Article
Biochemistry & Molecular Biology
Eunho Song, Seungha Hwang, Palinda Ruvan Munasingha, Yeon-Soo Seo, Jin Young Kang, Changwon Kang, Sungchul Hohng
Summary: In this study on bacterial Rho factor-dependent terminators, it was found that the three Rho-dependent termination routes operate compatibly and their efficiency depends on the termination pauses. The most abundant route involves Rho catching up with a paused RNA polymerase, leading to simultaneous release of transcript RNA and template DNA. The fastest route results in RNA-only release and recycling of RNAP, while the slowest route facilitates simultaneous releases. The termination efficiency of stand-by Rho positively correlates with pause duration, contrary to previous speculation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Ferenc Fekete, Katalin Mango, Annamaria Minus, Katalin Toth, Katalin Monostory
Summary: The impact of CYP1A2 genetic variants on enzyme activity is inconsistent. CYP1A2-genotyping is not suitable for predicting CYP1A2 function, but CYP1A2 mRNA expression in leukocytes can provide information about patients' CYP1A2-metabolizing capacity.
Article
Multidisciplinary Sciences
Sayanur Rahaman, Simone Faravelli, Sylvia Voegeli, Attila Becskei
Summary: The stability gain of mRNA in yeast depends on the mRNA coding sequence length. Codon optimality affects mRNA stability and polysome propensity above a threshold length. The untranslated regions (UTR) can tune this threshold length and some UTRs can destabilize mRNAs without reducing translation, which is important for controlling the oscillatory expression of cell cycle genes.
Article
Plant Sciences
Gaochao Cai, Andrea Carminati, Mohanned Abdalla, Mutez Ali Ahmed
Summary: The study revealed that although root hairs play a minor role in maize compared to barley in water uptake, they still have some impact on root hydraulics under soil drying conditions. Additionally, the response of root hydraulics to drought varies depending on soil textures, indicating that the role of root hairs cannot be generalized across different species.
Article
Oncology
Kristen E. Schratz, Diane A. Flasch, Christine C. Atik, Zoe L. Cosner, Amanda L. Blackford, Wentao Yang, Dustin L. Gable, Paz J. Vellanki, Zhimin Xiang, Valeriya Gaysinskaya, Robert H. Vonderheide, Lisa M. Rooper, Jinghui Zhang, Mary Armanios
Summary: Patients with short telomere syndromes (STS) have a predisposition to certain types of solid cancers, specifically squamous cell carcinomas of the head and neck, anus, or skin. This predisposition is not due to increased chromosome instability but rather acquisition of telomere maintenance mechanisms and T cell immunodeficiency. The findings suggest that the susceptibility to solid cancers in STS patients is driven by T cell exhaustion.
Article
Microbiology
Rocio Espinosa, Michael Askvad Sorensen, Sine Lo Svenningsen
Summary: Protein synthesis is a highly regulated and energetically costly process in cells. This study investigates the response of Escherichia coli to phosphate starvation and reveals that protein synthesis is primarily limited by the availability of template mRNA rather than the capacity of ribosomes. This limitation is an adaptive response to prevent overcommitting resources to protein synthesis. Furthermore, the degradation of ribosomal RNA is influenced by the availability of idle ribosomal subunits.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Xiaoyan Jiang, Xin Jia, Shengjie Gao, Yan Jiang, Ningning Wei, Cong Han, Tianshan Zha, Peng Liu, Yun Tian, Shugao Qin
Summary: The study found that leaf and fine-root traits of desert plants partially align with the global leaf economics spectrum (LES) theory, but fine-root traits do not exhibit a leaf-trait syndrome. Functional traits related to nutrient allocation and use are coordinated between leaves and fine roots in desert ecosystems, with differences observed among functional groups.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Ophthalmology
Yingyan Ma, Senlin Lin, Ian G. Morgan, Jos J. Rozema, Rafael Iribarren, Jianfeng Zhu, Rong Zhao, Bo Zhang, Yao Yin, Yueqin Shao, Xiangui He, Xun Xu, Haidong Zou
Summary: In preschool children, changes in refraction and refractive components over one year were observed. Loss of lens power in eyes with lower baseline spherical equivalent refraction resulted in hyperopic shifts, while in eyes with higher baseline spherical equivalent refraction, the loss of lens power compared to axial elongation was reduced, leading to myopic shifts. This study highlighted the homeostasis of human refraction and how it leads to a preferred state of mild hyperopia.
ACTA OPHTHALMOLOGICA
(2021)
Article
Biochemistry & Molecular Biology
Jose Garcia-Martinez, Daniel A. Medina, Pablo Bellvis, Mai Sun, Patrick Cramer, Sebastian Chavez, Jose E. Perez-Ortin
Summary: The study found no genetic compensation of NMD mRNA targets in yeast, and total mRNA buffering primarily uses a global system rather than a gene-specific one.
Article
Multidisciplinary Sciences
Hiromi Mutsuro-Aoki, Hiroshi Teramura, Ryoko Tamukai, Miho Fukui, Hiroaki Kusano, Mikhail Schepetilnikov, Lyubov A. Ryabova, Hiroaki Shimada
Summary: This study revealed that the UTRc splice variant of rice OsMac1 mRNA has a 38-nt sequence, sp38, which significantly enhances translation efficiency of the downstream ORF. Additionally, the first 100 nucleotides of the CU-rich region play a role in translational enhancement. Computational prediction identified structural motifs in UTRc, with SL4 binding to Region-A and base pairing between Region-B and the UTRc 3'end being critical for translational enhancement.
Article
Nursing
Dillon J. Dzikowicz, Mary G. Carey
Summary: Among firefighters, career length rather than age moderately correlates with IHD ischemic severity. This suggests that occupational exposure history plays a significant role in the development of IHD, and should be considered by health practitioners when providing risk reduction services.
WORKPLACE HEALTH & SAFETY
(2021)
Article
Multidisciplinary Sciences
Mateen A. Khan, Taj Mohammad, Ajamaluddin Malik, Md. Imtaiyaz Hassan, Artem V. Domashevskiy
Summary: The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was studied using molecular docking and multi-spectroscopic techniques. Molecular docking analysis revealed 11 residues involved in hydrogen bonding as the main driving force. Fluorescence binding results showed a strong interaction with a binding affinity of 31.3 x 10(6) M-1. Addition of Fe2+ decreased the binding affinity. The thermodynamic parameters indicated an enthalpy-driven and entropy-favored event. Stopped-flow kinetics confirmed complex formation and iron-induced structural changes.
SCIENTIFIC REPORTS
(2023)
Article
Pharmacology & Pharmacy
Anders Fuglsang
Summary: The study found that estimates based on REML are closer to true values than those based on linear models, with significant differences shown in only two out of seven scenarios tested. REML-based estimators have less variability, but both types of estimates are negatively biased, leading to a narrower acceptance range.
JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES
(2021)
Editorial Material
Health Care Sciences & Services
Fran Baum, Julia Anaf
Summary: This paper provides a commentary on the emerging tactics of ultraprocessed food transnational corporations (TNCs), discussing the growth in power and influence of TNCs and their impact on health and health equity. The article suggests five changes are required to create a more human-centered and health-promoting economy, including improved measurement of economic outputs, regulation of finance and TNCs, development of local economic models, reversal of privatizations, and making the reduction of economic inequalities a goal of financial policy.
INTERNATIONAL JOURNAL OF HEALTH POLICY AND MANAGEMENT
(2022)
Article
Law
Anne Hewitt, Laura Grenfell
Summary: This article examines the impact of a lack of work experience on university students' job prospects and proposes feasible reforms to alleviate these barriers.
ALTERNATIVE LAW JOURNAL
(2022)
Article
Multidisciplinary Sciences
Griffin M. Schroeder, Chapin E. Cavender, Maya E. Blau, Jermaine L. Jenkins, David H. Mathews, Joseph E. Wedekind
Summary: Riboswitches are non-coding RNAs that regulate gene expression in bacteria by recognizing specific cellular effectors. This study reveals the crystal structure of a preQ(1)-sensing riboswitch, showing two effectors stacked in a single binding pocket. The recognition of stacked effectors expands the effector recognition capabilities of riboswitches and has implications for antimicrobial development.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Eliezra Glasser, Debanjana Maji, Giulia Biancon, Anees Mohammed Keedakkatt Puthenpeedikakkal, Chapin E. Cavender, Toma Tebaldi, Jermaine L. Jenkins, David H. Mathews, Stephanie Halene, Clara L. Kielkopf
Summary: This study reveals the flexibility of U2AF2 in recognizing polypyrimidine tracts of nascent transcripts and the tolerance of nucleotide substitutions at the central position of the Py tract. The results highlight the importance of RNA flexibility for protein recognition and provide insights into the relationship between splice site motifs and pre-mRNA splicing efficiencies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jeffrey Zuber, Susan J. Schroeder, Hongying Sun, Douglas H. Turner, David H. Mathews
Summary: Nearest neighbor parameters are commonly used for estimating the folding stability of RNA secondary structures. In this study, we curated an expanded database and found that the terminal penalties for helices depend on the sequence identity of the adjacent penultimate base pair. By including this additional sequence dependence, new nearest neighbor parameters accurately predict the stabilities of helices and improve the fitting of base pair stacks with GU pairs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Elzbieta Kierzek, Xiaoju Zhang, Richard M. Watson, Scott D. Kennedy, Marta Szabat, Ryszard Kierzek, David H. Mathews
Summary: This study addresses the issue of predicting the secondary structure of RNA with covalently modified nucleotides. The researchers developed software and determined thermodynamic parameters to enable the prediction of secondary structure for sequences containing N-6-methyladenosine (m(6)A). The study also revealed the effects of N-6-methylation on folding stability in different contexts.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Wan-Jung C. Lai, Mingyi Zhu, Margarita Belinite, Gregory Ballard, David H. Mathews, Dmitri N. Ermolenko
Summary: Adding unstructured sequences to the 3'UTR of mRNA decreases translation, resulting in a weakened ability of the poly(A) tail.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
He Zhang, Sizhen Li, Liang Zhang, David H. Mathews, Liang Huang
Summary: This study presents a new RNA sampling algorithm, LazySampling and LinearSampling, which address the speed and computational complexity issues of conventional algorithms by eliminating redundant calculations and providing linear time runtime. Benchmarking tests demonstrate that LinearSampling outperforms standard tools in terms of sampling quality and speed, and identifies potential high-accessibility regions in the SARS-CoV-2 genome for COVID-19 diagnostics and therapeutics.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Barbara Mirska, Tomasz Wozniak, Dagny Lorent, Agnieszka Ruszkowska, Jake M. Peterson, Walter N. Moss, David H. Mathews, Ryszard Kierzek, Elzbieta Kierzek
Summary: Studying the RNA secondary structure of the respiratory virus influenza A virus (IAV) is important for understanding its biology and developing new antiviral drugs. In this study, we used chemical RNA mapping and mutational profiling techniques to analyze the RNA secondary structure of IAV in both in virio and in cellulo environments. The experimental data accurately predicted the structures of all eight viral RNA segments in virio and revealed the structures of three segments in cellulo for the first time. Further analysis identified highly conserved motifs in the predicted viral RNA structures, which could be potential targets for new antiviral strategies against IAV.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ananya Das, Nichole Adiletta, Dmitri N. Ermolenko
Summary: Translational G proteins released by GTP hydrolysis regulate protein synthesis by affecting the rotation of ribosomal subunits. LepA shifts the ribosome towards a non-rotated conformation while EF-G favors the rotated conformation. Despite stabilizing the non-rotated conformation, the presence of P-site peptidyl-tRNA and antibiotics only moderately reduces EF-G binding. These findings provide new insights into the mechanisms of LepA and EF-G and highlight the importance of ribosome structural dynamics in translation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ananya Das, Chen Bao, Dmitri N. Ermolenko
Summary: In this study, two independent FRET assays were used to confirm that pre-translocation ribosomes without EF-G can undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. The fraction of spontaneously fluctuating molecules changes depending on experimental conditions, highlighting the importance of using multiple FRET assays in studies of ribosome dynamics and emphasizing the role of thermally-driven large-scale ribosome rearrangements in translation.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Griffin M. Schroeder, Olayinka Akinyemi, Jeffrey Malik, Caroline M. Focht, Elizabeth M. Pritchett, Cameron D. Baker, James P. McSally, Jermaine L. Jenkins, David H. Mathews, Joseph E. Wedekind
Summary: The article investigates the regulation of downstream gene expression by riboswitches through binding cellular metabolites. It suggests that riboswitches regulate translation initiation by sequestering the Shine-Dalgarno sequence with metabolites. The study also reveals that in certain riboswitches, cellular metabolites can bind to the gene-regulatory sequence, thereby influencing gene regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Omar M. Hedaya, Kadiam C. Venkata Subbaiah, Feng Jiang, Li Huitong Xie, Jiangbin Wu, Eng-Soon Khor, Mingyi Zhu, David H. Mathews, Chris Proschel, Peng Yao
Summary: By analyzing ribosome profiling data, researchers identified a dsRNA structure in the uORF of the GATA4 gene that enhances uORF translation and inhibits mORF translation. The RNA helicase DDX3X inhibits the activity of the GATA4 uORF-dsRNA and regulates the translation balance of uORF and mORF. ASOs that disrupt the dsRNA structure promote mORF translation.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Jeffrey Zuber, Sudisht K. Sah, David H. Mathews, Elena Rustchenko, Elisabetta Blasi
Summary: Drugs from the ECN class are recommended as first-line treatments for infections caused by C. albicans, but their increased use has led to rising resistance. Identifying factors associated with decreased ECN susceptibility is important, as resistance is seen as a multistep evolution.