Of Fungi and Life

Congratulations to Dr Kangzhen Dong (February 2016)

KD Heatley-PayneKangzhen received the Microbiology Society’s Heatley-Payne Award supporting early career researcher exchange visits. The award will enable Kangzhen to attend the ASM Microbe meeting in Boston this year and to visit our collaborator Prof Anja Forche at Bowdoin College. In Anja’s lab, Kanghzen will learn to analyse ddRAD sequencing data.

 

Magdalena Lewoniec – In2Science Student (August 2015)Magdalena Lewoniec

Magdalena, a student at Brendan’s Sixth Form collage in Bristol, visited the lab for two weeks in August. Through the In2Science program, Magdalena was able to collect some valuable work experience.

Ishmael Akalanne – Lab Work Experience (July 2015)Ishmael Akalanne

Last week, Ishmael Akalanne, a Year 12 student at Sheldon Sixth Form from Chippenham, visited the lab. Ishmael is considering to get a degree in Natural Sciences and thought it a good idea to get some prior experience before committing to a three-year program. It was a pleasure to have Ishmael in the laboratory and I sincerely hope we could answer all his questions, there were a lot, which is a good thing.

Here is Ishmael’s experience in his own words.

Having been lucky enough to obtain a three day work experience placement at Yeast Genetics, this week marked my first real-world experience of lab work.

Every moment of work experience at Yeast Genetics was rich with new experiences and opportunities for learning. After meeting with Stephanie Diezmann, who kindly bought me a hot chocolate and helped me understand the general gist of affairs, I joined Chris Apark, whose sound explanations and easy manner won me over quickly. He proceeded to show me in the most entertaining way how the moth Manduca sexta is raised in a lab, and explained to me how their use can ensure that mammals such as mice need not be used for experiments, making the process of research more ethical and cheap. I was particularly fascinated by how the diet of the Manducas affected their colour. Because the food these lab Manducas were fed did not contain nutrients that would give the Manducas pigment, the larval ones grew to be a pretty turquoise colour. It follows that part of the reason that Manducas are a model species is how their skin colour will change depending on their environment.

I was also lucky enough to bear witness to some gel electrophoresis with Leenah Alaalm and Carolyn Williamson. Carolyn showed me how this process works with DNA, whereas Leenah showed me how it can be applied to proteins. This being the first time I was exposed to this process, I found this standard biological procedure most incredible, for in it I could see physics, biology and chemistry working in harmony to produce results that could easily be understood by humans. Its beautiful simplicity intrigues me, and I will be very excited to see it in action again in future.

When we saw the results of the electrophoresis under an imager, I was able to tell which samples had been successful and the one which had not by observing the position of bands of DNA. This illustrated to me how easily the basic outline of electrophoresis can be picked up and understood, and I was pleased to see I had made progress since my arrival.

The welcoming and friendly vibe of all of the lab members positively concreted my opinion that I had been most fortunate to procure a work experience in Stephanie Diezmann’s lab, and upon working with each person I discovered that each had various specialties. Therefore, in shadowing each member, I was able to learn about a different facet of the overall research process and I also gained a deeper insight into the teamwork aspect of lab research. I would like to express that in the short space of three days, I have acquired more experience of lab work and practice than I have had in the rest of my life, and that this practical lab work has also added a dimension of depth and understanding to my previously purely theoretical knowledge, which will certainly be of great use in future. Because of all of these positive points, I would vigorously recommend the Yeast Genetics lab to others searching for work experience.

 

19th Congress of the International Society for Human and Animal Mycology in Melbourne (May 2015)

A few weeks ago, I attended the 19th ISHAM congress in Melbourne. Here, several hundred mycologists from around the world had gathered to discuss the latest in human and animal mycology. Topics covered were very diverse, ranging from how next-gen sequencing methods inform and improve public health to rare fungal pathogens, such as Dr Lobo’s fungus that affects people and animals in Brazil. There was so much to hear and learn. Here is my storify account of #ISHAM2015 and the official program.

I very much enjoyed the keynote and plenary sessions, which are the highlights of any science meeting. For these special talks, senior scientists are invited to talk about their, often life-long, research programs. The keynote was presented by Prof Sarah Gurr from the University of Exeter. Sarah talked about the scary and wonderful world of fungi. Scary because plant pathogenic fungi spread faster than anyone thought thereby threatening the world’s food supply and wonderful because they can clean up unstable depleted uranium. Two of my favorite ISHAM plenaries were given by Profs Joe Heitman and John Perfect from Duke University. Both eloquently conveyed their passion for mycology and fungal pathogens. For his outstanding achievements in medical mycoloyg John Perfect received the Lucille K. Georg ISHAM medal.

For any new PI it is a special honor to be invited to speak at an international meeting. I used this opportunity to present our recent advances in developing the Tobacco Hornwom Manduca sexta in the “Virulence of fungal pathogens” session. This entirely student-run project aims to optimize employment of caterpillars of the Tobacco Hornworm moth as a novel model system for the study of fungal disease. Yes, we can.

Conferences are so much more than just learning about science though. They are more than welcome opportunity to catch up with old friends and to make new ones. I had a fabulous time with my former collegues from Duke University and my new fellow-UK myco friends from Aberdeen. I am looking forward to seeing everyone again at #ISHAM2018 in Amsterdam.

 

Naomi’s first impressions of graduate school and embarking on a PhD (October 2014)

I am joining the Diezmann lab to embark on my PhD, having finished my MRes at the University of Bath. I originally studied at the University of Liverpool, where I did a BSc in Microbiology before taking two years out to work in industrial labs and travel. I worked as a technician in two different food testing labs because I wanted to get some practical experience outside of the academic bubble and affirm that academia was really where I wanted to be.

When I had confirmed my place on the MRes course at Bath I upped and left to go and see the world before life tied me down again. One of the projects I did in my MRes year was in Dr Diezmann’s lab, where I found the research really interesting and the laboratory atmosphere enjoyable, so I applied for the PhD position when I saw that it was available. I remember hearing on the radio when I was about 14 that there was a worldwide shortage of mycologists and saying, “that’s what I’m going to do”, but I don’t think I seriously expected it to happen.

Embarking on the research, I’m looking forward to having a significant body of work to call my own and being one of the initial members of the Diezmann lab adds to the excitement. Having spoken to people who already have PhDs, I’m expecting a hard slog, lots of disappointments and the occasional disaster, but that should make the breakthroughs that much sweeter… I think for the first year I’ll feel like a floundering idiot in the lab and probably regularly wonder how on earth I got myself hired, but, as with learning anything, there’ll be an almost imperceptible transition when I become more comfortable in the position and contribute my own ideas, some of which might be intelligent and worthwhile.

I also hope, as I expand my knowledge, to improve my skills in fungal punnery, which are, as yet, pretty weak <insert pun here>.

Possible puns:

How many Hsp90 co-chaperones does it take to change a light bulb?

10; it’s a complex job.

I’m hoping the findings from my research will enable me to change the light bulb part to something more relevant.

 

Good Bye Emily!

Emily’s time in our lab has come to an end. Here she describes her experience and shares some photos.

Emily

HeaderDuring my placement within Dr Diezmann’s laboratory I have not only experienced first hand scientific research and the effects that this has towards reducing the amount of humans contracting fungal diseases but have also had the opportunity to work alongside a variety of different people throughout the two weeks, all of whom have explained their pathways into science to me and all the different aspects of the subject which are actually available to research into broadening my knowledge. Speaking to Stephanie and asking questions was helpful and gave me an idea as to how she became interested in yeast and how science projects are created and carried out. My first week allowed me to learn many of the basic skills required for work in the lab such as pippetting to certain measures of accuracy, creating basic medias to grow the yeast strains in and ensuring research was done in uncontaminated areas. It also focused on analysing the DNA and therefore genetics of the yeast strains and by shadowing Steve, Kangzhen and Jawaher. I learnt all about the process of PCR, with many opportunities to run gels filled with samples taken from colonies of cells and then use UV light to show bands indicating the amount of base pairs present and whether the sample could be used for their experiments later on in their projects. During day four, tubes of cells in media which had been incubated had only shown one tube to produce cells demonstrating a real life scientific problem whereby something had prevented cell growth and led to further investigations (which I have not undertaken before, for example during school) using different YPD medias and discussions about the amount of cells added to solve the problem rather than carrying on and producing incorrect results.

The second week at the lab gave me the chance to work alongside Debra on a project whereby Manduca sexta caterpillars were infected with different types of the pathogen Candida too see what phenotypes were expressed when death occurred and the effects of the different strains or dilutions on the animals. After a centrifuge had been used to clean the cells of toxins and they had been re suspended I learnt how to count cells using a microscope to check that there was enough for infection. Each caterpillar had to be injected in the back left hand leg, under the hood to avoid contamination and used sterile equipment to prevent other pathogens entering and was then monitored by measuring their weights and visually checking for a change in colour every day. I participated in two infections and was allocated my own set of Manduca to monitor during the week and obtain results from. The practical element of this task was exciting and allowed the effects of the fungal pathogens to be seen through the Manduca sexta’s appearance and not just through a microscope showing me how the different parts of lab work come together. Through Debra and others work it has been shown that high enough doses of Candida make the caterpillars turn from a bright turquoise to dark purple and then black whilst also causing a weight loss rather than the average healthy weight gain of 1g a day. This was clear within my set of Manduca results with all but one larger caterpillar that was infected loosing weight and turning purple, with five dying by the end of the weeks experiment. I also attended Andrews’s master talk learning even more about the benefits of using Manduca sexta as model systems. The experience overall gave me a great insight into science and research at a much higher level through practicals and talking to Stephanie and other lab members, showing me the huge range of topics available to work with and learn more about, convincing me that I definitely do want to pursue science after leaving senior school to discover new scientific interests. I hope that I can return to the Diezmann lab in the future!Summary Photo

 

Emily BullerWelcome Emily!

Emily Buller is a high school student from Devizes School and joins the lab this August through the In2Science program.

Since part of the experience is finding out what life as a scientist is like, we sat down for a chat. Here are some of Emily’s questions.

How did you initially start your science career and how did you become more involved with Candida albicans and Hsp90? I always knew I wanted to be a scientist but was not quite sure in what role. So to learn the ropes first, I went to lab tech school after highschool. After three years of training as a laboratory technician, I knew that science was for me. I then went to Humboldt Universität in Berlin to study Biology and did my PhD in Genetics at Duke University in Durham. Just before graduating from Duke, I saw this very inspiring talk from a young and enthusiastic scientist about her work on Candida albicans and Hsp90. Leah Cowen had just started her lab at the University of Toronto and I asked her for a postdoc position. This is how I got into Candida and Hsp90. I did a four year postdoc in Leah’s lab working on the Hsp90 network in Candida albicans.

Are there any particular qualities that you recommend that future undergraduates should look for when applying to University? I am not an expert on the UK undergraduate experience but when committing to a place for three or four years, I would also look at the living experience. Spending three years in one place can be very very long if you are unhappy. How do undergraduates live? What is the community like? What support structures are in place? These are the questions, I would ask.

Would you suggest taking a gap year and are science seminars and talks beneficial to people considering studying science? I never took a gap year as it is not part of the German education system. But given the time constraints later in life and once you have settled on a chosen career path, I would definitely do it. There is no other time to travel for extended periods of times, for example. As for science seminars and talks, most of them are open to the public as far as I know. Go and sit in, try it. You may not understand everything the speaker is talking about but you will get exposure.

Is choosing a specific science degree as an undergraduate beneficial or is it better to undertake a more general degree and specialise in the future? Both are good options and it depends on what you are interested in. If you are certain that you want to be a biochemist, study biochemistry. You are not quite sure yet, pick a more general topic, like biology. Science is moving very fast and you will specialise later no matter what. That being said, it is very important to get a solid knowledge foundation. So, look what is covered in the respective curricula at your University of choice.

How are projects decided within your lab and how is all the data and research used afterwards? We are in the lucky position that all the projects we work on are based on interest. Last year, I successfully submitted several grant applications and we are now working on these. The Manduca project is not externally funded but we use the bench fees of our students to push it forward. So far this has been working out very well. The data generated through our research will be published, used for future grant applications, made publicly available on figshare, and generally stored and treated in compliance with the University’s and the research funders’ data management policies.

What are the main aspects of science that interest you within the science that you do? There are a few basic questions that our science program revolves around and that we are trying to crack. We are trying to understand how chaperone networks change over time, how Hsp90 is regulated and what different sorts of regulation do to the downstream cascade, and how Hsp90 affects genome integrity. In addition to the science itself, I try to make sure everyone in the lab has a learning experience. Something that will move them along on their paths.

If you could study a completely new part of Science which part would you chose and why? This is a difficult question. There are many other parts of science that I would like to know more about. Neuroscience is interesting. What is the underlying chemistry of decision making? I also have a soft spot for physics but my maths skills are way too weak.

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