BioCurious Glossary of Terms:

If you encounter a term you find unfamiliar, please list it here. If there is a term you learn about, define it here, if possible, in your own words using facts.

 

A

Abcam: An English biotech company with an SF office selling primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.

 

Ag-staining: a sensitive way to detect small amounts of proteins in cells and other macromolecules using silver; it is 50X more sensitive than Coomassie Brilliant Blue staining.

 

Alfalfa: Medicago Sativa; a small flowering perennial often used in hay bales for feeding livestock. 

 

Anderson Lab: 327 Stanley Hall in the Department of Bioengineering at UC Berkeley; a synthetic biology lab helmed by J. Christopher Anderson. 

 

Antibodies: Also known as immunoglobulins, these are a class of proteins generated by B(one marrow) lymphocytes (white blood cells) that bind to proteins and other molecules that are foreign to the organism. Most vertebrate species generate antibodies, which contribute to humoral immunity. 

 

Antigen: Any substance that generates an immune response stimulating the production of antigens.

 

API: Application Programming Interface. Allows software to communicate with other software...people keep talking about API at BioCurious! (Anitha)

 

Arabinose: a five-carbon monosaccharide found in gum arabic; frquently used in media to grow bacteria. 

 

AraC: 

 

Arabidopsis thaliana:

 

Astaxanthin:

 

Astrobiology:

 

Auxin: plant hormone

 

B

BioBricks:  standard biological parts that are DNA sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems. 

 

BioFab: now-defunct company

 

BioSteel:  a trademark name for a high-strength based fiber material made of the recombinant spider silk-like protein extracted from the milk of transgenic goats, made by Nexia Biotechnologies. 

 

C

cDNA (Library): complementary DNA is DNA synthesized from a messenger RNA (mRNA) template in a reaction catalyzed by reverse transcriptase and  DNA polymerase. cDNA is often used to clone eukaryotic genes in prokaryotes, as prokaryotes lack the equipment to remove introns from transcribed DNA.

 

cDNA library: A pool of complementary DNA clones produced by cDNA cloning of total messenger RNA from a single source (cell type, tissue, embryo), the libraries lack information about enhancers, introns, and other regulatory elements found in a genomic DNA library. 

 

CFP: Cyan Fluorescent Protein

 

Cis-element or Cis Regulatory Element: RNA or DNA controlling expression of a gene on the same chromosome.

 

Codon Optimization:

 

C. elegans:

 

Coomassie-staining:

 

CRISPR: stands for clustered, regularly interspaced, short palindromic repeats. They silence foreign nucleic acids in bacteria.

 

D

Danio Rerio: Zebrafish; a popular model organism to study regenerative medicine

 

Decontamination

 

DNA ladder:

 

Drosophila melanogaster:

 

Dyad Symmetry: two sections of a DNA strand having sequences that are inverted repeats of each other; i.e. 5'...GAGTAC...CTG...GTCTTC...3'

 

 

E

ELISA:

 

Endy Lab: Headed by Drew Endy,...

 

Epitope:

 

Exon:

 

Exon Skipping:

 

F

 

 

G

Gel Green:

 

Gel Red:

 

GFP: green fluorescent protein is a protein composed of 238 amino acid residues (26.9kDa) that exhibits bright green fluorescence when exposed to light in the blue to ultravioletrange.^[1][2]Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the jellyfish Aequorea victoria. 

 

 

George Church:

 

 

Gibson Assembly:

 

 

Golden Braid Assembly:

 

 

Golden Gate Assembly:

 

Good Lab Practices (GLP):

 

Graphene: Pure carbon, but one atom thick, graphene is said to be the strongest material ever. It is difficult to synthesize much of, but carries potential in biofuel and rapid, inexpensive electronic DNA sequencing applications.

 

H

 

I

IDT: Integrated DNA Technologies

 

Immunocytochemistry(ICC) /Immunohistochemistry(IHC) :

 

Immunofluorescence:

 

Immunoglobulin: Antibodies! There are several types:

 

     IgA looks like this >=<. It is a dimer, which means it is composed of two subunits linked together. The v-shaped ends each bind to two anitgens. IgA can be      found in mucosa, or tissues lining the digestive system, respiratory system, and the genitourinary tract. It is also secreted into tears, saliva, and breast milk.

 

     IgD is a monomer, and looks like this >=. It is composed of a single subunit. IgD is not as well understood as the other immunoglobulins. It is found on the      surface of B cells embedded in the plasma membrane. Here, it is thought to act as a receptor-when it binds an antigen, it activates the B cell and makes it      produce more antibodies similar in shape to the receptor/IgD. IgD also seems to bind with and activate basophils and mast cells, causing them to release      antimicrobial agents.

 

     IgE is also a monomer. It is exclusively found in mammals, and protects against certain parasitic worms. It also plays a role in type 1 hypersensitivity (most      allergies). Allergens bind to T-helper cells, which results in their activation of B-cells and the production of IgE. IgE then binds to Fc receptors on mast cells.      These receptors bind to part of the "base" of the "Y," the Fc region, of IgE. When these Fc receptor-IgE complexes bind to the same allergen, the mast cell is      activated, releasing histamines and cytokines that result in the inflammatory response we associate with allergies, asthma, and other related conditions.      (Medicines like Benadryl bind to histamines, blocking their action.) 

 

     IgG is the main type of antibody found in blood and extra-cellular fluid (ECF). IgG is important in the secondary immune response--basically, its the antibody        that confers highly specific immunity to people who have been vaccinated against or exposed to a certain strain of pathogen. IgG is in breast milk, and is the      only antibody that can cross the placenta, making it and IgA important antibodies for neonates, who get their humoral immunity from their mothers. It is a      monomer.

 

     IgM is a pentameric immunoglobulin that is important in the early phases of an infection. It is very effective at activating the complement system (its      complicated, but if antibodies are the heat-seeking missiles of the immune system, complement would be the proximity mines.) Complement   

 

 

Immunostaining:

 

Invitrogen:

 

J

JBEI: Joint BioEnergy Institute in Emeryville - one of three national labs working towards using synthetic biology to develop and improve biofuels. 

 

K

Keasling Lab:

 

L

LCMS: Liquid Chromatography/Mass Spectrometry. This device uses high performance liquid chromatography (HPLC) to separate out the component parts of a solution, and then measures their atomic weight by mass spectrometry. A highly sensitive technique for detecting small-to-midsize organic molecules in solution.

 

Lygos:

 

M

MasterMix:

 

Mini Prep:

 

Monoclonal vs Polyclonal:

 

Mycobacterium avium: Found in showerhead biofilm in high concentrations, especially plastic ones.

 

N

NEB: New England BioLabs (http://www.neb.com/nebecomm/default.asp) NEB is a popular reagent producer and supplier. Additionally, it offers the largest supply of recombinant and native enzymes. NEB has two environmentally-oriented nonprofit foundations. 

 

Next Generation Sequencing (NGS):

 

Nickel Column:

 

Northern Blot:

 

O

Oligos: The prefix "oligo" roughly means more than two, but not all that many (less than "poly"). In the context of genetics, "oligos" usually refers to single stranded molecules of DNA that are short enough to be chemically synthesized without undue effort or expense. Often used in PCR.

 

Origin of Replication:

 

P

Patent:

 

PCR: Polymerase Chain Reaction. A method for creating huge numbers of copies of a DNA sequence. Requires short DNA "primers" and a DNA polymerase. A good basic introduction is here: http://www.youtube.com/watch?v=2KoLnIwoZKU

 

Phytochrome:

 

Plasmid: A circular piece of double-stranded, non-genomic DNA often incorporated in bacteria via transformation. 

 

Promoter:  the region of DNA "upstream" of a gene, that determines where, when, and how much the gene is turned on.

 

Pyrocystis: Lunula, Fusiformis, etc. A genus of dinoflagellates...

 

Q

 

R

RBS (Ribosome-Binding Site):

 

Recombineering:

 

Repressor:

 

Restriction Enzyme:

 

RFP: Red Fluorescent Protein

 

RNA interference (RNAi):

 

RuBisCO: Ribulose-1,5-bisphosphate carboxylase oxygenase; the most common protein in the world, RuBisCO is an enzyme that catalyzes carbon fixation, helping convert carbon dioxide into sugar. 

 

S

Sanger Sequencing:

 

SCOBY: Symbiotic Colony of Bacteria and Yeast. 

 

SEM: Scanning Electron Microscopy

 

Site-specific Mutagenesis:

 

Southern Blot:

 

Sterilization:

 

 

T

TEM:

 

TALENs:

 

Touchdown PCR: This type of PCR makes use of primers that don't bind nonspecific sequences. By using primers with a higher melting point, more specific base pairing occurs between the template and the primer. After each cycle, the annealing temperature is decreased, as the correct binding arrangement is likely being amplified.

 

Trademark:

 

Transcription factor:

 

Trichomes: Epidermal outgrowths like hairs or papillae found on plants and protists. 

 

U

 

V

Vibrio fischeri:

 

W

Western Blot:

 

Winogradsky Column:

 

X

X-gal: aka BCIG (5-bromo-4-chloro-indolyl-β-D-galactopyranoside); used to test for prescence of the enzyme β-galactosidase in a blue/white screening. The enzyme and X-gal interact, forming galactose and 5-bromo-4-chloro-3-hydroxyindole. 5-bromo-4-chloro-3-hydroxyindole then dimerizes, oxidizing into a bright blue insoluble product. The end. 

 

Y

Y Combinator: A venture capital LLC headquartered in Mountain View, California funding startups like Dropbox and reddit. In computer science, a program that runs programs.

 

Z

Zinc Fingers: