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Masterclass

6 July 2009

Things You Can’t See

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General Introduction

Welcome to the Masterclass – Things You Can’t See. This

information pack includes introductions to the people who will be working with you today, and summaries of the activities you will

participate in. It also contains important information about how to

keep safe during today’s activities.

Table of Contents

People involved 3

Safety and Responsibility 4

What is DNA? What does it look like? 8

Watching the Spread of Disease 9

An Introduction to Animal Parasites 10

Activated Porous Carbon for Separation and Gas storage 13

Further Information and Links 14

Timetable

Time Activity

11.00-11.15 Arrival/Housekeeping/Agenda

11.15-11.35 Mini lecture by Dr Aziz Aboobaker

11.40-12.40 Lab Session 1

12.45-1.15 Lunch and info on courses

1.20-1.40 Mini lecture by Prof John Brookfield

1.45-2.45 Lab Session 2

2.50-3.00 Q & A Session

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People involved Prof John Brookfield studied for a BA in Zoology at the University of Oxford before going on to work at University College Swansea, the

National Institute of Environmental Health Sciences in North Carolina, and the University of Leicester. He then moved to the University of Nottingham where he is Professor of Evolutionary Genetics. His

research looks at genome evolution with a focus on the evolution of DNA sequences which control development, and on the evolution of mobile

repetitive DNA sequences. Prof Brookfield is also Vice-President (External Affairs) for the Genetics Society and Appointed Fellow of the

Institute of Biology.

Dr Aziz Aboobaker studied for a BA in Natural Sciences at the University of Cambridge before going on to complete a PhD. He has

also worked as a scientist in Edinburgh, Berkeley (California), and Nottingham. He is an evolutionary developmental biologist studying the

genetic basis for the diversity of animal body plans, given that so many of the genes that control what animals look like seem to be the same.

He uses flat worms in his research to look at the role of micro RNAs during the evolution of developmental processes.

Dr Jess Tyson is a Senior Research Fellow in the Institute of Genetics. She works in the field of Human Genetics, in particular her work looks at

DNA variation and its consequence. To prepare for this, she completed A levels in Biology, Chemistry, Maths and General Studies, did a degree in

Biological and Biochemical Sciences and completed a PhD on the

Genetics of Deafness.

Emma Langford completed Art and Design AS and Geography,

Chemistry and Biology A-levels before studying a degree in Microbiology (BSc Hons.) at the University of Nottingham. This led her to study

environmental microbiology at PhD level with an aim to reducing heavy metal pollution around a disused mine.

Eric Masika is a PhD student in Chemistry working on synthesis of

zeolite materials to use as a hard template for the highly sought after high surface area and morphologically controlled carbon materials. This course was preceded by a BSc in Chemistry at JKUAT- Kenya and an

MSc Nanoscience at the University of Nottingham.

Job de Roij is a PhD student in evolutionary biology. During his undergraduate degree in Zoology at the University of Nottingham he

developed an interest in the study of parasites and how they interact with their hosts (the organisms they infect). After taking a gap year to

go travelling, he returned to Nottingham to start a PhD looking at how parasites influence the evolution of different populations of three-spined

stickleback fish.

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Safety and Responsibility

We want to make sure your visit to the University of Nottingham is as

safe and interesting as possible. Please read the notes below and, while on campus today, please ensure you follow all instructions from your

teachers and the researchers leading the activities.

Please be aware of where you and your belongings are at all times. In

every building you visit, you will be told where the nearest emergency exit is. If you hear an alarm, please make your way quickly and calmly

to the exit.

No bags or coats should be taken into laboratories. In laboratories, please do not touch any equipment unless you are specifically invited to

do so.

If at any point in the day you are injured, you must inform the researcher you are working with or another member of staff

immediately. Certified First Aiders will be available to help you.

Thank you very much. With your cooperation we can have a safe and productive day. A full risk assessment has been completed for today’s

activities. If you would like to see a copy, please ask.

Laboratory Safety

The laboratories are equipped and run so that with appropriate care,

you can work without risking the health and safety of yourself and others. Accidents are unexpected or undesirable events, but they are

avoidable with due care and attention.

You have a duty of care to work in a way that will not harm the health and safety of yourself and/or others.

All experimental procedures are assessed for risks, any necessary safety

measures put in place, and documentary evidence kept. All containers in the laboratory are labelled with their relevant hazards and any

equipment that may present a hazard or needs instruction before use will carry clear notices.

Ensure that you read any methods before and during the practical class, listen to instructions from staff and watch carefully any demonstrations

of experimental procedures.

REMEMBER: Any mishap with a chemical (or apparatus) MUST be reported to a member of staff IMMEDIATELY so that they can deal with

the problem and remove any hazards correctly.

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Safety is an integral part of good laboratory practice. Even LOW HAZARD chemicals may be hazardous if misused. Risks from hazardous

chemicals are minimised by handling them correctly.

HAZARDOUS chemicals require careful handling at all times because of one or more of the following characteristics:

(a) flammability (b) explosive nature

(c) toxic, hazardous, irritant, etc: with effects on or through the skin.

with effects on or through the respiratory tract. with effects on or through the eye.

with effects following ingestion. (d) reactive with water.

(e) reactive with air. (f) detrimental effect on the environment – especially to

aquatic life. Containers of hazardous chemicals carry a pictogram indicating

the type of danger.

Toxic Highly Flammable Explosive Biological

Hazard

Corrosive Harmful, Irritant Oxidising

Ensure that you know how to deal with any spillage BEFORE you embark on an experiment.

Do not ignore the warning signs displayed in the School. They are there

for your protection. The British and European standard safety signs are used:

Prohibitory Signs: e.g. “No Smoking”, are circular with a red border and crossbar over a black symbol on a white

background.

Warning Signs: e.g. “Caution, risk of ionising radiation”, are

triangular with a black border on a yellow background.

(Yellow with black border/text)

(Orange with black text)

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Mandatory Signs: e.g. “Eye Protection”, are circular on a blue background with symbols in white; used when there is

an obligation to wear safety equipment.

Emergency Signs: e.g. “Emergency Shower”, square or rectangular,

on a green background with symbols in white.

Fire doors must be kept closed at all times. Know where the fire-fighting, first-aid equipment, eye-wash and emergency showers are

situated.

Ensure that you know the location of fire exits.

In the event of a FIRE ALARM or an EMERGENCY EVACUATION of the laboratory, turn off all your equipment as you leave the laboratory and follow staff to the fire assembly point.

Working Safely in the Masterclass

Before commencing any operation in the laboratory give due care and

attention to how the procedure can be carried out without risk to yourself or fellow workers. If you are in doubt, consult a member of

staff before you start.

Risks from hazardous chemicals are minimised by handling them

correctly.

Check that the container has the correct chemical you require. Read the hazard information on the label before opening.

• Pour liquids carefully to avoid spillage and splashing.

• Containers should be opened with caution and away from the face. • Take care not to ingest or breathe in vapours or powders.

• Some containers should only be opened and the chemical used in a fume hood, especially for those likely to produce fumes or vapours.

• Handle any chemicals in the fume hood that the schedule advises. • Wear nitrile gloves when handling hazardous chemicals.

• Open wounds, e.g. cuts on hands, should be covered/protected. • Turn back over-long cuffs on clothes and laboratory coats to reduce

the chances of knocking over equipment or contaminating cuffs / sleeves.

• Do not put pens / fingers etc in mouths and do not eat or drink anything, including sweets or gum.

• Do not rub eyes / face with contaminated hands /nitrile gloves.

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• Risks are minimised by working tidily, cleanly and avoiding spillages. • All spillages must be wiped up immediately.

• Dispose of all products and surplus chemicals correctly. • IF IN DOUBT – ASK

• Wash hands at the end of your laboratory session.

Spillages / accidents / FIRST AID • Spillages / splashes on the skin should be rinsed off immediately with

plenty of cold running water, then washed with soap and warm water.

• Any splashes in the eye(s) should be washed out immediately with an eye wash bottle and / or with plenty of cold running water.

• All cuts and scrapes on hands should be rinsed with cold running water.

• Any burns should be held under cold running water for at least 10 minutes.

Seek advice from a member of staff if you have an accident or if you feel unwell. A trained first aider will give advice, ensure any injuries are

treated and that relevant documentation is completed.

Safe use of equipment

Glassware

• Do not use any glassware that has chips or cracks – hand it to a member of staff for disposal.

• Take care when rinsing out glassware for reuse or to send for

washing – if there are any chipped edges or cracks – hand to a member of staff – do not rinse out.

• In the event of breakages, do not pick up the pieces of glass. Ask a member of staff to sweep up the pieces with a brush and dustpan.

Sharps The glass Pasteur pipettes and microscope slides should be handled with

care and disposed of in the 1.5% Trigene containers provided.

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What is DNA? What does it look like? Jess Tyson

DNA is amazing. We have loads of the stuff. Inside almost every

cell in our body is a nucleus and inside each nucleus is about 2m of

DNA. Because the cell is very small, and because organisms have

many DNA molecules per cell, each DNA molecule must be tightly

packaged. This packaged form of the DNA is called a chromosome. DNA spends a lot of time in its chromosome form. But during cell

division, DNA unwinds so it can be copied and the copies transferred

to new cells. DNA also unwinds so that its instructions can be used to

make proteins and for other biological processes.

Before we can work on DNA in the

laboratory we need to be able to

extract it from whichever source,

(be it blood, buccal cells or tissue) that we have been given. DNA is

extracted from human cells for a

variety of reasons. With a pure

sample of DNA you can test a

newborn for a genetic disease for

example, or analyze forensic

evidence, or study a gene involved

in cancer.

Today, we will be extracting DNA,

but not from humans! Instead we will be using spinach and

strawberries as examples!

DNA extraction is typically the first step in a longer laboratory

process. Its an important part because DNA needs to be purified

away from proteins and other cellular contaminants. Once we’ve

extracted the DNA we will look at techniques to study DNA which are

used everyday in the research lab.

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Watching the Spread of Disease Emma Langford

Swine ‘flu H1N1 is a very high profile health issue today. With the

number of cases increasing daily it has recently been announced as a

pandemic (globally distributed human-human transmitted disease).

Another pandemic the world is suffering from today is HIV, initially

transmitted to humans from simians.

But a key part of coping with any disease – be it on a global scale or

an outbreak of food poisoning from a local food outlet – is tracking

the spread of the disease and finding the initial point of infection. In this activity we will be looking at how quickly a disease can spread

through poor hygiene, and how the initial point of infection can be

identified on a small scale. We will do this using fluorescent dyes to represent micro-organisms and ‘infecting’ one of you, then tracking

the spread of the ‘infection’ through the group. We will also use

microscopy and culturing techniques to look at how the micro-

organisms (in this case bacteria not viruses) can be identified to confirm a disease.

At the end of the activity we will discuss some of the factors that

make real life epidemiology (studying the spread of disease) more

challenging than our simulation.

For more information on the number of swine ‘flu cases across the

globe look at

http://gamapserver.who.int/h1n1/atlas.html?select=ZZZ&filter=filter

4,confirmed.

For more information about swine ‘flu and why it was declared a

pandemic, look at http://www.who.int/mediacentre/news/statements/2009/h1n1_pand

emic_phase6_20090611/en/index.html.

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An Introduction to Animal Parasites Job de Roij

Parasites are all around us. In fact, many biologists believe that they

make up over half of the total number of species on the planet. Every

animal species has at least one parasite species that infects it.

Parasites are organisms that live in or on another organism (the

host), obtaining from it part or all of its nutrients and causing some

degree of real damage to its host. Parasites include a range of

organisms, from microscopic viruses, fungi and bacteria to macroscopic worms and insects. The aim of today’s activity is to

introduce you to a range of parasites, by dissecting a three-spined

stickleback fish.

Three-spined stickleback fish are common in many areas of the

Northern Hemisphere such as North America and Europe. You often

find them in lakes, streams and rivers. However, they are originally a marine species. The main reason why they are interesting to study is

because since the last ice age, when sea levels changed dramatically,

they colonised many freshwater areas. As a result they have evolved

very rapidly into different body sizes and shapes, and are a great

example of natural selection in action. Below is a diagram that

captures just how diverse three-spined sticklebacks are:

A three-spined stickleback

Because they have evolved so much in terms of body size and body

shape, we think they may also have evolved differences in other

traits such as growth, how they reproduce and how well they resist

certain parasites. Sticklebacks are an important host for a number of

parasites, but the ones you will be coming across today are:

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Schistocephalus solidus

- A tapeworm that lives in the body cavity

- The worms can grow to be extremely large - heavy infections

may make up 50% of the total body weight of the fish! Can

you imagine something similar in human beings?

- Fortunately it doesn’t exist, but it’s easy to picture why being

infected with this parasite has serious consequences for the

fitness of the fish

- It has been shown to slow down growth of the fish as well as

making it virtually impossible for female fish to develop eggs

and reproduce

- They also change the behaviour of sticklebacks, making them

less able to escape predator attacks. This is very handy for the

parasite, as it needs to be eaten by stickleback-eating birds to

complete its life cycle

Schistocephalus solidus Diplostomum

spathaceum

Diplostomum spathaceum

- Belongs to a group of worms called flatworms

- It lives in a very abnormal place in the body: the lens of the

eye

- Evolutionary biologists think this evolved because it is safe

from any attack from the host immune system in the eye

- As with Schistocephalus, heavy infections can be very

damaging to the fish; in this case they may lead to blindness

- This makes them more prone to attack by bird predators,

which again is in the interest of the parasite, as it completes its

life cycle in birds as well

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Gyrodactylus spp.

- Belong to a class of flatworms called Monogenea

- They are ectoparasites (‘ecto’ = outside) that live on the gills,

skin and fins of fish

- Infections with certain Gyrodactylus species can lead to very

high mortality

- Biologists are interested in studying gyrodactylid parasites

because they have a very unusual way of reproducing: each

worm is born with a developed embryo inside it, which itself

contains a developing embryo – for this reason they are named

the ‘Russian Doll’ killers!

Gyrodactylus salaris

There are also some microscopes slides with samples of human

parasites. Don’t worry: these parasites are dead and not infective.

They have been preserved in special chemical solution. These will

give you an idea of just how diverse parasitic worms can be.

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Activated Porous Carbon for Separation and Gas storage

Eric Masika

Porous carbon materials with well ordered pores systems represent an exciting, intellectually challenging and rapidly expanding area of

research with many applications. They are of high performance in catalysis, separation, as energy storage materials and components of

electrodes. The growing list of application is attributed to the unique properties of the highly sought after materials such as high surface

area, large pore volume, chemical inertness and mechanical stability. It is desirable to control the morphology of the solid-templated porous

carbon materials, because the morphology (including particle size and shape) since it is a vital factor in the use of porous carbon on the

various applications. Though, it is not possible to create carbon frameworks on its own necessitating the use of scaffolds. In this case,

the use of zeolite materials with generous structural composition and morphologically tuneable has provided a timely solution making it an

area of intensive research in the recent past.

The practical use of porous carbon materials demonstrated in this work is separation in which students will be exposed to how carbon materials

carbon are used as Molecular Sieves. The diagram below illustrates simple filtration process using carbon as a sieve.

Based on the unique properties of these materials, demonstration using

potassium permanganate is used to show how molecules can be adsorbed. Then students will then use food colours to investigate what happens when activated carbon is used as a sieve. In addition, will

investigate whether it is possible to retrieve the dyes from carbon materials which make the process complete in the case of hydrogen

storage as reversibility is crucial for hydrogen economy to scale up.

WE

ARE

BIG

we are small

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Further Information and Links

Thank you for coming to the Masterclass! We hope you enjoyed the

day!

For further information on anything you have seen today or details

about studying at the University of Nottingham, please email

scienceoutreachproject@nottingham.ac.uk, or go to the project

website at www.nottingham.ac.uk/sop.

For additional information about any of the departments involved in

the Science Outreach Project or today’s event, check out the

following webpages:

School of Biology: www.nottingham.ac.uk/biology

School of Biosciences: www.nottingham.ac.uk/biosciences

School of Chemistry: www.nottingham.ac.uk/chemistry