Review
Biochemistry & Molecular Biology
Raffaele Sciaccotta, Giuseppe Murdaca, Santino Caserta, Vincenzo Rizzo, Sebastiano Gangemi, Alessandro Allegra
Summary: This article investigates the role of circular RNAs in the pathogenesis of multiple sclerosis. Circular RNAs influence post-transcriptional control, affecting microRNA and epigenetic factors, and promoting the development of typical MS abnormalities such as neuroinflammation and neuronal cell damage.
Article
Biochemical Research Methods
Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis
Summary: The study of viruses' genetic composition is crucial for their identification and classification, especially during times of pandemic turmoil. New technologies in nucleic acid sequencing can introduce artifacts into viral genomes, and this study proposes an algorithm to help remove problematic regions while retaining essential genetic information. This approach aims to improve the accuracy and integrity of viral genomes for novel virus identification and characterization in public databases.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Tomasz Wozniak, Malgorzata Sajek, Jadwiga Jaruzelska, Marcin Piotr Sajek
Summary: RNAlign2D is a fast Python tool that converts RNA sequences to pseudo-amino acid sequences, aligns them with the multiple protein sequence alignment tool MUSCLE, and produces accurate results in a short time. The pseudo-amino acid substitution matrix approach used in RNAlign2D is applicable for virtually all protein aligners.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Bankala Krishnarjuna, Thirupathi Ravula, Edgar M. Faison, Marco Tonelli, Qi Zhang, Ayyalusamy Ramamoorthy
Summary: In this study, polymer-based nanodiscs were used to measure RDCs from nucleic acids. The nanodiscs were characterized and their alignment stability was confirmed. RDCs from a labeled nucleic acid molecule were successfully measured using the aligned nanodiscs. This demonstrates the potential of SMA-EA-based lipid-nanodiscs for structural and dynamical studies of nucleic acids.
Article
Biochemistry & Molecular Biology
Geun Young Chae, Woo-Jong Hong, Min Jeong Jang, Ki-Hong Jung, Seungill Kim
Summary: TE-derived FAR1 genes play crucial roles in agriculturally important crops, with updated annotations revealing structural divergence, adaptation, and function of these genes. CRISPR/Cas9 genome editing and transcriptome analysis identified a novel gene involved in rice pollen fertility regulation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Giovanni Di Liberto, Angel Morales-Garcia, Stefan T. Bromley
Summary: From grain boundaries and heterojunctions to manipulating 2D materials, solid-solid interfaces have important applications in various technologies. However, understanding and predicting properties of these complex systems remains a challenge. In this paper, the authors present an unconstrained and generally applicable non-periodic screening approach for systematic exploration of material's interfaces, providing a detailed and comprehensive understanding of interface structure and energetic stability. They validate the method with the TiO2 anatase (101)/(001) and TiO2 anatase (101)/rutile (110) interfaces.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Bingkun Lei, Matias Capella, Sean A. Montgomery, Michael Borg, Akihisa Osakabe, Malgorzata Goiser, Abubakar Muhammad, Sigurd Braun, Frederic Berger
Summary: The diversification of histone variants is achieved through the acquisition of specific motifs and functional properties through convergent evolution. H2A variants are distinguished by specific C-terminal motifs and are often segregated within defined domains of the genome. The timing of evolution of these motifs in relation to segregation mechanisms remains unclear.
Article
Biochemistry & Molecular Biology
Xu Hong, Jinfang Zheng, Juan Xie, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu, Shiyong Liu
Summary: The three-dimensional structure of RNA is important in its recognition with RNA-binding proteins. RR3DD is an RNA classification database based on RNA fold and global 3D structural similarity, containing a large number of RNA chains classified and clustered. Through structural alignment, some unannotated RNAs can be annotated in RR3DD.
Article
Plant Sciences
Zhikai Liang, Sarah N. Anderson, Jaclyn M. Noshay, Peter A. Crisp, Tara A. Enders, Nathan M. Springer
Summary: This study reveals that although TEs can generate transcripts under heat or cold stress conditions, genome-wide activation of TEs did not occur. There is substantial variation in the stress-responsive expression of TE families among different genotypes, with the driving factors being largely concentrated on specific elements within TE families lacking DNA methylation. The differences in TE expression between genotypes are attributed to genetic and epigenetic variations, where fully methylated elements tend to be inactive while those with regions lacking DNA methylation are more likely to be expressed.
Article
Multidisciplinary Sciences
Madiha Kamal, Ambreen Fatima
Summary: The jobless growth of Pakistan's economy and the frequent changes in the government's power have an impact on its economic growth. A qualitative analysis of the structural transformation on the disaggregated level is conducted to determine its connection or impact on different sectors of the economy. The study explores how the sectoral transformation affects economic development, employment, and their relationships, as well as investigates its impact on sustainable employment generation. The results indicate that the military regimes perform better in terms of economic performance, but further research is needed to determine the employment elasticity of Pakistan's main political powers. The decline in the agriculture sector highlights the need for reforms to create additional jobs and sustain employment power.
Article
Multidisciplinary Sciences
Caillan Crowe-McAuliffe, Victoriia Murina, Marje Kasari, Hiraku Takada, Kathryn Jane Turnbull, Yury S. Polikanov, Arnfinn Sundsfjord, Kristin Hegstad, Gemma C. Atkinson, Daniel N. Wilson, Vasili Hauryliuk, Susanne Huch, Lilit Nersisyan, Vicent Pelechano
Summary: PoxtA and OptrA are ABC proteins of the F subtype that confer resistance to oxazolidinone and phenicol antibiotics. In this study, the researchers provide structural insights into how PoxtA binding to the ribosome indirectly promotes drug dissociation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Rosemary J. Cater, Geok Lin Chua, Satchal K. Erramilli, James E. Keener, Brendon C. Choy, Piotr Tokarz, Cheen Fei Chin, Debra Q. Y. Quek, Brian Kloss, Joseph G. Pepe, Giacomo Parisi, Bernice H. Wong, Oliver B. Clarke, Michael T. Marty, Anthony A. Kossiakoff, George Khelashvili, David L. Silver, Filippo Mancia
Summary: This study presents the structure of MFSD2A, revealing how it mediates the uptake of lysolipids into the brain through Na+-dependent conformational changes. The transporter features an amphipathic cavity and a lateral gate, facilitating the release of substrates into the membrane.
Article
Computer Science, Interdisciplinary Applications
Tianci Gao, Zihan Li, Yan Gao, Paul Schonfeld, Xiaoyun Feng, Qingyuan Wang, Qing He
Summary: This study utilizes deep reinforcement learning (DRL) to optimize railway alignments in mountainous areas in order to minimize construction costs. By integrating human experience and the DRL algorithm, the automated exploration and optimization of alignment designs is achieved, leading to a significant decrease in construction costs.
COMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING
(2022)
Article
Biochemical Research Methods
Mengyi Tang, Kumbit Hwang, Sung Ha Kang
Summary: This study proposes a new deterministic methodology for predicting the secondary structure of RNA sequences, which uses a simple algorithm to predict the structure of short RNA and tRNA sequences and provides a deterministic answer.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Harsha Doddapaneni, Sara Javornik Cregeen, Richard Sucgang, Qingchang Meng, Xiang Qin, Vasanthi Avadhanula, Hsu Chao, Vipin Menon, Erin Nicholson, David Henke, Felipe-Andres Piedra, Anubama Rajan, Zeineen Momin, Kavya Kottapalli, Kristi L. Hoffman, Fritz J. Sedlazeck, Ginger Metcalf, Pedro A. Piedra, Donna M. Muzny, Joseph F. Petrosino, Richard A. Gibbs
Summary: A capture sequencing methodology was developed to obtain SARS-CoV-2 genomic and transcriptome sequences from infected patients. Analysis of samples with varying viral titers revealed differential transcriptional activity and allelic frequencies. Hybridization-based capture proved to be effective and scalable for sequencing SARS-CoV-2 from patient samples.
Article
Engineering, Biomedical
Wei-Kee Ong, How-Foo Chen, Cheng-Ting Tsai, Yun-Ju Fu, Yi-Shan Wong, Da-Jen Yen, Tzu-Hao Chang, Hsien-Da Huang, Oscar Kuang-Sheng Lee, Shu Chien, Jennifer Hui-Chun Ho
Article
Biotechnology & Applied Microbiology
Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Tzu-Hao Chang, Dray-Ming Shien
Article
Computer Science, Artificial Intelligence
Tzu-Hao Chang, Li-Ching Wu, Jun-Hong Lin, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
EXPERT SYSTEMS WITH APPLICATIONS
(2010)
Article
Biochemistry & Molecular Biology
Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang, Jorng-Tzong Horng
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2013)
Article
Computer Science, Interdisciplinary Applications
Tzu-Hao Chang, Li-Ching Wu, Yu-Ting Chen, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING
(2011)
Article
Biochemistry & Molecular Biology
Tzu-Hao Chang, Hsien-Da Huang, Li-Ching Wu, Chi-Ta Yeh, Baw-Jhiune Liu, Jorng-Tzong Horng
Article
Biochemistry & Molecular Biology
Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, Jorng-Tzong Horng
NUCLEIC ACIDS RESEARCH
(2006)
