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Research projects for Bachelor and Master students 2013-2014 Student projects for Plant Ecology & Phytochemistry


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Research projects

for Bachelor and Master students
2013-2014


Student projects for Plant Ecology & Phytochemistry
Section leader Prof. Peter G. L. Klinkhamer

p.g.l.klinkhamer@biology.leidenuniv.nl

http://science.leidenuniv.nl/index.php/ibl/pep
Themes:


  1. Green plant protection

  2. Plant defence

  3. Invasive plants

  4. Pollination biology

The group works on these four themes. Theme 1 and 2 are important for the development of alternative pest management to reduce energy and pesticide inputs in agri- and horticulture. Theme 3 relates both to agriculture and to biodiversity. Invasive plants disrupt the ecosystem. There is also concern that Genetically Modified plants escape into the environment. For both questions we are interested in why some plants become invasive and others not. In theme 4 we make pollinator webs of ecosystems and are concerned about how the pollination crisis would affect biodiversity of plants and yield in agriculture.


Bachelor research projects start at the end of your bachelor program (c. February) and are 24 EC. At the start you make a project proposal and in the end give a final presentation in the research group. You attend the scientific meetings of Plant Ecology (each Monday at 9.30).
Master projects can start anytime and we make an agreement about the number of Ec’s.

We are member of the Research School Experimental Plant Sciences that is very active in organizing courses and meetings, which you can attend free of charge. The Research School also has funding for MSc students that are excellent and want to do a PhD in this field

Our students become familiar with a variety of techniques, which could involve using NMR, measuring alkaloids, molecular genotyping, estimating herbivory with imaging software, doing herbivory experiments. There is an emphasis on setting up experiments with a clear hypothesis and rigorous statistical testing. Students find amongst others jobs as PhD’s in ecological research or at seed breeding companies.

BACHELOR PROJECTS


THEME 1
1 + 1 ≠ 2 but 1 + 1 =3!
Info: Kirsten Leiss/Rita Rakmawati

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss





Carrot is a healthy vegetable containing high amounts of phenols. A phenol rich diet is known to reduce the risk of cancer and cardiovascular diseases. Phenols are also involved in host plant resistance to western flower thrips (Frankliniella occidentalis), a key agricultural pest worldwide. The phenols sinapic acid and luteolin as well as the amino acid β-alanine have been identified to confer thrips resistance in carrot (Leiss et al., 2013). All three metabolites increased thrips mortality at plant concentrations ranging from 25 to 100%, when tested singly in in-vitro bioassays. In a recent BSc internship we discovered that the combination of sinapic acid with either luteolin or β-alanine led to an even stronger resistance then the compounds alone.

This is the first report of synergistic effects in thrips resistance. In this project you will investigate whether it is a general rule that the combination of these compound classes leads to synergistic effects. You will test the effect of different phenylpropanoids, flavanoids and amino acids at various concentrations, singly and in 1:1 mixtures on thrips mortality. The findings are of relevance for healthy plant protection using compounds with positive effects on human health and negative effects for thrips.
- Reference: Leiss et al. (2013) An eco-metabolomic study of host plant resistance to Western flower thrips in cultivated, biofortified and wild carrots. Phytochemistry 93: 63-70.

- Techniques: Preparing solutions and dilutions, in-vitro thrips bioassays

- Level: Bachelor student

Can light improve control of thrips?
Info: Kirsten Leiss

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss




Western flower thrips (Frankliniella occidentalis) is a major insect pest in vegetables worldwide leading to substantial economic losses. Thrips is mainly controlled by synthetic pesticides, which leads to problems with insecticide resistance, human health and environmental contamination. As an alternative we investigate host plant resistance to thrips. As such we maintain a tomato, which is resistant to thrips based on secondary metabolites excreted by leaf hairs.

Increasing evidence suggests that the perception of light at different wavelengths is strongly influencing leaf hair density as well as the production of secondary metabolites. Therefore, in this project you will investigate whether UV light changes leaf hair density and whether this has effects on thrips resistance. The findings are of relevance for sustainable plant protection in tomato.


-Techniques: Rearing plants, microscopy, whole plant thrips bioassays, collection of plant material for metabolomic analysis

- Level: Bachelor student



Do thrips biotypes affect host plant resistance in chrysanthemum?
Info: Kirsten Leiss/Suzanne Kos

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss




Western Flower Thrips (Frankliniella occidentalis) is one of the major pests in chrysanthemum, which represents one of the most important ornamentals in Dutch horticulture. The main form of thrips control is the use of pesticides. However, high pesticide use is problematic in relation to human health and environmental risks. To diminish the use of pesticides we work on chemical host plant resistance to thrips. We established that different biotypes of western flower thrips do occur in the Netherlands (Mirnezhad et al., 2012). In this internship you will investigate whether different WFT biotypes affect host plant resistance in chrysanthemum.


- Reference: Mirnezhad et al. (2012) Variation in genetics and performance of Dutch western flower thrips populations. Journal of Economic Entomology 105: 1816-1824.

-Techniques: Rearing plants, plant thrips bioassays

- Level: Bachelor student

Host plant resistance as a tool for sustainable plant protection in sweet pepper

Info: Kirsten Leiss

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss

Western flower thrips (Frankliniella occidentalis) is a major insect pest in vegetables worldwide leading to substantial economic losses. Thrips is mainly controlled by synthetic pesticides, which leads to problems with insecticide resistance, human health and environmental contamination. As an alternative we investigate host plant resistance to thrips. In this project you will investigate host plant resistance in sweet pepper varieties regarded to be resistant or susceptible as provided by one of the Netherlands major seed companies. You will look at morphological characters, thrips damage and reproduction. The findings are of relevance to sustainable plant protection in sweet pepper.

-Techniques: Rearing plants, whole plant thrips bioassays, thrips reproduction assays, measurement of morphological characters, collection of plant material for metabolomic analysis

- Level: Bachelor student




Natural plant defence compounds against evil doing leaf miners

Info: Kirsten Leiss/Rita Rakmawati

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss

The wild ragwort plant (Jacobaea vulgaris), occurring in the Dutch sand dunes, produces many different pyrrolizidine alkaloids (PAs) to defend itself against herbivores. In preliminary observations we established that plants rich in otosenine-like PAs showed less damage to serpentine leaf miner (Liriomyza trifolii) a serious threat to vegetable growers worldwide. We are the only University having a rearing of this quarantine pest. In this project you will investigate whether plants with high or low concentrations of otosenine PAs differ in leaf miner damage. You will conduct plant bioassays as well as in-vitro bioassays with isolated PAs. The findings are of relevance to the evolution of alkaloids as secondary plant defence compounds and may be used for sustainable plant protection against leaf miner.


- Techniques: Rearing plants, plant leaf miner bioassays, in-vitro leaf miner bioassays

- Level: Bachelor student



Can natural compounds from endemic Canary Island plants control human and plant pathogens?

Info: Kirsten Leiss

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss


Endemic Canary Island plants contain plant defence compound active against herbivores Extracts of these plants containing pyrrolizidine alkaloids (PAs), as well as PA free extracts, showed negative effects against different insects (Dominguez et al., 2008). Their effect on pathogens is assumed but has never been tested. In collaboration with this Spanish research group we established some preliminary negative effects of the extracts on the fungus Aspergillus niger, which attacks plants and humans alike. In this project you will test a range of extracts from endemic canary island plants with and without PAs at different concentrations on negative effects on A. niger. You will further investigate whether combinations of PA and PA free abstracts may increase negative effects in comparison to activity of single compounds. The findings are of relevance to natural pathogen control.


- Reference: Dominguez et al. (2008) Pyrrolizidine alkaloids from Canarian endemic plants and their biological effects. Biochemical Systematics and Ecology 36: 153-166.

- Techniques: Preparing solution and dilutions, in-vitro pathogen bioassays

- Level: Bachelor student
Herbivore and pathogen in Carrot: do they interact with each other?
Info: Kirsten Leiss/Rita Rakhmawati

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss


Understanding the indirect interaction between a plant pathogen and herbivore requires further study. This interaction can occur when infestation by a first attacker changes the host plant in a way that affects a second attacker that is spatially or temporally separated from the first. Production of secondary metabolites may have an important role in antagonistic and/or synergistic interactions. In our previous research, we discovered that three metabolites (sinapic acid, luteolin and the amino acid alanine) in carrot (Daucus carota) have been identified to confer thrips resistance in carrot (Leiss et al., 2013). This is the first report of synergistic effects in thrips resistance.


In this project you will investigate the indirect plant-mediated interactions among two pests and assess their effect on herbivore and plant pathogen performances. You will use a piercing-sucking thrips (Frankliniella occidentalis) and necrotropic fungus Alternaria dauci on the experiment. You will measure lesion size of the pathogen (A. dauci) and the number of thrips larvae. The findings could be useful for Integrated Pest Management (IPM) purposes and lead to reduction of the use of pesticides and fungicides. Students with this sort of skills often find jobs in plant breeding and related companies.



  • Reference: Leiss et al. (2013) An eco-metabolomic study of host plant resistance to Western flower thrips in cultivated, biofortified and wild carrots. Phytochemistry 93: 63-70.

  • Techniques: Preparing solutions, study of insect behaviour, practical work (experiment) with thrips and fungi.

  • Level: Bachelor student


THEME 2

Cross-resistance between ragwort and its insect herbivore

Info: Xianqin Wei and Klaas Vrieling

Phone: 071-5275136

Email: k.vrieling@biology.leidenuniv.nl;


Background:

Green plants cover most of the land on planet earth and they are under continuous herbivore pressure of insects, the dominant and numerically diverse plant consumers. Plants and insects have been evolving together for over one hundred million years with varying levels of interactions leading to the selection of characters.

In this interaction between plants and herbivorous insects, plants are trying to avoid consumption, and insects are trying to optimize food exploitation. Why is the earth still green even there are so many insect herbivores eating plants every day? Why are some plants eaten by many herbivores while others by almost none? To experimentally test these questions, we use ragwort and its herbivores as a model system.
Research question:

If you have interests in exploring the secrets between plants and insects, we have a research project focusing on cross-resistance. If a plant has built up resistance against one herbivore, would that plant also be partially resistant against other herbivores?



Duration: 5 months

Starting date: February 2014

Techniques: The techniques you would learn in this project: plant tissue culture; culturing plants; culturing different insect herbivores; developing and performing bioassay tests.


THEME 3
Are slugs the exception to the rule?
Info: Tiantian Lin and Klaas Vrieling

Phone: 31(0)684403593

Email: t.lin.2@biology.leidenuniv.nl; k.vrieling@biology.leidenuniv.nl
Globalization of the world has led to an unprecedented transport of plants and animals over the world. Many plants species did establish in new areas and developed into a pest in their new ecosystem. Knowledge of what makes species become invasive is important for predicting the potentially invasive species before introduction and controlling the existing invasive species.

A generalist herbivore is able to thrive on a wide variety of environmental conditions and feed on a variety of different food resources. A specialist herbivore can only thrive on a narrow range of environmental conditions or feed on a limited diet. Theory predicts that when plants are introduced into a new habitat, they leave their co-evolved natural specialist enemies behind and are released from detrimental herbivore pressure, therefore they can fast increase their distribution and abundance.

Slugs can feed on a wide variety of vegetables and herbs, which can be considered as generalists. In our previous study, we fed the Deroceras reticulatum (grey garden slug) with native and invasive Jacobaea vulgaris (common ragwort) and in contrast with theory we found this slug species preferred the invasive plants. We now want to know if this is a general trend for slug species and we like to know why they prefer invasive plant genotypes over native plant genotypes. A follow up experiment showed the slugs also preferred the leaf juice from the invasive genotypes. Therefore we would like to continue testing Jacobaea vulgaris with different slug species to see whether it is a common preference among other slug species or it is only species specific. Furthermore we will continue doing some morphologic and chemical analysis to test the difference between native and in invasive Jacobaea vulgaris, which might give us an explanation of such an extraordinary feeding preference of slugs.
Duration: 5 months

Starting date: February 2014

Techniques: rearing plants and culturing slugs, morphologic and chemical analysis





Do mice discriminate between seeds of different Brassica varieties and why?
Info: Tom de Jong

Phone: 071-5275118

E-mail: t.j.de.jong@biology.leidenuniv.nl
Oilseed rape (Brassica napus) is a common crop in Europe that is grown for making oil, animal feed and bio fuel. It can also establish population along roads that grow together with its wild relative Brassica rapa. Because Genetically Modified varieties of the crop exist and are imported (farmers are not yet allowed to grow them here) there is concern that these seeds form feral populations. Which varieties of oilseed rape are most persistent and why?

It turns out that old varieties of Brassica napus are more persistent and these cultivars have high concentrations of both erucic acid and glucosinolates. Modern canola varieties with low concentrations of these substances disappear rapidly from roadsides. It is unclear why this is the case. Insects do not discriminate, slugs and birds do. The role of mice as seed predators is totally unknown.


Seeds with different concentrations of glucosinolates and erucic acid are presented to mice in a natural environment and seed predation is observed.
Techniques: estimating seed predation by counting and weighing seeds, video observations on mouse feeding behaviour

MASTER PROJECTS


THEME 1

Can plants leach plant defence compounds into the soil to keep pathogens at bay?

Info: Kirsten Leiss/Ria Mustafa

Phone: 071 5275135

E-mail: K.A.Leiss@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/leiss

The wild ragwort plant (Jacobaea vulgaris), occurring in the Dutch sand dunes, produces many different pyrrolizidine alkaloids to defend itself against insects and pathogens. So far, research focused on their effect against insects while relatively little is known about their role in defence against pathogens. The alkaloids are produced in the roots. In this project we want to investigate whether Senecio can leach alkaloids from the roots into the soil and whether this has an effect on soil pathogens. Using a colorimetric assay you will first study the leaching of alkaloids from tissue culture plants into agar. Thereafter, you will study leaching of alkaloids from potted plants into sterilized and non-sterilized soil establishing an adequate extraction procedure. These extracts can then be used in in-vitro bioassays to establish their effect against pathogens. Time permitting, the extracts can be used to identify the alkaloids involved using LC-MS. The findings are of relevance to the evolution of alkaloids as secondary plant defence compounds.


Techniques: Rearing plants, soil sterilization, colorimetric PA assay, PA extraction, in-vitro pathogen bioassays

Level: Master student




THEME 2
The effect of nutrients on pyrrolizidine alkaloids in Senecio and their interactions with soil microbial community
Info: Yan Yan and Peter Klinkhamer

Phone: 071-5275117

Email: Y.Yan@biology.leidenuniv.nl and p.g.l.klinkhamer@ biology.leidenuniv.nl
Secondary metabolite concentration and composition depends on the genetic factor, but also on other circumstances. Nutrients (NPK) enrichment could influence the growth and abundance of many organisms. Plant growth varied in response to increase fertilization. The role of nutrients affects on secondary metabolites production especially pyrrolizidine alkaloids (PAs). Senecio with low PAs should increase plant growth and make host plants resistance to herbivores and microorganims attack. Besides, PAs in senecio are selected with different microbial community. The aim of this experiment is to combine the effect of nutrients on pyrrolizidine alkaloids (PAs) in Senecio with those studies of interactions with soil-borne micro organisms.
In this study, we would like to study how does nutrient serials affect plant growth? Does the plant behaviour different in the same soil during study? Does the PAs content differ among nutrient manipulation in different soil types? Does the microbial community change after increasing nutrients?
Study system

Sj6 genotype will be used. Five types of natural soil from different sites (three parts from Ede station, Lisse, Meyendel) will be included. Combine sterilized soil with inoculated 5% nonsterilized soil into their own sterilized soil to establish. The nutrient availability in those soils will be measured. The soil microbial community of those soils will be determined before and after nutrients manipulating. Five nutrient serials with 5 replicates in each group will be used.


Previous experiment with nutrient series to study whether or not the effect of inoculation is through the effect of microbes on the nutrients (Fig 1). It shows the negative effect of microbes immobilized of nutrients in non-sterilized soil and influence plant growth. The optimum nutrient shifted between those sterilized and non-sterilized soil.

THEME 3

Does the invasive slug Arion lusitanicus have a different food preference than the native A, rufus?


Info: Tom de Jong

Phone: 071-5275118

Email: t.j.de.jong@biology.leidenuniv.nl

The slug community in the Netherlands has changed. The slug Arion lusitanicus was extremely rare 10 years ago but is now found everywhere in the Netherlands. It relative, the native Arion rufus, rapidly disappears. It is unclear why this is the case, but one of the reasons might be that A. lusitanicus accepts a wider range of food plants. The slugs feed at night and mostly unnoticed on seedlings so if the slugs indeed have a preference for different food plants this change in the slug community will have profound effects on the vegetation. Slugs eat seedlings of some species but totally reject seedlings of other species. Insect herbivory has been frequently studied but it is unknown how plants can defend against slugs. In this project you will grow different plants and genotypes and will then examine whether the preference of the two slugs is the same of different. You will also put extra substances in the diet (like glucosinolates) to see whether they discourage feeding.

Duration 4-8 months
Start March-April
Reservation: we have now grown several generations of A. lusitanicus in the lab without problems. We are in the process in setting up lines for A. rufus but this must go well (many slugs to be used in experiments) before this project can start.


Arion lusitanicus. A. rufus looks very similar and can only be distinguished by looking at the reproductive organs.

THEME 4



Male fitness of radiate and non-radiate flowers of ragwort

Info: Klaas Vrieling/Peter Klinkhamer

Phone: 071 5275135

E-mail: K.Vrieling@biology.leidenuniv.nl

Web page: http://science.leidenuniv.nl/index.php/ibl/vrieling

Ragwort (Jacobean vulgaris), is quite common in The Netherlands and a polymorphisms exists in ray morphology. The subspecies dunesis lacks ray flowers and is abundant in the dunes of Meijendel. Next to the rayless subspecies dunensis there is also the variety "nudus" of the subspecies vulgaris that occurs in inland populations.

We are interested to know if male fitness of ragwort plants is influenced by the presence or absence of ray flowers. We have raised several plants of a polymorphic population of Jacobaea vulgaris vulgaris. We would like to measure pollinator visitation rates in artificial population and couples this to female fitness (seed production) of the plants and male fitness (pollen transport). Male fitness of plants will be estimated by pollinator behaviour and SNP genotyping of the offspring using the SNP line. The SNP line allows accurate measuring of male fitness, which is unique in the world. This project combines fieldwork and molecular work.

This project can only be carried out during the natural flowering period of ragwort starting half of May.


Techniques: Pollinator behaviour, growing plants, DNA extraction, SNP genotyping.

Level: Master student



Who visits whom in plant – pollinator networks?
Info: Martina Stang (Peter Klinkhamer and Eddy van der Meijden)

Phone: +31 71 527 5126



E-Mail: m.stang@biology.leidenuniv.nl
 

Understanding interaction patterns between flowers and pollinators at the level of whole communities is important for biodiversity conservation because species form a complex web of interactions. A change in species composition due to species loss might change the interaction patterns of the remaining plants and animals and thus influence the stability of the whole community. Previous studies revealed (Stang et al. 2006, 2007, 2009) that interaction patterns could be explained surprisingly well by nectar depth, tongue length and the abundance of plant and pollinator species. It is likely that the knowledge about who visits whom and especially how often will be further improved by including additional factors, e.g. those based on potential allometric scaling relationships between body mass and visitation rate, and number and size trait offs for plants. Potential questions are: Is visitation rate of flower visitors related to body mass or tongue length? Is nectar production rate of flowers related to nectar depth? Are nectar depth or nectar production rate related to visitation rate of flower visitors? The setup of the study can be observational (using a subset of the plant and insect species of a meadow or dune community) or experimental (using potted plants in experimental arrays). The analysis of the data will be based on simple probabilistic models, regression analysis or analysis of variance, depending on the chosen study set up.

Duration: 6-9 months (Bachelor or Master)

Period: March – December

Techniques: Fieldwork at the community level, determination of species, measuring of size parameters of flowers and flower visitors, measuring flower visitation, nectar production.

Place field work: In the dunes of Meijendel (NL) or the Rocky Mountains (Rocky Mountain Biological Laboratory, Colorado (RMBL), USA), 6 to 12 weeks (between May and September (NL) or June and August (USA). Stay in the US together with Martina. Car or driving license is not needed. Application for housing at RMBL until 15th of January.

Costs for stay at RMBL: Between 2000 and 3000 Euro (depending on length, cabin, meal plan, and flight costs). Good chance that this money can be raised by the student via funding organizations (e.g. RMBL, LISF, deadlines: 15th of January and 30th of March).
For more info: website Martina Stang (Plant Ecology) and RMBL (http://rmbl.org)



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