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Journal of Biotechnology Nov 2017Metabolomics is the modern term for the field of small molecule research in biology and biochemistry. Currently, metabolomics is undergoing a transition where the... (Review)
Review
Metabolomics is the modern term for the field of small molecule research in biology and biochemistry. Currently, metabolomics is undergoing a transition where the classic analytical chemistry is combined with modern cheminformatics and bioinformatics methods, paving the way for large-scale data analysis. We give some background on past developments, highlight current state-of-the-art approaches, and give a perspective on future requirements.
Topics: Biomedical Research; Computational Biology; Mass Spectrometry; Metabolomics
PubMed: 28554829
DOI: 10.1016/j.jbiotec.2017.05.018 -
American Journal of Botany Jan 2019
Review
Topics: Biochemistry; Botany; Genomics; Metabolic Networks and Pathways; Plants
PubMed: 30629738
DOI: 10.1002/ajb2.1216 -
Biochemistry and Molecular Biology... 2014
Topics: Biochemistry; Carbon Dioxide; Ecosystem; Humans; Molecular Biology; Oxygen; Photosynthesis; Plants; Thinking
PubMed: 25052343
DOI: 10.1002/bmb.20814 -
Biochemistry and Molecular Biology... Jan 2020
Topics: Biochemistry; Humans; Molecular Biology; Publishing; Reproducibility of Results
PubMed: 31868993
DOI: 10.1002/bmb.21329 -
Biochemistry and Molecular Biology... Nov 2020Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I...
Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process.
Topics: Biochemistry; Computer Simulation; Humans; Software; Students
PubMed: 32203640
DOI: 10.1002/bmb.21347 -
Postepy Biochemii 2016Collaborations between the Wlodawer and Skalka laboratories have covered a period of almost 30 years. During that time our groups have co-authored 18 publications,... (Review)
Review
Collaborations between the Wlodawer and Skalka laboratories have covered a period of almost 30 years. During that time our groups have co-authored 18 publications, including several much cited journal articles, book chapters, and scholarly reviews. It has therefore been most rewarding for us to share enthusiasm, insights, and expertise with our Frederick colleagues over the years, and also to enjoy lasting friendships.
Topics: Biochemistry; Crystallography; History, 20th Century; History, 21st Century; Protein Conformation; Retroviridae; Retroviridae Proteins; United States
PubMed: 28132482
DOI: No ID Found -
IUBMB Life Jun 2021
Review
Topics: Australia; Biochemistry; Editorial Policies; History, 20th Century; History, 21st Century; Molecular Biology; Periodicals as Topic; Publishing
PubMed: 33861518
DOI: 10.1002/iub.2473 -
Trends in Biotechnology Nov 2020Biochemical production faces economic and environmental challenges that need to be overcome to enable a viable and sustainable bioeconomy. We propose an assessment... (Review)
Review
Biochemical production faces economic and environmental challenges that need to be overcome to enable a viable and sustainable bioeconomy. We propose an assessment framework that consistently combines environmental and economic indicators to support optimized biochemical production at early development stages. We define internally consistent system boundaries and a comprehensive set of quantitative indicators from life cycle assessment (LCA) and techno-economic assessment (TEA) to combine environmental and economic performance in a single score. Our framework enables the identification of trade-offs across environmental and economic aspects over the entire biochemical life cycle. This approach provides input for the optimization of future biochemicals in terms of overall sustainability, to overcome prevailing obstacles in the development of biochemical production processes.
Topics: Biochemical Phenomena; Biochemistry; Chemical Industry; Economics; Environment; Humans; Sustainable Development
PubMed: 32423725
DOI: 10.1016/j.tibtech.2020.04.011 -
Omics : a Journal of Integrative Biology Sep 2014The concept of tissues appeared more than 200 years ago, since textures and attendant differences were described within the whole organism components. Instrumental... (Review)
Review
The concept of tissues appeared more than 200 years ago, since textures and attendant differences were described within the whole organism components. Instrumental developments in optics and biochemistry subsequently paved the way to transition from classical to molecular histology in order to decipher the molecular contexts associated with physiological or pathological development or function of a tissue. In 1941, Coons and colleagues performed the first systematic integrated examination of classical histology and biochemistry when his team localized pneumonia antigens in infected tissue sections. Most recently, in the early 21(st) century, mass spectrometry (MS) has progressively become one of the most valuable tools to analyze biomolecular compounds. Currently, sampling methods, biochemical procedures, and MS instrumentations allow scientists to perform "in depth" analysis of the protein content of any type of tissue of interest. This article reviews the salient issues in proteomics analysis of tissues. We first outline technical and analytical considerations for sampling and biochemical processing of tissues and subsequently the instrumental possibilities for proteomics analysis such as shotgun proteomics in an anatomical context. Specific attention concerns formalin fixed and paraffin embedded (FFPE) tissues that are potential "gold mines" for histopathological investigations. In all, the matrix assisted laser desorption/ionization (MALDI) MS imaging, which allows for differential mapping of hundreds of compounds on a tissue section, is currently the most striking evidence of linkage and transition between "classical" and "molecular" histology. Tissue proteomics represents a veritable field of research and investment activity for modern biomarker discovery and development for the next decade.
Topics: Histology; Immunohistochemistry; Laser Capture Microdissection; Proteomics; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 25105455
DOI: 10.1089/omi.2014.0033 -
International Journal of Molecular... Dec 2021[...].
[...].
Topics: Biochemistry; History, 20th Century; Humans; Zinc
PubMed: 34948190
DOI: 10.3390/ijms222413393