Article
Mathematical & Computational Biology
Kuo-Feng Tung, Wen-Chang Lin
Summary: This study introduces a new transcript database that provides a unified representative transcript for human protein-coding genes. By utilizing a dataset based on a long-read sequencing platform, the researchers provide expression profiles of these transcripts in various normal human tissues, and establish an online database for user queries.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Plant Sciences
Peina Cao, Youning Wang, Zhaolan Ma, Xiao Xu, Dongfang Ma, Lijun Yang
Summary: This study analyzed the noncoding RNAs in wheat before and after powdery mildew infection and identified lincRNAs that may be involved in the pathogen response. The target genes of these lincRNAs were predicted and functional annotations were performed. Co-expression analysis showed significant correlation between certain lincRNAs and their potential target genes, suggesting their involvement in the pathogenic mechanism of wheat powdery mildew.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Ke Yi, Weiyi Yan, Xiang Li, Shuqing Yang, Jiaqi Li, Yifan Yin, Fengping Yuan, Haiying Wang, Zhensheng Kang, Dejun Han, Qingdong Zeng
Summary: Wheat sharp eyespot caused by Rhizoctonia cerealis is a severe threat to worldwide wheat production. Currently, there are no resistant wheat cultivars, and the use of fungicides is the primary method for controlling this disease. Elucidating the mechanisms of R. cerealis pathogenicity can accelerate the pace of the control of this disease.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agriculture, Multidisciplinary
Li Cen-cen, Yu Shu-long, Ren Hai-feng, Wu Wei, Wang Ya-ling, Han Qiu, Xu Hai-xia, Xu Yong-jie, Zhang Peng-peng
Summary: The study collected data on long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle development, identified differentially expressed lincRNAs during early pig embryonic development, predicted their potential target genes and functions, and laid the foundation for further research into lincRNAs functions.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2021)
Article
Multidisciplinary Sciences
Cecilia Blikstad, Eli J. Dugan, Thomas G. Laughlin, Julia B. Turnsek, Mira D. Liu, Sophie R. Shoemaker, Nikoleta Vogiatzi, Jonathan P. Remis, David F. Savage
Summary: Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation and play a central role in the bacterial CO2 concentrating mechanism. This study reveals the structural basis of carbonic anhydrase encapsulation into alpha-carboxysomes and highlights the importance of Rubisco as a central hub for mediating assembly through protein interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Oncology
Joanna Kozlowska, Tomasz Kolenda, Paulina Poter, Joanna Sobocinska, Kacper Guglas, Maciej Stasiak, Renata Blizniak, Anna Teresiak, Katarzyna Lamperska
Summary: Head and neck squamous cell carcinoma is a common and deadly cancer, requiring more research to find new personalized treatment options. Studying the tumor microenvironment and the role of non-coding RNAs in disease progression is crucial. Long intergenic non-coding RNAs play an important role in cancer biology and can serve as valuable biomarkers.
Article
Biology
Osama Abdin, Satra Nim, Han Wen, Philip M. Kim
Summary: Protein-peptide interactions are important but understudied and difficult to model. The authors developed PepNN-Struct, a structure-based approach, and PepNN-Seq, a sequence-based approach, to predict peptide binding sites on proteins. The models use a reciprocal attention mechanism to update encodings of peptides and proteins, and incorporate graph neural network layers and transfer learning to overcome the lack of complex information. Experiment results show consistently high performance of PepNN-Struct and its ability to predict novel peptide binding proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemical Research Methods
Syed Danish Ali, Waleed Alam, Hilal Tayara, Kil To Chong
Summary: piRNAs are a class of small RNAs that play important roles in maintaining germline cells, gene stability, and genome integrity, and are associated with various cancers. A predictor based on a deep learning architecture has been proposed, showing significant improvements in piRNA prediction and target mRNA deadenylation compared to existing computational methods.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Mathematical & Computational Biology
Anna Bernasconi, Luca Cilibrasi, Ruba Al Khalaf, Tommaso Alfonsi, Stefano Ceri, Pietro Pinoli, Arif Canakoglu
Summary: EpiSurf is a web application that selects viral populations and analyzes amino acid changes distribution within epitopes. It supports user-friendly testing of epitope conservancy for designing vaccines, drugs or serological assays.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Plant Sciences
Tian Wan, Bai-xue Qiao, Jing Zhou, Ke-sen Shao, Liu-yi Pan, Feng An, Xu-sheng He, Tao Liu, Ping-ke Li, Yu-liang Cai
Summary: This study reports the chloroplast genome sequences of 11 Cerasus species to investigate the evolution of their plastome. The results reveal the typical quadripartite circular structure of Cerasus chloroplast genomes and the presence of 115 unique genes. Several genes were found to have high nucleotide diversity and more polymorphic sites, including matK, rps16, and rbcL. The phylogenetic analysis sheds light on the relationships between different Cerasus species, providing insights for further research on their phylogenetics and phylogeography.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Jinjun Gao, Xinlei Sheng, Jianfeng Du, Di Zhang, Chang Han, Yue Chen, Chu Wang, Yingming Zhao
Summary: We developed a new database search strategy called CHiMA, which uses 50% matched fragment ions as the key criterion to identify high-confidence PSMs. Compared to conventional methods, CHiMA identified twice as many histone modification sites in benchmark datasets. Reanalysis of previous proteomics data using CHiMA led to the discovery of 113 new histone marks, almost doubling the number of previously reported marks. This tool not only offers a valuable approach for identifying histone modifications but also greatly expands the repertoire of histone marks.
Article
Biochemistry & Molecular Biology
Sahar Ghulam Mohyuddin, Yan Liang, Yuxin Xia, Mengqi Wang, Huimin Zhang, Mingxun Li, Zhangping Yang, Niel A. Karrow, Yongjiang Mao
Summary: This study analyzed the expression profile and characteristics of lncRNAs in the mammary gland tissues of Holstein cows during both lactation and non-lactation stages. The results showed significant differences in the expression of 96 lncRNAs between the two stages, with 83 genes upregulated and 53 genes downregulated. Enrichment analysis revealed abundant gene ontology (GO) terms related to cellular processes and predominant metabolic pathways, fatty acid biosynthesis, the immune system, and glycosphingolipid biosynthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Mark H. Griep, Michael S. Sellers, Bijil Subhash, Alexis M. Fakner, Abby L. West, Nicholas M. Bedford
Summary: Elucidating the location of stabilized nanoclusters within their protein hosts is a challenge, with the ability to synthesize protein-nanoclusters in a consistent and high-throughput fashion highly desirable. Density functional theory simulations were used to locate high probability regions within the trypsin enzyme for Au25 cluster stabilization, which suggested cluster location is likely near the trypsin active region. Microwave-based syntheses of gold nanoclusters showed slight structural differences compared to standard methods, while maintaining native structural attributes. This work highlights the importance of understanding the connections between synthetic conditions, atomic-scale structure, and materials properties in metal cluster-protein materials for future applications.
Article
Biochemistry & Molecular Biology
Zhiyuan Zhao, Kongfu Zhu, Dexiang Tang, Yuanbing Wang, Yao Wang, Guodong Zhang, Yupeng Geng, Hong Yu
Summary: The mycoparasite fungi of Clonostachys play a role in biological control, with their mitochondrial genomes showing gene rearrangements. The analysis of protein-coding genes suggests a high degree of conservation and purifying selection among the Clonostachys species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Astronomy & Astrophysics
Enrique Mestre, Diego F. Torres, Emma de Ona Wilhelmi, Josep Marti
Summary: The Cherenkov Telescope Array aims to conduct the deepest survey of the Galactic Plane in very-high-energy gamma-rays, but it will face the challenge of source confusion. Through simulations and analysis, it has been found that CTA can resolve about 60% of confused sources above 500 GeV.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
K. Wethmar, J. Schulz, E. M. Muro, S. Talyan, M. A. Andrade-Navarro, A. Leutz
Article
Biochemistry & Molecular Biology
Jonas Ibn-Salem, Enrique M. Muro, Miguel A. Andrade-Navarro
NUCLEIC ACIDS RESEARCH
(2017)
Article
Genetics & Heredity
Kivia A. P. de Oliveira, Eva Kaergel, Matthias Heinig, Jean-Fred Fontaine, Giannino Patone, Enrique M. Muro, Stephan Mathas, Michael Hummel, Miguel A. Andrade-Navarro, Norbert Huebner, Claus Scheidereit
Article
Biochemistry & Molecular Biology
Enrique M. Muro, Nancy Mah, Gabriel Moreno-Hagelsieb, Miguel A. Andrade-Navarro
NUCLEIC ACIDS RESEARCH
(2011)
Review
Cell Biology
Paul M. Krzyzanowski, Enrique M. Muro, Miguel A. Andrade-Navarro
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2012)
Article
Genetics & Heredity
Enrique M. Muro, Jonas Ibn-Salem, Miguel A. Andrade-Navarro
EPIGENETICS & CHROMATIN
(2019)
Article
Cardiac & Cardiovascular Systems
Torsten Mueller, Etienne Boileau, Sweta Talyan, Dorothea Kehr, Karl Varadi, Martin Busch, Patrick Most, Jeroen Krijgsveld, Christoph Dieterich
Summary: Pigs are valuable models for cardiovascular research, but their genome and transcriptome annotation lack diversity. Researchers used high-throughput sequencing and proteomics to enhance pig cardiac transcriptome annotation, providing a valuable data resource.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2021)
Article
Clinical Neurology
Miguel A. Andrade-Navarro, Katja Muhlenberg, Eike J. Spruth, Nancy Mah, Adrian Gonzalez-Lopez, Tommaso Andreani, Jenny Russ, Matthew R. Huska, Enrique M. Muro, Jean-Fred Fontaine, Vyacheslav Amstislavskiy, Alexei Soldatov, Wilfried Nietfeld, Erich E. Wanker, Josef Priller
FRONTIERS IN NEUROLOGY
(2020)
Article
Cell Biology
Piyush More, Sweta Talyan, Jean-Fred Fontaine, Enrique M. Muro, Miguel A. Andrade-Navarro
Summary: LincRNAs are long non-coding RNAs that lack functional evidence and their biogenesis is not well-understood. They are thought to originate from genomic duplication of coding material, resulting in pseudogenes, some of which may retain similarity to the parental gene for potential functional reasons.
Article
Cell Biology
Sweta Talyan, Samantha Filipow, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kuehne, Linus Butt, Heike Gobel, K. Johanna R. Hoyer-Allo, Felix C. Koehler, Janine Altmuller, Paul Brinkkoeter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman-Ulrich Mueller, Christoph Dieterich
Summary: Diseases of the glomerulus are a common cause of chronic kidney disease, with FSGS being a classic example leading to proteinuria and scarring. Current lack of targeted treatments is due to limited understanding of podocyte defects. Emerging studies on lncRNAs in FSGS reveal a potential for new insights, with the bioinformatic pipeline CALINCA offering a solution for further exploration.
Article
Immunology
Melinda Czeh, Sina Stable, Stephen Kramer, Lena Tepe, Sweta Talyan, Joana Carrelha, Yiran Meng, Barbara Heitplatz, Marius Schwabenland, Michael D. Milsom, Christoph Plass, Marco Prinz, Matthias Schlesner, Miguel A. Andrade-Navarro, Claus Nerlov, Sten Eirik W. Jacobsen, Daniel B. Lipka, Frank Rosenbauer
Summary: This study reveals the important role of DNA methylation in the development of dendritic cell subsets. Reduction of methylation can deplete plasmacytoid dendritic cells and alleviate systemic lupus erythematosus.
JOURNAL OF IMMUNOLOGY
(2022)