Article
Biochemistry & Molecular Biology
Eric W. Deutsch, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J. Carver, Luis Mendoza, Deepti J. Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaino
Summary: This article describes the recent developments in the ProteomeXchange (PX) consortium, which aims to standardize data submission and dissemination of MS proteomics data. The article highlights the increase in the number of datasets submitted to PX resources and the growing data re-use activities.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Genetics & Heredity
Mengqi Ma, Matthew J. Moulton, Shenzhao Lu, Hugo J. Bellen
Summary: The use of fruit flies in studying the function of genes associated with rare neurological diseases can enhance our understanding of common disease mechanisms.
TRENDS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
David Ben-Menahem
Summary: Genomic and phylogenetic analyses of various invertebrate phyla have revealed the existence of genes related to vertebrate's decapeptide gonadotropin-releasing hormone (GnRH) and its receptor genes. Research has identified AKH and CRZ in insects, which have similar sizes to GnRH and serve as neurohormones, with pleiotropic activities in metabolism and stress responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Qiong Zong, Bin Mao, Hua-Bao Zhang, Bing Wang, Wen-Juan Yu, Zhi-Wei Wang, Yu-Feng Wang
Summary: This study reveals the deubiquitylating effects induced by Wolbachia infection, suggesting that Wolbachia can widely deubiquitinate proteins that have crucial functions in male fertility of their hosts, but are not involved in cytoplasmic incompatibility (CI). The findings provide new insights into the regulatory mechanisms of endosymbiont/host interactions and male fertility.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Olga V. Andreenkova, Olga D. Shishkina, Alexandra I. Klimenko, Aleksandra E. Korenskaia, Margarita A. Bobrovskikh, Natalja V. Shatskaya, Gennady V. Vasiliev, Nataly E. Gruntenko
Summary: Several methods for extracting Wolbachia DNA from insect hosts have been described, but the low quantity of the bacteria made these techniques labor-intensive. This paper proposes a simplified and accelerated method for isolating high-purity Wolbachia DNA from Drosophila melanogaster, using centrifugation, filtration, and a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in total DNA was quantified using sequencing and bioinformatic analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Gabriel E. Rech, Santiago Radio, Sara Guirao-Rico, Laura Aguilera, Vivien Horvath, Llewellyn Green, Hannah Lindstadt, Veronique Jamilloux, Hadi Quesneville, Josefa Gonzalez
Summary: High-quality reference genomes are essential for understanding genome function and evolution. However, a single reference genome is not sufficient to capture global genetic diversity. This study generates 32 high-quality reference genomes for the model species D. melanogaster and explores transposable element variation, linking it to gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Pikam Pun, Jacobs Brown, Tyler Cobb, Robert J. Wessells, Dal Hyung Kim
Summary: The study developed a Transparent Omnidirectional Locomotion Compensator (TOLC) that allows a fruit fly to navigate freely in infinite space without tethering, providing a new solution for fruit fly behavior research.
Article
Multidisciplinary Sciences
Ching-Tai Chen, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, Ting-Yi Sung
Summary: Multi-Q 2 is an isobaric-labeling quantitation tool that offers the largest quantitation coverage and improved accuracy compared to other state-of-the-art methods. It supports various quantitation algorithms and allows for customization to improve quantitation accuracy. The use of complementary algorithmic combinations can enhance sensitivity in searching for biomarkers in proteomic experiments.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Ya Zheng, Bin Mao, Qian Wang, Xin Duan, Meng-Yan Chen, Wei Shen, Chao Li, Yu-Feng Wang
Summary: Knockdown of ocn gene in Drosophila testes resulted in smaller testis without germ cells. Through proteomics sequencing, 606 proteins were identified as significantly changed in expression after ocn knockdown. The down-regulation of ocn disturbed key signaling pathways related to cell survival and differentiation.
Article
Biochemistry & Molecular Biology
Yang Yue, Mengting Wang, Zhangping Feng, Yanyun Zhu, Jianchu Chen
Summary: The study demonstrated that rice protein hydrolysates (RPH) can enhance the antioxidant system and prolong the lifespan of fruit flies by cooperating with the intrinsic stress protection system, age-related signaling pathways, and longevity genes. This suggests potential applications of RPH in food and healthcare industries.
JOURNAL OF FOOD BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Ronald D. Smith, Joshua R. Puzey, Gregory D. Conradi Smith
Summary: In an empirical analysis, it was found that transposable element count in natural populations of Mimulus guttatus and Drosophila melanogaster showed a surprisingly high variance. This variance is likely due to copy-and-paste proliferation dynamics rather than purifying selection on total element load.
Article
Chemistry, Multidisciplinary
Mai H. Philipsen, Elias Ranjbari, Chaoyi Gu, Andrew G. Ewing
Summary: The changes in brain lipids induced by Modafinil treatment in Drosophila melanogaster show a decrease in phosphatidylcholine and sphingomyelin species, while an increase in phosphatidylethanolamine and phosphatidylinositol levels, which is consistent with previous studies on cognition-related drugs. These alterations offer insight into the potential mechanism of action of Modafinil in the brain and provide a potential target for the treatment of certain disorders.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Yaoyao Wu, Dawei Li, Yong Hu, Hongbo Li, Guillaume P. Ramstein, Shaoqun Zhou, Xinyan Zhang, Zhigui Bao, Yu Zhang, Baoxing Song, Yao Zhou, Yongfeng Zhou, Edeline Gagnon, Tiina Sarkinen, Sandra Knapp, Chunzhi Zhang, Thomas Stadler, Edward S. Buckler, Sanwen Huang
Summary: Hybrid potato breeding can transform the crop from tetraploid to diploid, enabling seed reproduction. Accumulation of deleterious mutations has hindered the development of elite inbred lines and hybrids. By utilizing a whole-genome phylogeny, we identified deleterious mutations and found that diploid lines with high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. The inclusion of these mutations improves genomic prediction accuracy for yield by 24.7%.
Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Review
Biochemistry & Molecular Biology
Greta Elovsson, Liza Bergkvist, Ann-Christin Brorsson
Summary: Alzheimer's disease is a neurological disorder associated with proteotoxic events caused by the misfolding and aggregation of the amyloid-beta peptide. Drosophila melanogaster is utilized as a model organism to study the proteotoxicity of the amyloid-beta peptide and screen for drug candidates, which may provide insights into disease progression and potential treatments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Marina T. DiStefano, Scott Goehringer, Lawrence Babb, Fowzan S. Alkuraya, Joanna Amberger, Mutaz Amin, Christina Austin-Tse, Marie Balzotti, Jonathan S. Berg, Ewan Birney, Carol Bocchini, Elspeth A. Bruford, Alison J. Coffey, Heather Collins, Fiona Cunningham, Louise C. Daugherty, Yaron Einhorn, Helen Firth, David R. Fitzpatrick, Rebecca E. Foulger, Jennifer Goldstein, Ada Hamosh, Matthew R. Hurles, Sarah E. Leigh, Ivone U. S. Leong, Sateesh Maddirevula, Christa L. Martin, Ellen M. McDonagh, Annie Olry, Arina Puzriakova, Kelly Radtke, Erin M. Ramos, Ana Rath, Erin Rooney Riggs, Angharad M. Roberts, Charlotte Rodwell, Catherine Snow, Zornitza Stark, Jackie Tahiliani, Susan Tweedie, James S. Ware, Phillip Weller, Eleanor Williams, Caroline F. Wright, Thabo Michael Yates, Heidi L. Rehm
Summary: This study addresses the lack of universal standards and terminologies in defining gene-disease relationships. The Gene Curation Coalition (GenCC) was formed to establish harmonized definitions and develop a unified database. The results show that conflicts in gene-disease validity assertions exist, highlighting the importance of standardization and collaboration in genetic testing and variant interpretation.
GENETICS IN MEDICINE
(2022)
Article
Biochemical Research Methods
Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L. Kelleher, Paul M. Thomas, Juan Antonio Vizcaino
Summary: It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence. The ProForma 2.0 notation aims to unify the representation of proteoforms and peptidoforms, supporting different proteomics approaches and allowing the encoding of highly modified proteins and peptides using a human- and machine-readable string.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Anton Kalyuzhnyy, Patrick A. Eyers, Claire E. Eyers, Emily Bowler-Barnett, Maria J. Martin, Zhi Sun, Eric W. Deutsch, Andrew R. Jones
Summary: This study profiles the human phosphoproteome to estimate the false discovery rate of phosphosites and predict a more realistic count of true identifications. It highlights significant potential of false-positive data in phosphorylation databases and emphasizes the importance of quality control for such data.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Kerry A. Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaino, Eric W. Deutsch, Andrew R. Jones
Summary: Phosphoproteomic methods are used to identify and quantify phosphorylation sites on proteins. This study introduces the concept of scoring modifications on a decoy amino acid to estimate the global false localization rate (FLR) independently.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Genetics & Heredity
L. Sian Gramates, Julie Agapite, Helen Attrill, Brian R. Calvi, Madeline A. Crosby, Gilberto dos Santos, Joshua L. Goodman, Damien Goutte-Gattat, Victoria K. Jenkins, Thomas Kaufman, Aoife Larkin, Beverley B. Matthews, Gillian Millburn, Victor B. Strelets
Summary: As FlyBase celebrates its fourth decade, it highlights its unique aspects and expresses its commitment to collaborate with other research communities. They emphasize the reports and tools dedicated to fly researchers' needs and provide multiple avenues for researchers to interact with FlyBase.
Article
Genetics & Heredity
Paul W. Sternberg
Summary: The Alliance of Genome Resources is a collaborative effort of 7 knowledgebase projects aimed at providing better service, a harmonized view of data, and a sustainable infrastructure. It offers comparative views of gene function, gene expression, and human disease relevance. The information is presented on uniform gene pages for easy summarization.
Article
Biochemistry & Molecular Biology
Ruth L. Seal, Susan Tweedie, Elspeth A. Bruford
Summary: The HGNC is the only organization authorized to approve symbols for human genes, ensuring clarity and ease of search in scientific literature and databases.
Article
Biochemistry & Molecular Biology
Ruth L. Seal, Bryony Braschi, Kristian Gray, Tamsin E. M. Jones, Susan Tweedie, Liora Haim-Vilmovsky, Elspeth A. Bruford
Summary: The HUGO Gene Nomenclature Committee (HGNC) is responsible for assigning unique symbols and names to human genes. Their database contains over 43,000 approved gene symbols, including protein-coding genes, pseudogenes, and non-coding RNA genes, which are displayed on their public website along with links to genomic, clinical, and proteomic information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Eric W. Deutsch, Juan Antonio Vizcaino, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C. E. Tosatto, Sandra E. Orchard
Summary: The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been developing guidelines and standards for the proteomics community for 20 years. The organization describes its operation, the current state of existing standards, and the proposals currently being developed. They emphasize the importance of community participation and collaboration with other organizations to promote data sharing and accelerate progress in proteomics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Tobias G. Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric W. Deutsch
Summary: Data set acquisition and curation are challenging in machine learning, particularly for proteomics-based LC-MS data sets due to data reduction. ProteomicsML is introduced as an online resource for accessing proteomics-based data sets and tutorials. It simplifies data access and provides tutorials for interacting with advanced algorithms. ProteomicsML enables comparison of machine learning algorithms and offers introductory material for newcomers in the field. The platform is freely available at https://www.proteomicsml.org/, and contributions are welcome at https://github.com/ProteomicsML/ProteomicsML.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, Robert L. Moritz
Summary: The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has undergone continuous development and refinement since the publication of its first tools, PeptideProphet and ProteinProphet, 20 years ago. The latest release offers a wide range of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. These tools incorporate machine-learning modeling to maximize information extraction and establish robust statistical models for accurate information derivation. This article presents an overview of the latest TPP tools, their deployment on different platforms, tutorials for their usage, and synergistic projects leveraging TPP. The article concludes with outlined plans for future TPP development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Klaas J. van Wijk, Tami Leppert, Zhi Sun, Eric W. Deutsch
Summary: A recent paper in Science Advances suggests that intrachloroplast proteins in Arabidopsis can be polyubiquitinated and transferred to the cytosol for degradation, challenging the existing belief that chloroplast organelles lack polyubiquitination mechanisms. However, a reanalysis of the raw mass spectrometry data revealed discrepancies and issues with the results, including extensive artifactual modifications caused by the use of alkylating agent iodoacetamide. As a result, the conclusions regarding intra-chloroplast polyubiquitination cannot be supported by these data. Recommendations for future research are provided to avoid similar pitfalls.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yanhui Hu, Aram Comjean, Helen Attrill, Giulia Antonazzo, Jim Thurmond, Weihang Chen, Fangge Li, Tiffany Chao, Stephanie E. Mohr, Nicholas H. Brown, Norbert Perrimon
Summary: PANGEA is a new GSEA tool that allows flexible and configurable data analysis using various classification sets. It enables GO analysis on different sets of GO annotations and provides visualization of results and comparison of multiple input gene lists.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Klaas J. van Wijk, Stephane Bentolila, Tami Leppert, Qi Sun, Zhi Sun, Luis Mendoza, Margaret Li, Eric W. Deutsch
Summary: This study investigates the impact of RNA editing on the protein accumulation of organelle-encoded proteins in Arabidopsis. It identifies the nonredundant set of protein identifiers and predicted editing sites, and determines the accumulation of edited and unedited proteoforms at the protein level. The results show that major RNA editing sites are required for stable protein accumulation.
