Article
Cell Biology
Christopher P. Johnstone, Kate E. Galloway
Summary: This study investigates the role of supercoiling-mediated feedback in multi-gene systems. By modeling transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, the study identifies how gene syntax determines expression profiles and correlation, and how supercoiling can enhance or weaken biochemical regulation.
Article
Oncology
Ruth Q. Jacobs, Kaila B. Fuller, Stephanie L. Cooper, Zachariah Carter, Marikki Laiho, Aaron L. Lucius, David A. Schneider
Summary: This study evaluates the specificity of the compound BMH-21 on transcription by Pols I, II, and III. The results show that Pol I is more sensitive to inhibition by BMH-21 compared to Pols II and III. These findings support the ongoing development of BMH-21 and its derivatives as potential therapeutic agents.
Article
Multidisciplinary Sciences
Florian B. Heiss, Julia L. Daiss, Philipp Becker, Christoph Engel
Summary: RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in eukaryotes. Here, the authors present three cryo-EM structures of S. pombe Pol I in different functional states, including a dimer structure, and discuss conserved and organism-specific features of Pol I.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ricardo Pires das Neves, Monica Chagoyen, Antonio Martinez-Lorente, Carlos Iniguez, Ana Calatrava, Juana Calabuig, Francisco J. Iborra
Summary: This study reveals the importance of thiol groups from cysteines in cellular response to ROS and their role in signaling. Different subcellular compartments have different amounts of these thiol groups, with the nucleolus having the highest concentration. These findings provide insights into the differential sensitivity of cells to ROS.
Article
Ecology
William A. Argiroff, Donald R. Zak, Peter T. Pellitier, Rima A. Upchurch, Julia P. Belke
Summary: The study reveals that ectomycorrhizal fungi with peroxidases decrease with increasing inorganic nitrogen availability in northern temperate forests, while ligninolytic fungal saprotrophs show no response. Soil organic matter and soil carbon are negatively correlated with ECM fungi with peroxidases and positively correlated with inorganic nitrogen availability, indicating that these ECM fungi contribute to the decay of lignin-derived soil organic matter and reduce soil carbon storage. The correlations observed suggest a tradeoff between tree nitrogen nutrition and ECM composition, influencing soil organic matter dynamics in temperate forests.
Review
Biochemistry & Molecular Biology
Tomasz W. Turowski, Magdalena Boguta
Summary: RNAPI and RNAPIII are multi-heterogenic protein complexes specialized in transcribing highly abundant non-coding RNAs, more complex than RNAPII synthesizing mRNAs. They share associated subcomplexes formed by specific subunits in yeast and establish an assembly platform co-translationally during the synthesis of the Rpb10 subunit.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Virology
Nan Zhou, Yue Huang, Lu Zhou, Mingma Li, Hui Jin
Summary: Norovirus is the major viral cause of gastroenteritis in humans. The GI RdRp gene of norovirus can be categorized into three groups, with a common ancestor dating back to 1484. The overall evolutionary rate of GI RdRp is 1.821 x 10(-3) substitutions/site/year. Most amino acids in the GI RdRp gene are under negative selection, with only a few sites showing positive selection. Accumulation of amino acid substitutions in the GI RdRp gene is a slow process. Different P-genotypes exhibit diverse molecular evolutionary characteristics. Sequencing of RdRp and VP1 should be encouraged in the surveillance system to understand the role of RdRp in norovirus activity.
Article
Biochemistry & Molecular Biology
Shinzi Ogasawara, Sae Ebashi
Summary: Researchers have developed an RNA editing technology called RNA overwriting, which utilizes the RNA-dependent RNA polymerase (RdRp) of the influenza A virus to overwrite the sequence downstream of a designated site on target RNA. By introducing mutations and fusing with catalytically inactive Cas13b, the modified RdRp can knock down target mRNA and perform sequence overwriting within living cells. This versatile editing technique allows for the repair of aberrant mRNA caused by dysregulation of mRNA processing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Kristin E. N. Watt, Julia Macintosh, Genevieve Bernard, Paul A. Trainor
Summary: Ribosomes are essential macromolecular machines involved in protein translation in all cells. Ribosome biogenesis begins with the transcription of various RNAs by RNA Polymerases I and III. Disruptions in the function of these polymerases result in tissue-specific developmental disorders and distinct syndromes. This review discusses the global roles of Pol I and III transcription, the consequences of disruptions in their function, and the mechanisms underlying tissue-specific phenotypes.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Biology
Sofya K. Garushyants, Igor B. Rogozin, Eugene Koonin
Summary: The study reveals the presence of various insert sequences in the SARS-CoV-2 genome, which not only reflect virus variance but may also affect its pathogenicity and immune escape. The independent insertion mechanisms play a crucial role in the evolution of the novel coronavirus.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Eun-Bee Choi, Munender Vodnala, Madeleine Zerbato, Jianing Wang, Jaclyn J. Ho, Carla Inouye, Lai Ding, Yick W. Fong
Summary: ABCF1 is identified as a coactivator for OCT4/SOX2, utilizing its LCD to undergo phase separation in vitro and mediate multivalent interactions with SOX2 and other coactivators critical for pluripotency gene expression. The disruption of these interactions by DNA damage results in cells exiting pluripotency, highlighting the importance of ABCF1 in regulating stem cell self-renewal.
Article
Biochemistry & Molecular Biology
Cinzia Caggiano, Marco Pieraccioli, Consuelo Pitolli, Gabriele Babini, Dinghai Zheng, Bin Tian, Pamela Bielli, Claudio Sette
Summary: This study uncovers a new role for androgen receptor (AR) in alternative cleavage and polyadenylation (APA) in prostate cancer. AR inhibition affects the rearrangement of APA subcomplexes and regulates transcriptome reprogramming. These findings are important for understanding the adaptive response of prostate cancer cells to hormonal therapy.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yongzhi Chen, Xuqiu Lei, Zhaozhao Jiang, Katherine A. Fitzgerald
Summary: CNBP plays a crucial role in the production of type I interferons in response to RNA virus infection. It controls the recruitment of IRF3 and IRF7 to IFN promoters and directly binds to the promoter of IFNb in the nucleus. This provides an additional layer of control for the antiviral innate immune response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Adriana Calaca Serrao, Felix T. Daenekamp, Zsofia Meggyesi, Dieter Braun
Summary: The initial nucleotide bias in short DNA pools disappears after isothermal replication, but the nucleotide composition at each position in the elongated sequences remains biased, with variations depending on the position and initial bias. Highly periodic dimer and trimer motifs emerge in the rapidly elongated sequences. These findings are important for understanding how biased prebiotic pools undergo molecular evolution and give rise to complex functional nucleic acids.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Runhua Han, Jessie Jiang, Jaden Fang, Lydia M. Contreras
Summary: 8-Oxo-7,8-dihydroguanine (8-oxoG) is a major RNA modification caused by oxidative stresses and is associated with carcinogenesis, neurodegeneration, and aging. This study identified four proteins in an extremophilic bacterium that preferentially bind to 8-oxoG-modified RNA, including PNPase and RhlB. These proteins reduce the cellular availability of 8-oxoG-modified RNA and enhance the bacterium's resistance to oxidative stress.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Marcela B. Prieto, Raphaela C. Georg, Fernando A. Gonzales-Zubiate, Juliana S. Luz, Carla C. Oliveira
BMC MOLECULAR BIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Rodrigo Bernardi Miguel, Philippe Alexandre Divina Petersen, Fernando A. Gonzales-Zubiate, Carla Columbano Oliveira, Naresh Kumar, Rafael Rodrigues do Nascimento, Helena Maria Petrilli, Ana Maria da Costa Ferreira
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Fernando A. Gonzales-Zubiate, Ellen K. Okuda, Julia P. C. Da Cunha, Carla Columbano Oliveira
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Biochemistry & Molecular Biology
Mahavir Singh, Fernando A. Gonzales, Duilio Cascio, Nathanael Heckmann, Guillaume Chanfreau, Juli Feigon
JOURNAL OF BIOLOGICAL CHEMISTRY
(2009)
Article
Biochemistry & Molecular Biology
Cyril Saguez, Fernando A. Gonzales, Manfred Schmid, Andreas Boggild, Chrysa M. Latrick, Francisco Malagon, Andrea Putnam, Lee Sanderson, Eckhard Jankowsky, Ditlev E. Brodersen, Torben Heick Jensen
Article
Biochemistry & Molecular Biology
Ellen K. Okuda, Fernando A. Gonzales-Zubiate, Olivier Gadal, Carla C. Oliveira
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biology
Oscar Chang, Fernando A. Gonzales-Zubiate, Luis Zhinin-Vera, Rafael Valencia-Ramos, Israel Pineda, Antonio Diaz-Barrios
Summary: This paper presents a computer simulation of a virtual robot that can learn efficient protein folding policies by itself and solve folding episodes of the Hemaggluanin-Esterase protein from human coronavirus. The robot is driven by a self-taught neural agent and uses reinforcement learning to explore new folding forms. The agent's memory is implemented with neural networks trained to satisfy future conditions required by the Bellman equation.
Review
Biotechnology & Applied Microbiology
Evelyn C. Mollocana-Lara, Ming Ni, Spiros N. Agathos, Fernando A. Gonzales-Zubiate
Summary: Although the study of RNA therapeutics was overshadowed by DNA-based therapies for many years, it is now back with force, elucidating the important role of RNA in cell regulation and disease development. Current research focuses on introducing various RNA molecules and the latest advancements in synthetic and delivery technologies, highlighting FDA-approved RNA therapies and ongoing clinical investigations.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Proceedings Paper
Computer Science, Information Systems
Nayeli Y. Gomez-Castillo, Pedro E. Cajilima-Cardenaz, Luis Zhinin-Vera, Belen Maldonado-Cuascota, Diana Leon Dominguez, Gabriela Pineda-Molina, Andres A. Hidalgo-Parra, Fernando A. Gonzales-Zubiate
Summary: The study proposes a machine learning model to accurately predict future blood glucose levels in diabetic patients. By processing the dataset using different methods, the study finds the best prediction accuracy. This research is of great importance for addressing healthcare issues related to glucose forecasting and avoiding complications in diabetic patients.
SMART TECHNOLOGIES, SYSTEMS AND APPLICATIONS, SMARTTECH-IC 2021
(2022)
Article
Biochemical Research Methods
M. Mitne-Neto, C. R. R. Ramos, D. C. Pimenta, J. S. Luz, A. L. Nishimura, F. A. Gonzales, C. C. Oliveira, M. Zatz
PROTEIN EXPRESSION AND PURIFICATION
(2007)
Article
Biochemistry & Molecular Biology
J. S. Luz, J. R. Tavares, F. A. Gonzales, M. C. T. Santos, C. C. Oliveira
Article
Biochemistry & Molecular Biology
DC Granato, FA Gonzales, JS Luz, F Cassiola, GM Machado-Santelli, CC Oliveira
Article
Biochemistry & Molecular Biology
FA Gonzales, NIT Zanchin, JS Luz, CC Oliveira
JOURNAL OF MOLECULAR BIOLOGY
(2005)
Article
Biochemistry & Molecular Biology
CC Oliveira, FA Gonzales, NIT Zanchin
NUCLEIC ACIDS RESEARCH
(2002)