- There is a button for you to access my google calendar so you can see when I am available and when I am busy. You might find this useful if you want to phone me so you can call when I am not in a seminar, class or meeting. I'm not entirely sure what info you can see, I believe that you can only see busy/free rather than the details of my diary. Also this may only work if you have a google account. Whatever, let me know if there are problems with it.
- PhD comics is a fun site ideal for procrastination and hits on some funny and scarily true issues relating to my situation as a grad student in the US.
- the Meebo widget is a tool for instant messaging me if I am logged in, or leaving a message for me even if I am not online. This is a bit new to me but give it a go, I don't think you need a log in to message me, the OSU library uses this for students to ask questions to the library staff online.
- I added my facebook profile so add me if you haven't already.
- I recently discovered a new breed of charity of which KIVA.org is one. They facilitate microfinance initiatives in developing countries. You chose an entrepreneur and loan them money for their business. You should get the money back after 6 months and are free to re-loan or retrieve the money. Money dealing is through paypal so if you are in the UK you can still sign up through the US based KIVA plus pounds buy a lot of dollars these days so your money can go a long way.
- Finally I added a slide show of my photos from Kenya this summer (2007). At the moment there are only about 5 pictures but I plan on putting more up at some point.
News from my blog
In case you haven't been paying attention to the stuff on the left had side of this page I have been adding some new features I would like to point out to you, from the bottom up.
More on the Lwet sensors
OK - with the help of Tom, Walt and Nik we re-wired the C sensor and it is now giving sensible resistance output data (brown line) so three sensors are now mounted and wired and programmed successfully to the data logger and the remaining sensor is almost ready to go, however it is a little different as it links to a different data logger and gives % data rather than raw output so that will make comparisons difficult. Below is a graph of test data from my office, and below that is a photo and a diagram of the sensor set up.
Classes and Grades
The term is over and I got an A- in Mycology and an A in Statistics. Next term I will be taking the follow on Stats class which I expect to struggle in as this term we had a professor who was lenient with grades but who I didn't fully understand so I fear I will find it hard to move onto next terms syllabus. Anyway, I will also be taking a class in environmental physiology of plants which sounds interesting. It is nice to have two A's in the first term, it gives me a kind of buffer so that when I am in the midst of research I can focus on that more than classes and if I get the odd C I can still average a B grade, which is what I need to maintain my research assistantship (which is what pays me). This week I am frantically trying to make progress with my 2 research projects so that I can get to a point where I will be ready to dive into more practical stuff at the start of the winter term and start collecting data. I also want to find a bunch of papers to take home to read over the break.
TBA report
I have posted the TBA sponsors report that I have finally written on the reports page of this site. I have not sent the letter off yet so I am open to comments or advice on the letter. You can read it here. I'll e-mail it to the TBA office next week. It is supposed to give a summary of what I learnt and what were the highlights of the course. I think I might send this letter also to the Biology Dept at Nottingham to encourage other students to apply for it.
Woooo Data!
Well I've finally wired and programmed the sensors and I'm getting some sensible data from the data-logger! Yay. So here are a couple of graphs. As you can see when I added water to the capacitance sensor the capacitance increased and gradually decreased as it dried. And as expected the resistance decreased in the resistance sensor with the application of the same spray of water. Well these are just the first steps, I still have to get the other 2 sensors working and then move to the growth chambers for the real experiment.
Leaf wetness sensors
Here are three of the leaf wetness sensors I will be looking at. The dark green one is plastic coated, the middle one is a resistance sensor and I have sprayed it with a coating of latex paint, and the right sensor is a device which uses filter paper or felt to make the connection between the electrodes.
This is one of the data loggers I will be wiring up to collect the data from the sensors:
This is the stand I made last week on which to mount the sensors:
Here is my office space! More data loggers and bits and bobs for stands, batteries and other stuff:
This is one of the data loggers I will be wiring up to collect the data from the sensors:
This is the stand I made last week on which to mount the sensors:
Here is my office space! More data loggers and bits and bobs for stands, batteries and other stuff:
USDA site and making sensor stands
Today was quite productive, I found some materials and tools in the workshop and having measured the growth chambers I built the first of 4 frames on which to mount the sensors that I shall be comparing. I have cut all the pieces of PVC piping to make all 4 frames but there were not enough joint fittings to get them all assembled. I've also now got my hands on all the datalogger boxes which are taking up a lot of space in the office so I'm not sure what my office mates think of that, but I've assured them that it is temporary. I'm going to try to wire them all exactly the same so that I can use the same program to collect all the data from each replication of the experiment. Unfortunately I have a midterm test on Friday morning so all of this exciting stuff will have to go on hold while I study for that.
Here is an image of where I work. If you look closely there are some tiny yellow numbers, 1 is where my office is, 2 is where Nik's office is and also the lab, 3 is my greenhouse, 4 is the workshop and 5 is the growth chamber building.
Here is an image of where I work. If you look closely there are some tiny yellow numbers, 1 is where my office is, 2 is where Nik's office is and also the lab, 3 is my greenhouse, 4 is the workshop and 5 is the growth chamber building.
Oomycete Biology - an alternative version
following on from the post Oomycete biology, and alternative version by David Brock:
Phytophthora is the beautiful wife of the Greek tycoon Genius. A bunch of speculators work with the Genius plotting to overthrow the Pathogens, the economically significant supporters of Phytophthora. She is in love with Oomycetes (better known as Walter Mitty). With his sister Oomycota he escapes her by taking a taxi to Phylum in the Kingdom of Stramenophila, leaving her in the Kingdom of Fungi where she listens to classical music. The Fungi fight off Oomycetes who forever after is called Pseudofungi by the people of Fungi.And by Clare - by way of an update on my cultures, and inspired by David to use as much mycological jargon as possible:
In Act II Queen Stramenophila, from her cell high above the Chitin, distinguishes Oomycetes far off, separates from her husband Septae and, to defeat Mycelial (who has deployed nuclear weapons), sends her servant Sporangia to Oomycetes with the key to her cell.
Unfortunately, Flagella, the composer, died before he could finish the work though notes for Act III suggest there was the usual hanky panky you get in opera.
Phytophthora cactorum and P. citricola are homothallic (they don’t need a partner) and therefore are individually prolific in their production of sexual oospores invitro. P. cinnamomi has produced a few chalymidospores (asexual resting spores) but refuses to produce any sporangia invitro without an offering of soil extract. P. cambivora is beginning to produce the sporangia desired for the preparation of zoospore inoculum to infect my rhododendrons. The others are still in the hyphal state but I have made some three plug plates in the hope that this may excite some of the isolates to reproduce. If not then further action must be taken to induce the production of sporangia.
The general plan so far
So far Nik and I have discussed rough plans for three projects to possibly result and a publication each and therefore form three chapters in my thesis.
One project will be to compare different leaf wetness sensors available (with the use of a weather station and data logger). This could result in a methods type paper.
Another project will be characterising the disease symptoms and comparing disease progress of various Phytophthora spp over the seasons of the year on Rhododendron starting in controlled environments and then moving to the field with non quarantine Phytophthora spp (this will also utilise weather station data which is an important consideration in epidemiology).
Finally a similar project but to looking at quarantine Phytophthoras such as P. ramorum and P. nemorosa so this work will not be in the field but in the quarantine chamber unless we set up a field station in an infected county in Oregon or California at a later date.
The first two projects are underway and I hope to complete the first in my first year.
One project will be to compare different leaf wetness sensors available (with the use of a weather station and data logger). This could result in a methods type paper.
Another project will be characterising the disease symptoms and comparing disease progress of various Phytophthora spp over the seasons of the year on Rhododendron starting in controlled environments and then moving to the field with non quarantine Phytophthora spp (this will also utilise weather station data which is an important consideration in epidemiology).
Finally a similar project but to looking at quarantine Phytophthoras such as P. ramorum and P. nemorosa so this work will not be in the field but in the quarantine chamber unless we set up a field station in an infected county in Oregon or California at a later date.
The first two projects are underway and I hope to complete the first in my first year.
Midterms
While last week turned out to be rather unproductive on the research front due to midterm exams, this week has been jam packed. I have been in the office/lab most of the time and I've started to play around with the brand new weather station equipment, it's all here set up in my office and I've been wiring different sensors into the data logger and I'm learning to program the software to instruct the data logger on how to collect and manipulate the signals into data. I also went through my cultures with Virginia yesterday and they are all going really well, they are growing fast and there were sporangia on one of the species, chlaymidospores on one, and lots of oospores on two of the Phytophthora spp so that is encouraging. I now need to come up with some strategies for continuing with these isolates and a rough experimental design so that I can start to do something with them. I have a meeting with Walt and Nik tomorrow to talk about the weather stations and plan the experiment in more detail.
Progress
At last I have got to doing some practical work. This week I obtained isolates of Phytophthora species from the long term storage in our lab and from another lab on campus also working on Phytophthora spp. and I transfered them onto bigger plates to get them going a little and hopefully begin to play with them and try to get some of them sporulating so that I can move on to inoculate some Rhododendron leaves. I also had a meeting with Nik and Walt about an idea to study leaf wetness sensors so I am going to learn to use the weather station and try to get things set up in my office for that too. Aside from these things it is midterms week so I have had two tests and on Friday I have a lab practical exam for mycology.
Oomycete Biology
Not a lot has happened this week. I have spent a lot of time identifying the mushrooms that I have collected for my mycology class. I am waiting for the lab technicians to grow some of the Phytophthora spp. I asked for from storage onto plates so that I can begin to work with them.
I thought I’d take this opportunity to explain a little of the biology of the organism that I am working with. Phytophthora is the genus and there are a bunch of species within this genus which are economically significant plant pathogens. Phytophthora spp. are Oomycetes (commonly termed the water moulds). ‘Oomycota’ is the taxonomic Phylum, and this is in the Kingdom ‘Stramenophila’, not the Kingdom Fungi as they were once classified. Oomycetes are sometimes termed pseudofungi as they closely resemble Fungi.
The key features which distinguish the oomycetes from the real fungi are their cell walls and their spores. Real fungal cell walls contain chitin, but the oomycete cell walls contain cellulose (as do plant cell walls). The hyphae of pseudofungi are not separated by septae, and the mycelial nucleus is diploid, with two sets of chromosomes. Oomycetes can reproduce both sexually (oospores) and asexually (sporangia, zoospores, chlamydospores). Zoospores are motile with two hair-like flagella propelling the zoospore through liquid, oospores, on the other hand, are non motile. In general sporangia are the survival and dispersal mechanism and zoospores are the infection mechanism.
Federal Holiday
So I went into work at around noon today, after classes this morning only to find the office shut, the doors locked and hardly anyone there and it turns out that it is Columbus day which means a bunch of people skip work for the day, but schools are still in session. Well, Nik was still in his office so I was able to talk to him and we discussed a bit about the directions of my research and the possibilities for the content of my thesis. He suggests that I should plan for between 3 and 6 chapters and that I should treat each chapter like a paper with the potential for publication. He also came up with a new idea about doing a study on the differences between various leaf wetness sensors which could result in a methods paper publication which has a guaranteed high citation rate and would be a good starter project for me to get me familiar with the weather station equipment and the statistical tools used in epidemiological studies.
Aside from this I am still working on identifying the isolates I am going to work with initially and then getting them growing on plates so that I can actually begin some detached leaf inoculations and stuff.
And one other thing - I just added a new link to my photography page which at the moment only has some photos from the work I did at Rothamsted this summer, but there will be more to come, including microscopy images and specimens from my mycology collection for a class I am taking this term.
Aside from this I am still working on identifying the isolates I am going to work with initially and then getting them growing on plates so that I can actually begin some detached leaf inoculations and stuff.
And one other thing - I just added a new link to my photography page which at the moment only has some photos from the work I did at Rothamsted this summer, but there will be more to come, including microscopy images and specimens from my mycology collection for a class I am taking this term.
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.
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.
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.
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
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
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
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