Article
Horticulture
Yuhan Zhou, Yushan Qiao, Zhiyou Ni, Jianke Du, Jinsong Xiong, Zongming Cheng, Fei Chen
Summary: In this study, a Genome Database for Strawberry (GDS) was developed to facilitate the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools. The database integrates data from eight strawberry species and provides user-friendly tools for researchers in the field.
Article
Biochemical Research Methods
Yujia Xiang, Quan Zou, Lilin Zhao
Summary: Posttranslational modifications (PTMs) play essential roles in the life cycle of viruses, and understanding viral PTMs is crucial for studying viral infections and potential drug targets. The development of the comprehensive viral posttranslational modification database (VPTMdb) provides systematic information on PTM sites in human viruses and infected cells, aiding in the investigation of virus-host interactions. The analysis of viral PTM sequences, protein disordered regions, and domain-domain interactions reveals important insights into the roles of viral PTMs in infections and can contribute significantly to the field of virus-human interactions. Additionally, the creation of the VPTMpre classifier and the implementation of the VPTMdb online web server offer valuable tools for users to predict viral protein phosphorylation sites and access viral PTM data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jeffrey Molendijk, Rui Yip, Benjamin L. Parker
Summary: We have developed a database for underrepresented post-translational modifications (PTMs) to accelerate the discovery of enriched protein modifications in experimental data. The database provides curated lists of proteins reported to be substrates of underrepresented modifications. We demonstrated the utility of the database through the analysis of previously published data. Additionally, we developed an online tool that integrates upstream transcription factor enrichment analysis with downstream pathway analysis through an easy-to-use interactive interface.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Biochemical Research Methods
Tianjiao Zhang, Liang Chen, Rongzhen Li, Ning Liu, Xiaobing Huang, Garry Wong
Summary: PIWI-interacting RNAs (piRNAs) are short molecules found in various species, with the main function of monitoring and protecting the genome from transposons. They have limited bioinformatics resources compared to microRNAs (miRNAs). This review provides an overview of piRNA-specific and non-specific databases, computational models, and their role in disease associations, particularly in cancer and neurodegenerative conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Panna Liptak, Attila Kiss, Janos Mark Szalai-Gindl
Summary: The article presents a novel approach for comparative analysis of sequences within a database environment, taking advantage of database management systems to expedite alignment algorithms. The authors work with the column-oriented MonetDB and discuss the key benefits of this database system in relation to their proposed heuristic approach.
Article
Biochemistry & Molecular Biology
Junhao Zhuge, Xiang Zhou, Lifeng Zhou, Jiafu Hu, Kai Guo
Summary: This study developed the Plant Parasitic Nematodes Database (PPND), a platform that provides genomic, transcriptomic, protein, and functional annotation data for plant parasitic nematode research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shiro Uchida, Takashi Sugino
Summary: This study identified genes associated with breast cancer progression mechanisms and potential therapeutic targets using bioinformatic tools. It found several genes involved in breast cancer progression and identified potential novel therapeutic targets.
Article
Biology
Susrita Sahoo, Soumya Ranjan Mahapatra, Bikram Kumar Parida, Satyajit Rath, Budheswar Dehury, Vishakha Raina, Nirmal Kumar Mohakud, Namrata Misra, Mrutyunjay Suar
Summary: DBCOVP is the first manually curated, web-based resource providing comprehensive information on structural virulent glycoproteins from coronavirus genomes. The database offers various sequence-structural properties for users to browse and analyze information in different ways, as well as predicted T-cell and B-cell epitopes that may play a significant role in immune responses. The database also provides an easy-to-use interface with built-in tools for a variety of analyses, making it an important resource for coronavirus research and vaccine development.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biology
Sedigheh Sadat Mortazavi, Zahra Bahmanpour, Yousef Daneshmandpour, Faranak Roudbari, Roghayeh Sheervalilou, Somayeh Kazeminasab, Babak Emamalizadeh
Summary: MicroRNAs are small endogenous non-coding RNAs that play crucial regulatory roles in biological processes through translational repression or mRNA degradation. The importance of miRNAs has led to the development of multiple databases, each with specific parameters and characteristics for researchers to benefit from. Understanding the classification and information contained in these databases is essential for scientists to quickly find suitable bioinformatics tools and relevant information.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Agronomy
Lei Jia, Lingjuan Xie, Sangting Lao, Qian-Hao Zhu, Longjiang Fan
Summary: Rice, as one of cereal crops and a model species for monocots, has seen significant progress in genomic research thanks to the rapid development and efficient utilization of bioinformatics methods and tools. Single-cell sequencing and machine learning are examples showing how bioinformatics integrates emerging technologies for future rice research.
Article
Biology
Xinyu Zhao, Huan Zhao, Yupeng Liu, Zhiyun Guo
Summary: This article provides a comprehensive overview of the methods, bioinformatics tools, and database resources used in ecDNA research, highlighting their significance in tumor initiation and progression, and offering suggestions for current analysis and future research directions.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
Summary: Deciphering the relationship between human genes/proteins and abnormal phenotypes is crucial for disease prevention and treatment, requiring computational predictions. The HPODNets model, with features including multiple network input, semi-supervised learning, and deep graph convolutional network, outperforms other methods in predicting human protein-phenotype associations.
Review
Biochemical Research Methods
Mattia Forcato, Oriana Romano, Silvio Bicciato
Summary: Recent advances in single-cell technologies are providing exciting opportunities for dissecting tissue heterogeneity and investigating cell identity, fate and function. However, combining different single-cell genomic signals is computationally challenging and requires integrative analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Rui Zhang, Xuan Xu, Xi Chen, Chunshu Hao, Zhenjun Ji, Pengfei Zuo, Mingming Yang, Genshan Ma, Yongjun Li
Summary: This study identified key pathogenic genes in hypertension-induced cardiac hypertrophy through gene expression analysis. The upregulated genes Eln and Tgfb3 were found to be positively correlated with the severity of cardiac hypertrophy, suggesting their potential as therapeutic targets for the disease.
Article
Entomology
Clauvis Nji Tizi Taning, Shunhua Gui, Kristof De Schutter, Mona Jahani, Nathaly Lara Castellanos, Olivier Christiaens, Guy Smagghe
Summary: This study confirmed the susceptibility of bumblebees to ingested dsRNA targeting specific genes, and found no significant off-target effects on gene expression in bumblebees following exposure to a fusion dsRNA product designed for pest control.
JOURNAL OF PEST SCIENCE
(2021)
Editorial Material
Biology
Buzz Baum, David A. Baum
Article
Biochemistry & Molecular Biology
Andrea Dimitracopoulos, Pragya Srivastava, Agathe Chaigne, Zaw Win, Roie Shlomovitz, Oscar M. Lancaster, Mael Le Berre, Matthieu Piel, Kristian Franze, Guillaume Salbreux, Buzz Baum
Review
Cell Biology
Anna Taubenberger, Buzz Baum, Helen K. Matthews
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Anna-Katharina Pfitzner, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Andela Saric, Aurelien Roux
Article
Biochemistry & Molecular Biology
Isabelle Anna Zink, Thomas Fouqueau, Gabriel Tarrason Risa, Finn Werner, Buzz Baum, Udo Blasi, Christa Schleper
Summary: CRISPR type III systems in archaea can be utilized for gene knockdown technologies to study essential genes, with results showing gene-specific silencing thresholds which can induce growth retardation phenotypes. Strong miniCRISPR constructs exceeding these thresholds can lead to specific mutation of the silencing miniCRISPR array and phenotypical reversion in cultures, with over two thirds of sequenced reverted cultures exhibiting precise excision of targeting spacers from the miniCRISPR array, suggesting an active recombination system acting on CRISPR arrays.
Article
Cell Biology
Jooske L. Monster, Lisa Donker, Marjolein J. Vliem, Zaw Win, Helen K. Matthews, Joleen S. Cheah, Soichiro Yamada, Johan de Rooij, Buzz Baum, Martijn Gloerich
Summary: During mitosis, epithelial cells exert tensile forces on neighboring cells by recruiting vinculin to maintain cell-cell junctions. Vinculin recruited from neighbors creates asymmetric cadherin junctions. Lack of vinculin in mitotic cells is essential for successful cell rounding.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jiwei Liu, Matteo Tassinari, Diorge P. Souza, Souvik Naskar, Jeffrey K. Noel, Olga Bohuszewicz, Martin Buck, Tom A. Williams, Buzz Baum, Harry H. Low
Summary: Membrane remodeling and repair are essential for all cells, and proteins involved in these processes, such as Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes, share a common ancient evolutionary origin. Cryo-electron microscopy structures of Vipp1 rings from cyanobacterium Nostoc punctiforme show homology and suggest conserved mechanistic principles underlying membrane remodeling in different domains of life.
Review
Cell Biology
Gautam Dey, Buzz Baum
Summary: The defining feature of eukaryotic cells, the nucleus, is bounded by a double envelope with nuclear pores critical for separating the genome from the cytoplasm. Eukaryotes have evolved various strategies to remodel the nuclear compartment boundary during mitosis, from disassembling and reassembling the nucleus in daughter cells to maintaining an intact boundary throughout division. This review discusses common features of the division process, topological challenges, and the selective pressures that may drive the evolution of distinct modes of division.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nitya Ramkumar, Jigna Patel, Jannis Anstatt, Buzz Baum
Summary: The isotropic metaphase actin cortex polarizes and reorganizes independently during mitotic exit, with different events coordinated in time. Aurora B kinase is identified as a regulator of actin clearance at cell poles, with a novel role in facilitating DNA-mediated polar relaxation, actomyosin cortex polarization, and cell division.
Article
Multidisciplinary Sciences
Ute Jungwirth, Antoinette van Weverwijk, Rachel J. Evans, Liam Jenkins, David Vicente, John Alexander, Qiong Gao, Syed Haider, Marjan Iravani, Clare M. Isacke
Summary: The study reveals that the genetic deletion of Endo180 in a subset of cancer-associated fibroblasts impairs tumor fibroblast contractility and viability, resulting in reduced tumor growth and metastasis. These findings provide important insights into how tumor cells adapt to non-activated stroma during early stages of metastatic colonization.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Agata Nyga, Jose J. Munoz, Suze Dercksen, Giulia Fornabaio, Marina Uroz, Xavier Trepat, Buzz Baum, Helen K. Matthews, Vito Conte
Summary: The study found that activation of the RAS oncogene induces changes in cell morphology and tissue mechanical properties, driving the transformation from 2D to 3D.
Review
Microbiology
Marleen van Wolferen, Andre Arashiro Pulschen, Buzz Baum, Simonetta Gribaldo, Sonja-Verena Albers
Summary: This review explores archaeal morphology, internal organization, and cell division, and discusses their importance in ecology, biotechnology, and human health. Recent studies have revealed the diversity and ubiquity of archaea in nature, expanding the phylogenetic scope of archaea and shedding light on their role in the evolutionary origins of eukaryotes. Advances in culturing and live imaging techniques have contributed to a better understanding of archaeal biology. The review also highlights technical challenges and discusses the potential of new technologies to address key unanswered questions.
NATURE MICROBIOLOGY
(2022)
Article
Oncology
Elizabeth R. Tucker, Irene Jimenez, Lindi Chen, Angela Bellini, Chiara Gorrini, Elizabeth Calton, Qiong Gao, Harvey Che, Evon Poon, Yann Jamin, Barbara Martins Da Costa, Karen Barker, Sumana Shrestha, J. Ciaran Hutchinson, Simran Dhariwal, Angharad Goodman, Elaine Del Nery, Pierre Gestraud, Jaydutt Bhalshankar, Yasmine Iddir, Elnaz Saberi-Ansari, Alexandra Saint-Charles, Birgit Geoerger, Maria Eugenia Marques Da Costa, Cecile Pierre-Eugene, Isabelle Janoueix-Lerosey, Didier Decaudin, Fariba Nemati, Angel M. Carcaboso, Didier Surdez, Olivier Delattre, Sally L. George, Louis Chesler, Deborah A. Tweddle, Gudrun Schleiermacher
Summary: ALK-activating mutations are present in approximately 10% of neuroblastomas and ALK amplifications in a further 1%-2% of cases. Lorlatinib, a third-generation ALK inhibitor, is being considered as a treatment for children with ALK-aberrant neuroblastoma. Resistance to single-agent treatment has been reported, and combination therapies with chemotherapy or MDM2 inhibitor are being explored to improve treatment efficacy.
CLINICAL CANCER RESEARCH
(2023)
Article
Multidisciplinary Sciences
Agata Nyga, Katarzyna Plak, Martin Kraeter, Marta Urbanska, Kyoohyun Kim, Jochen Guck, Buzz Baum
Summary: Animal cells undergo repeated changes in shape, such as rounding up and respreading during division. The process of cell rounding can also be observed in interphase cells, particularly when cancer cells switch from a mesenchymal to an ameboid mode of migration. However, the mechanism of interphase cell rounding remains unclear.
Review
Microbiology
Buzz Baum, Anja Spang, Amy K. Schmid
Summary: This article explores the origin of the eukaryotic nucleus and proposes a model for the archaeal origin of the nucleus.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
