Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Maxime Francois, Avinash Karpe, Jian-Wei Liu, David J. Beale, Maryam Hor, Jane Hecker, Jeff Faunt, John Maddison, Sally Johns, James D. Doecke, Stephen Rose, Wayne R. Leifert
Summary: The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer's disease (AD) is not well understood. This study examined the plasma samples of individuals with MCI or AD, as well as age- and gender-matched cognitively normal individuals, to identify cellular pathways and biomarkers associated with the diseases. The analysis revealed specific proteins that distinguish AD from MCI and cognitively normal groups, and identified various metabolic pathways affected in AD. These findings contribute to the understanding of the diseases and may be useful for future clinical trials.
Review
Biochemistry & Molecular Biology
Marina Amaral Alves, Santosh Lamichhane, Alex Dickens, Aidan McGlinchey, Henrique Caracho Ribeiro, Partho Sen, Fang Wei, Tuulia Hyotylainen, Matej Oresic
Summary: Lipids play important roles in biology, such as energy storage and cell membrane structure. Lipid metabolism is tightly regulated, and disturbances in lipid-related pathways are involved in the pathogenesis of common diseases. Advances in lipidomics provide new methods for lipid research.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2021)
Editorial Material
Microbiology
Jennifer Geddes-McAlister
Summary: The beauty within biological systems can be revealed through advanced technological platforms. Improvements in genome, transcriptome, proteome, and metabolome investigations, as well as data integration, have accelerated our understanding of diverse biological systems. For fungal pathogens, innovation is driven by exploring mechanisms of antifungal resistance, uncovering new relationships and interactions between host and pathogen, improving characterization of virulence determinants, and discovering new antifungal targets.
Review
Biochemistry & Molecular Biology
Munazza Ahmed, Ahlam M. Semreen, Waseem El-Huneidi, Yasser Bustanji, Eman Abu-Gharbieh, Mohammad A. Y. Alqudah, Ahmed Alhusban, Mohd Shara, Ahmad Y. Abuhelwa, Nelson C. Soares, Mohammad H. Semreen, Karem H. Alzoubi
Summary: Glioblastoma (GB) is a type of aggressive brain tumor with unclear biology and challenges in diagnosis and prognosis due to its heterogeneity. Omics techniques, including proteomics and metabolomics, have shown promise in understanding the regulatory network of enzymes and metabolites in GB. This review highlights the significant contributions of these tools in GB research and treatment, emphasizing the impact of integrative omics approaches in overcoming therapeutic challenges.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Immunology
Denise Battaglini, Miqueias Lopes-Pacheco, Hugo C. Castro-Faria-Neto, Paolo Pelosi, Patricia R. M. Rocco
Summary: This article summarizes the commonly used biomarkers in COVID-19, which play important roles in predicting disease severity, hospitalization, ICU admission, and mortality. It also discusses how novel analytical strategies can be applied in clinical practice, emphasizing the need for future research to focus on identifying a limited but essential number of laboratory biomarkers for predicting prognosis and outcomes in severe COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Tomasz Pienkowski, Tomasz Kowalczyk, Noemi Garcia-Romero, Angel Ayuso-Sacido, Michal Ciborowski
Summary: The diagnosis of glioma relies on imaging methods that cannot differentiate between different stages and subtypes. Patients are usually diagnosed in the symptomatic stage. Molecular alterations and tumor biomarkers can be used to diagnose asymptomatic gliomas. A multiomics approach can track physiological changes and serve as a non-invasive diagnostic method.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: This study characterized the early effects of salt stress on the proteome and metabolome of rice tissues. It identified numerous signaling pathways that were rapidly induced or partially induced by salt stress. Through a combined analysis, it revealed the most sensitive components of signaling pathways causing salt-susceptibility in rice and suggested potential targets for crop improvement.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: Rice, a staple food crop worldwide, is estimated to have its global production reduced by 50% due to salinity stress. However, limited knowledge exists regarding the initial molecular signaling and proteins associated with sensing salinity in crop plants. In this study, we characterized the early effects of salt on the proteome and metabolome of rice tissues and identified numerous signaling pathways induced by salinity. By combining omics data and physiological changes, we identified the most susceptible proteins and metabolites in each pathway, providing potential targets for improving rice's sensitivity to salinity.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Martin Rumbo, Mihai Oltean
Summary: Intestinal transplantation (ITx) is a life-saving option for patients with irreversible intestinal failure. However, ITx is highly immunogenic due to the unique immunobiology of the intestines and the lack of reliable non-invasive biomarkers for rejection surveillance. Various assays have been tested, but none have shown sufficient sensitivity and specificity for diagnosing acute rejection. This review integrates the mechanistic aspects of graft rejection with the current knowledge of ITx immunobiology and summarizes the search for a noninvasive biomarker of rejection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Food Science & Technology
Paulo E. S. Munekata, Mirian Pateiro, Maria Lopez-Pedrouso, Mohammed Gagaoua, Jose M. Lorenzo
Summary: Foodomics is a valuable tool that utilizes four main strategies to comprehensively understand the biochemistry and compounds associated with meat quality traits, in order to produce high-quality cuts of meat.
CURRENT OPINION IN FOOD SCIENCE
(2021)
Article
Medicine, Research & Experimental
Pengyu Liu, Wenxuan Wang, Fei Wang, Jiaqi Fan, Jinan Guo, Tao Wu, Dongliang Lu, Qingchun Zhou, Zhuohao Liu, Yuliang Wang, Zhiqun Shang, Franky Leung Chan, Wei Yang, Xin Li, Shan-Chao Zhao, Qingyou Zheng, Dinglan Wu
Summary: In this study, proteomic and metabolomic analysis of exosomes from prostate cancer (PCa) patients was performed. Several potential biomarkers for PCa and castration resistant prostate cancer (CRPC) were identified, including the proteins LRG1 and ITIH3. Metabolomic evaluation also revealed differentially expressed metabolites. These findings suggest the potential of exosomal proteins and metabolites as markers for CRPC and confirm the important role of the protein LRG1 in PCa progression.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Review
Nutrition & Dietetics
Lynnette Ferguson, Matthew Barnett
Summary: Nutrigenomics New Zealand (NuNZ) was a collaborative research programme established by three organizations with the aim of studying the application of nutrigenomics in New Zealand and exploring its potential benefits in the plant food and agricultural sectors. The programme divided nutrigenomics into personalized nutrition and nutrigenomics, utilizing various science laboratories for comprehensive analysis to understand the impact of food products and diets on health.
Article
Biotechnology & Applied Microbiology
Haiyu Zhang, Lu Wang, Dechun Yin, Qi Zhou, Lin Lv, Zengxiang Dong, Yuanqi Shi
Summary: This study integrates proteomics and metabolomics analyses to explore the dysregulated proteins and metabolites in AF patients with and without HF. Several significant pathways and potential biomarkers were identified, and a subclassification of HF based on metabolomics was conducted. This study provides novel insights into the mechanisms of AF-induced HF progression and identifies potential biomarkers for prognosis of AF with HF.
Editorial Material
Multidisciplinary Sciences
Bart P. Braeckman
Summary: Reduced tagging of certain proteins for clearance in ageing nematode worms can result in the accumulation of unnecessary proteins, ultimately impairing cellular and tissue function.
Article
Geriatrics & Gerontology
Daniel E. L. Promislow
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2020)
Article
Geriatrics & Gerontology
Daniel E. L. Promislow
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2021)
Article
Geriatrics & Gerontology
Cara L. Green, Sharon E. Mitchell, Davina Derous, Libia A. Garcia-Flores, Yingchun Wang, Luonan Chen, Jing-Dong J. Han, Daniel E. L. Promislow, David Lusseau, Alex Douglas, John R. Speakman
Summary: Calorie restriction is an effective intervention to extend lifespan and improve healthspan. This study revealed graded changes in the cerebellar metabolome after calorie restriction, involving various metabolites and pathways regulation.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2021)
Article
Cell Biology
Claudio de Lucia, Michela Piedepalumbo, Lu Wang, Fausto Carnevale Neto, Daniel Raftery, Erhe Gao, Domenico Pratico, Daniel E. L. Promislow, Walter J. Koch
Summary: This study aimed to evaluate the effects of aging and ischemia/reperfusion injury on plasma metabolomic profiling in mice. The results showed that aging significantly affects circulating metabolite levels, while ischemic injury did not have a drastic impact on LV function in aged mice compared to young mice.
Article
Multidisciplinary Sciences
Libia Alejandra Garcia-Flores, Cara L. Green, Sharon E. Mitchell, Daniel E. L. Promislow, David Lusseau, Alex Douglas, John R. Speakman
Summary: Caloric restriction affects the metabolome in a tissue-specific manner, with only a small number of common metabolic features responding in the same way across all tissues. The top modulated pathways were related to biosynthesis and degradation processes, suggesting each tissue has its own unique way of coping with reduced energy intake, supporting the clean cupboards hypothesis over the disposable soma interpretation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Geriatrics & Gerontology
Matt Kaeberlein, Alessandro Bitto, Maitreya J. Dunham, Warren Ladiges, Su-In Lee, Michael J. MacCoss, Alexander Mendenhall, Daniel E. L. Promislow, Peter S. Rabinovitch, Judit Villen, Lu Wang, Yuliang Wang, Jessica E. Young
Summary: The University of Washington Nathan Shock Center of Excellence provides leadership and resources for the geroscience community, supporting aging-related studies, organizing seminars and training programs, and partnering with other institutions for strategic initiatives.
Article
Cell Biology
Xiaqing Zhao, Forrest T. Golic, Benjamin R. Harrison, Meghna Manoj, Elise Hoffman, Neta Simon, Richard Johnson, Michael J. MacCoss, Lauren M. McIntyre, Daniel E. L. Promislow
Summary: Activity levels and metabolome-wide profiles are strongly associated with age, and many individual metabolites show a strong association with lifespan. The metabolome provides a biological clock that predicts not only sample age but also future mortality rates and lifespan.
Article
Biochemistry & Molecular Biology
Benjamin R. Harrison, Jessica M. Hoffman, Ariana Samuelson, Daniel Raftery, Daniel E. L. Promislow
Summary: Comparative phylogenetic studies have shed light on the evolution of metabolites across 50 million years in the genus Drosophila, revealing the conserved effects of sex and age on the metabolome. Modules in the metabolome show evidence of coevolution, enriched for specific biochemical pathways, and potentially influenced by functional relationships. These coevolutionary patterns differ between sexes and are affected by age, with some modules associated with lifespan variation, particularly in older flies, suggesting a role of metabolic associations in lifespan evolution over millions of years.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Kate E. Creevy, Joshua M. Akey, Matt Kaeberlein, Daniel E. L. Promislow
Summary: The Dog Aging Project aims to study the aging process in companion dogs through long-term research, collecting extensive data and samples to investigate the genetic, environmental, and lifestyle factors associated with aging.
Article
Geriatrics & Gerontology
Hannah Lee, Devin Collins, Kate E. Creevy, Daniel E. L. Promislow
Summary: This study investigates the relationship between age and activity in dogs based on dog and owner characteristics. The findings suggest that older dogs are less active, rural dogs are more active, and larger dogs are more active. Surprisingly, older owners tend to have more active dogs.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Daniel Promislow, Rozalyn M. Anderson, Marten Scheffer, Bernard Crespi, James DeGregori, Kelley Harris, Barbara Natterson Horowitz, Morgan E. Levine, Maria A. Riolo, David S. Schneider, Sabrina L. Spencer, Dario Riccardo Valenzano, Michael E. Hochberg
Summary: Aging research involves diverse disciplines, but lacks communication between them. Researchers propose that the concept of resilience can act as a bridge to connect these disciplines, thereby advancing research in the biology of aging.
Correction
Multidisciplinary Sciences
Kate E. Creevy, Joshua M. Akey, Matt Kaeberlein, Daniel E. L. Promislow
Article
Genetics & Heredity
Ming Yang, Benjamin R. Harrison, Daniel E. L. Promislow
Summary: This study focuses on gene coexpression in diverse cell types of the fruit fly using single-cell RNA sequencing data. The researchers discovered a set of highly coordinated genes that form a core cellular network, which accounts for only a minority of essential functions.
G3-GENES GENOMES GENETICS
(2022)
Article
Geriatrics & Gerontology
Emily E. Bray, David A. Raichlen, Kiersten K. Forsyth, Daniel E. L. Promislow, Gene E. Alexander, Evan L. MacLean
Summary: This study explores the association between physical activity and cognitive health in companion dogs. The research findings indicate that higher levels of physical activity are associated with lower severity of cognitive dysfunction symptoms, less symptom worsening, and lower prevalence of canine cognitive dysfunction. This highlights the value of companion dogs as a model for studying the relationship between physical activity and cognitive aging.
Article
Geriatrics & Gerontology
Cornelia Kraus, Noah Snyder-Mackler, Daniel E. L. Promislow
Summary: The study found that small size and genetic diversity are both associated with increased lifespan in dogs. The lifespan and proportion of old age mortality decrease with increasing body size and increase with increasing genetic diversity. The lifespan and proportion of cancer mortality follow the same patterns.