Team:Oxford/Chemicals
Chemicals
Sodium Fluorescein
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- Not a hazardous substance
Use in our project
Sodium Fluorescein was a very useful chemical in our project for several aspects; the interlab study and in relation to the beads.
Its main use was during the creation of a fluorescence calibration curve in the interlab study and also for detecting diffusion out of the beads.
After diffusion of sodium fluorescein out of the beads was trialled experimentally, we fitted a diffusion model to our data.
Facts
- Fluorescein gets its name from the intense green fluorescence it gives in alkaline solutions, visible even at dilutions of 1 in 50,000,000!
- It is used in optometry to reveal damaged areas of the cornea, as well as in the diagnosis of several important eye conditions including “dry eye”. The eye shown below is normal and healthy.
- Synthetic biologists and microbiologists use it to stain cells and cell structures under the microscope - such as the cell cytoskeleton marked out in bright green in the picture below!
- Fluorescein can be used to fight crime - investigators spray a watery fluorescein mist over a crime scene to reveal bloodstains that might have been cleaned away by the perpetrator.
- During World War II, German aircrews carried small containers of fluorescein with them into battle. If they were shot down and forced to parachute out of the plane, the fluorescein produced a vivid and highly conspicuous marking in the water that helped air-to-sea rescue teams find them.
- A more familiar and everyday use of fluorescein might be as the pigment in spirit levels, helping to make the air bubble more visible in contrast to the alcohols filling the tube.
Crystal Violet (aka Gentian Violet)
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- H302 - Harmful if swallowed
- H318 - Causes serious eye damage
- H350 - May cause cancer
- H410 - Very toxic to aquatic life with long lasting effects
- P201 - Obtain special instructions before use
- P273 - Avoid release to the environment
- P280 - Wear protective gloves/ eye protection/ face protection
- P305 + P351 + P338 - IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing
- P308 + P313 - If exposed or concerned: Get medical advice/ attention
- P501 -Dispose of contents/ container to an approved waste disposal plant
Use in our project
Crystal Violet was used in two different sections of our project.
It's first use was to stain the biofilms ready for the biofilm assays. It was also was used along side Sodium Fluorescence to aquire data for the diffusion rates out of the beads.
Facts
- It is most famous for its use in the Gram method of classifying bacteria - “Gram positive” = walls are stained purple, “Gram negative” = walls are not stained
- Used to develop fingerprints in forensics
- Crystal violet is a main component of black and navy inks for printers and ballpoint pens
- It can also be used as an antiseptic/antifungal in resource-limited settings, but has otherwise been superseded by other more modern antiseptics
Sodium Alginate
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
Not a hazardous substance
Use in our project
In combination with calcium chloride to form calcium alginate beads.
Facts
- Alginate (alginic acid or algin) is a polysaccharide found in the cell walls of brown algae (this includes most seaweeds)
- In its extracted form, it produces a gelatinous matrix that can hold 200 to 300 times its weight in water. This property helps seaweed remain buoyant
- It is used in the food industry as a flavorless additive for emulsification/making food more viscous (soups etc) and to make chunks out of fruit, cat food, and reformed ham
- Pioneering molecular gastronomers have started to use it more recently to trap small spheres of liquid in thin layers of jelly - including cocktail bubbles
- As a chelating agent it can also be used to pull radioactive heavy metal ions out of the body, and to immobilize enzymes
Calcium Chloride
Chemical Structure (chlorine is green, calcium is grey)
Control of Substances Hazardous to Health (COSHH) Assessment
- H319 - Causes serious eye irritation
- P305 + P351 + P338 - IF IN EYES: rinse cautiously for several minutes; remove contact lenses, if present and easy to do. Continue rinsing
Use in our project
As a component of M9 media, and in combination with sodium alginate to form the AlgiBeads
Facts
- Calcium chloride is highly soluble in water as well as being good at absorbing it; a property which makes it simultaneously a strong ice-melting salt and, ironically, a drying agent
- Because of its strong affinity for water (hygroscopy) it has to be stored in tightly closed containers
- It it also used to control dust on roads, as the thin film of water it attracts holds the dust in place
- It acts as a pH buffer in swimming pools, as well as controlling the water hardness.
- It is the firming agent for tofu!
Agarose
Control of Substances Hazardous to Health (COSHH) Assessment
- Not a hazardous substance
Use in our project
We made gels for electrophoresis by dissolving in TBE, for microscopy, and for making agar plates.
Facts
- Forms agar gel when combined with agaropectin
- This gel matrix is used in the lab to separate macromolecules such as DNA (via gel electrophoresis) and proteins (for purification)
- Depending on how the agarose gel is made, the properties can be adjusted to suit different purposes
- The only use for agarose outside of the lab is to produce agar tea; a rare oriental delicacy
Ethyl Acetate
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- H225 – Highly flammable liquid and vapour
- H319 – Causes serious eye irritation
- H336 – May cause drowsiness or dizziness
- P210 – Keep away from heat, hot surfaces, sparks, open flames and other ignition sources. No smoking
- P261 – Avoid breathing vapours.
- P305+P351+P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do so. Continue rinsing
Use in our project
Ethyl Acetate played a small but important role in our project, it was used to dissolve a petri dish in an attempt to create a coating for our beads...It was somewhat unsuccessful!
- It is the most common ester in wine, and is responsible for their fruity taste and smell
- It is used as an asphyxiant by insect collectors, which allows them to kill insects without physically damaging the specimen
- It is used industrially as a solvent - we used it to dissolve petri dishes to coat our bacterial beads!
Polystrene
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- Not a hazardous substance
Use in our project
As a candidate for the outer coating of our AlgiBeads, but unfortunately was unsuccessful.
- A synthetic polymer made by joining molecules of styrene (a liquid) together
- It is thermoplastic, meaning that if heated it can be freely molded but becomes rigid again after cooling
- It is one of the most widely used plastics, familiar to most in its foamed form but also present in trays, disposable cutlery, lids, and bottles
- It is infamously slow to biodegrade but sadly is not recycled due to how cheap and easy it is to produce more
Ethidium Bromide
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- H331 - Toxic if inhaled
- H341 - Suspected of causing genetic defects
- P261 - Avoid breathing dust/ fume/ gas/ mist/ vapour/ spray
- P281 - Use personal protective equipment as required
- P311 - Call a POISON CENTRE or doctor/ physician
Use in Our Project
Ethidium Bromide was one our biggest hazards in the lab, however it was one of our most useful chemicals. We used it to stain gels and visualise bands of DNA.
Without it Mabel, our Queen of molecular cloning would have had a much tougher time cutting out her bands of DNA.
Facts
- Ethidium bromide intercalates and binds between the layers of DNA helices
- It fluoresces orange under UV light, but this light is 20x as intense while it is bound to DNA - making it incredibly useful as a fluorescent tag for nucleic acids
- Its tight binding to DNA is also what makes it toxic, mutagenic and carcinogenic
- It can be used to treat trypanosome infections in cattle, but has fallen out of favor more recently due to a high incidence of resistance
Ampicillin
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- H315 - Causes skin irritation
- H317 - May cause an allergic skin reaction
- H319 - Causes serious eye irritation
- H334 - May cause allergy or asthma symptoms or breathing difficulties if inhaled
- H335 - May cause respiratory irritation
- P261 - Avoid breathing dust
- P280 - Wear protective gloves
- P305 + P351 + P338 - IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing
- P342 + P311 - If experiencing respiratory symptoms: Call a POISON CENTER or doctor/ physician
Use in Our Project
The use of the antibiotic ampicillin was vital in our project. It acted a selectable marker for transformed cells as those that haven't taken up the plasmid with the ampicillin resistance gene will not grow on ampicillin plates. Therefore we could ensure that the bacteria that was growing on our plate containted the plasmid that we wanted.
Facts
- It is an antibiotic used to treat several bacterial infections, including urinary tract infections, salmonella, and meningitis
- It is a variant of penicillin, and when it was first produced in 1961 it was the first penicillin therapy to show activity against gram negative bacteria
- Very cheap (a 10 treatment for a patient only costs $13) making it ideal for use in synthetic biology research
Chloramphenicol
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- H350 - May cause cancer
- P201 - Obtain special instructions before use
- P308 + P313 - IF exposed or concerned: Get medical advice/ attention
Use in Our Project
Chloramphenicol had the same role in our project as ampicillin, however some plasmids contained the Chl resistance gene rather than the Amp gene.
Facts
- An antibiotic that stops bacterial growth by preventing protein synthesis
- Outside of the lab it can be useful for the treatment of severe bacterial infections such as plague, cholera, and typhoid fever
- It is used sparingly due to its serious side effects - including suppression of blood cell production in the bone marrow, which can lead to death. Patients must be carefully monitored during treatment
Dimethyl Sulfoxide (DMSO)
Chemical Structure
Control of Substances Hazardous to Health (COSHH) Assessment
- Not a hazardous substance
Use in Our Project
DMSO was used in our war against the stubborn construcst that would just refuse to PCR. It was used as it prevents DNA secondary structure formation.
Facts
- Dimethyl sulfoxide (DMSO) is a solvent that has the useful property of being able to dissolve both polar and nonpolar compounds while still mixing well with other organic solvents and water
- DMSO can be used for drug delivery due to the fact that it passes through the skin very easily while carrying dissolved chemicals with it
- It is also used an an industrial solvent and a solvent for several chemical processes in chemistry labs
- It can be used as a cryoprotectant in cell media by reducing the freezing temperature of the medium
- Bizarrely, in many individuals it causes a garlic-like taste in the mouth after skin contact
Thiamine Hydrochloride
Control of Substances Hazardous to Health (COSHH) Assessment
- Not a hazardous substance
Use in Our Project
Thiamine hydrochloride had a small but useful role in our project as a part of M9 media which was used for a lot of interlab work and in relation to the beads. The tube of Thiamine must be kept wrapped in foil as it is unstable to light.
Facts
- Thiamine is more commonly know as Vitamin B
- It is an essential part of animal diets, since only bacteria, fungi, and plants can natively synthesise it
- Thiamine deficiency results in optic neuropathy and degeneration of the peripheral nervous and cardiovascular systems
Sodium Dodecyl Sulfate
Control of Substances Hazardous to Health (COSHH) Assessment
- H228 - Flammable as a solid
- H302 - Harmful if swallowed
- H332 - Harmful if inhaled
- H318 - Causes serious eye damage
- H335 - May cause respiratory irritation
- H412 - Harmful to aquatic life with long lasting effects
Use in our project
As a protein denaturant in SDS-PAGE
Facts
- Sodium dodecyl sulfate (SDS) is an organic detergent used to denature proteins, and therefore reduce inaccuracies in determination of molecular weight arising from folded protein shape
- SDS is also used in a variety of cleaning and hygiene products, often under the more familiar name of sodium lauryl sulfate
- It can be cheaply produced from coconut and palm oils
- It can act as a microbicide against some viruses, including HIV and Herpes simplex
- Also used as a shark repellent!