The 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.
Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
The plastid is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cyanobacteria. Examples include chloroplasts, chromoplasts, and leucoplasts.
Thylakoids are membrane-bound compartments inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as grana. Grana are connected by intergranal or stromal thylakoids, which join granum stacks together as a single functional compartment.
Glufosinate is a naturally occurring broad-spectrum herbicide produced by several species of Streptomyces soil bacteria. Glufosinate is a non-selective, contact herbicide, with some systemic action. Plants may also metabolize bialaphos and phosalacine, other naturally occurring herbicides, directly into glufosinate. The compound irreversibly inhibits glutamine synthetase, an enzyme necessary for the production of glutamine and for ammonia detoxification, giving it antibacterial, antifungal and herbicidal properties. Application of glufosinate to plants leads to reduced glutamine and elevated ammonia levels in tissues, halting photosynthesis and resulting in plant death.
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families.
Fenoxycarb is a carbamate insect growth regulator. It has a low toxicity for bees, birds, and humans, but is toxic to fish. The oral LD50 for rats is greater than 16,800 milligrams per kilogram (0.269 oz/lb).
Acephate is an organophosphate foliar and soil insecticide of moderate persistence with residual systemic activity of about 10–15 days at the recommended use rate. It is used primarily for control of aphids, including resistant species, in vegetables and in horticulture. It also controls leaf miners, caterpillars, sawflies, thrips, and spider mites in the previously stated crops as well as turf, and forestry. By direct application to mounds, it is effective in destroying imported fire ants.
60S ribosomal protein L28 is a protein that in humans is encoded by the RPL28 gene.
BIOBASE is an international bioinformatics company headquartered in Wolfenbüttel, Germany. The company focuses on the generation, maintenance, and licensing of databases in the field of molecular biology, and their related software platforms.
Interleukin 34 (IL-34) is a protein belonging to a group of cytokines called interleukins. It was originally identified in humans, by large scale screening of secreted proteins; chimpanzee, murine, rat and chicken interleukin 34 orthologs have also been found. The protein is composed of 241 amino acids, 39 kilodaltons in mass, and forms homodimers. IL-34 increases growth or survival of immune cells known as monocytes; it elicits its activity by binding the Colony stimulating factor 1 receptor.
Fluvalinate is a synthetic pyrethroid chemical compound contained as an active agent in the products Apistan, Klartan, and Minadox, that is an acaricide, commonly used to control Varroa mites in honey bee colonies, infestations that constitute a significant disease of such insects.
Oryzalin is an herbicide of the dinitroaniline class. It acts through the disruption (depolymerization) of microtubules, thus blocking anisotropic growth of plant cells. It can also be used to induce polyploidy in plants as an alternative to colchicine.
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).
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.
SWISS-MODEL is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. Homology modelling methods make use of experimental protein structures ("templates") to build models for evolutionary related proteins ("targets").
Oxydemeton-methyl is an organothiophosphate insecticide. It is primarily used to control aphids, mites, and thrips.
The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). This replaces and expands upon the original 2009 IUPHAR Database. The Guide to PHARMACOLOGY aims to provide a concise overview of all pharmacological targets, accessible to all members of the scientific and clinical communities and the interested public, with links to details on a selected set of targets. The information featured includes pharmacological data, target, and gene nomenclature, as well as curated chemical information for ligands. Overviews and commentaries on each target family are included, with links to key references.
