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!

 

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Halloween Science at the Institute of Integrative Biology

spooky science

Post by Dr Jill Madine

On Wednesday 31st October 2018 IIB and SoLS held the first Institute-wide School Engagement event within the Life Sciences Building. 82 children from Banks Road, Litherland Moss Primary Schools and home-schooled pupils from the local area attended the morning session with 128 Secondary school children from Notre Dame Catholic College, Prescot School, Kings Leadership Academy Hawthornes, Academy of St Nicholas, Archbishop Blanch and St Michaels High attending the afternoon session.

Pupils took part in a range of fun spooky science activities:

  • exploring relationships between skulls and other features of animals (e.g. diet and faeces!) with Michael Berenbrink and PhD student Kelly Ross
  • finding out about blood flow and gravity, how holding your breath slows your heart and which animals that make your heart race with SoLS Terry Gleave and Rachel Floyd
  • making zombie proteins out of magnetic beads with Luning Liu and Fang Huang, assisted by many students
  • looking at model organisms under the microscope with the Centre for Cell Imaging (CCI – Violaine See, Dave Mason, Jen Adcott, Daimark Bennett, Anne Herrmann, Marco Marcello and PhD students Kit Sampat, Hammed Badmos, Rebecca Kelly)
  • finding out how much protein is in the foods we eat including fishing in cauldrons for the answers from the Centre for Proteome Research (CPR – Kimberley Burrow, Jos Harris, Victoria Harman and PhD students Max Harris, Rosie Maher, Iris Wagner, Natalie Koch)
  • pupils could also get up close and find out more about a range of animals kindly provided by staff from World Museum and from within SoLS with Carl Larsen

Additional student and staff helpers including Alice Clubbs Coldron, Lauren Tomlinson, members of Jill Madine group (Hannah Davies, James Torpey and Alana Maerivoet), Louise Colley and Laura Winters were invaluable in organising the day and logistic arrangements on the day.

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

pic1

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!

Student’s Biochemical Society summer placement in IIB

Student’s Biochemical Society summer placement in IIB

Ravina Mistry, summer student working with James Torpey, supervised by Jill Madine and funded by Biochemical Society

Investigating peptide inhibition of alpha-synuclein as a potential therapeutic option for Lewy Body diseases

The two most common forms of dementia after Alzheimer’s disease are Dementia with Lewy bodies (DLB) and Parkinson’s disease (PD). These diseases are associated with intracellular inclusions of misfolded protein aggregates called Lewy bodies (LBs). The major protein component of LBs is the misfolded protein α-synuclein (asyn). Asyn and its associated aggregation/misfolding pathway is therefore a therapeutic target for these diseases. Collaborators in Bristol have identified a ten residue peptide that can prevent asyn aggregation and in turn prevent its associated toxicity. James had carried out NMR experiments to investigate the interaction between peptide and asyn and gain insight into the mode of action of the peptide in preventing aggregation. This data suggested that over time the peptide undergoes a structural rearrangement that is only detectable by a highly sensitive technique such as NMR, and that this is required before the peptide and protein are able to interact. This has implications for understanding the role of asyn aggregation in disease-associated toxicity and how it can be targeted therapeutically.

In her project Ravina investigated whether the peptide can also interact with and prevent aggregation of the six known disease associated mutants of asyn. Furthermore, she also used modified versions of the peptide (using amino acid substitutions) to further probe the mode of action and enhance the future progress of this peptide into a viable therapeutic avenue. She gained experience in a range of techniques including protein expression and purification, NMR, isothermal titration calorimetry, electron microscopy and fluorescence assays.