Settling in

During this first week of my graduate program I have met with my supervisor to discuss the direction of my initial research in his lab. I have been reading up on the latest research into Phytophthora spp and I met with other scientists in the field here at OSU. Initial ideas are for me to study a number of Phytophthora spp on Rhododendrons. I will be studying the epidemiology of the pathogen species in greenhouse and field inoculation experiments. This will hopefully provide a set of comparable data about the similar but different pathogen species and disease development throughout the different seasons of the year in conditions which aim to mimic the commercial nursery environment.

I have been talking to people who have conducted similar studies to learn from them the pitfalls and working methods and modifications to use. I have had a look around the culture lab and the molecular lab. I also visited the farm site where I will be able to carry out field experiments. It is really exciting, there are a whole bunch rhododendron plants waiting for me to use. There is a lot of greenhouse space available both at the lab/office site and at the farm. Also at the farm they have just constructed a gravel lot with a shade structure to shield the potted plants from wind and intense sun in the summer, and this is where I shall be working so I have all this space in which I can design my experiments.

Starting Grad School

I arrived in Corvallis on Monday this week and I've got all of this week to get myself organised, registered and on the pay roll etc. I have met with my supervisor, department head, and cohort. There are about 12 students beginning a graduate program in the botany and plant pathology department (BPP) this year, some of whom are on Masters and others are on PhD programs, some are on graduate teaching assistantships (GTA's) and others are on graduate research assistantships (GRA's). This indicates the source of funding and the type of work you will be doing. I am working for a PhD on a GRA in a lab working on Phytophthora spp, so my funding comes primarily from the USDA, and my work will lab and field research. I have registered for two classes this term, one in applied statistics and data handling, and the other is an introductory course in mycology (the study of fungi). In addition for the duration of my course I will be attending weekly 1hr seminars which will give me a broad understand in the field of plant pathology.

Botany and Plant Pathology

I am about to embark on a PhD program at OSU, where I studied previously. I will be in the botany and plant pathology (BPP) department and I will be working in Dr Niklaus Grunwald's lab on a graduate research assistantship (GRA). Nik's lab is involved in the study of Phytophthora spp. which are oomycete plant pathogens which cause a number of significant plant diseases. Of note are potato late blight (P. infestans), which caused the Irish potato famine, and sudden oak death (P. ramorum) which threatens to be as significant to the worlds oak populations as dutch elm disease was to Elm trees in the UK.

Plant Pathogen Interactions

In addition to attending the TBA field course in Kenya I also obtained BSPP funding for a summer student position at Rothamsted Research in Harpenden, Hertfordshire. I worked with Dr Jon West in the plant pathogen interactions division. I carried out a project on ergot and fusarium of wheat. I arrived at Rothamsted at the time when the wheat was flowering and is susceptible to infection so I was able to carry out inoculation and air sampling experiments in the field. The project aimed to look at the airborne inoculum of the two diseases.

The short report: A study of the airborne inoculum of two mycotoxin producing wheat pathogens

Tropical Biology

Having graduated with a degree in Biology and having spent time in several different laboratories I went looking for opportunities to gain more field experience. I found that the Tropical Biology Association run courses every summer in four different African countries to give graduates in biological sciences training in tropical biology, field work, ecology and conservation. I attended the TBA field course in Kenya in the summer of 2007. During this one month course I worked alongside 23 other course participants from 18 different European and African countries and so apart from gaining training in tropical ecology and field studies I learned a vast amount about different cultures and made friends in many different countries.

During the four week course we spent 10 days camping near the Mpala Research Centre in Laikipia, Central Kenya where we were given a series of research talks and field exercises. This was followed by a one day conference in Nairobi run by the TBA and hosted my the National Museums of Kenya (NMK) and the Kenya Wildlife Service (KWS). We then moved to Lake Naivasha in the Rift Valley where we stayed at the Elsamere field studies centre and worked in Hells Gate National Park (HGNP). During this time we broke into groups of two or three to conduct our own field projects in HGNP and the Lake Naivasha area.

I worked with Christina Ieronymidou (Cyprus) and Evelyn Fosuah (Ghana) on a project looking at the ant acacia interaction in HGNP. We looked at the differences between the ant behaviour and the host tree characteristics of Acacia drepanolobium hosting two different species of ant. We designed the study, carried out the field work, conducted a statistical analysis of our data and produced a written report and presentation.

The written report: Variation in Acacia drepanolobium defence by Crematogaster mimosae and a previously undescribed acacia ant at Hell’s Gate National Park, Kenya

Molecular Plant Pathology

Having enjoyed my time in the plant pathology department at OSU and then learning some molecular techniques at Dstl's microbiology department I was keen to put these new skills into practice when it came to my final year dissertation project at Nottingham. I joined Dr Matthew Dickinson's molecular microbiology lab in the school of Biosciences at Nottingham's Sutton Bonington campus. I worked closely with graduate student Jennifer Hodgetts on a project looking at the sequences of the SecA gene in the bacterial plant pathogens, the phytoplasmas. This project involved the PCR amplification of SecA genes from several different candidata phytoplasma and also the design and optimisation of new primers for this purpose. Upon successful amplification of the SecA gene it was cloned into E.coli for propagation and subsequent purification and sequencing. The SecA gene sequences obtained were analysed to establish the phylogenetic relationships between the SecA genes and to see how these relationships compared with the existing classification system of the phytoplasmas.

View the abstract and discussion here: Phylogenetic Analysis of the SecA gene in Phytoplasmas

Microbiology

During the second summer (2006) of my degree I worked in the Microbiology department at Dstl, with Dr Sarah Maddocks. I undertook a project to construct a suicide vector plasmid to create knockout mutants of a bacterial human pathogen. I went about this work by amplifying flanking regions of the desired gene/DNA fragment and then inserting these into a vector, propagating the vector in E.coli and then amplifying the constructed region of the DNA in the vector and inserting it into another vector to become the suicide vector. I learnt a number of valuable molecular techniques during the course of my time in this lab. I was only just able to succeed in getting the final vector product in the last days of my time here and therefore I was unable to produce a formal written report. I left the project ongoing for others to continue.

Plant Pathology

During the second year of my biology degree at the University of Nottingham I took the opportunity to study at Oregon State University (OSU) on the biology exchange program between the two schools. While at OSU I was able to take up an internship in a plant pathology laboratory run by Dr Walter Mahaffee. I worked for 6 months alongside a graduate student, Amy Peetz, to assist her in her research. The project I helped with involved a series of controlled environment experiments to assess the effect of temperature on the sporulation of hop powdery mildew caused by Podosphaera macularis. It was a challenging project as there were many environmental variables which had to be controlled in order to get results. During the time that I spent working there we did not complete the project, however I did gather enough data to be able to write a short report.

The report: The Effect of Temperature on Sporulation of Hop Powdery Mildew

Animal Behaviour

During the first summer (June - Sept 2005) of my undergraduate degree I worked at the Defence science and technology laboratories (as a Dstl sponsored student) for Drs Peter Pearce and Leah Scott, where I carried out an observational study into the behaviour of the common marmoset with the aim of improving the living environment for the animals in laboratory housing. The study looked at the use of a play cage as a form of environmental enrichment and assessed the animals' use of the facility and the behaviours that were displayed. I worked alongside another student, Rebecca Ross, whose work focused on the effect on the animals behaviour of different flooring types in the marmosets home cages. We each produced a written report of our respective findings. Subsequently I compiled our results into a poster which I presented at the European Marmoset Research Group (EMRG) conference in Milan, in September, 2006.

My report: How the common marmoset (Callithrix jacchus) makes use of the play cage facility in addition to its home environment

The Poster: Quantitative assessment of space in laboratory housing