Article
Food Science & Technology
Marie-Caroline Lecrenier, Aline Marien, Pascal Veys, Ikram Belghit, Marc Dieu, Nathalie Gillard, Jean Henrottin, Uta M. Herfurth, Daniela Marchis, Sara Morello, Eystein Oveland, Oliver Poetz, Josef Daniel Rasinger, Andreas Steinhilber, Vincent Baeten, Gilbert Berben, Olivier Fumiere
Summary: One of the main challenges after implementing the ban on processed animal protein (PAP) in feed has been to develop methods to detect and identify the type and origin of PAP or animal products. The study shows that liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a promising method to address this challenge, with inter-laboratory tests confirming its potential to resolve analytical gaps in detecting and differentiating PAP.
Article
Multidisciplinary Sciences
Kevin L. Yang, Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser, Alexey I. Nesvizhskii
Summary: This article presents an accessible method to improve peptide spectrum match rescoring using deep learning predictions in bottom-up proteomics. The authors demonstrate significant improvements in peptide/protein identifications across various experiments, including single-cell proteomics and immunopeptidomics. They introduce a new tool called MSBooster, which incorporates deep learning-based predictions of peptide properties to rescore peptide-to-spectrum matches, and show its utility in different workflows, such as immunopeptidomics and single-cell proteomics.
NATURE COMMUNICATIONS
(2023)
Article
Agriculture, Multidisciplinary
Marie-Caroline Lecrenier, Lisa Plasman, Alexandra Cordonnier, Vincent Baeten
Summary: This study aimed to evaluate the improvement in sensitivity and specificity of mass spectrometry-based proteomics detection of animal-processed proteins (PAPs) using sedimentation. The optimized method was able to achieve adulteration levels below the European Commission's requirement of 0.1% PAPs. This approach provides a simple and cost-effective solution without the need for new equipment or expertise.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Plant Sciences
Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, David L. Tabb
Summary: Proteomics has been more valuable in model organisms with genome sequence annotations than in nonmodel organisms lacking such annotations. This study aimed to establish a protein sequence set for the nonmodel organism chia using RNA-Seq experiments. The results showed that assembling RNA-Seq datasets for chia resulted in high completeness of transcript sequences, though the number of sequences and genes varied. After six-frame translation, orthologs were detected among other species within the same taxonomic order.
Article
Biochemical Research Methods
Christopher Burgoyne, Rob Smith
Summary: Glycans are important in biochemical processes, but the computational interpretation of glycans in mass spectrometry analysis can be challenging. The C++ implementation of the Sweet-SEQer algorithm, called C-SEQer, outperforms the original algorithm in terms of time and memory usage, making glycan analysis more efficient and effective. The implementation is freely available with an MIT license.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Eleni Stamoula, Eleana Sarantidi, Vasilis Dimakopoulos, Alexandra Ainatzoglou, Ioannis Dardalas, Georgios Papazisis, Konstantina Kontopoulou, Athanasios K. Anagnostopoulos
Summary: This study aimed to identify the serum proteome characteristics of anti-SARS-CoV-2 vaccinated individuals who had previously contracted the virus and compare them to virus-naive vaccine recipients. The results showed that there were 47 significantly differentially expressed proteins in the serum of previously infected patients, with the majority being down-regulated. These findings support the crucial role of the humoral immune response in the protection against SARS-CoV-2 infection provided by COVID-19 vaccination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Zohaib Iqbal, Helene A. Fachim, J. Martin Gibson, Ivona Baricevic-Jones, Amy E. Campbell, Bethany Geary, Rachelle P. Donn, Dashne Hamarashid, Akheel Syed, Anthony D. Whetton, Handrean Soran, Adrian H. Heald
Summary: Bariatric surgery induces metabolic pathway recalibration, potentially contributing to the remission of type 2 diabetes mellitus. Analysis of plasma samples identified several proteins that may serve as biomarkers for T2DM remission after surgery.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Clinical Neurology
Jan Kucera, Katerina Horska, Pavel Hruska, Daniela Kuruczova, Vincenzo Micale, Jana Ruda-Kucerova, Julie Bienertova-Vasku
Summary: Schizophrenia patients have reduced life expectancy due to metabolic disturbances, with antipsychotic medications playing a major role. Research shows that antipsychotic drugs trigger dysregulation of multiple energetic and metabolic pathways in adipose tissue, particularly in schizophrenia-like animal models.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2021)
Article
Biochemistry & Molecular Biology
Henrik Tonner, Selina Hunn, Nadine Auler, Carsten Schmelter, Vanessa M. Beutgen, Harald D. von Pein, Norbert Pfeiffer, Franz H. Grus
Summary: In this study, intravitreal injection of anti-HMGB1 Ab was found to reduce HMGB1-dependent inflammatory signaling and improve RGC neuronal survival in an experimental animal model of glaucoma. Mass spectrometric analysis demonstrated increased abundance of RNA metabolism-associated hnRNPs in animals injected with the antibody, while microarray analysis showed a decreased expression of inflammatory mediators in the HMGB1 group. These findings suggest that anti-HMGB1 Ab may play a neuroprotective role in glaucoma by modulating inflammatory processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Iris Ribitsch, Andrea Bileck, Alexander D. Aldoshin, Maciej M. Kandula, Rupert L. Mayer, Monika Egerbacher, Simone Gabner, Ulrike Auer, Sinan Gultekin, Johann Huber, David P. Kreil, Christopher Gerner, Florien Jenner
Summary: This study introduces an ovine model of tendon injury for comparing adult scarring repair and fetal regeneration. The results show that fetal tendons can completely regenerate within 28 days, while adult tendon defects remain evident five months post-injury. Proteome analyses reveal distinct differences in inflammation and repair processes between adult and fetal tendons, highlighting the potential therapeutic implications of understanding fetal healing mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Food Science & Technology
Jing Pu, Bingye Zhao, Xin Liu, Shugang Li, Beibei Wang, Di Wu, Jinqiu Wang, Fang Geng
Summary: This study comprehensively compared the protein profiles and properties of chicken egg white and its three components. The proteomes of thick and thin egg white are similar, but thick egg white has higher abundance of ovomucin subunits and lysozymes. The properties of thick and thin egg white are significantly different. Additionally, the chalaza component has higher abundance of insoluble proteins and lower abundance of soluble proteins, which explains its insolubility. These findings are important for further research and development of egg white, such as thinning of egg white, understanding changes in egg white properties, and differential application of thick and thin egg white.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Pharmacology & Pharmacy
Parul Kamboj, Soumalya Sarkar, Sonu Kumar Gupta, Neema Bisht, Deepika Kumari, Md. Jahangir Alam, Sagar Barge, Bhaswati Kashyap, Barsha Deka, Simanta Bharadwaj, Seydur Rahman, Partha Pratim Dutta, Jagat C. Borah, Narayan Chandra Talukdar, Sanjay K. Banerjee, Yashwant Kumar
Summary: The study demonstrates that the extract from Lysimachia candida Lindl. can improve the pathophysiology of fatty liver and reverse metabolic syndrome through altering metabolic pathways. Metabolomics analysis reveals the metabolic changes between diseased rats and treatment group, providing potential mechanisms for preventing metabolic syndrome.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Diana Canetti, Francesca Brambilla, Nigel B. Rendell, Paola Nocerino, Janet A. Gilbertson, Dario Di Silvestre, Andrea Bergamaschi, Francesca Lavatelli, Giampaolo Merlini, Julian D. Gillmore, Vittorio Bellotti, Pierluigi Mauri, Graham W. Taylor
Summary: Amyloidosis is a rare human disease caused by abnormal protein deposition in tissues, with proteomic analysis playing a crucial role in clinical diagnosis and amyloid typing. Inter-center data exchange is effective for testing and validating the accuracy of different software platforms in proteomics analysis.
Article
Multidisciplinary Sciences
Tzu-Yun Kuo, Jen-Hung Wang, Yung-Wen Huang, Ting-Yi Sung, Ching-Tai Chen
Summary: In this study, a novel quantitation pipeline that combines sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter is proposed to improve the quantitation accuracy of isobaric labeling-based mass spectrometry. The results demonstrate that this pipeline can enhance the overall quantitation accuracy at both the PSM and protein levels. This is the first study to utilize spectral library searching to improve isobaric labeling-based quantitation.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Kyle J. Juetten, Jennifer S. Brodbelt
Summary: MS-TAFI is a free Python-based program for analyzing and visualizing deconvoluted MS/MS data of intact proteins, offering a streamlined approach to data analysis. It also includes tools for native mass spectrometry experiments, allowing for the search of fragment ions with retained ligands and visualization of charge site locations.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Antoine H. Chaanine, LeeAnn Higgins, Todd Markowski, Jarrod Harman, Maureen Kachman, Charles Burant, L. Gabriel Navar, David Busija, Patrice Delafontaine
Summary: Metabolic remodeling plays a significant role in the pathophysiology of heart failure, and the crosstalk between PKA and AMPK signaling governs metabolic remodeling in myocardial remodeling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Meeting Abstract
Endocrinology & Metabolism
Mirza Muhammad Fahd Qadir, Weiwei Xu, Daniela Nasteska, Manika Bhondeley, Paula Mota de Sa, Charles R. Evans, Jochen Buck, Lonny Levin, Charles Burant, David Hodson, Franck Mauvais-Jarvis
Article
Biochemistry & Molecular Biology
Carolyn F. McCabe, Jennifer L. LaBarre, Steven E. Domino, Marjorie C. Treadwell, Ana Baylin, Charles F. Burant, Dana C. Dolinoy, Vasantha Padmanabhan, Jaclyn M. Goodrich
Summary: Maternal prenatal status plays a crucial role in offspring health and disease, and alterations in DNA methylation may be a mechanism through which suboptimal prenatal conditions confer disease risk later in life. This study investigated the association between maternal one-carbon metabolites and DNA methylation patterns in newborns. The findings highlight the importance of maternal diet and cellular methylation potential in shaping offspring health.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Neurosciences
Cheehoon Ahn, Benjamin J. Ryan, Michael W. Schleh, Pallavi Varshney, Alison C. Ludzki, Jenna B. Gillen, Douglas W. Van Pelt, Lisa M. Pitchford, Suzette M. Howton, Thomas Rode, Scott L. Hummel, Charles F. Burant, Jonathan P. Little, Jeffrey F. Horowitz
Summary: Even without weight loss, 12 weeks of exercise training can alter adipose tissue structure and factors that regulate metabolism and the inflammatory signal pathway in adults with obesity.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Multidisciplinary Sciences
Xianyong Yin, Lap Sum Chan, Debraj Bose, Anne U. Jackson, Peter VandeHaar, Adam E. Locke, Christian Fuchsberger, Heather M. Stringham, Ryan Welch, Ketian Yu, Lilian Fernandes Silva, Susan K. Service, Daiwei Zhang, Emily C. Hector, Erica Young, Liron Ganel, Indraniel Das, Haley Abel, Michael R. Erdos, Lori L. Bonnycastle, Johanna Kuusisto, Nathan O. Stitziel, Ira M. Hall, Gregory R. Wagner, Jian Kang, Jean Morrison, Charles F. Burant, Francis S. Collins, Samuli Ripatti, Aarno Palotie, Nelson B. Freimer, Karen L. Mohlke, Laura J. Scott, Xiaoquan Wen, Eric B. Fauman, Markku Laakso, Michael Boehnke
Summary: The Finnish population has a high frequency of genetic variants that are rare in other populations. This study identifies new genetic loci associated with 1391 circulating metabolites in Finnish men, highlighting the potential of metabolite genetic associations in understanding disease mechanisms. The results reveal novel genes and mechanisms related to diseases and disease-related traits.
NATURE COMMUNICATIONS
(2022)
Article
Geriatrics & Gerontology
Alexander D. Brown, Claire E. Stewart, Jatin G. Burniston
Summary: This study used novel isotopic labelling and proteomic methods to investigate protein turnover in ageing cells, and found that the loss of proteome quality may contribute to the lack of fusion in aged myoblasts.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2022)
Article
Endocrinology & Metabolism
Mary Ellen Vajravelu, Emily Hirschfeld, Acham Gebremariam, Charles F. Burant, William H. Herman, Karen E. Peterson, Jennifer L. Meijer, Joyce M. Lee
Summary: This study evaluated the prospective test performance of different screening measures for identifying dysglycemia in youth. The results showed that HbA1c and nonfasting glucose tests had reasonable longitudinal discrimination in identifying adolescents at risk for dysglycemia, but their performance depended on the definition of the outcome.
HORMONE RESEARCH IN PAEDIATRICS
(2023)
Article
Endocrinology & Metabolism
Johanna Y. Fleischman, Nathan R. Qi, Mary K. Treutelaar, Steven L. Britton, Lauren G. Koch, Jun Z. Li, Charles F. Burant
Summary: Caloric restriction improves metabolic health and shares similarities with high cardiorespiratory fitness in terms of adiposity reduction, enhanced cardiometabolic health, and increased longevity. This study investigates whether the mechanisms through which heritable high cardiorespiratory fitness occurs are similar to those promoting health and longevity through caloric restriction. The results suggest that caloric restriction has positive effects on physiological parameters in low cardiorespiratory fitness rats that resemble those seen in high cardiorespiratory fitness rats.
MOLECULAR METABOLISM
(2023)
Article
Genetics & Heredity
Muhammad Shoaib, Qiang Ye, Heidi IglayReger, Meng H. H. Tan, Michael Boehnke, Charles F. F. Burant, Scott A. A. Soleimanpour, Sarah A. Gagliano A. Taliun
Summary: Polygenic risk scores (PRS) can quantify the genetic susceptibility to disease by analyzing summary statistics from genome-wide association studies (GWAS). Differentiating between type 1 (T1D) and type 2 (T2D) diabetes accurately is crucial for diagnosis and treatment. PRS have the potential to address misclassification of T1D and T2D.
GENETIC EPIDEMIOLOGY
(2023)
Article
Endocrinology & Metabolism
Michael W. W. Schleh, Benjamin J. J. Ryan, Cheehoon Ahn, Alison C. C. Ludzki, Pallavi Varshney, Jenna B. B. Gillen, Douglas W. W. Van Pelt, Lisa M. M. Pitchford, Suzette M. M. Howton, Thomas Rode, Thomas L. L. Chenevert, Scott L. L. Hummel, Charles F. F. Burant, Jeffrey F. F. Horowitz
Summary: The objective of this study was to assess the relationship between insulin-mediated glucose uptake and clinical outcomes, as well as deep-phenotyping measures. The study also aimed to examine how adipocyte size, fibrosis, and proteomic profile contribute to the regulation of fatty acid rate of appearance.
Article
Cell Biology
Weiwei Xu, M. M. Fahd Qadir, Daniela Nasteska, Paula Mota de Sa, Caroline M. Gorvin, Manuel Blandino-Rosano, Charles R. Evans, Thuong Ho, Evgeniy Potapenko, Rajakrishnan Veluthakal, Fiona B. Ashford, Stavroula Bitsi, Jia Fan, Manika Bhondeley, Kejing Song, Venkata N. Sure, Siva S. V. P. Sakamuri, Lina Schiffer, Wandy Beatty, Rachael Wyatt, Daniel E. Frigo, Xiaowen Liu, Prasad V. Katakam, Wiebke Arlt, Jochen Buck, Lonny R. Levin, Tony Hu, Jay Kolls, Charles F. Burant, Alejandra Tomas, Matthew J. Merrins, Debbie C. Thurmond, Ernesto Bernal-Mizrachi, David J. Hodson, Franck Mauvais-Jarvis
Summary: Male mice without androgen receptor (AR) in pancreatic 0 cells have reduced insulin secretion and develop hyperglycemia. Testosterone activates an extranuclear AR, which enhances glucagon-like peptide-1 (GLP-1) insulin action. This study investigates the mechanisms through which testosterone enhances GLP-1-stimulated insulin secretion in male 0 cells, including the activation of cAMP production and the recruitment of Gas to GLP-1 receptor and AR complexes. Additionally, testosterone promotes insulin secretion in human islets through an actin remodeling cascade. The study provides insights into the genomic and non-genomic actions of AR in regulating insulin exocytosis.
Article
Neurosciences
Jan Krzysztof Blusztajn, Nurgul Aytan, Thekkelnaycke Rajendiran, Tiffany J. Mellott, Tanu Soni, Charles F. Burant, Geidy E. Serrano, Thomas G. Beach, Honghuang Lin, Thor D. Stein
Summary: This study identified monogalactosyl diglycerides (MGDGs) as a central correlate of clinical and pathological progression in Alzheimer's disease (AD). The levels of MGDGs were found to be positively associated with AD-related traits in postmortem brain samples. These findings suggest the importance of MGDG metabolism in the progression of AD.
JOURNAL OF ALZHEIMERS DISEASE
(2023)
Article
Endocrinology & Metabolism
Johanna Y. Fleischman, Francoise Van den Bergh, Nicole L. Collins, Madelyn Bowers, Daniel A. Beard, Charles F. Burant
Summary: This study investigates the differences in substrate preference and mitochondrial respiration between high capacity runner (HCR) and low capacity runner (LCR) rat lines. The results show that HCR rats have upregulated mitochondrial gene expression and higher fatty acid oxidative capacity compared to LCR rats. This increased fatty acid oxidation is likely a result of selection for running capacity and contributes to the healthy metabolic phenotype of individuals with high cardiorespiratory fitness.
MOLECULAR METABOLISM
(2023)
Article
Medicine, Research & Experimental
Allison C. Billi, Rachael Wasikowski, Feiyang Ma, Srilakshmi Yalavarthi, Claire K. Hoy, Yu Zuo, Matthew T. Patrick, Neha Shah, Christine Parker, Chad Aaronson, Alyssa Harbaugh, Matthew F. Lucido, Kerby Shedden, Krishna Rao, Heidi B. Iglayreger, Charles F. Burant, J. Michelle Kahlenberg, Lam C. Tsoi, Johann E. Gudjonsson, Jason S. Knight, Yogendra Kanthi
Summary: The risk of severe disease and death from COVID-19 is higher in certain patient demographic groups, such as older individuals, males, and those who are obese. A study found that there are distinct immune cell responses in these higher risk groups, including altered neutrophil maturation in older patients and enhanced cytokine responses in male patients. These findings emphasize the importance of studying diverse patient cohorts in COVID-19 immune therapy research.
Meeting Abstract
Environmental Sciences
Rebekah L. Petroff, Vasantha Padmanabhan, Raymond Cavalcante, Charles Burant, Dana C. Dolinoy, Jaclyn M. Goodrich
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)