Stellenbosch University
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From Stellenbosch to Stanford University and back
Author: Elbie Els
Published: 18/09/2017

After more than 10 years as Electron Microscopist and Senior Research Professional at the Cell Sciences Imaging Facility (CSIF) at Stanford University (USA), dr Lydia-Marie Joubert is back in South Africa to manage the Central Analytical Facilities' (CAF) Electron Microscopy unit.

 "I am very much a South African at heart, and Stellenbosch University (SU) provides me the opportunity to lead a team in Electron Microscopy (EM) at a core facility that is already very functional and bring South Africa prominently into the international microscopy, correlative imaging and 3D microscopy fields" Joubert said. "The niche I want to fill here is to develop the biological background that is lacking here currently." She strongly feels that people leaving South Africa should always look for an opportunity to give something back. "South Africans have made a great international contribution and I think our obligation is to, not necessarily come back physically, but to plough back intellectually and to create opportunities for collaboration."

In her role as EM specialist and manager at Stanford University, she was responsible for Scanning Electron Microscopy (SEM) related research projects, EM technique development, teaching and consultation, and management of an ongoing kidney stereology project involving TEM and light microscopy analysis. Her major interests are 3D SEM technique development and computation, as well as Correlative Light and EM techniques (CLEM) and she has focused a lot on 3D electron microscopy and application of novel techniques into new niche areas at Stanford.

"What I achieved at Stanford was connected to the people I worked with, and the developments there that are specifically in three dimensional analysis in biological electron microscopy, and to correlate high resolution fluorescence microscopy with the ultrastructural context provided by electron microscopy. One new big advantage in electron microscopy is that it is no longer a challenge imaging and capturing beautiful and informative pictures, since cutting-edge equipment has evolved rapidly over the last decade. Automation (of instruments) is still a challenge and then also computation." According to her, Stanford is probably the most interdisciplinary university in the world and they always had integration of the biological field with the engineering side. "Material development, biomaterials and the imaging of biomaterials under conditions that are needed for biomedical application (VP-SEM application) are some of the major things I learned and got involved in at Stanford."

Another breakthrough development by Joubert, some colleagues and postdoctoral students at Stanford University is Array Tomography. She explains that Array Tomography is based on serial sections of cells and tissues that are gathered on conductive glass panels that can be used for light microscopy and the sections can then be reconstructed in a three dimensional volume. The same sections can then be used for scanning electron microscopy, to obtain internal ultrastructure and stacks of images that can be correlated with the 3D volume from light microscopy. Comparisons between fluorescence microscopy and electron micros­copy result in a much better resolution than using only light microscopy, and gives us a better understanding of structure as well as function.

"I also hope to bring Array Tomography to Stellenbosch, because it is a novel and powerful technique, and people here haven’t tried it yet probably because they are not that familiar with the applications" she said. To prepare biological tissue for these applications they often delve into the publications of the 60s, 70s and 80s that were the initial high days of electron microscopy.

Her biggest challenge and vision for the SU Electron Microscopy unit is to expand onto the Tygerberg Campus. "Because of the clinical field I was in at Stanford at both the medical school and bioengineering, I would like to expand the EM unit to have a point of service in the medical research environment."
One of the things that she also wants to develop further at Stellenbosch is the CLEM (correlative light and EM) imaging platform that was launched in 2016. According to Joubert this is a strikingly new field to be in and there also is a learning curve for clients because it is at the front end of microscopy and a lot of troubleshooting is still needed. After talking to some of the staff at SU, Joubert said that the research questions and the equipment are here already and that it is a case of bringing them together.

"How can you answer the research questions with the equipment we have? I am very impressed with the current staff and the equipment here at Stellenbosch – there are a lot of cutting edge tools, and smart and dedicated staff here."

Joubert also feels that it is important to publish your work and attend conferences and network with other researchers. She plans to bring international collaborators and speakers to Stellenbosch. "Some of my colleagues from Stanford University and the greater Bay Area are specifically delighted about this opportunity, because from a medical side they have been looking for someone to connect to in SA to have a hub here and transfer technology and expertise." Joubert said that people in the
USA are usually very impressed by the level of science they find in SA. According to her it is also no longer expected that one person should do everything in a research project and therefore collaborators are very important. "One can move frontiers much more efficiently if a group of researchers work together, each applying their expertise in a niche area." Project management then becomes crucial for success.

She also has a creative side and was the winner in the illustration category at the International Science and Engineering Visualization Challenge (SciVis) in 2013 with her image "The Hand." She took multiple micrographs of colonies of live and dead bacteria, enlarged them 400 times, and superimposed them on a sculpture of a human hand. "I just played around with interesting images and then also had more time off to try different things." She is also focused on photography and explains that when she was a student in the 80s (and up to about 2000) they captured their images (‘electron micrographs’) on negatives. A photography course was compulsory before starting their electron microscopy course because they had to know how to develop their own negatives and make photographic prints. "Film was better resolution than you could capture with CCD cameras until very recently. You could visualize ultrastructure with the instruments in high resolution, but you couldn’t capture digital images in high resolution." She also received an American Microscopy Society Award in 2009 for her breakthrough development of new methods to investigate hydrogels – an honor that a scientist is allowed to win only once.

Her passion for the electron microscopy field comes from her graduate studies in the 1980s at SU with prof Jan Coetzee. "I was always a very visual person and I loved physics. I think applying the physics of electron microscopy in the biological field just put it all together." She also mentioned that the very inspiring people at the Botany Department at SU during her graduate studies, helped her choose between botany and her other major, mathematics, for her post-graduate studies. "The computational side of biological EM today indeed provides a full circle back to all my intellectual interests."

She is glad that she was part of electron microscopy in South Africa in the 70s and 80s. "In contrast to a few years ago, it nowadays is good to refer to sources from the 70’s in publications or talks, because that is when electron microscopy really started." Joubert matriculated as dux scholar at Outeniqua High School in George, obtained 4 degrees at Stellenbosch University and then obtained her PhD at the University of Pretoria, spent some time doing research at the Indiana University (USA) and started off her career as lecturer in Microscopy Techniques and Plant Sciences at Stellenbosch University. She also studied at Weizmann Institute in Israel during her post-graduate years, before getting married and raising 3 boys. After a few positions as researcher, doing world-class research in botany, microbiology and microscopy, Joubert headed to Stanford University in 2006.

With her passion and extraordinary knowledge and experience the CAF Electron Microscopy unit can surely look forward to a very exciting phase of growth and development.

(also published in CAF Annual Report)