, CDK4/6 inhibitors have been recognized for their potential as anticancer drugs. These inhibitors have demonstrated effectiveness in blocking the pRb-E2F pathway and inducing cell cycle arrest in pRb-proficient cells. However, recent evidence suggests unexpected effects of CDK4/6 inhibitors, particularly regarding DNA replication in pRb-deficient cell lines. This study highlights how palbociclib specifically impairs origin firing and affects the dynamics of DNA replication, providing potential therapeutic implications for targeting genomic instability in pRb-deficient cancers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Hongbiao Li, Song Gao, Siqi Zhang, Weizhu Zeng, Jingwen Zhou
Summary: Flavonoids have notable biological activities and are widely used in various industries. This study successfully integrated multiple flavonoid pathway genes in a single-step integration method in yeast, significantly improving the production of naringenin. Optimizing the supply of donor DNA and utilizing a high titer p-coumaric acid strain as a chassis were key factors in enhancing flavonoid production.
JOURNAL OF BIOTECHNOLOGY
(2021)
Review
Cell Biology
Evgeny Smirnov, Nikola Chmurciakova, Frantisek Liska, Pavla Bazantova, Dusan Cmarko
Summary: The review discusses the causes and types of human rDNA instability, the methods of detection, its distribution within the locus, and its biological significance. Literature data suggests that the variability of rDNA is not only a potential cause of pathology, but also an important but poorly understood aspect of normal cell physiology.
Article
Neurosciences
Vandre C. Figueiredo, Yuan Wen, Bjorn Alkner, Rodrigo Fernandez-Gonzalo, Jessica Norrbom, Ivan J. Vechetti, Taylor Valentino, C. Brooks Mobley, Gabriel E. Zentner, Charlotte A. Peterson, John J. McCarthy, Kevin A. Murach, Ferdinand von Walden
Summary: The study reveals the genetic and rDNA gene-wide epigenetic regulation of ribosome biogenesis in response to exercise, highlighting the roles of rDNA dosage and CpG methylation in skeletal muscle. This indicates a genetic predisposition for hypertrophic responsiveness and preferential up-regulation of ribosome biogenesis with resistance exercise. The findings expand our understanding of the genetic and epigenetic factors involved in exercise-induced changes in ribosome biogenesis.
JOURNAL OF PHYSIOLOGY-LONDON
(2021)
Article
Multidisciplinary Sciences
Songwei Ni, Baiyuan Li, Kaihao Tang, Jianyun Yao, Thomas K. Wood, Pengxia Wang, Xiaoxue Wang
Summary: The study reveals that the type II TA system, Pseudoalteromonas rubra plasmid toxin-antitoxin PrpT/PrpA, directly controls plasmid replication by acting as a negative regulator. The antitoxin PrpA binds to iterons in the plasmid origin to inhibit the binding of the replication initiator, preventing overreplication of the plasmid. This TA system is conserved and widespread on many conjugative plasmids.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Microbiology
Melia Bonnamy, Stephane Blanc, Yannis Michalakis
Summary: The replication of plant-infecting single-stranded DNA viruses, Geminiviridae and Nanoviridae, involves rolling-circle replication (RCR) and recombination-dependent replication (RDR) mechanisms. RCR relies on a virus-encoded Replication-associated protein (Rep) and specific sequences called iterons, while RDR is also observed in some double-stranded DNA viruses. This article provides a synthesis of the current understanding of these replication modes and discusses the potential role of gene copy number regulation in viral gene expression.
Review
Cell Biology
Selina M. Kindelay, Keith A. Maggert
Summary: The ribosomal DNA (rDNA) in Drosophila exists as two independent clusters of individual 35 S cistmns. The multiplicity of rDNA is crucial for ensuring proper translational demands, but the tandem arrays are susceptible to copy number variation within and between populations. This article discusses how cells respond to insufficient rDNA copy number, including the historical concept of rDNA magnification and recent discoveries of rDNA loss and potential mechanisms of magnification.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Cell Biology
Miao-Zhen Qiu, Qingjian Chen, Dan-Yang Zheng, Qi Zhao, Qi-Nian Wu, Zhi-Wei Zhou, Li-Qiong Yang, Qiu-Yun Luo, Yu-Ting Sun, Ming-Yu Lai, Sha-Sha Yuan, Feng-Hua Wang, Hui-Yan Luo, Feng Wang, Yu-Hong Li, Hui-Zhong Zhang, Rui-Hua Xu
Summary: Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a heterogeneous tumor composed of adenocarcinoma and neuroendocrine carcinoma. Whole-exome and multi-regional sequencing revealed that MANEC has four significantly mutated genes and shares similarities with chromosomal instability stomach adenocarcinoma. MANEC tumors are of monoclonal origin and the neuroendocrine carcinoma components exhibit more aggressive genomic properties. The phylogenetic trees demonstrate different patterns of tumor divergence, and immunohistochemistry confirms the transition from adenocarcinoma to neuroendocrine carcinoma in MANEC.
Article
Oncology
Seung-Hyun Jung, Hyeon-Chun Park, Youn Jin Choi, Sang Yong Song, Yeun-Jun Chung, Sug Hyung Lee
Summary: This study identified the histogenesis of GCTs through the analysis of single-nucleotide polymorphism array, revealing different genetic alterations between histologic areas within the same GCT. The findings suggest that GCTs may have various histogenesis and intratumoral genomic differences, which could be crucial for the identification of GCTs with different histologic areas.
JOURNAL OF PATHOLOGY
(2022)
Article
Plant Sciences
Xiaoxia Ding, Jieting Chen, Chunyan Dai, Peiqi Shi, Hengyu Pan, Yanqi Lin, Yikang Chen, Lu Gong, Linming Chen, Wenguang Wu, Xiaohui Qiu, Jiang Xu, Zhihai Huang, Baosheng Liao
Summary: This study characterized the ribosomal DNA (rDNA) of Artemisia annua and identified rich polymorphisms in rDNA copy number and sequence in A. annua populations. The study also found significant differences in the haplotype composition of the internal transcribed spacer 2 (ITS2) region among A. annua strains. These findings suggest that ITS2 haplotype analysis is an ideal tool for A. annua strain identification and population genetic homogeneity assessment.
Review
Biochemistry & Molecular Biology
Hisanori Fukunaga
Summary: Mitochondrial dysfunction is closely related to disease, and environmental factors during fetal life may influence health risks in offspring.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Liselot M. Mus, Stephane Van Haver, Mina Popovic, Wim Trypsteen, Steve Lefever, Nadja Zeltner, Yudelca Ogando, Eva Z. Jacobs, Geertrui Denecker, Ellen Sanders, Christophe Van Neste, Suzanne Vanhauwaert, Bieke Decaesteker, Dieter Deforce, Filip Van Nieuwerburgh, Pieter Mestdagh, Jo Vandesompele, Bjorn Menten, Katleen De Preter, Lorenz Studer, Bjorn Heindryckx, Kaat Durinck, Stephen Roberts, Frank Speleman
Summary: Human embryonic stem cells and embryonal tumors both exhibit compromised G1/S checkpoint, leading to replicative stress and genomic instability. Long-term in vitro cultured hESCs show a high incidence of DNA copy number gains, which may provide a proliferative advantage.
GENES CHROMOSOMES & CANCER
(2021)
Article
Biochemistry & Molecular Biology
Gregg W. C. Thomas, Richard J. Wang, Jelena Nguyen, R. Alan Harris, Muthuswamy Raveendran, Jeffrey Rogers, Matthew W. Hahn
Summary: The study analyzed patterns of CNV mutations in rhesus macaque individuals, finding a low rate of CNV mutations per generation and no correlation between parental age and the number of CNVs passed on to offspring. Rhesus macaques and humans differ in the proportion of segregating deletions, with both species having more segregating deletions than duplications.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Hematology
Jasper Hsu, Andreea Reilly, Brian J. Hayes, Courtnee A. Clough, Eric Q. Konnick, Beverly Torok-Storb, Suleyman Gulsuner, David Wu, Pamela S. Becker, Sioban B. Keel, Janis L. Abkowitz, Sergei Doulatov
Article
Genetics & Heredity
Kelsey L. Lynch, Gina M. Alvino, Elizabeth X. Kwan, Bonita J. Brewer, M. K. Raghuraman
Article
Biotechnology & Applied Microbiology
Jirasin Koonthongkaew, Yoichi Toyokawa, Masataka Ohashi, Christopher R. L. Large, Maitreya J. Dunham, Hiroshi Takagi
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Article
Genetics & Heredity
Anja R. Ollodart, Chiann-Ling C. Yeh, Aaron W. Miller, Brian H. Shirts, Adam S. Gordon, Maitreya J. Dunham
Summary: This study established a new method to simultaneously determine the mutation rate of multiple strains using continuous culture devices and deep sequencing, successfully applied to assay the mutation rate of Saccharomyces cerevisiae strains with mutations in the Msh2 gene. The method was proven to be accurate and reliable, and it can be applied to studying the mutation rate of various microbial species.
Article
Biology
Pengyao Jiang, Anja R. Ollodart, Vidha Sudhesh, Alan J. Herr, Maitreya J. Dunham, Kelley Harris
Summary: This study utilized natural polymorphisms to detect historical mutation spectrum differences among several wild and domesticated Saccharomyces cerevisiae strains. It found a 10-fold range of mutation rates and identified two strains with distinctive mutation spectra, indicating an enrichment for C > A mutations in certain strains. Additionally, a plasmid complementation test revealed that these strains share a mutator allele in the DNA repair gene OGG1, suggesting a potential underlying genetic cause for the observed mutation spectrum differences.
Article
Biochemistry & Molecular Biology
Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J. Dunham, Joseph Schacherer
Summary: This study analyzed the polyploid genomes of beer yeasts and revealed their evolutionary history. The results showed that different beer subpopulations originated from different population admixtures and had distinctive genomic patterns. Among them, the genes related to carbon metabolism, oxidoreduction, and cell wall organization, which are relevant to the brewing environment, showed the highest diversity. Furthermore, independent domestication, evolution, and adaptation events were highlighted across subpopulations.
Article
Multidisciplinary Sciences
Ishita Joshi, Jie Peng, Gina Alvino, Elizabeth Kwan, Wenyi Feng
Summary: This study compared replication origin activation in two yeast strains under hydroxyurea treatment, revealing the roles of S-phase checkpoint control, DNA sequence polymorphisms, and origin-transcription unit positioning. Rad53 protein plays a significant role in activation of origins, particularly in checkpoint-proficient cells.
Article
Hematology
Massiel Chavez Stolla, Andreea Reilly, Rochelle Bergantinos, Sintra Stewart, Neele Thom, Courtnee A. Clough, Rachel C. Wellington, Raisa Stolitenko, Janis L. Abkowitz, Sergei Doulatov
Summary: Autophagy is crucial for erythropoiesis, and ATG4A is identified as a cell type-specific regulator of autophagy in erythroid development.
Article
Developmental Biology
Sruti Patoori, Samantha M. Barnada, Christopher Large, John I. Murray, Marco Trizzino
Summary: The hippocampus is involved in important brain functions, and it has recently undergone expansion in humans compared to non-human apes. The gene networks active in hippocampal intermediate progenitor cells are significantly different between humans and chimpanzees, with transposon-derived enhancers playing a role in these differences. Human-specific SVAs serve as substrates for novel TBR2-binding sites.
Article
Genetics & Heredity
M. Bryce Taylor, Ryan Skophammer, Alexa R. Warwick, Renee C. Geck, Josephine M. Boyer, YEvo Students, Margaux Walson, Christopher R. L. Large, Angela Shang-Mei Hickey, Paul A. Rowley, Maitreya J. Dunham
Summary: Antifungal resistance is a growing concern in pathogenic fungi. The study successfully used experimental evolution to investigate antifungal resistance in laboratory strains of Saccharomyces cerevisiae, validating the approach. The collaboration between high school and university researchers can serve as a model for public involvement in biomedical research.
G3-GENES GENOMES GENETICS
(2022)
Article
Cell Biology
Elizabeth X. Kwan, Gina M. Alvino, Kelsey L. Lynch, Paula F. Levan, Haley M. Amemiya, Xiaobin S. Wang, Sarah A. Johnson, Joseph C. Sanchez, Madison A. Miller, Mackenzie Croy, Seung-been Lee, Maria Naushab, Antonio Bedalov, Josh T. Cuperus, Bonita J. Brewer, Christine Queitsch, M. K. Raghuraman
Summary: Timely completion of genome replication is crucial for mitosis, genome integrity, and cell survival. However, the replication of untranscribed rDNA poses a challenge to this process. By reducing the number of rDNA repeats in Saccharomyces cerevisiae, we observed early replication of rDNA, which subsequently delayed replication of other regions in the genome. Furthermore, cells with early-replicating rDNA and delayed genome-wide replication prematurely released the mitotic phosphatase Cdc14, leading to premature entry into anaphase. We propose that rDNA copy number determines the replication time of rDNA and the release of Cdc14 signals cell cycle progression.
Article
Hematology
Courtnee A. Clough, Joseph Pangallo, Martina Sarchi, Janine O. Ilagan, Khrystyna North, Rochelle Bergantinos, Massiel C. Stolla, Jasmine Naru, Patrick Nugent, Eunhee Kim, Derek L. Stirewalt, Arvind R. Subramaniam, Omar Abdel-Wahab, Janis L. Abkowitz, Robert K. Bradley, Sergei Doulatov
Summary: SF3B1 splicing factor mutations are a major cause of ring sideroblasts (RS) formation in myelodysplastic syndromes (MDS). In this study, an induced pluripotent stem cell model of SF3B1-mutant MDS was established, successfully recapitulating RS formation. Mutant SF3B1 induces missplicing of mitochondrial transporters TMEM14C and ABCB7, sequestering iron in mitochondria and causing RS formation.
Article
Immunology
Jacquelyn A. Gorman, Christian Hundhausen, Mackenzie Kinsman, Tanvi Arkatkar, Eric J. Allenspach, Courtnee Clough, Samuel E. West, Kerri Thomas, Ahmet Eken, Socheath Khim, Malika Hale, Mohamed Oukka, Shaun W. Jackson, Karen Cerosaletti, Jane H. Buckner, David J. Rawlings
FRONTIERS IN IMMUNOLOGY
(2019)