Article
Chemistry, Medicinal
Ricardo A. M. Serafim, Jonathan M. Elkins, William J. Zuercher, Stefan A. Laufer, Matthias Gehringer
Summary: More than 20 years after the approval of the first protein kinase inhibitor, imatinib, we still have limited understanding of the biological functions of many human kinases. Most research continues to focus on a small number of well-validated targets. However, the understudied fraction of the kinome holds great potential for future therapies. Chemical probes are essential tools for studying biology and validating novel kinase targets.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Oliver M. Crook, Chun-Wa Chung, Charlotte M. Deane
Summary: Proteomics is a data-rich science with complex experimental designs, and Bayesian statistics allows quantification of uncertainty through probability distributions, enabling scientists to ask complex questions of their data and explicitly revealing dependencies between data and parameters.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Plant Sciences
Ray Bacala, Dave W. Hatcher, Helene Perreault, Bin Xiao Fu
Summary: Wheat, as a critical global food source, faces the pressure of climate change and the need for increased yield, quality, nutrition, and safety. However, the progress in understanding the composition and structure of gluten proteins has been slow due to the difficulty in characterizing intact functional glutenin polymer. The sub-cellular trafficking of gluten proteins and the timing of cellular events play important roles in gluten strength and function. Proteomics technologies offer new tools for studying gluten protein composition and identifying patterns that can improve its functionality.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Review
Immunology
Carlos Avila-Nieto, Nuria Pedreno-Lopez, Oriol Mitja, Bonaventura Clotet, Julia Blanco, Jorge Carrillo
Summary: Syphilis is a sexually or vertically transmitted disease caused by Treponema pallidum subspecie pallidum (TPA) infection. Despite being an obligate human pathogen with a well-known infection route and effective treatment options, the incidence of syphilis has been increasing. Developing a syphilis vaccine is crucial in countries where current preventive measures are limited. Although previous vaccine prototypes in preclinical studies did not provide full protection against infection, they showed promising results in preventing bacteria dissemination and attenuating lesion development. It is important to integrate knowledge about TPA immune response and outer membrane protein (OMP) characterization to expedite vaccine development.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Medicine, General & Internal
Maria Kourti, Michalis Aivaliotis, Emmanouel Hatzipantelis
Summary: Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and risk-directed therapy based on clinical, biologic and genetic features has played a significant role in its treatment. Despite improvement in survival rates, ALL remains a leading cause of cancer-related deaths. Proteomics is a cutting-edge technology that aims to understand the impact of the proteome on leukemia subtypes and identify new biomarkers and targets for therapy.
Review
Chemistry, Physical
Tianyi Wang, Di He, Hang Yao, Xin Guo, Bing Sun, Guoxiu Wang
Summary: This review discusses the opportunities and challenges of using protein-based materials for high-performance energy storage devices. It summarizes the recent developments of directly using proteins as active components in rechargeable batteries. The advantages and disadvantages of using proteins are compared with traditional materials, and the working mechanisms of proteins in improving the electrochemical performances of rechargeable batteries are elucidated. Lastly, the future development of applying biomaterials to build better batteries is predicted.
ADVANCED ENERGY MATERIALS
(2022)
Article
Microbiology
Dana L. Carper, Manasa R. Appidi, Sameer Mudbhari, Him K. Shrestha, Robert L. Hettich, Paul E. Abraham
Summary: Microorganisms play a crucial role in plant sustainability and productivity. Recent research on plant holobiont theory and microbial invasion ecology has revolutionized our understanding of plant-microbe interactions. Omic technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have greatly advanced our knowledge in this field, although there are still limitations to overcome.
Review
Food Science & Technology
Richard A. Williams
Summary: The development of new forms of protein is rapidly advancing, as older forms like meat and poultry are criticized for various issues. Government agencies are currently sharing oversight of new technologies, such as genetic engineering and precision fermentation. The complexity and potential benefits of these new proteins may require a new regulatory system, with a super regulator overseeing specialized private companies.
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 12, 2021
(2021)
Review
Food Science & Technology
A. A. Anoop, Prasanth K. S. Pillai, Michael Nickerson, K. V. Ragavan
Summary: Plant-based proteins are gaining attention as alternatives to animal proteins in sustainable food systems. Utilizing plant leaf proteins has the potential to supplement a healthy diet and meet protein demands. Currently, leading economies are investing in the production and development of plant leaf proteins, considering their nutritional aspects, extraction methods, and impact on the environment.
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2023)
Article
Biochemical Research Methods
Brandon T. Ruotolo
Summary: Recent advancements have made it possible to comprehensively understand protein structure, oligomeric state, sequence, and modification status, providing new possibilities for treating human diseases. Mass spectrometry (MS) tools, especially those associated with ion mobility (IM) separation, have played a crucial role in this progress. However, the application of collision cross section (CCS) values in native proteomics still has limitations.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Pharmacology & Pharmacy
Zhuxuan Jiang, Yuxiu Chu, Changyou Zhan
Summary: This review provides insights into the impact of protein corona on targeted nanomedicine and discusses promising strategies to regulate protein corona for improved targeting.
EXPERT OPINION ON DRUG DELIVERY
(2022)
Review
Biotechnology & Applied Microbiology
Li-Hua Peng, Ting-Wei Gu, Yang Xu, Haseeb Anwar Dad, Jian-Xiang Liu, Jia-Zhang Lian, Lu-Qi Huang
Summary: There is a growing demand for pharmaceutical proteins, and genetic engineering of plant cells has emerged as a new strategy for protein production. However, current genetic manipulation techniques for plants have limitations and drawbacks. This review focuses on the use of nanovectors as novel gene delivery vehicles for plant cells, and discusses the potential advantages of combining nanotechnology with physical techniques to enhance protein yields. Challenges associated with these strategies and possible approaches to optimize protein production in plant bioreactors are also discussed.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Environmental Sciences
Angel Santiago Fernandez-Bou, J. Pablo Ortiz-Partida, Kristin B. Dobbin, Humberto Flores-Landeros, Leigh A. Bernacchi, Josue Medellin-Azuara
Summary: The study found that disadvantaged communities are underrepresented in scientific research, newspaper articles, and legislation bills, indicating a gap in understanding and recognition. Effective policies require collaboration with local stakeholders to address place-specific nuances and structural inequities.
ENVIRONMENTAL SCIENCE & POLICY
(2021)
Review
Chemistry, Multidisciplinary
Goran Angelovski, Ben J. Tickner, Gaoji Wang
Summary: The development of hyperpolarized bioresponsive probes for MRI applications is a rapidly growing topic in chemistry. These probes include small-molecule reporters that can be hyperpolarized using dynamic nuclear polarization and macromolecular conjugates hyperpolarized using optical pumping. This Perspective discusses how these probes can amplify MRI signals in response to biologically relevant stimuli, allowing for the rapid monitoring of various biological processes.
Review
Environmental Sciences
Sanghamitra Majumdar, Arturo A. Keller
Summary: With increasing global food demand and risks associated with climate change and agrochemicals, novel and sustainable agricultural practices are needed to improve crop yield and quality. Nanotechnology strategies have been explored widely, but limited understanding of nanomaterial safety constrains their application in the food industry. Interest in the potential of engineered nanomaterials in agricultural applications has led to increased crop exposure, posing unknown risks to plants, animals, and humans.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2021)
Article
Genetics & Heredity
Selina Casalino, Erika Frangione, Monica Chung, Georgia MacDonald, Sunakshi Chowdhary, Chloe Mighton, Hanna Faghfoury, Yvonne Bombard, Lisa Strug, Trevor J. Pugh, Jared Simpson, Saranya Arnoldo, Navneet Aujla, Erin Bearss, Alexandra Binnie, Bjug Borgundvaag, Howard Chertkow, Marc Clausen, Marc Dagher, Luke Devine, David Di Iorio, Steven Marc Friedman, Chun Yiu Jordan Fung, Anne-Claude Gingras, Lee W. Goneau, Deepanjali Kaushik, Zeeshan Khan, Elisa Lapadula, Tiffany Lu, Tony Mazzulli, Allison McGeer, Shelley L. McLeod, Gregory Morgan, David Richardson, Harpreet Singh, Seth Stern, Ahmed Taher, Iris Wong, Natasha Zarei, Elena Greenfeld, Limin Hao, Matthew Lebo, William Lane, Abdul Noor, Jennifer Taher, Jordan Lerner-Ellis
Summary: Rapid advancements in genome sequencing technology have improved our understanding of the relationship between genes and human disease. This study collected blood samples from COVID-19 patients and performed genome sequencing to analyze the data. The researchers developed a comprehensive report that includes information on disease risks, genetic variants, and ancestry. They emphasize the importance of genetic counseling and offer counseling and referrals for clinically significant findings.
Article
Biochemistry & Molecular Biology
Dmitri Segal, Stefan Maier, Giovanni J. Mastromarco, Wesley Wei Qian, Syed Nabeel-Shah, Hyunmin Lee, Gaelen Moore, Jessica Lacoste, Brett Larsen, Zhen-Yuan Lin, Abeeshan Selvabaskaran, Karen Liu, Craig Smibert, Zhaolei Zhang, Jack Greenblatt, Jian Peng, Hyun O. Lee, Anne-Claude Gingras, Mikko Taipale
Summary: This study maps the interactomes of all human 14-3-3 paralogs and characterizes their effect on client protein localization. It reveals that 14-3-3 proteins function as chaperone-like molecules and negatively regulate the localization and activity of certain proteins. These findings reshape our understanding of the function of 14-3-3 proteins.
Article
Microbiology
Stephan Kamrad, Clara Correia-Melo, Lukasz Szyrwiel, Simran Kaur Aulakh, Juerg Baehler, Vadim Demichev, Michael Muelleder, Markus Ralser
Summary: We developed a proteomics-based technology called differential isotope labeling by amino acids (DILAC) that can detect producer and consumer subpopulations within an isogenic cell population. By deconvoluting their proteomes using DILAC, we found evidence for in situ cross-feeding where rapidly growing cells ferment and provide the more slowly growing, respiring cells with ethanol. By combining DILAC with fluorescence-activated cell sorting, we showed that the metabolic subpopulations diverge phenotypically, as exemplified by a different tolerance to the antifungal drug amphotericin B.
NATURE MICROBIOLOGY
(2023)
Article
Medicine, General & Internal
Carmen Scheibenbogen, Judith Theresia Bellmann-Strobl, Cornelia Heindrich, Kirsten Wittke, Elisa Stein, Christiana Franke, Harald Pruess, Hannah Pressler, Marie-Luise Machule, Heinrich Audebert, Carsten Finke, Hanna Gwendolyn Zimmermann, Birgit Sawitzki, Christian Meisel, Markus Toelle, Anne Krueger, Anna C. Aschenbrenner, Joachim L. Schultze, Marc D. Beyer, Markus Ralser, Michael Muelleder, Leif Erik Sander, Frank Konietschke, Friedemann Paul, Silvia Stojanov, Lisa Bruckert, Dennis M. Hedderich, Franziska Knolle, Gabriela Riemekasten, Maria J. G. T. Vehreschild, Oliver A. Cornely, Uta Behrends, Susen Burock
Summary: The sequela of COVID-19, known as post-COVID-19 condition or syndrome (PCS), encompasses a range of symptoms caused by immune dysregulation, autoimmunity, endothelial dysfunction, viral persistence, and viral reactivation. However, it is unclear whether different clinical subgroups of PCS can be distinguished based on the expression of biomarkers. There is an overlap between symptoms and mechanisms of PCS and postinfectious myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Currently, there are no curative therapies available for ME/CFS or PCS, but the identified mechanisms provide targets for therapeutic interventions. To accelerate the development of therapies, it is proposed to evaluate drugs targeting different mechanisms in clinical trial networks using harmonized diagnostic and outcome criteria and subgroup patients based on comprehensive clinical profiling, including diagnostic and biomarker phenotyping.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Hamish J. C. McAuley, Rachael A. Evans, Charlotte E. Bolton, Christopher E. Brightling, James D. Chalmers, Annemarie B. Docherty, Omer Elneima, Paul L. Greenhaff, Ayushman Gupta, Victoria C. Harris, Ewen M. Harrison, Ling-Pei Ho, Alex Horsley, Linzy Houchen-Wolloff, Caroline J. Jolley, Olivia C. Leavy, Nazir I. Lone, William D. C. Man, Michael Marks, Dhruv Parekh, Krisnah Poinasamy, Jennifer K. Quint, Betty Raman, Matthew Richardson, Ruth M. Saunders, Marco Sereno, Aarti Shikotra, Amisha Singapuri, Sally J. Singh, Michael Steiner, Ai Lyn Tan, Louise Wain, Carly Welch, Julie Whitney, Miles D. Witham, Janet Lord, Neil J. Greening, HOSP-COVID Study Collaborat Grp
Summary: This study recruited COVID-19 survivors in the UK and objectively measured frailty using FFP. The results showed that frailty and pre-frailty are common after hospitalization with COVID-19, and comprehensive assessment and interventions targeting frailty are needed beyond the initial illness.
Article
Biochemical Research Methods
Fangfei Zhang, Augustin Luna, Tingting Tan, Yingdan Chen, Chris Sander, Tiannan Guo
Summary: COVIDpro is a web application based on proteomics data, including 41 original studies from 32 hospitals worldwide with 3077 patients. By identifying significantly dysregulated proteins, COVIDpro can classify COVID-19 patients into severe and non-severe disease categories with high accuracy. It serves as a valuable resource for researching potential treatments for COVID-19.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yichao Zhao, Daniel Tabet, Diana Rubio Contreras, Linjiang Lao, Arne Nedergaard Kousholt, Jochen Weile, Henrique Melo, Lisa Hoeg, Sumin Feng, Atina G. Cote, Zhen-Yuan Lin, Dheva Setiaputra, Jos Jonkers, Anne -Claude Gingras, Fernando Gomez Herreros, Frederick P. Roth, Daniel Durocher
Summary: To maintain genome integrity, cells accurately duplicate and repair DNA lesions. Through CRISPR-Cas9 screens, 160 genes causing spontaneous DNA damage and essential for cellular fitness were identified. Moreover, 227 genes causing DNA damage in replication-perturbed cells were also discovered. The study revealed the potential roles of DERA in suppressing DNA damage caused by Ara-C and GNB1L in PIKK biogenesis associated with 22q11.2 syndrome.
Article
Hematology
Felix Camirand Lemyre, Sewanou Hermann Honfo, Chelsea Caya, Matthew P. Cheng, Karen Colwill, Rachel Corsini, Anne-Claude Gingras, Agatha Jassem, Mel Krajden, Ana Citlali Marquez, Bruce D. Mazer, Meghan McLennan, Christian Renaud, Cedric P. Yansouni, Jesse Papenburg, Antoine Lewin
Summary: In this study, Bayesian latent class models (BLCMs) were used to estimate the seroprevalence of SARS-CoV-2 using blood donor samples. The results revealed a relatively low spread of SARS-CoV-2 in Quebec, but the seroprevalence could change rapidly.
Article
Engineering, Biomedical
Matthew E. H. White, Ludwig R. Sinn, D. Marc Jones, Joost de Folter, Simran Kaur Aulakh, Ziyue Wang, Helen R. Flynn, Lynn Krueger, Pinkus Tober-Lau, Vadim Demichev, Florian Kurth, Michael Muelleder, Veronique Blanchard, Christoph B. Messner, Markus Ralser
Summary: A technique named 'OxoScan-MS' allows for the large-scale quantification of glycopeptides in plasma samples. By applying this technique, the study identified differential glycosylation in COVID-19 patients compared to healthy controls in various disease-relevant plasma glycoproteins. This technique has the potential for the quantitative mapping of glycoproteomes in a large number of samples.
NATURE BIOMEDICAL ENGINEERING
(2023)
Book Review
Chemistry, Multidisciplinary
Markus Ralser, Nick Lane
NATURE REVIEWS CHEMISTRY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Claire Martin, James Knight, Kento Abe, Bhavish Rathod, Cassandra Wong, Brett Larson, Anne-Claude Gingras
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Kali R. Iyer, Sheena C. Li, Nicole M. Revie, Jennifer W. Lou, Dustin Duncan, Sara Fallah, Hiram Sanchez, Iwona Skulska, Mojca Mattiazzi Usaj, Hamid Safizadeh, Brett Larsen, Cassandra Wong, Ahmed Aman, Taira Kiyota, Mami Yoshimura, Hiromi Kimura, Hiroyuki Hirano, Minoru Yoshida, Hiroyuki Osada, Anne -Claude Gingras, David R. Andes, Rebecca S. Shapiro, Nicole Robbins, Mohammad T. Mazhab-Jafari, Luke Whitesell, Yoko Yashiroda, Yoko Yashiroda, Charles Boone, Leah E. Cowen
Summary: The rising drug resistance among pathogenic fungi is a growing threat to human health, with a limited number of antifungal compounds available. A compound called NPD6433 was identified through screening and showed broad-spectrum activity against major human fungal pathogens as well as Aspergillus fumigatus. NPD6433 targets the enoyl reductase domain of fatty acid synthase 1 (Fas1), inhibiting its activity and thus essential fatty acid biosynthesis. This compound has potential as a therapeutic tool to explore lipid homeostasis in pathogenic fungi.
CELL CHEMICAL BIOLOGY
(2023)
Article
Geriatrics & Gerontology
Jessica A. Breznik, Ahmad Rahim, Tara Kajaks, Megan Hagerman, Lucas Bilaver, Karen Colwill, Roaya M. Dayam, Anne -Claude Gingras, Chris P. Verschoor, Janet E. McElhaney, Jonathan L. Bramson, Dawn M. E. Bowdish, Andrew P. Costa
Summary: A longitudinal cohort study in nursing and retirement homes in Ontario, Canada, identified vaccine type, number of doses, and recent infection history as important factors for protection against Omicron variant infection in older adults.
JOURNAL OF THE AMERICAN MEDICAL DIRECTORS ASSOCIATION
(2023)
Article
Medicine, Research & Experimental
Laure Bosquillon de Jarcy, Bengisu Akbil, Baxolele Mhlekude, Johanna Leyens, Dylan Postmus, Greta Harnisch, Jenny Jansen, Marie L. Schmidt, Annette Aigner, Fabian Pott, Robert Lorenz Chua, Lilian Krist, Roberta Gentile, Barbara Muehlemann, Terence C. Jones, Daniela Niemeyer, Julia Fricke, Thomas Keil, Tobias Pischon, Juergen Janke, Christian Conrad, Stefano Iacobelli, Christian Drosten, Victor M. Corman, Markus Ralser, Roland Eils, Florian Kurth, Leif Sander, Christine Goffinet
Summary: The expression levels of 90K/LGALS3BP protein were found to be elevated in COVID-19 patients. The SARS-CoV-2 infection inhibited the levels of PBMC-associated 90K protein, suggesting increased release into the extracellular space. Monocyte-specific induction of LGALS3BP mRNA expression was also observed in COVID-19 patients.
CLINICAL AND EXPERIMENTAL MEDICINE
(2023)
Review
Microbiology
Christian Kost, Kiran Raosaheb Patil, Jonathan Friedman, Sarahi L. Garcia, Markus Ralser
Summary: Microbial communities are shaped by ecological and environmental interactions, where antagonistic and synergistic interactions play important roles in driving their structure and dynamics.
NATURE MICROBIOLOGY
(2023)
