Team:Edinburgh/tech/Hints

Hover over words in bold italics to see explanation.

iGEM is the International Genetically Engineered Machine competition. Each year during (Northern hemispheric) summer, undergraduate-led teams from all over the world compete to produce biological devices with standard, reusable parts.

Bacteriophage are viruses that infect bacteria. They are the world's most numerous biological replicators, believed to outnumber bacteria 10 to 1.

A bioreactor (as defined by Edinburgh) is a microscopic system containing multiple enzymes that work together in synergy to catalyse some reaction.

Note though that others use the term to mean a large container in which biological processes occur.

Two or more enzymes act in synergy if their efficiency is increased in the presence of each other.

A flagellum is a long appendage that allows bacteria to swim. Not every species has them, and some have more than one per cell.

M13 is a filamentous (long tubular) virus that infects E. coli bacteria but does not kill them.

Cellulases are a group of enzymes that break down the common plant material cellulose, ultimately producing glucose sugar.

A biorefinery is any system that converts biomass into useful products.

A promoter is a DNA sequence causing the following sequence to be transcribed into RNA.

A ribosome binding site is a region of RNA where the ribosome binds to start translation into protein.

The pVIII protein is the major coat protein of M13, present in about 2,700 copies per phage.

A leader or signal peptide is a sequence of amino acids present at the start of a protein which instructs the cell to send it to some specific location.

A linker is a chain of amino acids used to connect two protein domains while giving them space to fold.

A fusion protein contains the amino acid sequences of two or more proteins, effectively joining them together.

Ice Nucleation Protein is a protein isolated from the plant pathogen Pseudomonas syringae. It is present on the outer membrane of the bacteria and causes the formation of ice crystals, which harms the plant, helping the bacteria attack it. However, we will use it as a carrier to get other proteins displayed on the cell surface.

malS is a gene coding for amylase, which breaks down starch into its component glucose sugars.

The pIII protein is a minor coat protein of M13, present in 5 copies at the end of the phage.

An oligonucleotide is a short piece of DNA or RNA. DNA oligonucleotides are often used as primers for PCR.

The Polymerase Chain Reaction is a method for amplifying a section of DNA, producing many copies with the same sequence.

Ligation Independent Cloning is a method of assembling DNA fragments into a plasmid, which does not involve a ligase enzyme. Instead, long overhangs of homologous DNA are used to join the fragments, and the transformed bacterium repairs the phosphate backbone.

The F plasmid is present in some bacteria, and contains genes coding for a sex pilus, which the plasmid uses to spread itself to other bacteria. The M13 phage requires the pilus to be present in order to infect E. coli.

A codon is a sequence of three DNA bases, coding for one amino acid in a protein. Since there are four types of base, there are 64 possible codons. Three of these are stop codons which terminate translation (protein production).

The amylase family of enzymes break down starch into its component glucose sugars.

A BioBrick is a reusable biological part, containing a DNA sequence. BioBricks are designed to be joined together to produce new (composite) BioBricks.

Pseudomonas syringae is a species of Gram-negative bacteria and a pathogen of several plant species.

Escherichia coli is a species of Gram-negative bacteria commonly found in the mammalian gut. Most strains are harmless or even beneficial (though this is not a good reason to consume them). They have been well-studied and are often used in genetic engineering.

Help! Help! We're being held prisoners in an iGEM laboratory! They make us do minipreps and agarose gels all day long!

The C terminal of a protein is one end of the protein chain. That part of the protein is coded for by the end of the relevant DNA sequence.

The N terminal of a protein is one end of the protein chain. That part of the protein is coded for by the start of the relevant DNA sequence.

Sorbitol is a naturally occuring derivative of glucose. It can be used as a sweetener.

High Fructose Corn Syrup is a syrup containing a high level of fructose, making it very sweet.

The metagenome is all of the genetic information contained in the environment.

Green Fluorescent Protein is a protein which emits green light if illuminated with a blue light. It is often used in genetic engineering as a reporter; i.e. to prove that a system is working.

Fitness is the ability of an organism to compete with other organisms and successfully reproduce. If an organism outcompetes other organisms it is said to have greater fitness. Such an organism will spread.

An algorithm is a method of computing some function. It consists of a finite number of steps which you need to follow, to get the desired result.

Examples: The annoying program inside a PCR machine, a flight checklist, or a pasta recipe.

Recombination is a natural process in which different pieces of DNA are joined together. Complex organisms use this process to combine the DNA of two parents during sex, while simpler organisms use it to repair damaged DNA by replacing it with an undamaged copy.

Cellulose is a tough plant material composed of chains of glucose sugar. Unlike starch (which is also a glucose chain) it is difficult to digest or degrade, so making usable sugar from it is hard.

Starch is an easily degradable chain of glucose sugars used by plants as a food store.

In evolution, a selection pressure exists when some external factor causes some members of a species to outcompete others, due to their having a genotype that is more suitable for the environment.

In genetics, synonymous codons are different 3-base sequences that code for the same amino acid. For example, CAA and CAG both code for glutamine. By using synonymous codons, different DNA sequences can code for the same protein.

Plasmids are small circular pieces of DNA which replicate independently of the main bacterial chromosome. They are relatively easy to manipulate and so are used in genetic engineering.

Artificial selection is the process where humans choose or influence which members of a species reproduce the most, thus altering the genetic makeup of the population.

RFC10 is the original BioBrick standard. It specifies how restriction sites are to be placed in flanking positions around the BioBrick. Most iGEM-related parts are made in this format.

Two sequences of DNA have homology if the same sequence is present in both of them. Homology-based assembly relies on using base-pairing to join two pieces of DNA which have homologous ends, the start of one piece matching the end of the other.

A frameshift mutation in a gene involves the addition or deletion of a non-multiple of three bases. Because triplets of bases (codons) code for amino acids, subsequent codons will be "out of frame" and will code for the wrong amino acids.

Synthetic biology is a broad range of disciplines, unified by the desire to take an engineering approach to biology. It is like genetic engineering, only more so.

A presbyterian church is one governed by elected elders. At the highest level, policy is decided by a general assembly of these elders.

Switchgrass (binomial name: Panicum virgatum) is a grass that can be grown on land that is unsuitable for normal crops, to produce high yields of cellulose.

Blue skies research is research with no immediate practical use foreseen, though such uses often turn up later.

The cytoplasm is the internal volume of a cell; essentially everything that is contained within the cell's membrane(s).

A stochastic system is non-deterministic, meaning that the future state of the system cannot be predicted from the previous state, i.e. there is some random element involved.

An agent-based system is composed of many agents. Agents can perform actions of a varying level of complexity. Often, representing a system as many agents lets the programmer model complex behaviour using simple rules.

The syntax of a (programming) language is the set of rules that result in working programs.

The Runge-Kutta methods are ways of generating an approximately correct solution to an ordinary differential equation.

A system is deterministic if future states of the system can be perfectly predicted from past states. Such a system does not incorporate any genuine randomness.

A program is computationally intractable if it is possible to compute its output, but it takes an awful lot of time - e.g. exponential on the length of input.

Adsorption is the process in which molecules bind to a surface.

Hydrolysis is a type of chemical reaction in which water molecules are split up into a proton (H⁺) and a hydroxide (OH⁻) during the process of breaking down some other substance.

To call some piece of knowledge empirical is to say that it is derived from data and evidence, rather than purely theoretical considerations.

Cellobiose is a type of sugar containing two molecules of glucose bonded together in a certain way. There are other such sugars, such as maltose.

The Michaelis-Menten equation is a relatively simple formula predicting the rate of an enzymatic reaction from the concentration of the substance upon which the enzyme acts.

In bacteria that have two membranes, the periplasm is the space between them.

Genes are said to be cryptic if they are present in the genome but cannot normally be activated.

Brownian motion is a type of motion where, at any time, a particle can move in any direction. It is also called a "random walk".

An assay is a test of some biological agent's presence or activity.

A process flow diagram is an engineering design tool used to show plant layout and connections between components.

The phrase in silico was coined to refer to the study of biological processes in computer models, as opposed to in vivo (in life) or in vitro (in a test tube).

Hemicellulose is a weak sugar-based polymer found in plants. There are many possible forms.

Lignin is a tough plant material quite resistant to degradation by enzymes, though some species of fungi and bacteria can slowly degrade it.

Fractionation is a separation technique whereby mixtures are divided into a number of smaller components.

Depolymerisation is the chemical reaction which results in a polymer chain being broken up into monomer units.

Crystallisation is a chemical technique that separates solids and liquids using mass transfer.

'Aqueous' means 'in a solution of water'.

Distillation is a technique for separating chemicals based on differences in boiling points.

Hydrous pyrolysis is a chemical engineering technique whereby organic compounds are heated to high temperature with water.

Ordinary differential equations (ODEs) are differential equations in which the dependent variable is a function of a single independent variable.

The computational complexity of an algorithm is the type of relationship between the length of input to the program and the number of operations it needs to perform. This is usually proportional to the program's runtime. For example, logarithmic computational complexity is good, whereas exponential is very, very bad.

The random seed is a number used to initialise a pseudorandom number generator. Initialising the same generator with a defined seed means that the generated numbers will be consistent between runs of a program.

An RNA sequence is polycistronic if it codes for more than one protein.