Article
Biochemistry & Molecular Biology
Caroline Teyssier, Odile Rogier, Stephane Claverol, Florian Gautier, Marie-Anne Lelu-Walter, Harold Durufle
Summary: This study presents the first large-scale proteomic analysis of Douglas fir, revealing the protein composition and distribution in different plant organs or tissues. The findings provide an important foundation for future genomic annotations of conifers and other trees.
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Carmen Pena, Elio Diez-Feijoo, Pablo Hervella, Isabel Lema
Summary: This study utilized a qualitative approach to explore the tear proteome of patients with keratoconus (KC), finding that the expression of certain proteins in tears of KC patients differed from the control group. These differences were linked to processes such as cell death, oxidative damage, and inflammation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Enxhi Shaba, Claudia Landi, Alfonso Carleo, Lorenza Vantaggiato, Eugenio Paccagnini, Mariangela Gentile, Laura Bianchi, Pietro Lupetti, Elena Bargagli, Antje Prasse, Luca Bini
Summary: This study is the first to investigate the proteomics of EVs isolated from BALF of IPF patients, revealing that EV proteins are predominantly involved in cytoskeleton remodeling, signaling pathways, and lipid metabolism. These findings suggest a wider system involvement in the pathogenesis of IPF.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Delphine Vincent, AnhDuyen Bui, Doris Ram, Vilnis Ezernieks, Frank Bedon, Joe Panozzo, Pankaj Maharjan, Simone Rochfort, Hans Daetwyler, Matthew Hayden
Summary: This study optimized a LC-MS shotgun quantitative proteomics method to screen wheat genotypes for breeding lines with better performance. A large number of wheat proteins were identified using this method, and data mining tools were used to explore the flour proteome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Benjamin A. Neely, Michael G. Janech, M. Brock Fenton, Nancy B. Simmons, Alison M. Bland, Daniel J. Becker
Summary: Bats are increasingly studied for their longevity model systems and their natural host abilities with virulent viruses. This study demonstrated the use of proteomics to overcome limitations in characterizing immune mechanisms of viral tolerance and quantifying infection dynamics in wild bats. By analyzing the serum proteome of vampire bats, the study identified various immunological and viral proteins, providing insights for wildlife immunology and pathogen surveillance.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, Fernando J. Corrales
Summary: The analysis of biological fluids for disease-related proteins is an important field of research. However, challenges exist, especially in complex matrices like bile. A new procedure described in this study significantly improves protein recovery from rat bile, providing valuable resources for further understanding disease molecular markers.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Bastien Burat, Audrey Reynaerts, Dominique Baiwir, Maximilien Fleron, Gauthier Eppe, Teresinha Leal, Gabriel Mazzucchelli
Summary: Eccrine sweat has the potential to be used for personalized therapy, but the lack of in-depth characterization studies has hindered its evaluation. By using omics technology and accredited sweat collection methods, analysis of human sweat can now be standardized for personalized medicine. The sweat proteome, characterized in this study using shotgun proteomics, revealed diverse biological processes and molecular functions, highlighting its potential as a valuable biological matrix for further research in individualized monitoring and personalized medicine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Wojtek Bazant, Ann S. S. Blevins, Kathryn Crouch, Daniel P. P. Beiting
Summary: The study presents a tool called CORRAL for identifying eukaryotes in shotgun metagenomic data. It utilizes eukaryote-specific marker genes and Markov clustering to automate the detection of eukaryotes, even those not represented in the reference marker gene set, such as novel strains.
Article
Veterinary Sciences
Anja Ruud Winther, Vinicius da Silva Duarte, Davide Porcellato
Summary: The host response to invasive microbes in the bovine udder is crucial for animal health and the dairy industry. In this study, we used proteomics and amplicon sequencing to investigate the proteome expression and microbiota in quarter milk samples from naturally infected cows. The analysis revealed specific expression patterns in high somatic cell count samples, indicating immune response pathways. Different proteome profiles were also identified in quarter samples containing mastitis pathogens, highlighting the host's different responses. Weighted correlation network analysis identified protein modules correlated with somatic cell count, including immune response and metabolic pathways. This study provides insights into the host-microbe interaction in naturally infected cows.
VETERINARY RESEARCH
(2023)
Article
Plant Sciences
Meenakshi Arya, Satya Prakash, Yaiphabi Sougrakpam, Renu Deswal
Summary: The study identified leaf cuticle proteins from Brassica juncea using organic solvents, analyzing them through gel-based and quantitative shotgun proteomics. Most of the proteins had signal peptides supporting extracellular localization and were predicted to be involved in various activities such as defense response, fatty acid binding, and nutrient reservoir activity. The study also explored the roles of specific proteins like Myrosinase and GDSL esterase/lipase ESM1 in cuticle structuring and defense, as well as the glucosinolate-myrosinase system, PTM crosstalk, and antifreeze activity as stress adaptive strategies in B. juncea.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Biochemical Research Methods
Yang Wang, Wei Yang
Summary: Protein S-acylation, also known as palmitoylation, is a crucial reversible lipid modification that regulates protein functions. Recent advances in proteomic analysis of S-acylation have significantly improved our understanding of its biological processes. This research field is expected to play a key role in discovering new disease mechanisms and therapeutic targets.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Food Science & Technology
Gianfranco Mamone, Gianluca Picariello
Summary: Although the hydrolases from the intestinal brush border membrane (BBM) have physiological importance, they have not been included in the current protocols of in vitro digestion due to unavailability and lack of consensus. This study purified BBM vesicles from pig jejunum and identified 1428 proteins, including hydrolases, transporters, and protease inhibitors. Aminopeptidase N and sucrase-isomaltase were the most abundant enzymes, making porcine BBM suitable for simulating human small intestinal digestion.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Clinical Neurology
Daniel J. Panyard, Justin McKetney, Yuetiva K. Deming, Autumn R. Morrow, Gilda E. Ennis, Erin M. Jonaitis, Carol A. Van Hulle, Chengran Yang, Yun Ju Sung, Muhammad Ali, Gwendlyn Kollmorgen, Ivonne Suridjan, Anna Bayfield, Barbara B. Bendlin, Henrik Zetterberg, Kaj Blennow, Carlos Cruchaga, Cynthia M. Carlsson, Sterling C. Johnson, Sanjay Asthana, Joshua J. Coon, Corinne D. Engelman
Summary: A hallmark of Alzheimer's disease (AD) is the aggregation of proteins (amyloid beta [A] and hyperphosphorylated tau [T]) in the brain. Proteome-wide analysis of cerebrospinal fluid (CSF) identified 61 proteins significantly associated with the AD pathology and 636 significant protein-biomarker associations. The results suggest that glucose and carbon metabolic dysregulation and increased CSF succinylcarnitine levels are associated with amyloid and tau pathology in AD.
ALZHEIMERS & DEMENTIA
(2023)
Article
Nutrition & Dietetics
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, Bernhard Kuster
Summary: Plants are crucial for sustainable global food supply, but the understanding of crop proteomes is limited. The presence of secondary metabolites in crop plants has hindered proteomic analyses, requiring individually optimized protein extraction protocols. In this study, a universal protein extraction protocol combined with an automated SP3 protocol and optimized micro-LC-MS/MS conditions was developed for high-quality proteomic analysis of crop plants. The workflow was successfully applied to analyze the proteomes of mature tomato fruits, demonstrating its robustness and potential for large-scale projects mapping crop tissue proteomes.
Article
Endocrinology & Metabolism
Hongqun Yang, Lanlan Chen, Yahui Liu
Summary: Using Mendelian randomization analysis, this study identified and validated 13 plasma proteins associated with hypothyroidism. Some of these proteins could explain the association between the coagulation system and hypothyroidism. These proteins have the potential to be used as early screening biomarkers for hypothyroidism.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
