Thank You!

Finally,  would just like to say a massive thank you to everyone who I worked with at the John Innes Centre I had an absolutely fabulous time there. I made some great friends who I hope to stay in contact with and the experience of working in such an intellectual environment will be cherished.

This has been one of the best summers of my life, I have been so busy and learnt so much. Yes, it has been hard to be away from home but it pushed me to go out there and really put all my effort into my work! After working at the John Innes Centre, I now cannot wait to start my career after university, it has really enlightened me to the different paths I can go down.

I hope to go back to the John Innes Centre after I have graduated to see how everything has progressed.

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My Day of Microscopy!

So today I worked with Adrian, a key member of the GRU, in his work on meiosis and mitosis in crop genetics.

11741869_10152886279493204_2097733262_n11741714_10152886279463204_633771325_nMeiosis 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.

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11753839_10152886279573204_620490261_nMitosis 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.

The Beginning of the End…

So, I’ve had a totally busy weekend. I saw friends, family and had a great time in the sun!

11717085_10152880483008204_1918833402_n11739753_10152880483373204_355692889_nOn 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)!

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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.

A Day of Injuries and Field Work

Today I just sort of got on with things, I had a lot of work to do and I don’t have much time left to do it all in. I can’t believe I am nearing the end of my penultimate week, this has gone by so fast, which must mean I’m enjoying it!

This morning I got on with some computer analysis and uploaded photos into the database system to be checked over by Liz. After break we headed over to the glasshouses where we viewed the oats and harvested what we thought was ready. This was where I hit my head the first time! On the metal ledge by the window, it really hurt and it was quite warm in there, so I’m blaming the temperature on my craziness. Moreover, 5 seconds later I bashed my hand on a piece of metal by the pipes and I now have a few small cuts on my hand. The harvesting was fun, but was over quickly and before I knew it we were out on the field again!

In order to get to the fields where we have out test sites we have to drive as they are a few miles away from the main site. I got all my equipment ready and jumped in the car. Now, I have to say I think I was a bit keen to get in the car as I really enjoy this part of my work, however I was a bit too keen as I bashed my head in the same place on the car while I was getting in. What am I like?

I’ll let you know if I’m still alive tomorrow…

Inspection Day and Field Work

I arrived early to work today thinking that I would have to get along with some work alone while waiting for the others to arrive. However, I was happily surprised to find Mike there when I arrived, this was because he was preparing for an inspection official for plant health controls from Defra. It is essential that the facility is inspected so that they can be insured and all the seeds and plants are healthy and free from disease.

Mike and I got involved in quite an intense conversation about what constitutes a GM crop and where you can draw the line for genetic modification. We came to the conclusion that the media sensationalises GMO and makes people believe that it is a bad thing without all the facts.

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Anyway, when the inspector arrived I was involved in preparing the seeds for his inspection and then to be sent off to the lab. This was quite an easy job, as it is similar to things that I have done before, but it was relatively hard-working and kept me active for the morning. The boxes that the seeds were in, did however turn my hands temporarily green!

11721113_10152875165288204_1972301060_nAfter lunch, Liz and I headed out to the field to continue with our spike information and photographic evidence for the database. This was quite fun as I have got myself into a bit of a rhythm of it now, meaning that I actually did a lot more than I thought I did!

The only problem with the field work today was that the weather was extremely changeable. It went from being so warm that I had to take off my jacket to being quite chilly and pouring down with rain! We did have to stop at one point due to the rain, but we managed to get back out as it really brightened up. I would have continued to carry on with my work, but the issue is with taking photos, it becomes extremely difficult in poor light and rain. Towards the end of the day it did get much worse, so we had to give up and go back. Hopefully tomorrow will be a brighter day!

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My Day of Lab Work!

I was very excited today because today I was introduced to another working lab!

11696751_10152873483293204_1998726145_nI 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!

11292017_10152873483043204_626527450_nIt 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.

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Electronic multichannel
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Manual 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!

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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.

11714358_10152873482823204_1699936846_nThe 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!

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The E-Gel
Afterwards
The 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!

Surprisingly Muddy in the Glasshouse

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.

11715907_10152871731983204_1554618816_nSo 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.

11715983_10152871732078204_864449535_nWe 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!

Public Transport is My Enemy Number One!

Today was a very weird day! After yesterday’s fun outings with friends, today I decided to have a bit of a calmer one.

I woke up with a very weird feeling about my travels today, like I knew something bad was going to happen, but I pushed them aside and started on with the day. So I went into town for a bit of shopping, well I tell you, the world and his wife had the same idea, everyone was out. I’ve never seen so many people queue for the mall car park! My mum and I did a bit of shopping and I saw one of the friends I didn’t have an opportunity to chat to yesterday for a bit of a catch up!

11714954_10152870182138204_962442868_oBy the time we got home I had to pack for Norwich, still with this weird feeling. Packing has become extremely easy for this now as I know exactly what to bring and I only take a small case with me. I then wrapped up my brother’s birthday presents (I won’t be able to see him on his actual birthday) and handed them to him over tea and scones like proper English people, haha! He loved them!

After dinner the reccurring weird feeling had settled in properly and I just didn’t want to get the train. Although once I got on the first one I saw that I had nothing to worry about. My first issue when I arrived in London was that there were no escalators working going down, meaning that I have to carry my bag down the flights of stairs to the underground. This wasn’t a major issue but at the time I thought my worries were over and it would be plain sailing from there. Boy, was I wrong!

As soon as I stepped off the tube in London Liverpool Street there was a massive crowd running about, I got to see the departures board and I could see why. All the trains to Norwich and surrounding areas were cancelled or had severe delays! Why you say? Apparently a bridge broke and they had to fix it, fair enough, but why did nobody send me an email? There was a notice saying “please don’t travel unless absolutely necessary”. I don’t know about you, but I’m not on public transport for fun, I’m on there because I have to be anyway!

Ok, I thought I can figure out something out, so I went to the information office and the woman told me to run to platform 13 and get on that train so I ran, no questions asked. It went to Ipswich meaning that I had to get off there and change to Norwich. It was an extremely busy train as everyone had the same plan as me rushing about to get up to the east! Apparently though, Ipswich didn’t get the memo because the train left without all of us and we had to wait over an hour for the next one, this I didn’t really mind. I mean, it was annoying, but I got out my book while everyone else was arguing and floated into fantasy land! The train was later still, and not only that but another train arrived before only to dump more unknowing people onto the platform wanting the same train as me. It was so chaotic it was almost laughable, so disorganised. I couldn’t believe that I had had this bad feeling all day, it actually made me calmer not caring and just knowing I’d be back.

witch-clip-art-di6oAnei9My mum thinks it’s my witchy powers maturing because I’m an adult now (she’s mad) and a friend believes me to be a train psychic (also mad), I just believe that the UK public transport system has a vendetta against me (crazy).

To be fair though, when we got to Norwich they were extremely kind, they gave us all reclaim forms, booked a taxi for me to the house and even put on an extra train for people who were supposed to get a connection afterwards. So in the end the journey from home to the house I’m staying in took 5.5 hours and I’m exhausted!

All in all, it was by far not the worst journey I’ve had on public transport, but let’s save that horrendous tale for another day…or not.

Halfway Through

Today was the last day of my second week and I can honestly say I have enjoyed every day!

Some days have been more exhausting than others and sometimes I end up in pyjamas by 9pm, however, other days are so fun and inspiring that I stay up all night texting my friends all about the things I did and everything I’ve learned!

I have learnt about the full processes of harvesting, threshing, storing and sending off seeds and it has all been really interesting! Next week I am told that I will be spending some time in the labs to get to understand their processes and jobs. I can’t wait to learn all about some more processes and expanding my knowledge about the John Innes Centre as a whole.

Finally, I have to say that everyone I have met during my internship has been really friendly and interested in my work. I am so happy to be a part of this lovely organisation, even if it is only for a month! I can’t wait for the next two weeks and I’ll be so sad when it’s all over!