Tag Archives: University of Bath

Molly Monk and Issy Bolton at the University of Bath

Pawan Jolly, Molly and Issy

Photo: Issy and Molly with Pawan Jolly in the department of electronic & electrical engineering 

Within the department we were working with the Biosensor group. During our time there we were given lots of opportunities organised by our supervisor, Pawan Jolly, to experience and learn about research science. We visited chemistry, electronics and the nanofabrication labs and were kindly shown around by other post graduates who explained to us their work. It was very interesting to know how the researchers were working on the development of diagnostic tools for cancer diagnosis where one of the main focus was Prostate Cancer (PCa) diagnosis. It was also fascinating how the different groups around the Europe has come together on a common platform to work on the diagnosis of PCa and the network was called PROSENSE (http://www.prosense-itn.eu/).

Within the PROSENSE project, we individually fabricated DNA based biosensor for PCa, observed the absorbance of light by gold nanoparticles using spectrophotometer and used localised surface plasmon resonance technique (LSPR) among other things.

On the 24th Aug 2015, we started with preparation of buffers namely trisma base and sodium acetate and a bovine serum albumin (BSA) as a protein for our biosensor. The next day we adjusted the pH of the buffer using a pH meter, which detects the ion concentration of a solution, to raise or lower the pH of the buffers  bases and acids were used.

As we were working with DNA, everything used must be extremely clean. So first we prepared our gold working electrodes by cleaning it using techniques like sonication, polishing with aluminium oxide in a figure of eight motion. As we wanted our surface to be very clean, electrochemical cleaning was performed in sulphuric acid as an electrolyte with a three electrode configuration using cyclic voltammetry. The silver reference electrode is kept in a salt bridge in order to protect it from the acid, the platinum counter electrode goes straight into the solution and the gold working electrode again goes into the solution. The electrode are connected up to a potentiostat that will cycle a voltage through them and causes oxidation and reduction of the gold surface and hence, removes dirt from the surface of the working electrode. In our experiment the next step was to fill caps with a light sensitive solution together with probe (receptors to capture DNA) and electrode was dipped in it, they were then left overnight.

Next we produced two separate electrolytes using potassium(II) hexacyanoferrate and potassium(III) hexacyanoferrate salts mixed with our prepared buffer solution. Then we placed our electrodes into the same buffer solution that was being used in our electrolytes. Firstly for each electrode we carried out cyclic voltammetry again. After the first run some of the electrodes had DNA attached and the others had a protein attached and depending on the length of time the electrodes were allowed to sit in the solution they should decrease the oxidation peaks as they interfere with the flow of electrons. We also carried out the programme electrochemical impedance spectroscopy (EIS) which measures the amount of resistance of the system  this is affected by not only the surface modification because of binding but also the ion concentration in the electrolyte. With capture of DNA, we observed the increase in resistance and also the decrease in the oxidation peaks in the CV. By the end, we successfully developed our own DNA based biosensor for detection of circulating DNA in blood for Prostate cancer.

All in all, we had a great time and can’t thank enough everyone who took the time to talk to us about their respective fields. Most of all a massive thanks to Pawan, for having the patience of a saint and showing us the “realities” of research in the field of science.

Producing Biodiesel from Used Coffee Grounds by Transesterification

by Ben Laurie-Machin

The manufacturing of transportation fuels such as petrol produces around 20% of all greenhouse gases. Therefore, it is essential to find alternative, greener fuels. One such alternative fuel is biodiesel produced from waste products and resources. My group’s project was to turn used coffee grounds, taken from one of Bath University’s cafes, and turn them into biodiesel.

Extraction

First of all, we had to extract the coffee oil from the grounds. We did this by mixing the grounds with a solvent, hexane, and then filtering the mixture. We then took the mixture and heated it under reflux while stirring it. After that, we filtered out the solvent-oil solution.

Evaporation

Once the solvent-oil solution had been obtained, we had to evaporate the mixture. Evaporation is an important step as it allowed us to concentrate the solution by removing the hexane. We did this by heating the solvent in a rotary evaporation unit.

Coffee Biodiesel Synthesis

The final step was to turn the coffee oil into biodiesel. We did this through a process called transesterification. Transesterification is the process of exchanging the organic group on an ester with the organic group on an alcohol.

In our experiment, we used an alcoholic catalyst (ethanol) to turn the oil (triglycerides) into biodiesel.

fig 1

Analysis

Throughout the transesterification stage, which happened over 24 hours, we took samples from the solution and tested them to see how much biodiesel had been made throughout the experiment. To be able to test the samples, we put them in an NMR (nuclear magnetic resonance) machine. The NMR machine can detect the magnetic field around each proton within the sample. From this, we can determine what sort of bonds are near each proton and quantify the amount of biodiesel in the sample.

In the end, our experiment turned out to have a 0.170% efficiency. This is mainly due to the transesterification stage in which we heated the solution for 24 hours. A lot of energy was wasted here. If biodiesel was going to be produced on an industrial scale from coffee grounds, a more efficient process will need to be found.

HeLa Cell Line Culture Drug Testing: which concentration of three unknown drugs is most effective

by Rhia Buchan

While at Bath University under the supervision of Dr Momna Hejmadi we (Charlotte, Chloe, Laura, Pedro, Will and myself) carry out an investigation on a HeLa cancer cell line (taken originally from Henrietta Lacks who was an African-American women who died on 4th October 1951 from cervial cancer. Her cells from her tumour were then without permission cultured by George Otto Gey and is the first know human ‘immortal’ cell line to be used for medical research).

This investigation entailed growing a three separate cultures of the HeLa cell line in medium. We placed the cells into incubation over night and when we checked them the next day we found that they were growing quicker than expected. Due to this we moved our experiment forward.

To carry out it out we needed a 98 well plate and used it as shown below:

column 1-4 group 1 – Drug A

column 5-8 group 2 – Drug B

column 9-12 group 3 – Drug C

Row G and H were our positive (used bleach) and negative control (had no cells)

96 wells

The last column in each section was left as a control for each cell culture. We then had to work out the dilution for drug B from the stock (shown below):

Drug B stock 90% – 45×1/90 = 0.5 + 0.5 medium

15×1/90 = 0.16 + 0.84 medium

5×1/90 = 0.05 + 0.95 medium

After working out the dilutions we then diluted the drugs by using medium and p1000 and p20 pipettes as shown below:

  1. 500 microliters of drug + 500 microliters of medium
  2. 160 microliters of drug + 840 microliters of medium
  3. 50 microliters of drug + 950 microliters of medium

We then placed the cells back in incubation at 2:40pm. The next day 11:20am we took the plate out of the incubator. Then on blue towel carefully we blotted the plate to remove the medium then added 100 microliters of MTT then remove the same way the medium was. Then add 100 microliters of isopropanol. This results in the MTT causing crystals to form in intact mitochondria which when isopropanol is added will give a blue colour. Then we looked at the cells under the microscope and analysed the data we obtained.

We found that drug B (Hydrogen Peroxide) was the most effective however would not be an effective cancer treatment drug as it isn’t exclusive in killing only cancer cells but all cells. The next best drug was A (5-Flurorouracil) which is currently used as a cancer treatment and then C (Camptothecin) which is an unproven natural treatment for cancer.

CANCER AND GENETICS RESEARCH PLACEMENT by Laura Huynh

Having heard of how beneficial the in2scienceUK scheme was for students such as myself, applying for a STEM degree at university, my expectations were set high for the 2 week research placement – confirmed to be held at Bath University. It’s safe to say that I was not disappointed and that the experience I gained during my time in the labs has given me a truly valuable insight into research not only at a university level but as a remarkable career option too.

Though my group were fortunate enough to have the opportunity to carry out a multitude of experiments whilst at the university, our predominant investigation focused on mimicking the drug screening process by testing the effect of three different drugs (5-fluorouracil, camptothecin and hydrogen peroxide) on the viability of HeLa cancer cells.

We began by preparing the HeLa cells on which we would later test each drug and this involved growing the single strain provided on three separate agar plates – each containing Nematode growth medium. All petri dishes were incubated overnight at optimal growth conditions (38 degrees and 5% CO2) to ensure the rapid proliferation of the cells. We then proceeded to make up the required concentrations of each drug by calculating the correct ratio of stock (initial concentration of drug) and medium. A 96 well plate was used with 6 replicates for each concentration of each drug (3 per drug) and included a positive control (bleach to ensure induced cell death) as well as negative controls (no HeLa cells and no drug).

Laura H fig 1

After leaving the cell/drug mixture overnight, an MTT assay (a colorimetric assay used to assess cell metabolic viability) was carried out the following day. The principle of this technique is based on the fact that the mitochondria in viable cells contain functional enzymes that are capable of reducing the dye into insoluble purple crystals. Thus, the viability of cells is reflected in the richness of the purple colour produced which is assessed using a colorimeter.

Our results reflected findings from previous research as 5-fluorouracil was most effective at its highest concentration as this is a drug commonly used in chemotherapy. It works by acting as an analogue of uracil with a fluorine atom replacing the hydrogen attached to C5 thus preventing the biosynthesis of pyrimidines and has an inhibitory effect on DNA replication thus cancer cells cease to replicate. Camptothecin is a more experimental drug however it shows promise for future clinical use as demonstrated within our results.

Laura H fig 2

Computer Science at the University of Bath

by Gabriel Barnes & Robert Murray

We thoroughly enjoyed our two weeks at the University of Bath. We worked on augmented reality applications, which is projecting virtual objects into the real world. To do this we used the Unity game engine and experimented with two augmented reality packages, Vuforia and Metaio.

In the first week we expanded upon a project Gabriel has been working on called Plant Notes. The project involves collecting data about the environments of plants and we thought it would be an interesting idea to use augmented reality to visualise the data. We programmed the application to request data from the web server on the hub. We then processed the data so that when the phone was pointed at the hub data would magically pop out of it. Here is an example of such wizardry.

GB & RM 1

In the second week we embarked on a furthermore ambitious quest, that of positional tracking indoors. Unfortunately we didn’t have enough time to implement all of our ideas, but we did manage to calculate all of the distances and angles necessary and develop some proof of concept applications. We hope that our work will be useful to our supervisor, Daniela De Angeli, as this may contribute towards her PhD.

GB & RM 3
He we show a proof of concept, by measuring the distance from the trackable object to the camera and between two trackable objects.

GB & RM 2

Above are some rough sketches to show the thought processes and calculations behind our idea.
Above are some rough sketches to show the thought processes and calculations behind our idea.

By using tracking of objects in the real world we can calculate the position of the camera in real time which is useful for a whole host of applications. One that would be interesting to look at would be its application in virtual reality for mobile phones as this would provide a cheap method to implement positional head tracking to reduce motion sickness.

We then experimented with controlling sound pitch and volume when the camera changed its distance to the object which could be used to assist the visually impaired or as an interactive sound synthesizer made from objects in your home.

We would both like to thank the Department of Computer Science at Bath University and in2scienceUK as for without this amazing opportunity wouldn’t have been possible.

At the end of our placement we were asked to give a presentation with demos of our projects to people in the department, which was very well received.
At the end of our placement we were asked to give a presentation with demos of our projects to people in the department, which was very well received.

Yeasts are not only used in baking bread!

title

Over the two weeks spent in the laboratory I have learnt about how significant understanding and testing pathogens (particularly Candida albicans and Candida galbrata) is to preventing human fungal diseases being contracted. I spent time investigating the different strains of yeast at both a molecular level through polymerase chain reactions (PCR) which analysed the yeast strains DNA (see photo A) and therefore genetics alongside microscope studies and also visually by comparing phenotypes which Manduca sexta caterpillars (see photo B) expressed when different strains or dilutions were injected, monitoring them for changes in weight and colour.

Photo A: Agarose gel electrophoresis to analyse PCR products

photo A

Photo B: Manduca sexta

photo B

I had the opportunity to collect my own data which enabled me to see, from the beginning to the end of the life cycle how powerful fungal pathogens can be and relate that to the importance of all the studies within the lab to preventing illnesses. The members of the lab were varied, including PhD researchers and master students, all of whom have enlightened me as to the broad range of topics science has to offer and the overlap of many different aspects, whilst also explaining different pathways into their scientific careers which has shown me the vast amount of ways to work within the field and that there are opportunities to move on and complete different studies throughout your whole career.

Participating in this placement scheme, alongside Stephanie and other lab members I have learnt a huge amount in just two week and realised that the phrase ‘you learn something new every day’ really is true when working in a scientific career, with around 80% of experiments not actually working scientists have to be patient in order to achieve the end result which could one day save lives.

By Emily B

University of Bath August Placements

Becky Mead updates us about the varied and exciting range of placements taking place at the University of Bath

Another fantastic mixture of placements @UniofBath this month! First, the Department of Pharmacy and Pharmacology @PharmUnivBath. Our in2scienceUK student has been busy working alongside Dr Chris Bailey’s PhD students, investigating neuronal changes caused by drugs of abuse, and how they relate to drug tolerance and addiction. During my visit she was working with PhD student @AnnelisaSadler and preparing her first gel electrophoresis (see photo below). She has really enjoyed all aspects of the practical work and has a clearer idea about what degree she would like to study.

Photo 1

Next, the Department of Biology and Biochemistry where two students have been working with Dr Momna Hedjmadi. Both students have completed practical work with Momna into the effectiveness of anti-cancer drugs and have also worked with MSc student Grace, who investigates behaviour and genetic changes in the worm C. elegans (seen with the microscope in the photo below). Both students have thoroughly enjoyed the experience, especially the practical lab work, and don’t want to leave!

Photo 2

On to the Department of Chemistry where one student has been working in the group of Professor Aron Walsh @lonepair alongside Dr Keith Butler and other post docs and PhD students. Based mainly in a theoretical chemistry lab, out student has been learning to code and create scripts which search through the periodic table for possible new materials (see photo below). He has also been able to visit an organic chemistry lab. The lab have been incredibly welcoming and have helped our student to focus on which degree he wants to apply for and he is really grateful to all the researchers who have spoken to him about their degrees and shared their advice.

Photo 3

Staying in the Department of Chemistry, I visited Dr Judith Brown and her in2scienceUK student, who is hoping to study Dentistry. One of Judith’s current research themes is culturing biofilms to examine the effect of ultrasonic cavitation on plaque so this was a really interesting project for our student to be part of. He has been able to visit a Biochemistry lab and has learnt a number of lab techniques during his two weeks at Bath.

Finally, back to the Department of Biology and Biochemistry for our final two placements. Dr Stephanie Diezmann @diezmannlab has provided a fascinating project involving research into the yeast Candida albicans and the Manduca caterpillar. Our in2scienceUK student has been able to work alongside different researchers and complete lots of lab work and use techniques such as PCR. Stephanie arranged an interesting Q&A session for our student () and also for our student to meet with the department admissions tutor, both of which proved really helpful. Thank you to everyone in Stephanie’s lab for such an inspiring placement!

Last but certainly not least, Dr Daniel Henk and his lab hosted a placement looking into different aspects of fungal ecology and evolution. Our student has been directly involved in Dan’s research and has completed fieldwork collecting diseased fruit from which he has then isolated the disease-causing yeast Botrytis. This data will help Dan and his group to understand more about the ecology and genetics of this yeast and its biocontrol. Our student has spent a lot of time in the lab and has learnt many new techniques such as PCR and used equipment new to him, including pipettes. Talks with Dan and other lab members have helped him to think about his which degree to study at university and have inspired him work hard during his A Level studies in the forthcoming year.

This summer’s placements have been a huge success, thanks mainly to the incredible support and dedication from our supervisors and their groups, and also due to the enthusiasm and commitment of out students. Thank you again to everyone who has been involved this year! I look forward to seeing you all at our Celebration Evening next month.

By Becky Mead, in2scienceUK Bath Coordinator