Phosphatase Glossary

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Molecular biology and biochemistry

Warburg effect

In oncology, the Warburg effect is the observation that most cancer cells predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol, rather than by a comparatively low rate of glycolysis followed by oxidation of pyruvate in mitochondria as in most normal cells. See Warburg effect wikipedia page.

Fructose-2,6-bisphosphate

A signal molecule that controls glycolysis and overall intracellular reactive oxygen species (ROS) levels. Also see wikipedia.

Phosphoinositides

Phosphorylated forms of phosphatidylinositol (PI) are called phosphoinositides and play important roles in lipid signaling, cell signaling and membrane trafficking. See wikipedia page for more.

3-phosphoglycerate

See glycolysis in wikipedia.

2-phosphoglycerate

See glycolysis in wikipedia.

Taxonomy

Holozoa
  • Metazoan
  • + unicellular Choanoflagellates (sequenced genomes include Monosiga brevicollis and Salpingoeca rosetta)
  • + the more basal clades Filasteria (e.g. Capsaspora owczarzaki and Ministeria vibrans)
  • + Ichthyosporea (fish parasites including Amoebidium parasiticum)

These unicellular holozoa (sometimes called Choanozoa, though this is most likely to be paraphyletic) have a large number of kinases and other genes that were previously thought to be animal-specific and so are of strong interest to understand the origins of animals. The closest major out-group of the holozoa are the fungi.

Metazoa

Metazoans are the same as animals, a group of multi-cellular eukaryotes. They are a subset of the holozoan, which includes a few unicellular groups such as choanoflagellates. Within the Metazoa, the earliest branching lineages are sponges (they may be monophyletic or polyphyletic), which have little tissue structure. Eumetazoan ("true metazoans") consist of all metazoans other than sponges.

Eumetazoa
Opisthokont

Opisthokonts include holozoa (animals + close relatives) and fungi and a few of their close relatives. Opisthokonts are a major clade within the Unikonts.

Ecdysozoa

Ecdysozoa is the clade of animals that include arthropods (including insects and crustaceans) and nematodes. There has been a long controversy as to whether insects are more closely related to vertebrates (the coelomate hypothesis) or to nematodes, but molecular data now largely favor the ecdysozoa.

Lophotrochozoa

Lophotrochozoa ("crest/wheel animals") are a major grouping of protostome animals. One example is Caribbean reef squid. The Lophotrochozoa comprise two groups, the trochozoans and the lophophorata. The exact relationships between the different phyla are not entirely certain.

Bioinformatics

SCOP

Structural Classification of Proteins is a database of protein structural relationships. There are two versions: SCOPe at Berkeley and SCOP2 at MRC, Cambridge, UK.

Pfam

The Pfam database is a large collection of protein domain families. Each family is represented by multiple sequence alignments and hidden Markov models (HMMs). Link.

Double-conserved synteny

A method to detect whole-genome duplication [1].

Genomicus

A synteny browser.

References

  1. Kellis M, Birren BW, and Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004 Apr 8;428(6983):617-24. DOI:10.1038/nature02424 | PubMed ID:15004568 | HubMed [Kellis04]