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Biomolecules May 2021Homocysteine is a non-proteinogenic sulfhydryl-containing amino acid derived from methionine and is a homologue of cysteine [...].
Homocysteine is a non-proteinogenic sulfhydryl-containing amino acid derived from methionine and is a homologue of cysteine [...].
Topics: Animals; Biochemistry; Disease; Homocysteine; Humans; Molecular Biology
PubMed: 34063494
DOI: 10.3390/biom11050737 -
BioMed Research International 2018Extracellular vesicles (EVs) play an essential role in the communication between cells and transport of diagnostically significant molecules. A wide diversity of... (Review)
Review
BACKGROUND
Extracellular vesicles (EVs) play an essential role in the communication between cells and transport of diagnostically significant molecules. A wide diversity of approaches utilizing different biochemical properties of EVs and a lack of accepted protocols make data interpretation very challenging.
SCOPE OF REVIEW
This review consolidates the data on the classical and state-of-the-art methods for isolation of EVs, including exosomes, highlighting the advantages and disadvantages of each method. Various characteristics of individual methods, including isolation efficiency, EV yield, properties of isolated EVs, and labor consumption are compared.
MAJOR CONCLUSIONS
A mixed population of vesicles is obtained in most studies of EVs for all used isolation methods. The properties of an analyzed sample should be taken into account when planning an experiment aimed at studying and using these vesicles. The problem of adequate EVs isolation methods still remains; it might not be possible to develop a universal EV isolation method but the available protocols can be used towards solving particular types of problems.
GENERAL SIGNIFICANCE
With the wide use of EVs for diagnosis and therapy of various diseases the evaluation of existing methods for EV isolation is one of the key problems in modern biology and medicine.
Topics: Biochemistry; Extracellular Vesicles; Filtration; Humans; Microfluidics; Solubility; Ultracentrifugation
PubMed: 29662902
DOI: 10.1155/2018/8545347 -
Cell Dec 2017Methods for the targeted disruption of protein function have revolutionized science and greatly expedited the systematic characterization of genes. Two main approaches...
Methods for the targeted disruption of protein function have revolutionized science and greatly expedited the systematic characterization of genes. Two main approaches are currently used to disrupt protein function: DNA knockout and RNA interference, which act at the genome and mRNA level, respectively. A method that directly alters endogenous protein levels is currently not available. Here, we present Trim-Away, a technique to degrade endogenous proteins acutely in mammalian cells without prior modification of the genome or mRNA. Trim-Away harnesses the cellular protein degradation machinery to remove unmodified native proteins within minutes of application. This rapidity minimizes the risk that phenotypes are compensated and that secondary, non-specific defects accumulate over time. Because Trim-Away utilizes antibodies, it can be applied to a wide range of target proteins using off-the-shelf reagents. Trim-Away allows the study of protein function in diverse cell types, including non-dividing primary cells where genome- and RNA-targeting methods are limited.
Topics: Animals; Antibodies; Biochemistry; Protein Transport; Proteolysis
PubMed: 29153837
DOI: 10.1016/j.cell.2017.10.033 -
Biochemistry and Molecular Biology... Jul 2017To date, national interests, policies, and calls for transformation of undergraduate education have been the main drivers of research integration into the undergraduate...
To date, national interests, policies, and calls for transformation of undergraduate education have been the main drivers of research integration into the undergraduate curriculum, briefly described here. The New Horizons in Biochemistry and Molecular Biology Education conference at the Weizmann Institute of Science (Israel) this fall presents an exciting opportunity to discuss integration of undergraduate research into the curriculum and other cutting-edge topics in biochemistry and molecular biology education from a cross-national perspective. I look forward to exploring prospects for international collaboration on research and development of course-based undergraduate research experiences and on STEM education in general. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):293-298, 2017.
Topics: Biochemistry; Curriculum; Education, Medical, Undergraduate; Educational Measurement; Humans; Molecular Biology; Science; Students; Universities
PubMed: 28696054
DOI: 10.1002/bmb.21070 -
Molecular Plant Jan 2023Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to... (Review)
Review
Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.
Topics: Plant Breeding; Metabolomics; Genomics; Plants; Proteomics
PubMed: 36114669
DOI: 10.1016/j.molp.2022.09.007 -
The FEBS Journal May 2023Peter Macheroux is Professor of Biochemistry and Head of the Institute of Biochemistry at Graz University of Technology in Austria. Peter's research spans a diverse...
Peter Macheroux is Professor of Biochemistry and Head of the Institute of Biochemistry at Graz University of Technology in Austria. Peter's research spans a diverse selection of topics, and his work has contributed significantly towards advancing our understanding of bacterial enzymology, plant physiology and the molecular pathways that underlie human pathophysiology. Among Peter's many scientific achievements, he has led the team that recognised DPP3 as a biomarker for cardiovascular diseases, with the subsequent therapeutic implications of the development of DPP3 inhibitors. In this interview-based article, Peter provides an overview of his research focus and goals, recalls some of his great scientific breakthroughs and describes what the key current challenges in his research field are.
Topics: Male; Humans; History, 20th Century; Biochemistry
PubMed: 36308323
DOI: 10.1111/febs.16646 -
Cell Reports. Medicine Sep 2023We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with...
We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.
Topics: Humans; Proteogenomics; Deep Learning; Neoplasms; Proteomics; Machine Learning
PubMed: 37582371
DOI: 10.1016/j.xcrm.2023.101173 -
International Journal of Molecular... Jun 2022Cancer metabolism has been of interest for decades; however, the recent development of sophisticated techniques such as metabolomics or lipidomics have significantly...
Cancer metabolism has been of interest for decades; however, the recent development of sophisticated techniques such as metabolomics or lipidomics have significantly increased our understanding of processes taking place in tumour cells [...].
Topics: Humans; Lipid Metabolism; Lipidomics; Metabolomics; Neoplasms
PubMed: 35806215
DOI: 10.3390/ijms23137210 -
Annual Review of Nutrition Aug 2023An interview with James M. Ntambi, professor of biochemistry and the Katherine Berns Van Donk Steenbock Professor in Nutrition, College of Agricultural and Life... (Review)
Review
An interview with James M. Ntambi, professor of biochemistry and the Katherine Berns Van Donk Steenbock Professor in Nutrition, College of Agricultural and Life Sciences, at the University of Wisconsin-Madison, took place via Zoom in April 2022. He was interviewed by Patrick J. Stover, director of the Institute for Advancing Health through Agriculture and professor of nutrition and biochemistry and biophysics at Texas A&M University. Dr. James Ntambi is a true pioneer in the field of nutritional biochemistry. He was among the very first to discover and elucidate the role that diet and nutrients play in regulating metabolism through changes in the expression of metabolic genes, focusing on the de novo lipogenesis pathways. As an African immigrant from Uganda, his love of science and his life experiences in African communities suffering from severe malnutrition molded his scientific interests at the interface of biochemistry and nutrition. Throughout his career, he has been an academic role model, a groundbreaking nutrition scientist, and an educator. His commitment to experiential learning through the many study-abroad classes he has hosted in Uganda has provided invaluable context for American students in nutrition. Dr. Ntambi's passion for education and scientific discovery is his legacy, and the field of nutrition has benefited enormously from his unique perspectives and contributions to science that are defined by his scientific curiosity, his generosity to his students and colleagues, and his life experiences. The following is an edited transcript.
Topics: Humans; Agriculture; Metabolism; Nutritional Sciences; Nutritional Status; Uganda; United States; Wisconsin; African People; Malnutrition; Biochemistry
PubMed: 37253680
DOI: 10.1146/annurev-nutr-061021-020321 -
The FEBS Journal Aug 2021In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research focus, perspectives on the journal and future...
In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research focus, perspectives on the journal and future directions in their field and beyond. Angela M. Gronenborn is the UPMC Rosalind Franklin Professor and Chair of the Department of Structural Biology, University of Pittsburgh, School of Medicine and Professor of Bioengineering, Swanson School of Engineering, Pittsburgh, USA. She has served as an editorial board member of The FEBS Journal since 2009.
Topics: Biochemistry; Biophysics; History, 20th Century; History, 21st Century; United States
PubMed: 34342147
DOI: 10.1111/febs.15889