Article
Microbiology
Marjolein Bruijning, Julien F. Ayroles, Lucas P. Henry, Britt Koskella, Kyle M. Meyer, C. Jessica E. Metcalf
Summary: The study discusses the potential issues in estimating microbiome heritability using relative abundances instead of absolute abundances, uncovering three main problems and suggesting potential solutions. The findings underscore the need for caution when interpreting and comparing heritability estimates across studies.
Article
Chemistry, Multidisciplinary
Qinqin Hu, Zongxuan Tong, Ayimukedisi Yalikong, Li-Ping Ge, Qiang Shi, Xinyu Du, Pu Wang, Xi-Yu Liu, Wuqiang Zhan, Xia Gao, Di Sun, Tong Fu, Dan Ye, Chunhai Fan, Jie Liu, Yun-Shi Zhong, Yi-Zhou Jiang, Hongzhou Gu
Summary: Biomarker discovery is crucial for understanding and diagnosing malignant diseases, but the lack of sensitive methods to identify rare disease-specific molecules remains a challenge. This study presents MORAC, a method that utilizes DNAzymes to identify candidate biomarkers with low abundance. By exploiting the catalysis and affinity of DNAzymes, previously unknown biomarkers with clear clinical value can be identified.
Article
Chemistry, Analytical
Na Wu, Lingyi Jiao, Matthias Butikofer, Zhihui Zeng, Renato Zenobi
Summary: This study successfully utilized commercially available purified proteins as internal standards for high-mass MALDI-MS analysis, achieving absolute quantification of various high-mass analytes. By systematically evaluating four sample deposition methods and using a sandwich deposition method with saturated sinapinic acid, robust quantitative analysis by high-mass MALDI-MS was performed. Furthermore, combining this quantitative strategy with chemical cross-linking allowed for evaluation of the affinity of protein-protein interactions, providing dissociation constants between 10 nM and 5 mu M for the protein complexes formed.
ANALYTICAL CHEMISTRY
(2021)
Article
Pharmacology & Pharmacy
Laura Buyssens, Laura De Clerck, Wim Schelstraete, Maarten Dhaenens, Dieter Deforce, Miriam Ayuso, Chris Van Ginneken, Steven Van Cruchten
Summary: The study assessed hepatic cytochrome P450 (CYP) protein abundance in developing Gottingen Minipigs and found various age and sex-related differences. The data provided valuable insights for constructing a neonatal and juvenile Gottingen Minipig PBPK model, showing correlations between CYP protein abundance and enzyme activity.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Zhengyan Huang, Chi Wang
Summary: This review provides an overview of statistical methods for differential abundance (DA) analysis in mass spectrometry-based metabolomic data. The high-throughput data produced by mass spectrometry often contain a large fraction of zero values, and various statistical methods have been developed to characterize and analyze this zero-inflated data. The article discusses and compares different DA analysis methods in terms of their assumptions and statistical modeling techniques.
Review
Genetics & Heredity
Elena A. Ponomarenko, George S. Krasnov, Olga I. Kiseleva, Polina A. Kryukova, Viktoriia A. Arzumanian, Georgii V. Dolgalev, Ekaterina V. Ilgisonis, Andrey V. Lisitsa, Ekaterina V. Poverennaya
Summary: Transcriptomics methods are more routine and reproducible than proteomics methods, leading to a tendency to focus on mRNA content in scientific studies. However, protein content and its post-translational status play a crucial role in cell behavior, and the correlation between transcriptome-proteome levels is generally low. The ratio between mRNA and protein content is determined by multiple factors, including ribosome movement, tRNA availability, and transcript secondary structure. Technical features of experimental methods also influence the comparison outcomes.
Article
Biochemical Research Methods
Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L. Moritz, Mukunda Goswami, Sanjeeva Srivastava
Summary: Proteomic studies on Labeo rohita provided a comprehensive organ-based protein profiling, identifying a large number of proteins and global post-translational modifications. These findings offer important insights for basic and applied research in aquaculture field.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Pharmacology & Pharmacy
Theo Tasoulis, Tara L. Pukala, Geoffrey K. Isbister
Summary: Understanding snake venom proteomes is crucial for comprehending snake venom biology, evolution, as well as the clinical effects of venoms and approaches to antivenom development. This study reviewed a range of research on snake venom proteomes and found that different methodological strategies can enhance protein identification, while combining methods can maximize proteome coverage. Variation in protein diversity and abundance was observed among different snake species, with viper venoms being compositionally more complex than elapid venoms. To ensure equivalent comparisons between studies, it is necessary to clarify methodological differences and establish standardized protein classification, nomenclature, and reporting procedures.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Pharmacology & Pharmacy
Chiara Melchiorre, Cerina Chhuon, Vincent Jung, Joanna Lipecka, Francesca Di Rella, Alessandro Conforti, Angela Amoresano, Andrea Carpentieri, Ida Chiara Guerrera
Summary: Follicle-stimulating hormone (FSH) is a glycohormone that plays a crucial role in stimulating ovulation in women and spermatogenesis in men by binding to its receptor. The glycosylation of FSH significantly affects its binding affinity to the receptor and hence its biological activity. Current ELISA method for monitoring serum hFSH is unable to distinguish between different glycovariants, limiting the study of the hormone's biological activity.
Article
Biochemical Research Methods
Maria Isabel Alcoriza-Balaguer, Juan Carlos Garcia-Canaveras, Francisco Javier Ripoll-Esteve, Marta Roca, Agustin Lahoz
Summary: In this study, LipidMS 3.0, an R package, was introduced for the whole data analysis workflow from pre-processing to lipid annotation. Compared to existing tools, LipidMS 3.0 performs similarly in data pre-processing performance but provides a higher level of structural information and fewer incorrect annotations in lipid annotation.
Article
Biochemistry & Molecular Biology
Guillaume Postic, Jessica Andreani, Julien Marcoux, Victor Reyss, Raphael Guerois, Julien Rey, Emmanuelle Mouton-Barbosa, Yves Vandenbrouck, Sarah Cianferani, Odile Burlet-Schiltz, Gilles Labesse, Pierre Tuffery
Summary: Proteo3Dnet is a web server dedicated to analyzing mass spectrometry interactomics experiments by searching for structurally interacting molecules, short linear motifs, and physically validated protein-protein interactions, providing a clearer overview of the data. The server returns a graph of identified interactions that can be interactively explored to understand core complexes and suggest undetected partners.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Alexander Zhigunov, Josef Plestil
Summary: Both small-angle scattering methods, X-ray (SAXS) and neutrons (SANS), are effective in determining the molar mass of nanoparticles and tracking aggregation or degradation processes. This work presents a method to extract additional information, including molecular weight, from a single scattering curve, providing insight into the assembly and swelling of nanoparticles.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Mariela Gonzalez-Avendano, Simon Zuniga-Almonacid, Ian Silva, Boris Lavanderos, Felipe Robinson, Roberto Rosales-Rojas, Fabio Duran-Verdugo, Wendy Gonzalez, Monica Caceres, Oscar Cerda, Ariela Vergara-Jaque
Summary: The PPI-MASS web server provides an interactive platform for filtering protein sets based on biological features to identify protein-protein interactions with pharmacological potential. Users can manipulate filters to identify candidate proteins to establish physical contacts with a target protein, offering a powerful tool for the future design of associated therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Bohui Li, Maarten Altelaar, Bas van Breukelen
Summary: In this study, a deep learning framework was used to integrate large-scale protein abundance and interaction data, successfully predicting protein-protein interactions and identifying 5010 protein complexes using a two-stage clustering strategy. The predicted complexes were found to be mostly ubiquitously expressed in all cell types and tissues, providing a comprehensive map of protein-protein interactions and a novel perspective on protein complexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ozgur Yurekten, Thomas Payne, Noemi Tejera, Felix Xavier Amaladoss, Callum Martin, Mark Williams, Claire O'Donovan
Summary: MetaboLights is a global database for metabolomics studies that contains raw experimental data and associated metadata. It includes metabolite structures, reference spectra, and biological roles. This article discusses the growth and diversity of submissions to the database and highlights the development of MetaboLights Labs, a standardized workflow platform. The reuse of data by the community is also emphasized.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Organic
James L. Bachman, Cyprian I. Pavlich, Alexander J. Boley, Edward M. Marcotte, Eric V. Anslyn
Correction
Biotechnology & Applied Microbiology
Alexander A. Boulgakov, Andrew D. Ellington, Edward M. Marcotte
TRENDS IN BIOTECHNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Cecil J. Howard, Brendan M. Floyd, Angela M. Bardo, Jagannath Swaminathan, Edward M. Marcotte, Eric Anslyn
ACS CHEMICAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Claire D. McWhite, Ophelia Papoulas, Kevin Drew, Rachael M. Cox, Viviana June, Oliver Xiaoou Dong, Taejoon Kwon, Cuihong Wan, Mari L. Salmi, Stanley J. Roux, Karen S. Browning, Z. Jeffrey Chen, Pamela C. Ronald, Edward M. Marcotte
Article
Cell Biology
Heidi M. Blank, Ophelia Papoulas, Nairita Maitra, Riddhiman Garge, Brian K. Kennedy, Birgit Schilling, Edward M. Marcotte, Michael Polymenis
MOLECULAR BIOLOGY OF THE CELL
(2020)
Article
Genetics & Heredity
Riddhiman K. Garge, Jon M. Laurent, Aashiq H. Kachroo, Edward M. Marcotte
Article
Chemistry, Organic
Alexander A. Boulgakov, Sarah R. Moor, Hyun Hwa Jo, Pedro Metola, Leo A. Joyce, Edward M. Marcotte, Christopher J. Welch, Eric Anslyn
JOURNAL OF ORGANIC CHEMISTRY
(2020)
Article
Biochemical Research Methods
Brendan M. Floyd, Kevin Drew, Edward M. Marcotte
Summary: Protein phosphorylation is a crucial regulatory mechanism in eukaryotic cellular processes, with the majority of phosphorylation sites still having unknown functions. A method called phospho-DIFFRAC was developed to systematically identify phosphorylation-dependent protein assemblies and found that these interactions are enriched in RNA-binding proteins.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Kevin Drew, John B. Wallingford, Edward M. Marcotte
Summary: Researchers developed a machine learning framework to identify nearly 7,000 protein complexes in human cells, resulting in the creation of the more accurate and comprehensive resource hu.MAP 2.0 and proposing many new hypotheses. The study also identified promiscuous proteins that participate in multiple complexes, suggesting potential moonlighting roles.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Caitlyn L. McCafferty, David W. Taylor, Edward M. Marcotte
Summary: Electron microscopy (EM) provides near-atomic resolution structures for proteins, but some structures are limited. Researchers have developed a new method that incorporates co-evolutionary information to build three-dimensional models of atomic structures for fitting into EM maps. This method improves systematic fitting of atomic models into medium- to low-resolution EM maps, enhancing integrative models lacking spatial data.
Article
Developmental Biology
Elle C. Roberson, Anna M. Battenhouse, Riddhiman K. Garge, Ngan Kim Tran, Edward M. Marcotte, John B. Wallingford
Summary: This study found significant gene expression differences along the anteroposterior axis of the mouse oviduct, but relatively few changes in gene expression across the estrous cycle. The gene expression variances along the anteroposterior axis included genes related to embryonic development. The researchers speculated that the stable transcriptional dynamics in the mouse oviduct across the estrous cycle may be influenced by its extremely rapid five-day cycle.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Caitlin C. Devitt, Chanjae Lee, Rachael M. Cox, Ophelia Papoulas, Jose Alvarado, Shashank Shekhar, Edward M. Marcotte, John B. Wallingford
Summary: The study focuses on the role of Twf1 in vertebrate gastrulation and finds that Twf1 is crucial for convergent extension. Loss of Twf1 disrupts lamellipodial dynamics and polarity and prevents the assembly of polarized cytoplasmic actin cables necessary for convergent extension. This research provides new insights into the specific cell behaviors of embryonic morphogenesis and their connection to the core machinery of actin regulation.
JOURNAL OF CELL SCIENCE
(2021)
Article
Biochemical Research Methods
Javier Antonio Alfaro, Peggy Bohlander, Mingjie Dai, Mike Filius, Cecil J. Howard, Xander F. van Kooten, Shilo Ohayon, Adam Pomorski, Sonja Schmid, Aleksei Aksimentiev, Eric V. Anslyn, Georges Bedran, Chan Cao, Mauro Chinappi, Etienne Coyaud, Cees Dekker, Gunnar Dittmar, Nicholas Drachman, Rienk Eelkema, David Goodlett, Sebastien Hentz, Umesh Kalathiya, Neil L. Kelleher, Ryan T. Kelly, Zvi Kelman, Sung Hyun Kim, Bernhard Kuster, David Rodriguez-Larrea, Stuart Lindsay, Giovanni Maglia, Edward M. Marcotte, John P. Marino, Christophe Masselon, Michael Mayer, Patroklos Samaras, Kumar Sarthak, Lusia Sepiashvili, Derek Stein, Meni Wanunu, Mathias Wilhelm, Peng Yin, Amit Meller, Chirlmin Joo
Summary: Single-cell profiling methods have greatly impacted the understanding of cellular heterogeneity, although proteome profiling at the single-cell level is still in the early stages. The development of new technologies, such as single-molecule protein sequencing and innovations in mass spectrometry, will eventually enable broad sequence coverage in single-cell proteomics, leading to new biological discoveries and opportunities for ultra-sensitive disease diagnostics.
Article
Biochemical Research Methods
Claire D. McWhite, Ophelia Papoulas, Kevin Drew, Vy Dang, Janelle C. Leggere, Wisath Sae-Lee, Edward M. Marcotte
Summary: CF/MS is a flexible and powerful method for detecting physical associations of proteins, which can be applied to any tissue or organism without the need for protein-specific antibodies or epitope tags. Successful application of this approach relies on sample preparation protocols and a computational pipeline.
Article
Biochemistry & Molecular Biology
Caitlyn L. McCafferty, Edward M. Marcotte, David W. Taylor
Summary: Protein-protein interactions and the prediction of pairwise protein interaction interfaces were studied, utilizing a reduced representation of protein geometry and mapping of molecular properties. The research demonstrated comparable predictions to other structure-based tools and tolerance to conformational changes, highlighting the enhanced speed and capabilities of the simplified approach.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)