Team:Sheffield/glossary
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GLOSSARY |
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A
Aerobic Conditions
An environment that has free diatomic oxygen (O2)
Agarose gel electrophoresis
A technique used for separating DNA fragments according to their size by driving the molecules through a gel with an electric field.
Anaerobic Conditions
An environment that does not have free diatomic oxygen (O2)
Antibiotic Resistance
The ability of a bacterial strain to resist treatment with antibiotics
Antibiotics
Chemicals used to treat and prevent bacterial infection, by killing or limiting the growth of bacteria
Antibodies
Proteins produced by the immune system that specifically bind to certain antigens
Antigen
A foreign molecule that induces an immune response
B
Burkholderia cenocepacia (B. cenocepacia)
A species of bacteria commonly found in the environment. For the purposes of our project, we used a mutant strain that is deficient in siderophore uptake, but not siderophore production, in order to overproduce siderophores
C
Capillary action
The way in which liquid will travel up a narrow tube or an absorbent material such as paper due to its surface tension
Capillary stop valve
A particular microfluidics design where fluid is prevented from flowing into a bigger channel due to its surface tension until another fluid flows past the bigger channel
CFU
Colony Forming Units, a single viable cell forming a colony on an agar plate.
Chelator
A chemical species that binds with high affinity to metal ions (in this case iron)
Computer Aided Design (CAD)
Refers to the general activity and end product of designing components through a digital medium
D
Dcr-Hr
Bacterial hemerythrin domain originating from Desulphovibrio vulgaris
Deoxyribonucleic Acid (DNA)
The molecule used for information storage in all known living organisms
Diffusion
The movement of particles from a region of higher concentration to a region of lower concentration
Dimer
A macromolecule that consists of 2 identical molecules. E.g. the Fur protein exists in the E. coli cell as a dimer with 2 identical Fur subunits
Dissociation constant
The ratio of the equilibrium concentrations of unbound ligands to their bound complexes
Downregulate
A regulatory process wherein the cell to reduces the concentration of a certain cellular component
E
EDTA
A type of chelator that binds to iron
entC
A gene encoding for a protein involved in enterobactin synthesis pathway
Enterobactin
A specific type of siderophore which is produced by E. coli
Escherichia coli (E. coli)
A species of bacteria commonly used in molecular biology as a model organism
F
Fe2+/Fe3+
Charged forms of iron (iron ions)
Ferric Uptake Regulator (Fur)
A bacterial protein that regulates internal iron concentration, by repression of genes when bound to iron
Ferritin
A universal intracellular protein that stores and releases iron, to maintain iron homeostasis.
G
Gene
A region of DNA responsible for a phenotypic trait
Gram negative bacteria
A grouping of bacteria based upon it not responding to a gram stain. This group is often associated with having a thin cell wall and a second outer membrane
Gram positive bacteria
A grouping of bacteria based upon it responding to a gram stain. This group is often associated with having a thick cell wall
Green Fluorescent Protein (GFP)
A protein that is able to fluoresce green upon excitation by a particular wavelength. This fold very readily in many different organisms, so it is often used as a reporter protein
H
Hemerythrin (Hr)
A protein used for oxygen transport in bacteria and marine invertebrates that binds to iron and oxygen, this produces a colour change
Homeostasis
The ability of the cell or organism to regulate its own conditions to a particular equilibrium
I
J
JC28
A mutant strain of E. coli deficient in siderophore production
K
L
Laminar flow
Describes liquid particles that travel in an orderly manner parallel to the channel length and in a single direction. The velocity of the liquid is well represented using known equations
Light Dependant Resistor (LDR)
Changes resistance through the component based on the light intensity it receives
Lipocalin-2 (LCN2)
Protein produced by vertebrates that bind to siderophores, inhibiting bacterial iron uptake mechanisms. Also known as Neutrophil Gelatinase-Associated Lipocalin (NGAL), Human Neutrophil Lipocalin (HNL) or Lipocalin
M
Mc-Hr
Bacterial hemerythrin domain originating from Methylococcus capsulatus
Messenger RNA (mRNA)
RNA that is transcribed from DNA, that codes for the production of a protein
Microfluidics
The flow and mixing of microlitre volumes of fluids via capillary action, where the fluids are contained within a chip with wells and channels made of glass and polydimethylsiloxane (PDMS)
Mutant
A strain, gene, or characteristic that is distinct from the typical “wild type”
N
O
OD600
The optical density of a sample, which is indicative of the concentration of cells. This is determined by measuring absorbance at 600 nm using a spectrophotometer
P
Periplasm
The matrix in between the inner and outer membranes in gram negative bacteria
Plasmid
A piece of bacterial DNA which is separate from the chromosomal DNA, that can be transferred between bacteria by conjugation
Polydimethylsiloxane (PDMS)
The material that a microfluidics channel is made out of
Polymerase Chain Reaction (PCR)
A technique used to amplify DNA, utilising primers complementary in sequence at either end of the region that is amplified
Primer
A short strand of DNA that serves as a starting point for DNA synthesis during a polymerase chain reaction. This is needed as DNA polymerase cannot attach to single stranded DNA
Protein
Polymers of amino acids responsible for performing a function within an organism
Pseudo steady-state approximation
When one reaction happens at the much faster timescale than the other reactions, it can be assumed that this reaction has reached equilibrium and thus, its concentration remains constant
Q
R
Rate constant
The rate of a chemical reaction, which is dependent on the concentrations of the reactants
Reactive Oxygen Species (ROS)
Chemically reactive chemicals that contain oxygen, produced as a by-product from many biological reactions. These are able to damage DNA by reacting with the nucleotides, causing mutations
Red Fluorescent Protein(RFP)/mCherry
Proteins that are able to fluoresce red upon excitation with a particular wavelength
Restriction Digest
The act of cutting DNA into smaller pieces using restriction enzymes. Products can be run on an agarose gel to check for plasmid insertions of the correct size
Restriction Enzyme/Restriction Endonuclease
Enzymes that are able to cleave DNA sequences at or near a specific DNA sequence
Reynolds number
A value quantifying whether a flow is laminar or turbulent
Ribonucleic Acid (RNA)
Molecules produced by the transcription of DNA that perform various functions
RNA interference (RNAi)
The process in which RNA inhibits protein production by binding to the mRNA of the gene forming double stranded RNA which induces degradation
RyhB
A small regulatory RNA (srRNA) which down-regulates transcripts associated with iron storage and use. Is negatively regulated by Fur
S
Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE)
A technique used for separating proteins according to their size by driving the molecules through a polyacrylamide gel with an electric field
Serum
Protein-rich fraction of the blood not including clotting factor, white or red blood cells
Siderophores
Small organic molecules produced by some bacteria and fungi capable of binding iron with extremely high affinity, these can then be taken up by the organism where they release their bound iron
Small Regulatory RNA (srRNA)
Small, non-coding, RNA molecules that inhibit the expression of specific genes, by preventing RNA translation
Superfolder GFP (sfGFP)
A form of green fluorescent protein that folds more readily
Superoxide Dismutase
An antioxidant enzyme that helps to reduce concentrations of reactive oxygen species
T
Td-Hr
Eukaryotic hemerythrin gene derived from Themiste dyscrita
tonB
Gene encoding for a protein involved in siderophore uptake in Gram negative bacteria
Top10
A wild-type strain of E.coli that has high transformation efficiency
Translation
The process whereby a peptide polymer is produced by a ribosome, using an mRNA sequence as a guide
Turbulent flow
Describes a type of liquid flow where the direction and speed at which each particle moves is unpredictable
U
5’ Untranslated Region (5’UTR)
A sequence found upstream of the initiation codon on mRNA that is not translated. It is often important in the regulation of translation
Upregulated
A regulatory process wherein the cell to increases the concentration of a certain cellular component
V
Viscosity
A quantity describing a fluid’s resistance to flow when a pressure is exerted on it. E.g. honey has a higher viscosity than water
W
W3110
A wild-type strain of E. coli which JC28 strain derives from
Western Blot
A molecular biology technique used for detecting specific proteins in a sample
Wild Type
Wild type - A strain, gene, or characteristic which prevails among individuals in natural conditions, as distinct from an atypical mutant type.
