Speed Dating Scientists

Convincing school pupils that scientists are actually ordinary people is no small feat, but scientists from the IIB, along with the social enterprise Farm Urban have been doing just that.

Farm Urban, in conjunction with the University of Liverpool and funded by Shaping Futures, have developed a 12 week STEM club called the Future Food Challenge, where pupils form their own social enterprise to try and help fix the world’s food production problems using high-tech growing technologies such as aquaponics and hydroponics. Before starting the program, the pupils were invited to an introductory day at the Department of Engineering on Wednesday 6th February, where they were built their own mini aquaponics system and were given talks and advice by local business leaders about how to set up their own business. Matt Murphy from the Engineering Department, who helped to organise the day, also gave a talk to help the pupils understand the design and engineering problems they might face.

As part of the day, pupils took part in a Scientist Speed Dating session, where groups of 6-10 pupils got to sit down with a real life scientist and ask them questions about their work, and how they’d ended up in their job. The idea was to break down some of the barriers preventing the pupils seeing themselves as capable of being scientists and show them that some of the scientists had similar life experiences to their own.

Laurence Anderson, Hannah Davies, Jens Thomas and James Torpey from the IIB all took part. At first, students and academics were eyeing each other with some trepidation, but by the end of each session, the groups always had to be forcibly moved on as everyone was getting on so well and didn’t want to stop the conversation. The scientists had to contend with a bewildering array of questions, from what their most important experiment was, to what their favourite food or colour was, and although they were sometimes stuck for answers (I’m still not sure what my favourite colour is) the day went incredibly well.

We hope that the day and the program will broaden the horizons of the pupils and show them that they too could be scientists and entrepreneurs, just like the people they met on the Future Food Challenge.

IIB’s Iain Young, who helped to develop the programme and is now at the Institute of Clinical Sciences, was shortlisted for a public engagement award for his part in creating the Future Food Challenge.

 

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Inspiring the next generation of NMR scientists during British Science Week

On Friday 15th March 10 chemistry A-Level students from Range High School visited the Institute for the annual Analytics Day held in the NMR Centre for Structural Biology organised by Dr Jill Madine and Dr Marie Phelan. This visit has been an annual event for the past several years which the students look forward to in order to gain enhanced understanding of NMR to help with their A-level courses and also provide an opportunity to chat with PhD students about what is involved in University life and academic research.  The students were given lectures on the basic applications of mass spectrometry and NMR from Stephen Moss (School of Physical Sciences) and Dr Marie Phelan. This was the followed by practical workshops where the students carried out chromatography and learnt to prepare and run NMR samples along with how to interpret the data.  Prior to their visit, as part of a school practical, they have made salicylic acid – a precursor for aspirin. We obtained these samples and collected NMR spectra of their products ready for analysis on the day.  This enabled them to establish how successful their synthesis had been and compare their results across the class, with previous years’ students (and to the teacher!). The pupils response at the end of the day was that they had learnt a lot and they can now ‘do’ NMR. Watch out for future budding NMR Nobel Prize Winners inspired during British Science Week in IIB!

Pupils were assisted on the day by Michelle Tan, Adika Sen (visiting interns in the NMR Centre), Zain Ghanameh (IACD), Jeremy Chazot (IACD) and James Torpey (IIB).

Plant Power at the VGM

On Thursday 21 February 2019, during school half term the Walley group were at the Victoria Gallery and Museum (VGM).  We took with us a display of cultivated brassica crops, and their crop wild relatives to demonstrate how over many years the weedy Brassica oleracea crop wild relatives have been domesticated and bred into so many different vegetables through selection.

Visitors had a go at performing crosses between different brassica crops by transferring pollen between flowers using paint brushes and, inspired by how new vegetables can created, such as flower sprouts or ‘Kalettes’ (crossing a sprout with a kale plant), designed their ideal or fantasy brassica plants for us to display.

The methods of modern plant breeding that we are using within the BRESOV project (Breeding for Resilient, Efficient and Sustainable Organic Vegetable production) were discussed and compared to conventional plant breeding.

Visitors had the opportunity to taste many of the different vegetables derived from wild Brassica oleracea, including cauliflower, sprouts, kale, kalettes, red cabbage, pak choi, chinese cabbage and broccoli- they were very popular!

 

Summer school: “Big data Analytics and Machine Learning Meets Omics”

In summer 2018 the faculties of Health and Life Sciences, and Science and Engineering, hosted a ten week summer school for students interested in data science, analytics and machine learning. The five successful students received supervision from leading experts in the field, as well as a stipend.

The projects focussed on the application of data science techniques in the area of biological and biomedical research, called “omics”. These areas include the study of genomes and related technologies that produce large amounts of complex data, suitable for data mining. Researchers at Liverpool are using these techniques for “personalised health” research (e.g. to understand how your genetics relate to your likelihood of getting a disease), for cancer research (e.g. for understanding how certain genes are switched on or off during cancer progression), and to understand how infectious diseases can spread or how we can better detect them.

“Insightful, collaborative, applied”

We asked the students to explain their research project and experience of the summer school:

Di LiuDi Liu (BSC Computer Science) worked on the project “Topological data analysis for bioinformatics”.

 Can you tell us a little bit about your current research project

The intention of the project is to visualize the gene-gene interactions by analysing correlation coefficient of gene pairs as the pair’s weight score.

To achieve this we are analysing glioma gene scores by MPI and visualizing the analysis’ results on Cytoscape.

 How have you found the project? What has been the highlight?

The project has been excellent! Working with Drs Kurlin and Krishna broadened my vision and enriched my experience of using the knowledge I have learned.

Also, the project group is awesome. Two supervisors and one teammate, they helped me to overcome any obstacles during my internship.

The highlight for me was successfully using the C++ knowledge to fix the problem we met in the project, and learning how to use MPI to complete parallel programming to save a lot computer running time.

Has anything surprised you about the project?

I was expecting a more reserved role and have solo solved the data part of tasks because of the trust shown in me by Drs Kurlin and Krishna.

Have you seen the University in a different light as a researcher, compared to being here as a student?

Yes, the research side of the University is awesome. On the one hand, it practised the knowledge I have learned at University. On the other hand, it gave me a chance to learn more skills that can’t be learned in lectures. I think this will assist me in the future studies.

Has the research project changed your expectations of the future?

This project is relational with my expectation of the future. So, it let me realize my future’s expectation more clearly. Besides, it also let me see more possibilities to connect my subject with other subjects.

If you were to describe the experience in 3 words, what words would you choose?

Enjoyable, teamwork, rewarding.

Weiyi Ren (BSC Mathematics) worked on the project “Building a statistical model to help quantify molecules important for cell signalling and cancer”

Can you tell us a little bit about your current research project?

The project aims to understand how genetics relate to the likelihood of getting a disease, and to understand how infectious diseases can spread or how we can better detect them. My task was to build a statistic model to predict the change of intensity or retention time between the modified or unmodified peptide.

How have you found the project? What has been the highlight?

The team lead by Professor Andy Jones was searching for undergraduate students to help them build a statistic model. We tried several new approaches: random forest and neural network. The results were very successful comparing with the linear regression model.

Has anything surprised you about the project?

The project was very smooth. We met each week to talk about the progress. The supervisors were very passionate to help us with our difficulties. We could get detailed explanations from them on time.

Have you seen the University in a different light as a researcher, compared to being here as a student?

Yes, the research side of the University is excellent. Participating in a research is very different from being a student. It involves much more communication between the supervisor and the students, which would be no doubt a valuable experience for one’s future academic life.

Has the research project changed your expectations of the future?

Yes, this experience provides me with more possibilities for my future career. Data science is definitely a very good choice for me.

If you were to describe the experience in 3 words, what words would you choose?

Enjoyable, productive, full.

Ash Myall photo.jpg BSC e-Finance student Ash Myall worked on the project “Distributed computing and analytics to annotate the human genome”.

Can you tell us a little bit about your current research project

The intention of the project has been to develop a web-based visualization suite for results of Peptide Search Engines within proteomics analysis, focused specifically on the crowdsourced search engine which operates on a distributed network.

To develop this, we have used R and shiny, which together can quickly produce interactive dynamic visualizations.

In lay terms….producing visual representations of large scale data sets, to identify trends in the behaviour of proteins in samples (e.g. the human body).

How have you found the project? What has been the highlight?

The project has been incredibly insightful, which subsequently lead me to pursue postgraduate research in the field. My favourite part has been consolidating my understanding and confidence in using R.

Has anything surprised you about the project?

Yes, before I had little idea how essential data visualisations can be to understanding underlying trends, and how useful making interactive plots is; questions can be answered instantly about the data by a user.

Have you seen the University in a different light as a researcher, compared to being at here as a student?

Yes, I’ve found the independence to give greater flexibility in finding solutions to unseen problems.

Has the research project changed your expectations of the future?

Absolutely, I’m about to start an MRes in Advanced Biological Sciences with the bio informatics pathway following my interest in biological data analysis on the project.

If you were to describe the experience in 3 words, what words would you choose?

Insightful, collaborative, applied.

Is there anything else you would like add?

This has been a great opportunity, I’d recommend it to anyone who’s got an interest in biological sciences and comes from a computational background like myself. Not only has it provided an excellent application from my undergraduate skills, but it’s also set me in a great position for beginning a career or for going into a PhD.

Antoine Rohmer.jpgAntoine Rohmer (BSC Computer Science) worked on the project “Exploiting Graph Databases for bioinformatics” which included an internship at IBM.

Can you tell us a little bit about your current research project

The purpose of the project was to gain an understanding of the technologies underlying graph databases and parallel computing to create a large-scale visualization of gene-gene interactions from data provided by the University.

The technologies used in the project include Neo4j and the Cypher querying language on the graph database side. C++ and Python were used in tandem with supercomputers provided by IBM for data processing. Cytoscape was used for visualization. The open source pathway database reactome was used as the foundation of the database created for the project.

 How have you found the project? What has been the highlight?

The project was a great foray into the professional world. Working alongside experts in the field and absorbing their insight was a fantastic learning experience.

The highlight of the project for me was the moment the graph database and parallel computing sides of the project combined to form a coherent whole that until then seemed intangible.

 Has anything surprised you about the project?

Perhaps the biggest surprise was how largely independent I was in pursuing the project. Although a plan and structure existed, most of the meeting setups, deadlines, and choices in technologies were up to me. This in particular was a refreshing excursion from the otherwise rigid structure found in my studies.

 Have you seen the University in a different light as a researcher, compared to being here as a student?

Although at times the project felt like a continuation of my studies due to the large amount of research that had to be conducted, the knowledge that the end product will be used as a stepping stone to other research is a much greater motivator than grades.

 Has the research project changed your expectations of the future?

The project truly validated my interests in data analysis and got rid of any doubts previously had about which postgraduate program to pursue. More importantly it made me even more eager to enter the professional world.

If you were to describe the experience in 3 words, what words would you choose?

Insightful, refreshing, validating

Student’s Biochemical Society summer placement in IIB

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Christopher Steel exploring the role of proteoglycans and glycosaminoglycans in aortic aneurysm and dissection funded by Biochemical Society supervised by Hannah Davies and Jill Madine

Aortic aneurysm is a bulge in a section of the aorta. This causes weakening of the aortic wall and increased risk of the blood vessel bursting. A number of biochemical factors can complicate the local environment of an aorta which then has a direct consequence on the mechanical function of the vessel. One factor reported to affect the integrity of the vessel wall is the concentration and distribution of proteoglycans (PGs) and glysaminglycans (GAGs), particularly ‘pooling of PGs’ which may compromise the aorta wall and lead to delamination, aortic aneurysm, and dissection.

In his project Chris investigated the levels of PGs and GAGs in human tissue obtained during aortic surgery at Liverpool Heart and Chest Hospital using a range of gel-based techniques and dot-blots and employed immuno-staining to investigate the distribution of GAGs within the medial layer of the aorta wall. Data is being correlated with existing data on biomechanical properties and biochemical composition of collagen and elastin, along with clinical characteristics for the same patients to assess whether PG and GAG distribution could be contributing to altered aortic wall integrity in disease. PGs and GAGs could provide a future therapeutic biomarker to predict risk of aortic disease and rupture.

 

Wellcome Summer Studentship Award

Megan Souness completed a Wellcome Trust funded project with Elliott Stollar this summer titled “The role of electrostatic interactions in SH3 domain structure and function”. Megan was successful in purifying and thermodynamically characterising over 20 SH3 domains. She was also able to study the role salt played on the folding kinetics of the SH3 domain from Abp1p and found that salt affects the folding rate much more than the unfolding rate. Her work will be included in a publication which is hoped to be submitted soon.

Summer in the Dart Lab

Jagjit Binning (now Year 3 Biological Sci) and Mohamed Omar (now Year 3 Biochemistry) joined Caroline Dart’s group for 3 weeks in July to look at the expression and function of a specialized calcium influx pathway (the Orai/STIM system) in human skin cell lines.  This involved aseptic cell culture, SDS PAGE /immunoblot analysis and also learning how to record the tiny electrical currents carried by the movement of calcium ions using patch clamp electrophysiology.  The electrophysiological recordings are technically difficult and time-consuming so well done to Jagjit and Mohamed both managing to seal a microelectrode onto the surface of an individual cell at virtually their first attempt!