PhD projects round 4
1.
2.
3.
4.
5.
6.
Adaptive response of woody plants to grazing, burial and denudation stress in dry mobile sands in
Inner Mongolia
The role of the exocyst in targeting exocytosis during cell plate formation
Biological behaviour of optically addressable nanoparticles and the possibility to use them for
sensitive and highly specific detection of bacteria and malaria in blood
Super-THz receiver based on a quantum cascade laser and a HEB mixer for atmospheric space
research
UHP metamorphism of eclogites and subsequent retrograde metamorphism, magmatic and
hydrothermal activities in western Dabieshan and Qinling: investigations by 40Ar/39Ar stepwise
crushing, laser microprobe and laser stepwise heating techniques
Isolation and Characterization of Fusarium Mutants altered in virulence
1. Adaptive response of woody plants to grazing, burial and denudation stress in
dry mobile sands in Inner Mongolia
Starting date: 1 September 2008
PhD candidate: Liang Xu
Supervisors: Prof M J A Werger, Prof Ming Dong
Involved Netherlands Institute: Department Biology, Plant Ecology & Biodiversity, Utrecht University
Involved China Institute: Institute of Botany, Beijing
Abstract:
Globally desertification is occurring at an unprecedented rate, and this problem is mostly concentrated in
(semi)arid regions including large parts of Inner Mongolia. Probably the most important cause of
desertification is overgrazing. The opening up of the vegetation due to this overgrazing results in sands
becoming mobile. Consequently plants are either covered by sand (burial) or sand is being blown away
around their roots (denudation), both of which can aggravate the effects of overgrazing. Great costs are
made in attempts to stabilize the sands and regulate grazing. But the successful application of these
conservation measures requires extensive knowledge of how plants respond to different combinations of
burial/denudation and grazing.
Many plants species have characteristics by which they can mitigate the negative effects of grazing or sand
burial and the reduction in growth due to these stresses are consequently often much smaller than one
would expect. For some species growth can even be stimulated by low levels of grazing or sand burial.
Obviously knowledge of such responses is crucially important to optimize conservation measures and
limit their associated costs. Unfortunately growth responses of plants to either sand burial or denudation
has insufficiently been investigated, and almost nothing is known about how these factors affect growth
when they occur in combination with grazing. In addition most of the work on effects of sand burial has
focused on herbaceous plants, in spite of the fact that woody species are the most suitable candidates for
sand stabilization. Finally, clonal integration – i.e. the situation where plants produce several copies of
themselves which are physically connected and can thus exchange resources – might be an important
adaptation to sand burial but its contribution is not well understood.
In the proposed study we will compare the growth responses of six local woody species from Inner
Mongolia, to different levels of sand burial or denudation in combination with defoliation (which
simulates grazing). These species comprise both clonal and non-clonal species. We further develop a new
approach, designed by us in collaboration with Stanford University, to determine the contribution of
responses of plants at the organ level (e.g. increases in leaf photosynthesis or changes in biomass
allocation) to grazing, burial and denudation to whole-plant performance. In a related joint project the
population dynamics of four of these species are studied under different conditions of grazing and sand
movement.
In combination these studies will provide (1) crucially important data that are needed to optimize
attempts to control grazing and sand movements and thus slow down desertification, and (2) an
important fundamental insight into the way different species from (semi)arid regions are adapted to
combinations of grazing and moving sand.
2. The role of the exocyst in targeting exocytosis during cell plate formation
Starting date: 1 October 2009
PhD candidate: Wenjing Wang
Supervisors: Dr T Ketelaar & Prof A M Emons, Prof Chun Ming Liu
Involved Netherlands Institute: Laboratory of Plant Cell Biology, Wageningen University
Involved China Institute: Center for Signal Transduction and Metabolomics (C-STM), Institute of Botany,
Beijing
Abstract:
The budding of the yeast Saccharomyces cerevisiae is a model system for polarised exocytosis.
In S. cerevisiae, a multi-protein complex has been identified that targets exocytic vesicles during polarised
exocytosis to the cell surface area where they dock and fuse, the exocyst. In budding yeast and mammalian
cells, the exocyst has been characterized as a complex consisting out of 8 proteins: Sec3, Sec5, Sec6, Sec8,
Sec10, Sec15, Exo70 and Exo84. Since plant cells do not expand equally over their whole surface, and the
basis of plant cell growth, like yeast growth, is exocytosis, unequal plant cell expansion must involve polar,
targeted exocytosis. The exocyst is likely to be involved in the targeted delivery of growth materials in
plant cells.
Although the genes that encode the exocyst subunits are conserved in plants, the existence of a
functional exocyst and its precise functions remain to be analysed.
The cell plate is a new cell wall that is formed during cytokinesis after nuclear division of plant cells and
separates the newly formed daughter cells. It is formed by targeted, polarized fusion of vesicles,
containing building materials for the developing cell wall. We have found evidence that Sec5a, one of the
exocyst subunits, interacts with AtPAKRP1, a kinesin motor protein that moves over microtubules and
specifically is involved in cell plate formation. Our evidence provides a novel link between the exocyst and
formation of the plant specific cell plate.
In a series of experiments, we will pinpoint the exact role of the exocyst during cell plate formation and
explore the precise role of the interaction of Sec5a and AtPAKRP1. Firstly, we will perform Sec5a
localization studies, both by fusion of Sec5a to fluorescent proteins and by immuno-localization. We will
perform these experiments on both wild-type Arabidopsis plants and Arabidopsis lines in which
AtPAKRP1 and a homologue gene have been knocked out to test whether AtPAKRP1 is involved in
targeting the Sec5a to the forming cell plate or Sec5a targets AtPAKRP1 to the cell plate. In addition we
will test cell plate formation and Sec5a localization in Arabidopsis lines in which exocyst subunits other
than Sec5a have been knocked out. These experiments, combined with localization studies of other
exocyst subunits, will give information about the role of the exocyst in cell plate formation and more
specifically of the role of individual exocyst subunits in recruiting and targeting the exocyst to the forming
cell plate. Together, with the proposed experiments we will gain insight in cell plate formation, which is a
process that is pivotal during plant development, and the role of the exocyst in
targeting building materials to the cell plate.
3. Biological behaviour of optically addressable nanoparticles and the possibility
to use them for sensitive and highly specific detection of bacteria and malaria
in blood
Starting date: 1 December 2008
PhD candidate: Mr Kai Liu
Supervisors: Dr H Zhang1, Dr W J Buma1 & Dr A M Brouwer1 & Dr M C G Aalders2, Prof Xianggui Kong
Involved Netherlands Institute: 1Van 't Hoff Institute for Molecular Sciences, University of Amsterdam &
2Faculty of Medicine, Dept of Biomedical Engineering and Physics, Academic Medical Center/University of
Amsterdam
Involved China Institute: Changchun Institute of Optics, Fine Mechanics and Physics/Key Laboratory of
Excited State Processes
Abstract:
In nanomedicine, and more specific, in nanodiagnostics, the ultimate goal is to identify disease at the
earliest stage possible, ideally at the level of a single cell. To achieve this goal, research and development
activities in nanotechnology need to be undertaken to improve the effectiveness of in-vivo and in-vitro
diagnostics. Nanotechnology can offer diagnostic tools of better sensitivity, specificity and reliability. It
also offers the possibility to take different measurements in parallel.
Functionalization of the nanoparticles by conjugation with antibody (fragments) or proteins allows
targeting of specific cells or molecules, and by either using their inherent physical properties, or coupling
to therapeutic agents, complete molecular scale management of diseases like cancer and viral infections
may be feasible. Therefore, strategies for in vivo detection and triggering of the nanoparticles need to be
developed. Optical techniques are attractive because they allow miniaturization and cost reduction and
use non-ionizing radiation.
The proposed PhD project has two distinct goals.
The first is to study the behavior of the particles in physiologically relevant conditions where the physical
properties of the nanocrystals may change severely e.g. due to binding to biological molecules. In this
phase, the possibilities, limitations and, most important, the toxicity aspects will become clear. The results
of this phase will be fed back to the synthesis group at the CIOMP. In the second phase, several clinical
applications will be explored, specifically in the field of bacteriology and parasitology. These experiments
will be performed in close collaboration with experts in these fields who will provide us with bacteria
colonies and malaria infected red blood cells. First experiments will be performed in cell cultures to assess
the affinity of the functionalized nanocrystals for the target cells. After these initial experiments, we will
move on to more relevant and complex biological systems, such as the chick chorioallantoic membrane
(CAM) model, which enables measurements in a highly vasularized layer of tissue. With these experiments
we can determine the technical and biological requirements for detecting the particles in the blood
stream. The last step will comprise experiments in small animals.
4. Super-THz receiver based on a quantum cascade laser and a HEB mixer for
atmospheric space research
Starting date: 1 October 2008
PhD candidate: Mr Yuan Ren
Supervisors: Prof T M Klapwijk & Dr Jian-Rong Gao, Prof Sheng-Cai Shi
Involved Netherlands Institute: SRON Netherlands Institute for Space Research Kavli Institute of Nano
Science, Faculty of Applied Sciences, Delft University of Technology
Involved China Institute: Purple Mountain Observatory (PMO), National Astronomical Observatories of
China (NAOC)
Abstract:
Observations of ionic, atomic and molecular lines at terahertz (THz) frequency region provide important
and unique information on the history of the universe, and are the only means of getting insight in the
physical and chemical conditions and its evolution. Similar observations can also provide important and
unique information on the problems related to the Earth's atmosphere such as global warming and ozone
destruction. Hydroxyl (OH) radical is the dominant oxidizing chemical in the atmosphere. It destroys most
air pollutants and many gases involved in ozone depletion and the greenhouse effect. OH emission line at
3.5 THz has been identified as the best candidate for OH profile retrieval because of its brightness and
isolation, as predicted by modeling. To detect this, it is desirable to have sensitive heterodyne
spectroscopic instruments operated in a balloon-borne or a space-borne observatory. Cores of the
instrument are a mixer and a solid-state coherent source as local oscillator operating in the vicinity of
3.545 THz.
Up to now the region above 2 THz is hardly accessible due to lack of suitable heterodyne receivers. In the
existing CAS-KNAW joint research program, SRON/TU Delft together with the Chinese partner (PMO) has
been focusing on the development of THz mixers using superconducting NbN hot electron bolometers for
the 3.5 THz OH line. A breakthrough has been made recently, in which the Dutch team has demonstrated a
new mixer operating at 4.3 THz with an unprecedented high sensitivity (P. Khosropanah et al, Applied
Physics Letters, 2007). We expect even a higher sensitivity if it is operated at 3.5 THz. The reason to start
with 4.3 THz is the availability of a FIR gas laser as local oscillator.
A remaining challenge is the lack of solid-state local oscillators. In this CAS-KNAW joint PhD training
program, we propose to develop a THz quantum cascade laser (QCL), a THz source based on a
semiconductor chip, as local oscillator. As shown by us (TU Delft/SRON), THz QCL holds great promise for
this application. However, to make THz QCL ready for a practical instrument, we propose to focus on
several aspects of the performance, which needs either to be well understood or improved.
The proposed program fits ideally to a long-term R&D and instrument plan within SRON/TUDelft, as well
as PMO. The developed technology can lead to a new instrument to detect the OH line at 3.5 THz in TELIS
(TErahertz and sub-millimeter LImb Sounder) flying on a stratospheric balloon gondola for atmospheric
chemistry (jointly by Germany/UK/NL). It can also potentially lead to a new space mission to follow up
the Earth Observing System (EOS) Microwave Limb Sounder (MLS), which is one of four instruments on
the NASA's EOS Aura satellite, launched in 2004 (The Ozone Monitoring Instrument (OMI), a DutchFinnish contribution, is also one of the instruments) . Thanks to the HEB mixer and THz QCL, such an
instrument will be much more sensitive and compact.
Through this program, a young Chinese scientist will be trained in the field of THz QCL, and PMO will gain
the knowledge on the QCL-HEB system. The collaboration can potentially initiate a joint Chinese-Dutch
space instrument.
5. UHP metamorphism of eclogites and subsequent retrograde metamorphism,
magmatic and hydrothermal activities in western Dabieshan and Qinling:
investigations by 40Ar/39Ar stepwise crushing, laser microprobe and laser
stepwise heating techniques
Starting date: 1 September 2009
PhD candidate: Rongguo Hu
Supervisors: Dr J R Wijbrans & Dr F M Brouwer, Prof Hua-Ning Qiu
Involved Netherlands Institute: Faculty of Earth and Life Sciences Institute of Earth Sciences, Vrije
University Amsterdam
Involved China Institute: Guangzhou Institute of Geochemistry
Abstract:
Rare evidence for Ultrahigh Pressure metamorphism (UHPM) is found when continental crust is
subducted to >100 km depth and exhumed during continental collision. Central China is unique in that
there is evidence for repeated continental collision: 1) the current collision of India und Eurasia, 2)
collision in the Carboniferous-Permotriassic between the Sino-Korean block in the north and the Yangtse
block in the south, and 3) collision during the Ordovician. Together they resulted in the Central Orogenic
Belt of China, extending from Xinjiang to the Shandong Peninsula (Fig 2), the largest collisional orogen on
Earth. In the east, in Sulu and eastern Dabieshan, UHPM took place in the Triassic, whereas further west,
in western Dabieshan, Qinling, Qaidam and Altyn Tagh UHPM occurred in the Ordovician. However, Qiu &
Wijbrans (2006, 2008) retrieved Ordovician (U)HP ages for East Dabieshan eclogite garnets, whilst Jiang
et al. (2001) and others have proposed an additional Carboniferous UHPM phase in western Dabieshan.
Fieldwork in western Dabieshan in 2007 and subsequent U/Pb dating of zircons from eclogites of the
Hong’an block revealed that within the western Dabieshan block there must be different terranes that
recorded metamorphism and exhumation at different times: Ordovician, Carboniferous and Triassic (Wu
et al. Ms).
Thus a more complex evolution of the belt emerges, with evidence of continental collision during at least
two orogenic cycles. Western Dabieshan and Qinling are the areas to study this complex history in detail
because there, evidence for the two cycles is best preserved.
40Ar/39Ar ages of UHP micas are often too old to fit with other age constraints due to the presence of
extraneous argon. This extraneous argon is commonly divided into an excess and an inherited component.
Whereas 40Arexcess is absorbed by minerals during metamorphism from the outside and does not contain
any interpretable age information, 40Arinherited ages record events older than the last event, and thus may
contain interpretable age information. The interplay between inherited and excess components in the 40Ar
content of micas is an unsolved scientific problem. With insight into the argon evolution of metamorphic
fluid in eastern Dabieshan from our crushing experiments and the new information on the tectonic history
of the UHP rocks we expect to shed new light on this as yet unresolved problem.
Outstanding scientific questions to be addressed:
• How far west can we trace the Triassic UHP event, and how far east can we trace the Carboniferous and
Ordovician events?
• Consequently, the question arises whether eastern Dabieshan belongs to the main Ordovician UHP belt
of Central China, as well as to the Triassic belt?
• Do phengites under UHP conditions preserve interpretable inherited age signals from their protoliths?
Anticipated results :
1. New investigation of the UHP metamorphism of western Dabie and Qinling eclogites by 40Ar/39Ar
techniques, resulting in retrograde metamorphic histories for UHP eclogites from the Qinling and Dabie
terranes.
2. Definition of Pressure-Temperature-time paths for individual blocks in the orogen.
3. Testing of the inherited argon hypothesis for commonly observed extraneous argon in (U)HP micas.
4. New constraints on magmatic and hydrothermal activity after UHPM.
5. Comparison of 40Ar/39Ar ages between western and southern Dabie eclogites.
6. Isolation and Characterization of Fusarium Mutants altered in virulence
Starting date: 1 January 2009
PhD candidate: Zhao Chunzhao
Supervisors: Dr C Waalwijk & Dr Th A J van der Lee, Prof Bin Wang
Involved Netherlands Institute: Plant Research International B.V, Wageningen
Involved China Institute: Institute of Genetics and Developmental Biology, Beijing
Abstract:
All major world-wide grown crops suffer from diseases caused by fungi that can have devastating
economic effects on yield and quality of the harvested products. Fusarium species infect numerous plant
species including major crops like barley, wheat, maize, banana, and many ornamentals. In most of these
crops, Fusarium species dramatically affect yield as shown by recent devastating epidemics in the USA and
Canada that resulted in the highest agronomic losses since decades (Windels, 2000). In addition, they also
affect the quality of the harvested product due to the production of mycotoxins that can enter our food
and feed chains with health threatening consequences. The disease pressure of Fusarium in several
provinces in China is among the highest in the world. All available data indicate that Fusarium epidemics
are becoming more frequent, more severe, and more widely spread in China. Consumption of food and
feed contaminated with the mycotoxins (secondary metabolites) produced by Fusarium species poses a
great threat as they can cause serious illnesses and immuno-suppression in both humans and animals.
Intangible systems uncovered: The Barley-Fusarium model was a project of Programme Strategic
Scientific Alliances (PSA) within the Royal Netherlands Academy of Arts and Sciences (KNAW) that aims at
establishing a limited number of Strategic Scientific Alliances in the fields of material sciences,
biotechnology/drug research, and environmental science. The present project focuses on the diseases
caused by Fusarium using barley as a model. Many results have been achieved already including a large
collection of pathogens and resistant barley varieties. Primary molecular biology research of Fusarium and
Fusarium-infercted barley has been completed in China and in the Netherlands. A set of 26 genes required
for virulence of F. graminearum has been identified and these will be studied in detail in the proposed PhD
project using highly advanced phenotyping and expression platforms generated in the PSA.