So today I worked with Adrian, a key member of the GRU, in his work on meiosis and mitosis in crop genetics.
Meiosis is a cell cycle where cells divide into 4 with half the number of chromosomes (thread like structures made of DNA) which then go on to form plant spores e.g. pollen. This is incredibly interesting work, especially at this time of year with the allergy season!
We need the plants before the Metaphase stage of meiosis, the second stage of the cell cycle and where the chromosomes are aligned at the centre. For this we take anthers, a crucial part of the plant for reproduction as it produces pollen! There is then a series of acid mixtures, alcohols and dyes that are added in the process to stain the anther tips.
To obtain the anthers, we have to take an early ear formation from the cuttings of a stem of a plant such as wheat. We then dissect the plant to obtain 1 of the three anthers and do further dyes to see them under the microscope.
Mitosis is another cell cycle where the cell divides into only two as part of its growth processes.
There is a similar process in staining root tips as there is in the anthers, but this time we were looking for something slightly different. So the main process that we embarked upon was called root tipping where we take the concentration region of growth, or meristem and dye it to see the stage of mitosis that it is in. The plants are stopped in their cell cycle by freezing them for 24 hours. In root tipping, you take 2 out of three of the roots for the experiment, leaving the third so that the plant can continue to grow after it’s particular genetics have been discovered.
So, I’ve had a totally busy weekend. I saw friends, family and had a great time in the sun!
On Friday, however I fear I may have had a little too much sun. That’s right, I got sunburnt! My arms temporarily turned into lobsters and heated up like the sun!
However, all in all on Friday it was a great day I got loads of photos taken, all of the barley and the heritage wheats. Unfortunately Liz and I found some issue with some the Chinese wheat because it is harvest-able earlier as the seed ripens. This means that some of the seed is lost and some of it is eaten by birds before we have the chance to properly harvest it. So I took photos of them too and Liz began to harvest them.
It was such a hot day, I have no idea where I got my sudden burst of energy from!
On Sunday night I watched the film ‘Creation’ with my parents. It’s about Charles Darwin and how he came about to form his theory of evolution. I properly nerded out on all the Darwin stuff that I know and his connection to John Innes to my parents and explained throughout the film why I love it all so much. Long story short, my parents were impressed with my knowledge and passion and surprised that I was so quiet, (I normally talk through films, annoying everyone)!
Exhaustion kicking in after work at 5pm.
Today was a lot cooler, but a lot more tiring for me. The tiredness came from my early start at 4:40 am, which set into exhaustion by around 4pm. Why was I up at 4:40 am you ask? Well, I was at home all weekend and decided to travel up to Norwich on the Monday morning instead of the Sunday night thanks to all last week’s shenanigans! So, 2 trains, 1 tube and a bus later and I arrive at the JIC at 10am. This was quite good timing I thought!
I got on with a day’s work of sorting out orders for the seeds, a continuation of work I have done before, and we also spent a lot of time in the greenhouse where we harvested many barley plants, taking photographic spikes of information as we went along.
This week I am staying with my lovely friend Laura in Wymondham, so 1 bus and a train later I got to hers where we tucked into some delicious food cooked by her dad and had great conversation! This totalled my public transport for the day at 3 trains, 1 tube and 2 buses, approximating around 5.5 hours of travel!
Today was another great day at the John Innes Centre, but I can’t believe it is my last week this week. I am so thankful that I have had the opportunity for experience there. I will keep you all updated on my final week in the following blogs, apparently tomorrow I am being shown the mitosis and meiosis of seeds (oooh!) and how they are used in the GRU.
I was very excited today because today I was introduced to another working lab!
I was shown all sorts of things once Saleha brought me to her lab and had gone through all the particular protocols and safety procedure. I had arrived on a great day because the main job was to complete lots of PCR (polymerase chain reactions) and analysis for specific primers of a lotus plant gene. This was all part of RevGenUK who are named after the reverse genetics process. They offer a tilling service where they find mutations in a specific gene at a price to other scientists all around the world, some of whom I even recognised!
It was extremely exciting to be part of this service and I am just going to go through some of what I did there today:
Armed with a lab coat and a pair of glamorous luminous orange gloves, I learnt all about the process involved from getting a request to the procedure of microsatellite arrays and PCR. I even found out what is done with the results in some computer analysis afterwards.
Electronic multichannelManual multichannel
First I was given the task of setting up multiple tests for a PCR reaction in a microsatellite well. All sorts of different equipment was involved in this process, much of which was expensive and I wasn’t used to using.
I even got to use a multichannel Eppendorf that does multiple pipettes at the same time, this took loads of getting used to and Saleha allowed me time to practice it a little before I had to put my new-found skills to use in an actual experiment that she was using for her research.
Once I had mastered the use of this, she moved me on to an electronic one which was crazy because it took up all the liquid at once and dispensed it into every single hole at the touch of a button, it was so easy!
All labelled and packaged
Once I had put in all the ingredients (primers F1 and H2, water, dNTPs, taq polymerase) with the DNA, the boxes of tubes had to be sealed, vortexed and centrifuged before being placed into the PCR machine.
The PCR machine is great as it does all the heating and cooling for you. It had set specific regimens on there that can be altered and chosen for the specific array that is being done. The only problem is that these machines can be a little temperamental which can occasionally cause errors. these are however, easily identified by the machine and the plates can just be placed into a different machine to proceed. It even sets timers for the different stages of heat and cooling and repeats as many cycles as you want to specify.
The PCR machine can be left alone to complete the process by itself and it will tell you when to collect the finished product! It even keeps a track of the temperature on a graph that it displays for ease on screen!
The E-GelThe printout
Afterwards, we placed a sample from one of the rows into a gel electrophoresis machine using E-Gel. E-Gel is great because it means instead of waiting for hours or even days for results, the machine pushed the liquid through the gel to get faster results to see, they are also pre-cast meaning that it doesn’t take any time to set up. Just beware of the Ethidium Bromide! Anyway, so this only took 5 minutes and we got some cool results! We viewed these results by placing the gel into a UV light machine and printing off a photograph.
This shows us shockingly, that I didn’t make a mistake in the experiments and whatsmore, the primers actually worked. This is great news for Saleha’s research and it means that she will now hopefully be able to use these to identify more mutations on a specific gene.
Saleha uploaded the information into the computer and we looked at mutations in a gene spectrum of the species to see which were changing, this was very difficult work, although very interesting I think it is something that I definitely need a lot more practice on!
This day was amazing, so enlightening to the working world of labs as every lab that I visit is different. I really enjoyed my time today and although I was exhausted by the end of it, I was so happy to be a part of this research!
Today was my first day without Louise, nooo! I’ve had such great times with her and she’s been so helpful with getting me used to the work and equipment, I know I’ll really miss her today.
So when I got in I checked my emails to see if there was anything of interest or any induction stuff for my lab work tomorrow. There wasn’t much, most of it was admin stuff or invitations to seminars on site. I’m going to sift through them all and see if there are any in the area I’m interested in while I’m here. There was also an email about the lab code of conduct and a lab review report that I read over. I’m so excited for my lab day tomorrow, hopefully it should be a great one.
The rest of my day consisted mostly of collecting data on wheat and barley that was growing in the glasshouses. Liz told me that all this data is important in their research for specific varieties of seeds. Some of the phenotypes that we recorded included height, awned (bristles on the ear) and row number (2 or 6 this is about how many seeds are alongside each other). This information is then input into the database and checked with other information we have on the species varieties.
We then set out to harvest the seeds from the plant after I took photographic evidence of the phenotypes to cross reference with the notes that were taken. The plants most definitely were ready for harvest as they snapped off in our hands. This normally would not be a problem, but the greenhouse had just been watered so the soil was especially muddy and the ears of the plants got clogged with water. An easy way to solve this problem is the drying process that happens after we bunch them together. Because of the recently watered area, I found that my hands were a lot muddier than usual, making me look like a proper labourer!
I completed several other tasks throughout the day including separating out 2.00 grams of seeds to be analysed for the database out of an entire collection. this was quite fun as some of the seeds have really strange names ‘Inspiration’, ‘Lancelot’ and ‘Lynx’ to name a few.
I can’t wait to tell you all about my lab stuff tomorrow!
Today I completed several different tasks that I have mentioned previously in this blog, so I won’t bore you all with the repetition. Instead I am going to discuss the importance of the work that goes on in the John Innes Centre.
The John Innes Centre is the international centre of excellence for plant science and crop genetics. I should point out that “germplasm” is the living genetic resource of the seeds in this collection. Mike Ambrose is a senior scientist in crop genetics and manager of the GRU. His work involves curating and distributing strategically important germplasm for a wide range of crop species and their wild relatives.
The GRU maintains a range of web databases that help other scientists to utilise these collections by identifying useful nutrients and other useful materials, I am involved in part of the work on this database at the moment where I am photographing important reference spikes for the system. This is part of the international centre of seed banks, one of which I volunteered at last summer, Kew’s Millennium Seed Bank.
They maintain community engagement through scientific meetings, plant breeding, farming and public talks and demonstrations. Educating the public on the importance of our climate, plants and the future of species that we commonly eat.
Some of the heritage Barley plants I was working on today.
The important species in the collection here include the UKs public collections for wheat, barley and oats as well important legume and more recently brassica resources. Do you recognise any of these? Yes, they are all extremely important species for human survival, crops are 90% of the world’s daily intake. One that you may not have heard of before, brassica, is the cabbage family, and while it may seem like a random family to store and maintain, it is actually one of the most important, as one of the species in it, Arabidopsis is a model organism, meaning that it is used in many scientific experiments as a basis for how other species will react to certain conditions. Just google it and you’ll find out.
Crop wild relatives are important to breed plants to deal with the serious effects of climate change such as flooding and drought, so this is about finding a species that we could utilise better. The wide range of mutation reference collections that are stored in the GRU seed store frisges are important for many scientific experiments to identify genes that contribute to certain features of a plant.
Today was the hottest I ever remember England being, it was around 30C for pretty much most of the day and there were no clouds to cover under nor was there any wind to bring in cool air, the day was hot, and there was a lot of drama on site because of this!
Water… essential for life and general “not-fainting-ness”
First off, I should tell you that today was the first day of the Royal Norfolk Agricultural Association Show, much like the South of England show mentioned in ‘My Day of Pomp!’, I was first affected by this event this morning when all the buses were muddled as event buses were going round picking people up, meaning that I inadvertently got in 15 minutes later than expected. However, it was all ok when I arrived and quickly got on with numerous tasks throughout the day.
The first dramatic incident of the day was two separate callings over the tannoy system for first aiders in two different areas. We were sitting right in front of the window at this time so we saw everyone running about, it was crazy, but actually seemed to be really well organised. I believe it was all down to the heat, it seems that people are fainting as the temperature is rising! Keep hydrated folks!
The fridge doors…
It wasn’t only the people that were affected by the heat, but the GRU had an incident of its own today. Firstly I will explain that the fridge or ‘cold-store’ where all the seeds are kept was built around the 1960s and it was one of the first of its kind. This means that they did not have incidents like today’s to plan for. So the fridge, unlike that of the Millennium Seed Bank is above ground and made of a metal roof.
The control and alarm pad.
I think that you can guess what happened with this information… that’s right the fridge broke. It was overworking itself, and instead of being at the chilly 1.5C it rose to moderate 10.9C by the time I left. This is an incredibly high temperature at which to store seeds, some can even germinate at these kinds of temperature so the conditions for storage were not really great. Our jobs involved going in and out of the fridge a lot today which set off several violent alarms repeatedly throughout the day.
Mike gave us an extra job today while he was out in the show-grounds as we were close to finishing some of our bigger jobs. We had to measure out 2 grams of hundreds of packets of seed and place them into small plastic bags that were labelled with their code-names and numbers of the seed. I am not exactly sure what this was for, probably another order. This job was more complicated than expected as the scales were very sensitive, so even a movement of a fly on the table would alter it by 0.01 grams! We made it fun though, or should I say, Louise did, by putting on music and having great conversation!
We managed to finish a few major things today which means tomorrow we can go out on the field as it is supposed to be cooler!
Today must have been the hottest day of the year so far, and with no breeze there was no chance of a day in the glasshouses or out on the field. I took shelter in the GRU building away from the Sun and with the windows wide open!
Just some of the seeds
While Louise was counting seeds for the collection, I took to the computer to get started on the job he set out for me yesterday. A few years ago, a man come to Mike as a private collector for seeds, he wanted to donate everything to the John Innes Centre as he was elderly and could no longer keep up with his active hobby. My job was to enter these seeds into the database. However, this was not as easy as it would first appear, the problem was that the seeds were not labelled correctly and their taxonomy was all over the place! I spent hours searching databases and Googling around for the correct match and entering any extra information into the computer. It was quite a confusing job as I am not used to the specificities of plant species, however, this should all come in handy for uni next year!
The collection
After lunch, I was about to start helping Louise with some work to do with clearing the cool room, when Mike proposed us with an event that was being held in the library and we should go and check it out. I am so glad we did, we saw some amazing things!
So detailed, that’s a young Shakespeare on the right!
The historian who works at the library took out a collection for us all to look at to do with the history of the John Innes Centre. It was absolutely fascinating! I thought we were only going to pop in, have a look around and be out in a few minutes, but we were chatting to the lady and looking at things for almost an hour!
It was great! We saw all sorts of sets of work, from ‘The First Booke of the Historie of Plants’ that was so old to works of Gregor Mendel (genetics), Charles Darwin (evolution) and Carl Linnaeus (taxonomy)! These three were the geniuses of their time that uncovered the area of science that we all need and is so interesting today!
I got particularly excited when I got to hold a letter that Darwin had written himself, showing his signature, and a first edition of ‘The Origin of Species’ it was absolutely amazing to see! It was safe to say that I completely” nerded out” at this point and started asking the lady loads of questions about everything on show and where they came from. I have always wanted to see a first edition of this ground-breaking book and today, I’m pretty sure it made my year!
First edition!Me holding Darwin’s letter next to his book!A bit messy!
It was particularly funny to see the letter where the word ‘genetics was first used by William Bateson. It was so scruffy, but far easier to decipher than Darwin’s notorious handwriting! I was kind of shocked, if I was going to coin a new term I think I would have at least written it on a fresh piece of paper! This shows me that he clearly didn’t know how big the word would come to be and the field that it would create! I am so delighted to see that the word genetics was first used with plants as animal genetics is the field that is always heavily pushed in the media! Mendel would be proud!
A pedigree of heredity in a family
Something that I saw in the library collection was completely new to me and I had never before really associated it with the world of genetics. This is colour-blindness, one of the first tests that was done to see if Darwin’s theory of evolution could also be attributed to humans.
Testing to see if a child could determine different colours.
At the top of the picture the child was asked to identify the colour on the string and match it with any other colours in a pile of wool, they picked out the 7, there is a ‘confused’ remark. At the bottom of the picture the same 7 year old child is asked to pick out all the green colours and they pick out 17 that range all the way into the browns. This is fascinating to me as I am not colour-blind, it is amazing to see how one mutation can affect someone’s vision that much!
After our fascinating trip to the library, we came back to the GRU to continue with our work and told Mike all about the cool things we saw. The afternoon’s work comprised of going in and out of the fridge a lot, which was great because even the walk to and from the library across the site had me building up a sweat! One of the bigger jobs was to remove old transgenic seed from the cold storage and put it in bags to be autoclaved. This proved to be an interesting job as many of the seeds were from 1995 the year I was born! Although it may seem like a waste, these seeds have to be autoclaved so that the facility has permission from the government to do experiments like this, so we went on destroying the lot!
Today was a fabulous day, I am so happy about my trip to the library, I’ll look out for more events like that while I’m at the John Innes Centre!
I come to the end of today exhausted from all my travelling home and bewildered by how fast these past few days have gone! In the last week I have learnt all sorts of new things and met many interesting and wonderful people. I have had a tremendous amount of fun with my work and hope that this continues for the next 3 weeks!
Today was a great day! Louise and I finished of the threshing of the wheat for the University of Bristol in the morning and met a few other people in the threshing room to have a good old chat about our work! This is a difficult task as the job is quite intensive and requires plenty of concentration, we don’t want to mix up the packets, or worse accidentally chuck all the seeds down the ventilator!
My concentrating face
However, I managed to get through the task without any major slip-ups! So glad I made it through my week in an accommodating manner rather than a destructive one!
I then spent the rest of the afternoon compiling a database for the photos I had taken on the field. This was the first time I had used one of the site computers so I had to get IT to give me a new password as I couldn’t get access. After this bit of a palaver I was all set and ready to go on the system. This was quite a long winded task so I should be able to pick it up on and off throughout the weeks, ensuring my day doesn’t get too monotonous.
This evening I spent on buses, trains, tubes and cars trying to get home. I can finally say that I’m here for the weekend, hurrah! It was such a stressful journey, but then it always is with my mini-anxiety over public transport!
Today I started off my fulfilling more orders for the seeds in the cold storage, but not for long, soon Liz rushed up to Louise and I asking us to quickly check the oats in the greenhouse to see if the seeds were dropping. It’s all go in the land of seeds! There weren’t many dropping to be honest, the greenhouse visit today was not as exciting as I had hoped! I think it was mainly a way for Liz to get us out of the GRU while she was touring a class of school children around.
Threshing equipment: ventilator, ears, rubber grip, paper plate, seed packet and pencil
However, my luck turned around after break when we were told that the University of Bristol wanted us to collect and thresh some seeds for them. This was a new process that I was not trained in yet, it has quite a knack to it!
Confused face as I walk in.
Once I arrived in the threshing room I found a row of benches with a machine attached along the back of the wall. The hole through the desk was attached to the machine and once turned on,sucked everything in the workspace through the ventilator. This machine is supposed to make the job of threshing much easier and the cleaning up job afterwards faster!
The basic premise of threshing is to separate the grain or seeds from a crop plant usually in a violent manner. Now I can tell you, at the John Innes Centre this is not done in a violent manner; it is very precise and systematic, actually making the process a lot easier, we even get to sit down! I won’t go into specific details to bore you, but there is a lot of labelling of bags and shaking of seeds involved!
The stock that we were using was a precise genetic match so we could not risk any form of contamination to the packets that we would deliver. Instead, anything that we are unsure of its origin we have to destroy to prevent later issues. I continued with this for a while and managed to pick up the rhythm of it, so it was lots of fun!
I spent the rest of the afternoon in the field continuing with my photography work for the database. It was a boiling day so there was a lot of squatting beneath the barley for shade! I am told that tomorrow I will start to upload them into the database and begin the process of setting the system up for use.
This morning I arrived early with the help of my pass, meaning I could help Louise with the first task of the day, cleaning peas! Although, this didn’t take very long as they weren’t very dirty to begin with. It was quite a fun task really as some of the peas were really pretty up close. This took us to break time where I caught up with the other staff and once again observed the daily crossword challenge!
Trainers are a must!
After the break we headed over to the field trials for this we needed a car as the fields we grow on are about 2 miles away from the main site. Liz hired one of the company cars and drove us all over with our equipment. We were told to bring a jumper as the wind can really pick up in the fields as there’s no protection from buildings to cover us, however, the sun popped out on our way so I hastily applied sun-cream and ditched the jumper in the car.
Out in the sun!
The first job out in the field was to label the crops with bed, plot and row numbers so that they can be uniquely identified through all stages. This took a long time to go through as the species needs to be identified and checked before we can be certain that it’s labelled properly.
One of the jobs that I was assigned to by Mike Ambrose via email a few months ago was to “photograph reference spikes and upload into the GRUs information management system for a Doubled Haploid mapping population of wheat that was developed to study abiotic stress.” For those non-biologists out there, this basically means that I had to take photos of the labelled species and upload them into a computer database. This involves going through the fields and taking close-up photos. Kneeling down taking the photos, I could see that I may easily get lost beneath the grass!
Puke?!
This job was loads of fun, there were so many different names for the species and some of the seeds were all sorts of different colours, especially the barley species from Ethiopia. Moreover, many of the names of species were probably lost in translation (see right) and proved to be bundles of hilarity!
Scarecrow or scare-human?
We drove back to the main site at lunchtime so Louise and I sat down together over our food for a good chat! After our break we drove back to the field site and I continued taking photos while getting a bit of a tan on! When we continued with our work I got the scare of my life, the device used to scare away the birds (see left) is an explosive gas cannister on a random timer so you never get used to it going off! It is extremely loud so I’m going to have to psych myself up for a few more loud bangs through this month!
I can’t wait to continue with my new project and upload all the information into the database for many other scientists to use!
Meiosis is a cell cycle where cells divide into 4 with half the number of chromosomes (thread like structures made of DNA) which then go on to form plant spores e.g. pollen. This is incredibly interesting work, especially at this time of year with the allergy season!
Mitosis is another cell cycle where the cell divides into only two as part of its growth processes.
Intern Rachel 