Article
Plant Sciences
Chunyu Zhao, Mo Zhu, Yanying Guo, Jian Sun, Wenhong Ma, Xiaoxue Wang
Summary: Phosphatidylethanolamine-binding-protein (PEBP) domain-containing proteins are important in plant development. This study identified 20 OsPEBP genes in rice and found that they are not evenly distributed on the chromosomes. Phylogenetic analysis classified the OsPEBPs into six subgroups. The structure of these genes and their encoded proteins is similar. The expression of OsPEBP genes can be regulated by various factors, indicating their involvement in environmental signal responses.
Article
Multidisciplinary Sciences
Orhi Barroso-Gomila, Fredrik Trulsson, Veronica Muratore, Inigo Canosa, Laura Merino-Cacho, Ana Rosa Cortazar, Coralia Perez, Mikel Azkargorta, Ibon Iloro, Arkaitz Carracedo, Ana M. Aransay, Felix Elortza, Ugo Mayor, Alfred C. O. Vertegaal, Rosa Barrio, James D. Sutherland
Summary: SUMO-ID technology combines TurboID proximity biotinylation and protein-fragment complementation to study SUMO-dependent interactions, providing insight into the complexity of the ubiquitin code.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Software Engineering
Huu Tan Nguyen, Abhinav Bhatele, Nikhil Jain, Suraj P. Kesavan, Harsh Bhatia, Todd Gamblin, Kwan-Liu Ma, Peer-Timo Bremer
Summary: The Call context trees(CCTs) is an effective tool for understanding and analyzing the performance of parallel programs. However, existing visual representations do not scale well to applications running on a large number of processors. CallFlow is presented as an interactive visual analysis tool that provides a high-level overview of CCTs and semantic refinement operations to explore CCTs progressively.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Biochemical Research Methods
Wentao Gao, Dali Xu, Hongfei Li, Junping Du, Guohua Wang, Dan Li
Summary: Adaptor proteins play an important role in signal transduction pathways and are closely related to diseases. Previous studies used PSSM and neural network methods to identify adaptor proteins, but ordinary neural networks cannot handle the contextual information in PSSM profiles well. This study proposes an efficient method combining 1-D CNN and biLSTM, which shows better performance in identifying adaptor proteins.
Article
Genetics & Heredity
Zixiao Zhang, Yue Gong, Bo Gao, Hongfei Li, Wentao Gao, Yuming Zhao, Benzhi Dong
Summary: A method based on support vector machine was developed to effectively recognize SNARE proteins, utilizing PSSM to extract sequence features and SVM-RFE-CBR to rank feature importance. Independent tests showed sensitivity of 68%, specificity of 94%, accuracy of 92%, AUC of 84%, and MCC of 0.48, demonstrating superior performance compared to existing methods.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Benjamin Wiseman, Ram Gopal Nitharwal, Goeran Widmalm, Martin Hogbom
Summary: Lipopolysaccharides, crucial components of bacterial cell envelopes, are synthesized at the inner membrane through the Wzx/Wzy-dependent assembly pathway. The cryo-EM structure of intact E. coli WzzB provides insights into the transmembrane and cytoplasmic domains, as well as a conserved proline-rich segment near the C-terminal transmembrane helix.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Multidisciplinary
Qu Cheng, Wang Ran, Che Wu-nan, Li Feng-qi, Zhao Hai-peng, Wei Yi-yun, Luo Chen, Xue Ming
Summary: The study identified 19 OBPs in Harmonia axyridis and found that some OBPs were highly expressed in antennae of adult individuals, while most other OBP genes were highly expressed in non-olfactory tissues. These results provide valuable insights for further research on the olfaction of H. axyridis, potentially enhancing its biocontrol efficacy.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2021)
Article
Plant Sciences
Hao Zhang, Zhenjia Yu, Xiaodie Yao, Jingli Chen, Xing Chen, Huiwen Zhou, Yuxia Lou, Feng Ming, Yue Jin
Summary: The evolutionary analysis of the SAUR gene family from bryophytes to angiosperms, particularly in Fabaceae plants, shows a large expansion and specific distribution in different plant species. The conserved motifs and protein structures of SAUR proteins indicate their critical role in plant stability and function. Expression analysis of SAUR genes and functional similarity within the same clade highlight the importance of studying gene functions at a clade level.
Article
Biochemistry & Molecular Biology
Zhen Chen, Momoko Shiozaki, Kelsey M. Haas, Will M. Skinner, Shumei Zhao, Caiying Guo, Benjamin J. Polacco, Zhiheng Yu, Nevan J. Krogan, Polina Lishko, Robyn M. Kaake, Ronald D. Vale, David A. Agard
Summary: In this study, the authors used cellular cryoelectron tomography and AlphaFold2 modeling to investigate the construction of mammalian sperm and identified novel microtubule-associated proteins. The high-resolution reconstructions allowed for unbiased matching of protein models and shed light on the in vivo functions of Tektin 5.
Article
Multidisciplinary Sciences
Lukas M. Weber, Arkajyoti Saha, Abhirup Datta, Kasper D. Hansen, Stephanie C. Hicks
Summary: nnSVG is a scalable approach based on nearest-neighbor Gaussian processes for identifying spatially variable genes. It can identify genes that show continuous variation in expression across the entire tissue or within specific spatial domains, and it scales linearly with the number of spatial locations. We demonstrate its performance using experimental data and simulations.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Xiangtao Li, Shixiong Zhang, Ka-Chun Wong
Summary: Transcriptomic profiling is crucial in post-genomic analysis, and single-cell RNA-seq technology has advanced understanding of gene expression. A new algorithm, EMOBCS, is proposed to evolve transcriptomic profiles from single-cell RNA-seq data, optimizing two objective functions based on artificial bee colony. Experimental results show the effectiveness of the proposed algorithm compared to other algorithms.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Kevin Elias, Urszula Smyczynska, Konrad Stawiski, Zuzanna Nowicka, James Webber, Jakub Kaplan, Charles Landen, Jan Lubinski, Asima Mukhopadhyay, Dona Chakraborty, Denise C. Connolly, Heather Symecko, Susan M. Domchek, Judy E. Garber, Panagiotis Konstantinopoulos, Wojciech Fendler, Dipanjan Chowdhury
Summary: In this study, we found 19 miRNAs associated with BRCA1/2 mutations, and 10 of them were used for diagnostic classification. The logistic regression model achieved high sensitivity and specificity in an independent validation cohort, offering a potential cost-effective method to identify BRCA1/2 mutations in high-risk cancer patients.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Norbert Deutsch, Matyas Pajkos, Gabor Erdos, Zsuzsanna Dosztanyi
Summary: A novel visualization tool called DisCanVis has been developed for studying cancer-related intrinsically disordered proteins (IDPs). This tool aids in interpreting observed mutations by combining genome-level information with the structural and functional properties of proteins. Users can inspect individual proteins, collect examples with existing annotations of protein disorder and associated function, or discover uncharacterized examples with potential disease relevance.
Article
Physiology
Ranran Sun, Jin Liu, Yuanhao Xu, Liwei Jiang, Yun Li, Guohua Zhong, Xin Yi
Summary: This study performed a comprehensive genome-wide analysis of the ribosomal protein gene family in Spodoptera litura. The study identified 81 ribosomal protein genes and analyzed their properties, gene structure, phylogenetic relationships, and targeted microRNAs. The study also revealed the expression profiles of these genes in different stages of oogenesis, highlighting their potential roles in insect reproductive processes.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Food Science & Technology
Yuhong Mao, Lan Chen, Luyan Zhang, Yangyang Bian, Chun Meng
Summary: This study achieved immobilization of Alcalase and Flavorzyme using SiO2 microparticles, leading to improved activity and stability. Peptidomics and bioinformatics were used to identify bioactive peptides.
Article
Biochemistry & Molecular Biology
Edlyn Wu, Ajay A. Vashisht, Clement Chapat, Mathieu N. Flamand, Emiliano Cohen, Mihail Sarov, Yuval Tabach, Nahum Sonenberg, James Wohlschlegel, Thomas F. Duchaine
NUCLEIC ACIDS RESEARCH
(2017)
Article
Neurosciences
Yael Ben-David, Tehila Mizrachi, Sarah Kagan, Tamar Krisher, Emiliano Cohen, Talma Brenner, Millet Treinin
Article
Cell Biology
Anna Shteingauz, Emiliano Cohen, Yoav Biala, Millet Treinin
JOURNAL OF CELL SCIENCE
(2009)
Article
Biology
Emiliano Cohen, Eviatar Yemini, William Schafer, Dror G. Feitelson, Millet Treinin
JOURNAL OF EXPERIMENTAL BIOLOGY
(2012)
Article
Neurosciences
Emiliano Cohen, Marios Chatzigeorgiou, Steven J. Husson, Wagner Steuer-Costa, Alexander Gottschalk, William R. Schafer, Millet Treinin
MOLECULAR AND CELLULAR NEUROSCIENCE
(2014)
Review
Biochemistry & Molecular Biology
Lena Qawasmi, Maya Braun, Irene Guberman, Emiliano Cohen, Lamis Naddaf, Anna Mellul, Olli Matilainen, Noa Roitenberg, Danielle Share, Doron Stupp, Haya Chahine, Ehud Cohen, Susana M. D. A. Garcia, Yuval Tabach
JOURNAL OF MOLECULAR BIOLOGY
(2019)
Article
Microbiology
Emiliano Cohen, Maya Davidovich, Assaf Rokney, Lea Valinsky, Galia Rahav, Ohad Gal-Mor
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Pharmacology & Pharmacy
Emiliano Cohen, Rakesh Kumar, Tal Zinger, Avi Priel, Millet Treinin
FRONTIERS IN PHARMACOLOGY
(2020)
Article
Evolutionary Biology
Emiliano Cohen, Galia Rahav, Ohad Gal-Mor
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Maya Miller, Anna Mellul, Maya Braun, Dana Sherill-Rofe, Emiliano Cohen, Zohar Shpilt, Irene Unterman, Ori Braitbard, Jacob Hochman, Edit Y. Tshuva, Yuval Tabach
Article
Microbiology
Emiliano Cohen, Shalevet Azriel, Oren Auster, Adiv Gal, Carmel Zitronblat, Svetlana Mikhlin, Felix Scharte, Michael Hensel, Galia Rahav, Ohad Gal-Mor
Summary: Salmonella enterica is a highly diverse bacterial pathogen that infects humans and animals. While many serovars of S. enterica have a broad host specificity, some pathotypes have evolved to cause disease in limited host species. The mechanisms underlying the host specificity of Salmonella are not fully understood. This study provides genetic analysis, phenotypic characterization, and virulence profiling of a monophasic S. enterica serovar Typhimurium strain isolated from wild sparrows in Israel, revealing unique genetic features and phenotypic profiles that contribute to its adaptation to birds.
Article
Microbiology
Helit Cohen, Claire Hoede, Felix Scharte, Charles Coluzzi, Emiliano Cohen, Inna Shomer, Ludovic Mallet, Sebastien Holbert, Remy Felix Serre, Thomas Schiex, Isabelle Virlogeux-Payant, Guntram A. Grassl, Michael Hensel, Helene Chiapello, Ohad Gal-Mor
Summary: Salmonella enterica includes various serovars causing distinct diseases in humans. In this study, we compared the global gene expression and intracellular phenotypes of S. Typhimurium (STM) and S. Paratyphi A (SPA), representative serovars of non-typhoidal and typhoidal Salmonella, during human epithelial cell infection. We found different expression patterns in key virulence and metabolic pathways, cytosolic motility, and reinvasion ability of SPA after exiting infected cells. These differences may contribute to the invasive and systemic disease developed following SPA infection in humans.