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A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.
Structural biology, as defined by the Journal of Structural Biology, deals with structural analysis of living material at every level of organization.
Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.
Rudolf Aebersold is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. He was one of the founders of the Institute for Systems Biology in Seattle, Washington, United States where he previously had a research group.
RRP12-like protein is a protein that in humans is encoded by the RRP12 gene. It is currently thought to be involved in ribosome assembly of the precursor particles of both subunits in eukaryotes and was identified as a RNA binding protein.
Putative RNA-binding protein 3 is a protein that in humans is encoded by the RBM3 gene.
High throughput biology is the use of automation equipment with classical cell biology techniques to address biological questions that are otherwise unattainable using conventional methods. It may incorporate techniques from optics, chemistry, biology or image analysis to permit rapid, highly parallel research into how cells function, interact with each other and how pathogens exploit them in disease.
Marc R. Wilkins is an Australian scientist who is credited with the defining the concept of the proteome. Wilkins is a Professor in the School of Biotechnology and Biomolecular Sciences at the University of New South Wales, Sydney.
Edward S. Boyden is an American neuroscientist and entrepreneur at MIT. He is the Y. Eva Tan Professor in Neurotechnology, and a full member of the McGovern Institute for Brain Research. He is recognized for his work on optogenetics and expansion microscopy. Boyden joined the MIT faculty in 2007, and continues to develop new optogenetic tools as well as other technologies for the manipulation and analysis of brain structure and activity. He received the 2015 Breakthrough Prize in Life Sciences.
The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.
The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. In June 2023, version 23 was launched where a new Interaction section was introduced containing human protein-protein interaction networks for more than 11,000 genes that will add new aspects in terms of protein function.
In cell biology, single-cell analysis and subcellular analysis refer to the study of genomics, transcriptomics, proteomics, metabolomics, and cell–cell interactions at the level of an individual cell, as opposed to more conventional methods which study bulk populations of many cells.
The secretome is the set of proteins expressed by an organism and secreted into the extracellular space. In humans, this subset of the proteome encompasses 13-20% of all proteins, including cytokines, growth factors, extracellular matrix proteins and regulators, and shed receptors. The secretome of a specific tissue can be measured by mass spectrometry and its analysis constitutes a type of proteomics known as secretomics.
An imaging cycler microscope (ICM) is a fully automated (epi) fluorescence microscope which overcomes the spectral resolution limit resulting in parameter- and dimension-unlimited fluorescence imaging. The principle and robotic device was described by Walter Schubert in 1997 and has been further developed with his co-workers within the human toponome project. The ICM runs robotically controlled repetitive incubation-imaging-bleaching cycles with dye-conjugated probe libraries recognizing target structures in situ (biomolecules in fixed cells or tissue sections). This results in the transmission of a randomly large number of distinct biological informations by re-using the same fluorescence channel after bleaching for the transmission of another biological information using the same dye which is conjugated to another specific probe, a.s.o. Thereby noise-reduced quasi-multichannel fluorescence images with reproducible physical, geometrical, and biophysical stabilities are generated. The resulting power of combinatorial molecular discrimination (PCMD) per data point is given by 65,536k, where 65,536 is the number of grey value levels (output of a 16-bit CCD camera), and k is the number of co-mapped biomolecules and/or subdomains per biomolecule(s). High PCMD has been shown for k = 100, and in principle can be expanded for much higher numbers of k. In contrast to traditional multichannel–few-parameter fluorescence microscopy (panel a in the figure) high PCMDs in an ICM lead to high functional and spatial resolution (panel b in the figure). Systematic ICM analysis of biological systems reveals the supramolecular segregation law that describes the principle of order of large, hierarchically organized biomolecular networks in situ (toponome). The ICM is the core technology for the systematic mapping of the complete protein network code in tissues (human toponome project). The original ICM method includes any modification of the bleaching step. Corresponding modifications have been reported for antibody retrieval and chemical dye-quenching debated recently. The Toponome Imaging Systems (TIS) and multi-epitope-ligand cartographs (MELC) represent different stages of the ICM technological development. Imaging cycler microscopy received the American ISAC best paper award in 2008 for the three symbol code of organized proteomes.
CXorf66 also known as Chromosome X Open Reading Frame 66, is a 361aa protein in humans that is encoded by the CXorf66 gene. The protein encoded is predicted to be a type 1 transmembrane protein; however, its exact function is currently unknown.
The human interactome is the set of protein–protein interactions that occur in human cells. The sequencing of reference genomes, in particular the Human Genome Project, has revolutionized human genetics, molecular biology, and clinical medicine. Genome-wide association study results have led to the association of genes with most Mendelian disorders, and over 140 000 germline mutations have been associated with at least one genetic disease. However, it became apparent that inherent to these studies is an emphasis on clinical outcome rather than a comprehensive understanding of human disease; indeed to date the most significant contributions of GWAS have been restricted to the “low-hanging fruit” of direct single mutation disorders, prompting a systems biology approach to genomic analysis. The connection between genotype and phenotype remain elusive, especially in the context of multigenic complex traits and cancer. To assign functional context to genotypic changes, much of recent research efforts have been devoted to the mapping of the networks formed by interactions of cellular and genetic components in humans, as well as how these networks are altered by genetic and somatic disease.
Mathias Uhlén is a Swedish scientist and Professor of Microbiology at Royal Institute of Technology (KTH), Stockholm. After a post-doc period at the EMBL in Heidelberg, Germany, he became professor in microbiology at KTH in 1988. His research is focused on protein science, antibody engineering and precision medicine and range from basic research in human and microbial biology to more applied research, including clinical applications. He is member of several academies and societies, including Royal Swedish Academy of Science (KVA), National Academy of Engineering (NAE) and the Swedish Academy of Engineering Science (IVA). Dr Uhlen was the Founding Director of the national infrastructure Science for Life Laboratory (SciLifeLab) from 2010 to 2015.
Paola Picotti is an Italian biochemist who is Professor for Molecular Systems Biology at ETH Zürich. She is Deputy Head of the Institute for Molecular Systems Biology. Her research investigates how the conformational changes of proteins impact molecular networks with cells. She received numerous awarded awards, among which the 2019 EMBO Gold Medal.
Kathryn S Lilley is a professor of biochemistry at the University of Cambridge, director of the Cambridge Center for Proteomics, and an elected member of the European Molecular Biology Organization (EMBO).
Ilaria Testa is an Italian-born scientist who is a Professor at the Department of Applied Physics at the School of Engineering Science at the KTH Royal Institute of Technology. She has made major contributions to advanced microscopy, particularly superresolution microscopy.
References
- ↑ "Emma Lundberg". SciLifeLab. Retrieved 2022-03-13.
- ↑ "Mapping of cells and proteins improved with help of gamers and AI". KTH. Retrieved 2022-03-13.
- ↑ Armitage, Hanae (2018-08-22). "Massive online space game refines protein localization". Scope. Retrieved 2022-03-13.
- ↑ Vogt, Nina (October 2018). "Raising the game in image classification". Nature Methods. 15 (10): 759. doi:10.1038/s41592-018-0162-4. ISSN 1548-7105. PMID 30275575. S2CID 205573216.
- ↑ "Lundberg Lab". cellprofiling.org. Retrieved 2022-03-13.
- 1 2 3 Lundberg, Emma; Communications, Corporate (2022-01-10). "Applying AI and Machine Learning in Microscopy and Image Analysis".
{{cite journal}}: Cite journal requires|journal=(help) - ↑ "We might not know half of what's in our cells, new AI technique reveals". ScienceDaily. Retrieved 2022-03-13.
- ↑ Philippidis, Alex (2018-05-21). "Top 10 Under 40". GEN - Genetic Engineering and Biotechnology News. Retrieved 2022-03-13.
- ↑ "Latest RMS Scientific Achievement Award winners announced". Wiley Analytical Science. Retrieved 2022-03-13.
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