Article
Multidisciplinary Sciences
Andrew Keniry, Natasha Jansz, Linden J. Gearing, Iromi Wanigasuriya, Joseph Chen, Christian M. Nefzger, Peter F. Hickey, Quentin Gouil, Joy Liu, Kelsey A. Breslin, Megan Iminitoff, Tamara Beck, Andres Tapia del Fierro, Lachlan Whitehead, Andrew Jarratt, Sarah A. Kinkel, Phillippa C. Taberlay, Tracy Willson, Miha Pakusch, Matthew E. Ritchie, Douglas J. Hilton, Jose M. Polo, Marnie E. Blewitt
Summary: In this study, a replenishable female mouse embryonic stem cell system was developed to study X chromosome inactivation (XCI). Through a targeted genetic screen, the researchers identified the BAF complex as essential for creating nucleosome-depleted regions at promoters on the inactive X chromosome during the early stages of XCI establishment. This model system provides a valuable tool for discovering unknown factors involved in XCI and epigenetic silencing.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xiaotao Dong, Rong Guo, Tianrong Ji, Jie Zhang, Jun Xu, Yaoyi Li, Yingliang Sheng, Yuxiang Wang, Ke Fang, Yulin Wen, Bei Liu, Gongcheng Hu, Hongkui Deng, Hongjie Yao
Summary: This study reveals the important role of YY1 in EPSCs, where it regulates extended pluripotency through its impact on gene expression and epigenetic crosstalk. This finding contributes to a better understanding of the transcriptional regulatory mechanism differences between EPSCs and ESCs, and provides new insights for the applications and research of extended pluripotency.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Meena Kusi, Maryam Zand, Li-Ling Lin, Meizhen Chen, Anthony Lopez, Chun-Lin Lin, Chiou-Miin Wang, Nicholas D. Lucio, Nameer B. Kirma, Jianhua Ruan, Tim H. -M. Huang, Kohzoh Mitsuya
Summary: 2-hydroxyglutarate (2HG) suppresses DNA repair, affects chromatin plasticity, and induces cell differentiation and growth in breast cancer cells. Breast tumors with high 2HG exhibit enhanced heterogeneity and adverse prognosis. Ascorbate-2-phosphate can eliminate this heterogeneity and reduce the growth of high 2HG-producing cancer cells.
Article
Multidisciplinary Sciences
Jani de Vos, Richard P. M. A. Crooijmans, Martijn F. L. Derks, Susan L. Kloet, Bert Dibbits, Martien A. M. Groenen, Ole Madsen
Summary: This paper aims to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, which are of interest for the FAANG community and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq were used to investigate these cell lines. Heteroploidy of various chromosomes was observed, and higher gene expression was found in genes located on aneuploid chromosomes compared to diploid chromosomes. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was also explored.
Article
Genetics & Heredity
Stefan Butz, Nina Schmolka, Ino D. Karemaker, Rodrigo Villasenor, Isabel Schwarz, Silvia Domcke, Esther C. H. Uijttewaal, Julian Jude, Florian Lienert, Arnaud R. Krebs, Nathalie P. de Wagenaar, Xue Bao, Johannes Zuber, Ulrich Elling, Dirk Schuebeler, Tuncay Baubec
Summary: Genomic imprinting is regulated by DNA methylation of imprinting control regions (ICRs) with parental-specificity. The epigenetic states of ICRs, despite having an identical DNA sequence, are determined by genetic and epigenetic factors. Through iterative integration of ICRs and DNA sequences, this study identified the DNA sequence features required for maintaining the epigenetic states in embryonic stem cells. Additionally, ATF7IP and ZMYM2 were found to be important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
Article
Plant Sciences
Parveen Akhtar, Avratanu Biswas, Fanny Balog-Vig, Ildiko Domonkos, Laszlo Kovacs, Petar H. Lambrev
Summary: Cyanobacterial mutants with monomeric PSI show changes in the composition and abundance of phycobilisomes and in the excitation energy transfer to PSII and PSI. The oligomeric state of PSI impacts the excitation energy flow in Synechocystis.
Article
Cell Biology
Dandan Bai, Jin Sun, Chuan Chen, Yanping Jia, Yanhe Li, Kuisheng Liu, Yalin Zhang, Jiqing Yin, Yingdong Liu, Xiaoxiao Han, Jingling Ruan, Xiaochen Kou, Yanhong Zhao, Hong Wang, Zheng Wang, Miaoxin Chen, Xiaoming Teng, Cizhong Jiang, Shaorong Gao, Wenqiang Liu, Hong Wang, Zheng Wang, Miaoxin Chen
Summary: Assisted reproductive technology is widely used for treating human infertility, but in vitro fertilization (IVF) is associated with a low pregnancy rate and various health issues in offspring. This study reveals that IVF manipulation disrupts gene expression in extraembryonic tissues and leads to abnormal H3K4me3 modification, which is a major cause of implantation failure and abnormal placental development in IVF embryos.
Review
Genetics & Heredity
Sebastian Preissl, Kyle J. Gaulton, Bing Ren
Summary: This article discusses cell type-specific gene regulation and its changes during development and disease. Single-cell epigenomic methods and data analysis tools provide a deeper understanding of gene regulatory programs and their roles in different environments and diseases.
NATURE REVIEWS GENETICS
(2022)
Article
Water Resources
D. Magritsky, M. A. Samokhin, A. Goncharov, O. N. Erina, D. Sokolov, V. V. Surkov, M. A. Tereshina, P. G. Mikhailyukova, A. A. Semenova
Summary: The Agrakhan Bay, located at the mouth of the Terek River in the Caspian Sea, has undergone significant degradation over the past century. A comprehensive study and investigation of this area is crucial for the restoration of its wetlands and ecological potential.
Article
Cell Biology
Tasha A. Morrison, William H. Hudson, Danielle A. Chisolm, Yuka Kanno, Han-Yu Shih, Rafi Ahmed, Jorge Henao-Mejia, Markus Hafner, John J. O'Shea
Summary: Immunological memory is a complex concept with multiple molecular mechanisms. New sequencing technologies have improved the understanding of gene regulation and lymphocyte specification, shedding light on the epigenomic and transcriptomic programs underlying memory. The involvement of long noncoding RNAs (lncRNAs) is increasingly apparent, but their functions and knockout mouse studies are still limited.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Yuuki Matsushita, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Summary: Cellular reprogramming involves erasing epigenetic memories of differentiated cells to regain pluripotency, achieved by overexpressing a few genes. The interplay between oscillatory gene expression and slower epigenetic modifications is perceived as a global attraction in this process.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Psychiatry
Hye Yoon Park, Minji Bang, Eunchong Seo, Se Jun Koo, Eun Lee, Seung-Koo Lee, Suk Kyoon An
Summary: This study investigates the interaction between vulnerability and the environment on the neurobiological substrates of schizophrenia. The findings suggest that individuals with ultra-high risk for psychosis show reduced functional connectivity between the default-mode network and the frontoparietal network. Additionally, the study reveals that schizotypy level moderates the relationship between brain-derived neurotrophic factor methylation and network functional connectivity.
Article
Engineering, Civil
Benazir F. Ahmed, Kaustubh Dasgupta
Summary: The study evaluates the seismic limit states for bridge piles in sand, considering the parametric influences of pile and soil through PSI. The results show that various parameters affect the lateral response of piles, influencing the expected values of limit states and the fragility of bridge systems.
Review
Genetics & Heredity
Aled Parry, Steffen Rulands, Wolf Reik
Summary: Recent studies have shown that simultaneous activity of de novo methylation and demethylation mechanisms results in rapid DNA methylation turnover. This process may facilitate key lineage decisions and lead to large-scale oscillatory dynamics at gene distal regulatory elements.
NATURE REVIEWS GENETICS
(2021)
Review
Medicine, General & Internal
Eric F. Morand, Ruth Fernandez-Ruiz, Ashira Blazer, Timothy B. Niewold
Summary: This review provides a comprehensive summary of the current status of systemic lupus erythematosus, including recent advances in genetics and immunological pathogenesis, as well as the latest guidelines and strategies for diagnosis, classification, and treatment. The paper also reviews numerous recent clinical trials in SLE and suggests future research directions. The findings of these studies should contribute to personalized treatment, minimizing side effects, and achieving better outcomes in this challenging disease.
BMJ-BRITISH MEDICAL JOURNAL
(2023)
Article
Microbiology
Kyle Sander, Daehwan Chung, Doug Hyatt, Janet Westpheling, Dawn M. Klingeman, Miguel Rodriguez, Nancy L. Engle, Timothy J. Tschaplinski, Brian H. Davison, Steven D. Brown
Review
Biotechnology & Applied Microbiology
Regina L. Wilpiszeski, Jayde A. Aufrecht, Scott T. Retterer, Matthew B. Sullivan, David E. Graham, Eric M. Pierce, Olivier D. Zablocki, Anthony Palumbo, Dwayne A. Elias
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Kyle Sander, Meredith Yeary, Kristina Mahan, Jason Whitham, Richard J. Giannone, Steven D. Brown, Miguel Rodriguez, David E. Graham, Bertrand Hankoua
Article
Engineering, Environmental
Geoff A. Christensen, Caitlin M. Gionfriddo, Andrew J. King, James G. Moberly, Carrie L. Miller, Anil C. Somenahally, Stephen J. Callister, Heather Brewer, Mircea Podar, Steven D. Brown, Anthony Palumbo, Craig C. Brandt, Ann M. Wymore, Scott C. Brooks, Chiachi Hwang, Matthew W. Fields, Judy D. Wall, Cynthia C. Gilmour, Dwayne A. Elias
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2019)
Article
Microbiology
Shihui Yang, Mary Ann Franden, Xia Wang, Yat-Chen Chou, Yun Hu, Steven D. Brown, Philip T. Pienkos, Min Zhang
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Kyle B. Sander, Daehwan Chung, Dawn M. Klingeman, Richard J. Giannone, Miguel Rodriguez, Jason Whitham, Robert L. Hettich, Brian H. Davison, Janet Westpheling, Steven D. Brown
BIOTECHNOLOGY FOR BIOFUELS
(2020)
Article
Microbiology
Cynthia C. Gilmour, Ally Bullock Soren, Caitlin M. Gionfriddo, Mircea Podar, Judy D. Wall, Steven D. Brown, Joshua K. Michener, Maria Soledad Goni Urriza, Dwayne A. Elias
Summary: ND132T strain, isolated from Chesapeake Bay, USA, is a sulfate-reducing and mercury-methylating bacterium with high levels of mercury methylation. It belongs to the genus Pseudodesulfovibrio and has been proposed as a new species, Pseudodesulfovibrio mercurii.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Anne E. Otwell, Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, Serdar Turkarslan, Sean M. Gibbons, Dwayne A. Elias, David A. Stahl, Gary Siuzdak, Nitin S. Baliga
Summary: Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is influenced by intermediates of nitrogen and sulfur cycling, such as hydrogen sulfide and nitrite. Mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of NRB have been uncovered through transcriptomic and metabolomic analyses, providing insights into the competitive interactions between NRB and SRB in diverse environments. The study highlights the importance of understanding how reduced sulfur compounds affect the growth and activity of NRB and SRB, impacting their stratification in different ecosystems.
Article
Microbiology
Dmitry A. Rodionov, Irina A. Rodionova, Vladimir A. Rodionov, Aleksandr A. Arzamasov, Ke Zhang, Gabriel M. Rubinstein, Tania N. N. Tanwee, Ryan G. Bing, James R. Crosby, Intawat Nookaew, Mirko Basen, Steven D. Brown, Charlotte M. Wilson, Dawn M. Klingeman, Farris L. Poole, Ying Zhang, Robert M. Kelly, Michael W. W. Adams
Summary: Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono-and oligosaccharides to produce ethanol and other industrially important end products. Transcriptional regulation mechanisms of carbohydrate utilization genes were investigated using a comparative genomics approach, revealing a complex regulatory network controlling the expression of genes involved in degradation of plant biomass. The reconstruction of carbohydrate utilization regulatory network improved functional annotations of transporters and catabolic enzymes, providing insights for metabolic engineering strategies to optimize yields of bio-based fuels and chemicals from lignocellulose, with a focus on Caldicellulosiruptor bescii.
Article
Engineering, Environmental
Natalia Neal-Walthall, Udonna Ndu, Nelson A. Rivera, Dwayne A. Elias, Heileen Hsu-Kim
Summary: This study explored the use of DGT passive samplers to quantify the methylmercury (MeHg) bioaccumulation potential and inorganic mercury (IHg) methylation potential in freshwater wetlands. The results showed that the vertical distribution of bioavailable MeHg is important for macrofauna food sources, and DGT samplers can predict IHg methylation and MeHg bioaccumulation potentials without explicitly determining IHg and MeHg speciation.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Analytical
Grace E. Schwartz, Katherine A. Muller, Saubhagya S. Rathore, Regina L. Wilpiszeski, Alyssa A. Carrell, Melissa A. Cregger, Dwayne A. Elias, Mircea Podar, Scott L. Painter, Scott C. Brooks
Summary: The study demonstrates that the TAM can accurately describe MMHg production in sediments, with the need to revise the model structure to incorporate terms for concentration-dependent microbial activity. By including expressions accounting for such activity, the model description of the data can be improved in some cases.
ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS
(2022)
Correction
Chemistry, Multidisciplinary
Lahiru N. Jayakody, Christopher W. Johnson, Jason M. Whitham, Richard J. Giannone, Brenna A. Black, Nicholas S. Cleveland, Dawn M. Klingeman, William E. Michener, Jessica L. Olstad, Derek R. Vardon, Robert C. Brown, Steven D. Brown, Robert L. Hettich, Adam M. Guss, Gregg T. Beckham
ENERGY & ENVIRONMENTAL SCIENCE
(2021)
Article
Microbiology
Minjae Kim, Regina L. Wilpiszeski, Michael Wells, Ann M. Wymore, Caitlin M. Gionfriddo, Scott C. Brooks, Mircea Podar, Dwayne A. Elias
Summary: The study sequenced two metagenomes of sediments from East Fork Poplar Creek in Oak Ridge Reservation contaminated with Hg, resulting in the reconstruction of 28 metagenome-assembled genomes of novel prokaryotic species.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Peter T. Podar, Kellie Peyton, Ally Soren, Regina L. Wilpiszeski, Cynthia C. Gilmour, Dwayne A. Elias, Mircea Podar
Summary: Desulfobulbus oligotrophicus Prop6 is a sulfate-reducing, propionate-oxidizing bacterium from sewage sludge. They can thrive in anaerobic environments and some species are capable of producing the neurotoxin methylmercury.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)