Difference between revisions of "Team:Sheffield/glossary"

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                         <h1>Capillary stop valve</h1>
 
                         <h1>Capillary stop valve</h1>
 
                         <p>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</p>
 
                         <p>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</p>
 +
                        <h1>CFU</h1>
 +
                        <p>Colony Forming Units, a single viable cell forming a colony on an agar plate.</p>
 
                         <h1>Chelator</h1>
 
                         <h1>Chelator</h1>
 
                         <p>A chemical species that binds with high affinity to metal ions (in this case iron)</p>
 
                         <p>A chemical species that binds with high affinity to metal ions (in this case iron)</p>
 +
<h1>Cloning</h1>
 +
                        <p>A set of techniques used to insert recombinant DNA from a prokaryotic or eukaryotic source into a replicating vehicle such as a plasmids. Making numerous copies of a DNA fragment of interest.</p>
 
                         <h1>Computer Aided Design (CAD)</h1>
 
                         <h1>Computer Aided Design (CAD)</h1>
 
                         <p>Refers to the general activity and end product of designing components through a digital medium</p>
 
                         <p>Refers to the general activity and end product of designing components through a digital medium</p>
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                         <p>A type of chelator that binds to iron</p>
 
                         <p>A type of chelator that binds to iron</p>
 
                         <h1><i>entC</i></h1>
 
                         <h1><i>entC</i></h1>
−
                         <p>A gene encoding for a protein involved in enterobactin synthesis pathway</p>
+
                         <p>An <i>E. coli</i> gene coding for Isochorismate synthase, a key enzyme in the siderophore synthesis pathway. Knocked out in the JC28 mutant strain.</p>
 
                         <h1>Enterobactin</h1>
 
                         <h1>Enterobactin</h1>
 
                         <p>A specific type of siderophore which is produced by E. coli</p>
 
                         <p>A specific type of siderophore which is produced by E. coli</p>
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                         <h1>Ferric Uptake Regulator (Fur)</h1>
 
                         <h1>Ferric Uptake Regulator (Fur)</h1>
 
                         <p>A bacterial protein that regulates internal iron concentration, by repression of genes when bound to iron</p>
 
                         <p>A bacterial protein that regulates internal iron concentration, by repression of genes when bound to iron</p>
 +
<h1>Ferritin</h1>
 +
<p>A universal intracellular protein that stores and releases iron, to maintain iron homeostasis.</p>
 
</div>
 
</div>
 
<a name="G"></a>
 
<a name="G"></a>
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                         <h1>Gene</h1>
 
                         <h1>Gene</h1>
 
                         <p>A region of DNA responsible for a phenotypic trait</p>
 
                         <p>A region of DNA responsible for a phenotypic trait</p>
 +
                        <h1>GP</h1>
 +
                        <p>Abbreviation for general practitioner. A medical doctor that gives general treatment and diagnoses patients with more serious conditions by sending them to a hospital.</p>
 
                         <h1>Gram negative bacteria</h1>
 
                         <h1>Gram negative bacteria</h1>
 
                         <p>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</p>
 
                         <p>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</p>
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<div class="definition">
 
<div class="definition">
 
                         <h1>JC28</h1>
 
                         <h1>JC28</h1>
−
                         <p>A mutant strain of <i>E. coli</i> deficient in siderophore production</p>
+
                         <p>A mutant <i>E. coli</i> strain with the genotype: W3110 <i>∆fecABCDE ∆zupT ∆mntH ∆entC ∆feoABC</i>. Deficient in siderophore production. </p>
 
</div>
 
</div>
 
<a name="K"></a>
 
<a name="K"></a>
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                         <h1>Microfluidics</h1>
 
                         <h1>Microfluidics</h1>
 
                         <p>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)</p>
 
                         <p>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)</p>
 +
                        <h1>Mutant</h1>
 +
                        <p>A strain, gene, or characteristic that is distinct from the typical “wild type”</p>
 +
 
</div>
 
</div>
 
<a name="N"></a>
 
<a name="N"></a>
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                         <h1>Reactive Oxygen Species (ROS)</h1>
 
                         <h1>Reactive Oxygen Species (ROS)</h1>
 
                         <p>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</p>
 
                         <p>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</p>
 +
<h1>Reduction</h1>
 +
<p>A chemical reaction in which a species gains electrons. For example the reduction of iron(III) to iron(II).</p>
 
                         <h1>Red Fluorescent Protein(RFP)/mCherry</h1>
 
                         <h1>Red Fluorescent Protein(RFP)/mCherry</h1>
 
                         <p>Proteins that are able to fluoresce red upon excitation with a particular wavelength</p>
 
                         <p>Proteins that are able to fluoresce red upon excitation with a particular wavelength</p>
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<div class="letter-heading"><h1>S</h1></div>
 
<div class="letter-heading"><h1>S</h1></div>
 
<div class="definition">
 
<div class="definition">
 +
                        <h1>Stakeholder</h1>
 +
                        <p>A person with an interest or concern in something, especially a business</p>
 
                         <h1>Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE)</h1>
 
                         <h1>Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE)</h1>
 
                         <p>A technique used for separating proteins according to their size by driving the molecules through a polyacrylamide gel with an electric field</p>
 
                         <p>A technique used for separating proteins according to their size by driving the molecules through a polyacrylamide gel with an electric field</p>
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<div class="definition">
 
<div class="definition">
 
                         <h1>5’ Untranslated Region (5’UTR)</h1>
 
                         <h1>5’ Untranslated Region (5’UTR)</h1>
−
                         <p1>A sequence found upstream of the initiation codon on mRNA that is not translated. It is often important in the regulation of translation</p>
+
                         <p>A sequence found upstream of the initiation codon on mRNA that is not translated. It is often important in the regulation of translation</p>
 
                         <h1>Upregulated</h1>
 
                         <h1>Upregulated</h1>
 
                         <p>A regulatory process wherein the cell to increases the concentration of a certain cellular component</p>
 
                         <p>A regulatory process wherein the cell to increases the concentration of a certain cellular component</p>
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<div class="definition">
 
                         <h1>W3110</h1>
 
                         <h1>W3110</h1>
−
                         <p>A wild-type strain of <i>E. coli</i> which JC28 strain derives from</p>
+
                         <p>A common lab strain of <i>E. coli</i> K12, the wild type which JC28 strain derives from.</p>
 
                         <h1>Western Blot</h1>
 
                         <h1>Western Blot</h1>
 
                         <p>A molecular biology technique used for detecting specific proteins in a sample</p>
 
                         <p>A molecular biology technique used for detecting specific proteins in a sample</p>
 
</div>
 
</div>
 +
                        <h1>Wild Type</h1>
 +
                        <p>Wild type - A strain, gene, or characteristic which prevails among individuals in natural conditions, as distinct from an atypical mutant type.</p>
 +
 
<a name="X"></a>
 
<a name="X"></a>
 
<div class="letter-heading"><h1>X</h1></div>
 
<div class="letter-heading"><h1>X</h1></div>
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     <!-- Bootstrap core JavaScript
 
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Latest revision as of 09:48, 19 October 2016

A template page

GLOSSARY
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z

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)

Cloning

A set of techniques used to insert recombinant DNA from a prokaryotic or eukaryotic source into a replicating vehicle such as a plasmids. Making numerous copies of a DNA fragment of interest.

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

An E. coli gene coding for Isochorismate synthase, a key enzyme in the siderophore synthesis pathway. Knocked out in the JC28 mutant strain.

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

GP

Abbreviation for general practitioner. A medical doctor that gives general treatment and diagnoses patients with more serious conditions by sending them to a hospital.

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 E. coli strain with the genotype: W3110 ∆fecABCDE ∆zupT ∆mntH ∆entC ∆feoABC. 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

Reduction

A chemical reaction in which a species gains electrons. For example the reduction of iron(III) to iron(II).

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

Stakeholder

A person with an interest or concern in something, especially a business

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 common lab strain of E. coli K12, the wild type 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.

X

Y

Z