Research Opportunities

A number of postdoctoral fellowships and several post-graduate research projects, at M.Sc. and Ph.D. level, will be funded by the Hans Merensky Foundation as part of this Chair.

 

Please see the sections below, describing different areas of research that we are pursuing, and see here for details on how to apply to join us.

Research activities in EucXylo revolve around four main themes: (1) Understanding the physiology of the plant and, in that context, the developing xylem, (2) formulating the best models to capture our understanding of the ecophysiology and xylogenesis, (3) integrating models in a simulation system which provides flexibility and harnesses the available computational power and (4) characterization of fully differentiated wood, as our main basis for comparison.  The research will involve an ongoing cycle of experimentation and model formulation.

A range of research projects will be undertaken with a focus on measuring and quantifying the dynamics of xylogenesis.  Understanding plant responses to fluxes in environmental conditions will be a priority of the research.  In particular, measurements will be made of temporal and spatial variation in physiological processes, differentiation and developmental dynamics and proteomic/metabolomic adjustments influencing or occurring in the developing xylem.  Research projects might, for example, be focussed on how rates and duration of fibre expansion vary following release from a drought.  Or, how might wall thickening dynamics be adjusted purely due to variation in day length or circadian effects?

By linking detailed measurements of growth to high-resolution images of wood, it is possible to assess the timing of formation of parts of the wood of interest, and link changing properties to growth responses or particular conditions.

Wood properties in eucalypts change very quickly in response to changes in environmental conditions.  We will be making extensive use of high precision monitoring equipment in concert with detailed wood and cambial sampling techniques to get the bottom of what drives these fascinating responses.  All of the xylogenesis responses which can be observed and quantified need to be seen and understood in the context of the whole plant.  For this reason, a range of research projects will be developed to better understand (and ultimately model) a wide range of ecophysiological processes and phenomena.

High precision dendrometers are valuable equipment that will be used in Eucxylo research.

Ecophysiology and xylem development

One area of particular interest is carbohydrate allocation, and understanding how source-sink or the maintenance of carbohydrate balances by other mechanisms, will influence flows of sugar to the developing xylem. Another area of focus is the effect of environmental stressors such as drought on xylem development.

Linking sap flow and stem size dynamics in eucalyptus provides great insight into water movement and storage, and is an important part of understanding xylem development (see Zweifel et al. 2008).

A small, pilot project last year (just before EucXylo officially kicked off!) by Honours student, Mr. Francis Bouwer, explored the growth responsiveness of E. cladocalyx seedlings to re-watering following cycles of drought.

Collar diameter over time in periodically droughted and irrigated seedlings of E. cladocalyx.

While the periodically droughted trees showed reduced growth overall compared to continuously irrigated trees, the trees responded strongly to watering. But what was the xylem doing?  The underlying xylem formation processes will now be followed up as part of one of our student projects in EucXylo.  Hundreds of samples of developing xylem and the cambial zone were taken from the seedlings to elucidate the xylem developmental dynamics.

Cambial cell fate

A fascinating problem that we hope will be explored in a PhD project in Eucxylo will be to understand how and why cambial cells, after they have become xylem mother cells, become further determined as vessels or fibres (or other longitudinal cell types).

Some fascinating research in poplar has recently used sector analysis to better understand the replenishment/maintenance of cambial cells as initials/mother cells (Bossinger and Spokevicius, 2018).  Other researchers are also exploring a variety of molecular approaches to understanding what “gene switches” operate to determine cell fate.  But beyond that: what mechanisms and processes come into play?

It is particularly interesting to understand what it is that determines that a cell will become a large, conductive vessel.  We need to ask what switch it is that leads to this determined path, and we can learn from the amazing insights of modern molecular biology.  But once a cell is on the “vessel” path, what physiological and developmental mechanisms make it possible to grow to such a large size relative to its neighbours?  What happens to its neighbours?  And important, can we capture these decisions and processes in coherent, integrated mathematical models?

Tubulin is visible as green fluoresced light in a developing vessel in a Eucalyptus globulus tree.  how does such a cell come to be?

Visualising developing xylem

An exciting frontier which students and researchers in the Chair will be facing is that of non-destructively visualising the developing xylem in living, growing plants. What approaches can we use to see the cambium, and expanding and differentiating xylem in vivo, but without destroying the plant? We will be looking at using cutting-edge applications of techniques like MRI-PET and micro- and nano-CT.

One of the most critical “bottlenecks” in undertaking research on xylogenesis is being able to take enough samples of the cambial and developing xylem zones, with little/no damage, with high frequency.  Using traditional methods of embedding and careful sectioning is slow, intensive, and expensive.  It also involves making a wound in the tree, or in small trees, probably killing the specimen.  The images/analyses are very static, providing a “snap shot” of the developing xylem as it was at the point of sampling  One of our goals in EucXylo is to try to push the boundaries of how else we might be able to quickly see, and assess, and characterise the properties of living xylem quickly, inexpensibly and repeatably, with as little damage to the tree as possible.  Ideally, we’d like to be able to live cell imaging of the developing xylem

We’re in the lucky position to have quick and easy access to a Nano- and Micro-CT scanner in our building!  We will be working with the CT-scanner team to see if we can use our CT scanner (we wish we had a synchrotron!) to build on work like that recently published by Earles et al. (2018) to see what kind of detail, at or below cell level, we might be able to see in the cambial zone of fully intact plant stems.

Micro-CT imagery of a 2 year-old Eucalyptus grandis showing embolised xylem (following 24 hours of drying), and a high-density band of tissue between xylem and phloem regions.

Integrating ecophysiology and xylogenesis models

The approaches to undertaking the computational and mathematical analysis are also an important part of our research. How best can we attack some of the very interesting challenges inherent in modelling the differentiation occurring in a complex, three-dimensional tissue such as developing xylem?

Insights from our research will be the basis by which we continually build and improve predictive models at multiple scales. Where our models are weak, or we do not understand how to express or characterise a process in the models, we will go back to the lab to measure what needs to be measured to answer our question.

The models will be incorporated into a software-based simulation framework, which is envisaged to become a platform for scientific collaboration and the generation of new hypotheses and ideas within South Africa and around the world. We plan to implement these models in open-access languages/environments like R and Python, and harness the power of innovations like GEMS developed through our and the AgroInformatics partnership to bring everything together. We’ll be working closely with the new School of Data Science and Computational Thinking.

Wood properties characterisation

An important part of our research will involve characterising fully differentiated wood accurately, in order to make comparisons with the predictions of our models.

This will include a range of cell-scale or tissue-scale properties, including fibre cross-sectional and 3D dimensions (e.g. diameter, or wall thickness or length), vessel distributions, ray locations, etc.  But we’re also interested in being able to characterise physical and chemical characteristics of the cell walls.

Once again, we’ll be taking advantage of the opportunities provided by our local CT-scanning team.  We’ll also be working closely with colleagues like Dr Geoff Downes to use NIR as a non-destructive and lower cost means of getting information on pith-to-bark variability in various chemical properties.

Seeing wood in 3D, created from our Stellenbosch CT scanner

Ph.D. and M.Sc. scholarships

Students from a wide range of backgrounds are welcome to apply, including from applied fields like Forest and Wood Science, Plant Biology, Genetics and Horticulture, or more basic sciences, including Mathematics, Biochemistry, Physics, Chemistry or Biology.

However, we will only consider students who have achieved above-average results in prior degrees.  Some restrictions may apply and applicants can be expected to subject to certain biometric/competency testing.

Doctoral students will have at least one opportunity to present their work at an international conference during their candidature and/or spend some time working at an overseas research lab (e.g. Ghent, Belgium or Brisbane, Australia).  Students must register full time and be based on the Stellenbosch campus of the University.  At least three peer-reviewed publications will be expected from Ph.D. candidates by the time of graduation.

Please send questions, and applications to Dr David Drew (drew [at] sun [dot] ac [dot] za) including the following:

  • All previous degrees and academic records
  • A cover letter giving background to your application
  • A comprehensive and up-to-date Résumé including details of at least two referees.
  • A 1 – 2 page essay outlining your ideas for a possible research direction you would like to take in your Ph.D. project within the EucXylo program.

A wide range of topics are available within the program, and students have great scope to tailor their own research project to their interests and ideas.  Some ideas for potential Ph.D. projects are:

  • Modelling physiological and molecular drivers of vessel determination and formation
  • Fibre growth and wall formation dynamics during drought and with subsequent re-watering.
  • Control of fibre differentiation by regular seasonal variability: day length, temperature and vapour pressure deficit.
  • Sugar-hormone interactions and the mediation of xylogenesis
  • Cause or effect: Linking xylem hydraulic properties, stem stiffness and xylem differentiation
  • Approaches to modelling xylogenesis of reaction wood
  • Control and mechanisms of cellulose deposition and orientation in the secondary wall layers
  • Functional-structural models of  Eucalyptus tree form using L-systems
  • Individual-tree modelling of light interception and carbon fixation

Possible M.Sc. topics include:

  • Using Micro- and Nano-CT to see the living xylem
  • Using Positron emission tomography–magnetic resonance imaging (PET-MRI) to visualize living xylem OR xylem functioning
  • Rapid sample preparation and sectioning of developing xylem tissue
  • Fluorescence and “brightfield” imaging of developing and lignified xylem using stereomicroscopy
  • Tree-level carbon allocation models: a synthesis of available models
  • Estimating canopy conductance and transpiration from individual trees

Students will be provided with office space and computers and will have the opportunity to present at least one research paper at an international scientific conference in South Africa or abroad.  The Chair will also provide some students with the opportunity to be based for a period of time at an overseas lab; this could be in the Democratic Republic of Congo, Belgium, Australia, France, Germany… Please contact Dr David Drew (drew [at] sun [dot] ac [dot] za) for more information.