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Tuesday, June 27, 2006 By Any Other Name, Still... Rosa rugosa   ... a rose. Thanks to Mom our front and back yards have become a botanist's dream. You'd need a degree in Latin just to pronounce everything growing there. That would be Rosa rugosa pictured.      Master returned to the lab late tonight to stop his experiment on time. Actually, it's only the first part of an overall experiment that takes about six to seven days to complete, if everything goes well. What he's doing is a relatively routine protein separation using a 2D-Gel technique. Routine in the field of Proteomics anyway. Generally, a complex mixture of proteins can be separated (or focused) by their isoelectric value in one dimension, and then by molecular weight in a second dimension. But first, in order to be able to see a protein in the gel, all the proteins in the sample are first covalently labeled with a fluorophore. Different fluorophores will "glow" a distinct color when excited by a particular wavelength of laser light. Mixtures of protein from different samples (normal vs. tumor tissue, say) can be labeled with different fluorophores and run in the same gel. In this way, proteins from normal tissue will glow green, for instance, and those from the tumor sample red. In theory anyway.      Subsequent image analysis can then quantify the different expression (amount) of proteins common to both the normal and tumor samples. Proteins of interest can then be excised from the gel, trypsinized (i.e. cut into smaller pieces (peptides) by an enzyme), and then sequenced on a mass spectrometer. A bioinformatics search can then match the peptide to the parent protein, and Voila!, you've identified the protein on the gel. In theory anyway.     Once you know the proteins differentially expressed between samples, you might be able to tell a story about cell cycle regulation changes occurring in cancer, or better yet, identify biomarkers of the disease state. And a budding pharmacologist might even be sufficiently brazen to suggest novel pathways to target with therapeutics.      In the end you might be able to get a nifty paper or three published. And one could even write a PhD dissertation. And maybe even defend it! In theory anyway.      But we're getting ahead of ourselves.   9:27:58 PM    Comments disabled © Copyright 2008 Rufus. Nonsense, distribute widely and freely! Last update: 7/26/2008; 10:58:15 AM.			Readers Amused       Home About Me Airedale Philosophy How this all got started       FAQ What's an Upright? Upright: noun : a by and large bipedal companion, also referred to as a human being. What's a Cheechako? Cheechako: noun : a person new to Alaska who has come with the intention to live here. Who's Master? Master: pronoun : just the finest upright on the face of the earth, that's who! To read him is to love him. What's Dogdom? Dogdom: noun : Life's venue from a dog's point of view. What's a Sourdough? Sourdough: noun : A long time Alaskan who has an automatic suspicion of cheechakos. What does Outside mean? Outside: noun : A provincial reference to somplace other than Alaska; usually the lower 48. What's Breakup? Breakup: noun : A uniquely Alaskan season between winter and spring when the snow and ice begins to melt for good. Where is SquareBanks? SquareBanks: slang : A self-evident euphemism for a place widely known as Fairbanks, AK. Where can I read the Houston Trip? Houston Trip: vignette : Here What digital camera do you use? Camera: hardware : Canon Powershot A80 (4.0 MP) Who's Mom? Mom: Hottie : Have A Look What's a Squeakamunka? Squeakamunka: noun : your ordinary gray squirrel which can be seen everywhere in our Cleveland neighborhood! « Alaska Blogs »  Stories Fiction Boy Wonder Bat Girl Objects in Mirror Are Larger Than They Appear Used To Be Fish Skin Deep Essay Life Is Good Desert Nostalgia A Voice of Reason Fictional Four Realms of Darkness Poetry Lucky Chain  The Cycling Pages 1999 Canadian Tour 2000 Tour of Alaska "Yooper" : 2001 Tour of WI/Michigan UP 2001 Spine of Italy Tour 2002 Tour of New England 2004 Tour of New Zealand (coming soon!) 2005 Tour Of Nova Scotia Conways Game of Life (needs java plugin) Sometimes Interesting Billy Greg (Hiatus) Virginia Postrel Wendy McElroy Samizdata Atlantic Monthly Reason No Treason Slashdot Derke Lowe Heather Champ (Photo blog) T.C. Boyle Liquid Generation Improved Clinch Exquisite Corpse, A. Codrescu Fred On Everything Assymetrical Information The Daily Ablution (Hibernation) Lileks Frank Kelly (Hiatus) Up In Alaska