The Xanthophyll Cycle in Photosystem II

Friday, 30 May 2014

Analysis of results, from day 1 experiments

So this Friday we basically just went in and analysed our results from FPLC the other day, having not had time the other day~

So we found a mysterious curve at the end of our results~ which indicates that there a lot of protein in our final sample where we have solublised the photosynthetic membrane.
Despite that~ we have quite a large amount of photosystem II (PSII, which I will now refer to), which is the fraction we really need for the next step of analysing on HPLC.

We came to the conclusion, that next time we want less free pigment trimmers, indicated on the graph before, as we want more of the PSII.

The graph produced via FPLC. My analysis notes in my lab book! I'll talk about my lab book in another blog :)

Therefore next time when we repeat the experiment: we will use

·        A greater sample loop for injecting into the sample loop. This is because our fractions came out extremely pale and didn’t have much green at all. If we concentrate our fractions by having a greater volume, it means that next time our fractions will be a greener colour. We increased the sample loop of the FLPC from 100ul to 500ul. However, the use of 500ul might result in a poorer resolution in our results as 500ul is the maximum volume that the sample loop can hold.

·        There is a chance that our buffer could have over solubilised our supercomplexes, giving us more free pigments than expected. Hence next time we repeat this experiment, we can try changing the concentration of the buffet- alphaDM to 0.8% instead of using 1%. This will hopefully give us a larger amount of PSII complexes obtained in the fractions next time J

I find the analysis of results the best part of experiment. I enjoy seeing outcome after a long day of slaving in the lab. I can’t wait to repeat this experiment and see what changing one variable will have an effect on the results! Also, the next time I do this experiment I will be overall more confident and know what each step is~ hence be more efficient in the lab!

Due to the fact my summer project is supervised with the lab's technician, Petra, my entire timetabling depends around her timetable. For example I do not need to come in next monday, instead I can do extra reading. This means that I'm not in everyday at the lab~ some days I actually have off to do summer related things, like going out to see friends :D Which just makes me feel even more luckier to be awarded with such studentship, as the project itself is independent- its a project of my own and not a project or another phd student. Also, its a nice summer studentship as its not 9-5pm everyday, giving me the time to actually enjoy summer! Win Win Win!

Thursday, 29 May 2014

First day in labs!

Oh the excitement, I actually didn’t know what to expect! I’ve been in labs before obviously, but this was a project of my own now! Where I would be the only student doing this and basically discovering new results for my supervisor!

So starting at 9am and ending at 6pm, I can honestly say it was a long day! Obviously I had a lunch break and everything, but still very long!

Thing is with these types of experiments, there is a lot of centrifuging and treatment that needs to be done in order to get the final, correct medium that can be finally analysed via the chromatography machine- FPLC: fast protein liquid chromatography. In our experiment we are basically only wanted to separate the different supercomplexes in the photosynthetic membrane; to mainly get the fraction of photosystem II, so we can further analyse the pigments in the photosystem II via HPLC: high performance protein liquid chromatography that are involved in light stress. Obviously, understanding the underlying mechanisms of the photosystem II will really aid in my future plans of further being a researcher in artificial photosynthesis J

Anyways here is photos to explain the day:
This is a device which basically spins the spinach around in hand controlled speeds, hence drying washed spinach rapidly! We obtained the spinach fresh from Whitechapel market in the morning.

The nitrogen tank! Looks so scary :3 It actually looks like a nuclear bomb or something in real life.... stuff which i just generally think should have never been created in this world; we should all try to live in harmony, but sadly this is not the case in our world right now :( Anyways, the technician showing me how to switch on the supply/ off.
This is me chopping up the stems and midrib of the spinach preparing them for light treatment. I was initially quite slow as I didn't want to damage the spinach leaf and lose good material.

The spinach leaves ready for light treamtment.

The spinach leaves covers in cling film and starting light treatment.

Measuring the light intensity for the light treatment~ it was between 450-500 micro Eisenstein. This device is so cool it like an botanist stethoscope, haha!

Further measuring of light intensity and you can see the other plants grown by other researches at Queen Mary, in the plant room :)

Reading through the instructions and adding extra notes for next time.
While waiting for the centrifuge cycle, preparing of the buffers and mediums ready to add to the pellet of the centrifuge tubes.
The osmotic medium added after the break medium which breaks the photosynthesis membrane into smaller pieces, the break medium is added for 30 seconds, before the osmotic medium is added.
A centrifuge! You always learn about them throughout education in science. I always never really understood the true importance of them, till i actually used them in this studentship. They are such amazing devices and I've learnt to absolutely love this one in Ruban's lab! :D
Centrifuge walkthrough, left to right- Time: 1.41 seconds remaining of the spin, Rotations per minute: 4000, Temperature: 4 degrees and not sure about what the 9 means, think its pre-set!
Love my university lab coats, how they embroided the logo on every single one. Luckily for me X-smaller is in the colour of red and i love the colour red :) It's chinese lucky colour! However, if I'm honest pink is my favourite, it just makes me feel so happy and girlie, hahah...
Taking buffer from the FPLC machine~which we need for further steps in the instructions.

Other picture of the FPLC machine, looks pretty cool~ overwhelming at first.

So basically watching the different separation of fractions in the FPLC on the PC screen. The different wavelength of lights indicate what is observed. As we know wavelength of 670λ are of chorophyll A, 480λ is for both chorophyll A and B and pigments, 280λ gives proteins.
So by the end of the first full day in lab I have completed pretty much nearly all the steps in the protocol plan for the 8 weeks! I was initially worried if I would have enough time in the 8 weeks to do it all, as I didn't know anything about how long each step will take. However, after today I understand the whole project alot more! That 8 weeks is plenty time to get really nice results in this project. That mainly the 8 weeks will be analysing the fractions that I obtain from solubilisation, to find the efficiency of Violaxanthin de-epoxidation in PSII supercomplex. 

I am quite excited to move onto outline step B. I always think working with mutants is interesting as they can clearly indicate the purpose of certain complexes in each organisms.

Tomorrow I shall be analysing the results obtained from FPLC

Monday, 26 May 2014

Bank Holiday Monday: Back in London!

Bank holidays are always fun, or relaxing at least J

So today, me and my family went to a Chinese restaurant to eat and then had casual shop around Sheffield town centre, before I got on the train back to London! In ways it is always sad departing from loved ones, but London just offers more excitement for my outgoing nature so I’m always happy to go back. I think if I could drive, Sheffield would be a fun place too as I could visit all my friends easily, but London has the fast connection of the tube, so I can get anywhere practically J Plus the boyfriend to drive you around is a bonus as well ^_^

Anyways~ finally back and its around 7pm, I’ve started reading up on the chapters that my supervisor suggested. It’s really cool as he has written a book which is so condense and references many papers, it makes his research area sort of like a walk through.

Ruban's photosynthetic membrane book, just making notes on each page to help me further understand. Alot of the time in science there are words which confuse me so I always need to find out the definition or action of a certain pigment I'm reading about. I like to have the generalise view.
This is what my supervisor sent me, it's basically what I will be doing for the 8 weeks! OOOH excitment ^_^
Here is the experimental protocol, reading up on it so I know what I need to do tomorrow! I hate the feeling of not knowing the next share and uncertainty when following instructions for an experiment. Need to know everything before hand!
My first year lab book, we did a lot of practicals in first year and I wrote alot of notes on how to use micro pipettes, centrifuges and do calculations. All which are essential lab skills ^_^
My amazing corner study desk~ where all the geeking out happens :D Really into spacing saving designs, so this corner desk is just amazing !

Although, because I am mainly a Medical Geneticist, and my degree consist more of biology/ biomedical related modules than biochemistry, this research project I will have to read up extra on, as it is in a different field to mine. To be honest I was really considering to do biochemistry, as I enjoy remembering the pathways, different mechanisms…I love learning pattern. Lots of people told me to not do biochemistry because it’s boring and it’s all about remember all the long amino acids name and structures, so I didn’t. Little did I realise that when I did do my biochemistry modules in first year, I actually loved all the shizzle that people said were boring. Life lesson learnt never listen to others and follow your heart J In ways Medical geneticist offered a better degree in a sense if I decided to do medical research (which I do quite enjoy reading up on) or decide for graduate entry for Dentistry/Medicine/ Veterinary… it’s just good to keep options open, uncase I do change or discover my new passions for areas J Also, genetics is the fundamental science of life really, it what makes us all unique, so I do enjoy it!
Yeah, so I’ve been basically reading up on the chapters and relevant papers he has suggested. Although, personally I find it quite hard to see how they are relevant. Tomorrow is my first day in the lab so I’ll see how it all shall link. For me I always believe it’s easier to see how things relate in content than reading in book. Once I can see the link it all goes in and it’s easier to logically think about~

So why everyone is having those bank holiday Monday raves! I’m inside reading all this, it’s like exams all over again! Hahah, joke really. This is nothing like exams as there is no pressure of actually sitting an exam. I actually really enjoy learning, especially because this is area which is different to my actual degree. I’ve never learnt about photosynthesis in this depth before J People say to me omg you don’t get a break after exams, which is crazy! But I prefer life to be like this. I don’t really like sitting in my room all day and doing nothing. I actually like doing something, a mix of things, variety. My studentship was actually meant to start 2 weeks after my final exam but I decide to pull it forward to straight after my exams! It’s better to get started early, especially because I am eager. Also, I have a third year project to start as well after my studentship, on something different maybe… Ruban said we can decide that later on anways~

Super excited for tomorrow J Even though it’s an 9am start and that involves me going underground for 30minutes, which is quite depressing in the mornings, but I’ve gotten use to it now I’ve been in London for 2 years ! 

Saturday, 24 May 2014

The weekend of end of exams!

So basically it’s the weekend of the end of my exams! Woo! Crazy how I’ve taken 8 exams this summer, so glad that next year we only have to take 6, due to the third year project being worth 30 credits ^_^

Usually, people would be going to go clubbing to celebrate, but not all my friends have actually finished their exams, especially my closer friends from different universities. I guess one of perks of being in my course is that we always finish really early, compared to other universities in London/ around the U.K. Anyways, I decided to go home to visit my family, it’s been a while. I don’t always go back every week like a lot of students do. Sheffield is 2hours away from London on the train, also I always have something to do in London. This is the reason why I decided to come to London for University in the first place. It is the city that never seems to sleep! (I know everyone says that about New York too, but I think it’s true for London) There is always something to do in London, something new and exciting. It’s such a big city therefore a lot of areas and events are always going on. I never get bored! Also, it is so culturally enriched and I love being exposed to vast cultures- it just opens your mind more to the beautiful world we have J

So walking around Sheffield town centre with the family looking for something to give to my blog and I see a plant stores outside the town hall. Here are some pictures.

This actually got me really excited for the start of my studentship on Tuesday (Monday is a bank holiday, woo woo! Don’t we all love bank holidays?! :D) I’ve always thought plants were beautiful organisms, in ways seeing a plant is quite refreshing, especially because in London there is little greeny which surrounds me. I have always been interested in photosynthesis, its such a complex mechanism, I know at the time learning at A-levels it being very complex, when actually when you think back the way they thought it in A levels is so simple compared to what it is really….Anyways, I really like photosynthesis, it’s a really neat process, it basically is the reason how we and practically all of the other organisms evolved on life. We wouldn’t even be here if it wasn’t for plants. So it’s quite sad how people just overlook them and not really realised their importance.

I was recently reading a nature review about why we need plant sciences, as they are the scientist which would unlock the answers to. How will we feed the children of the future? How can plants contribute to the energy crisis? It’s true that this is an area in science that is often neglected. I don’t think that the UK education system really implements plant science careers into the minds of young children. Many aspire to be lawyers, doctors, football players, police men, business owners, but rarely does anyone actually want to be a plant scientist. To be honest I’ve always been interested in Medical sciences, hence the reason why I’m undertaking a degree in medical genetics, but it just hit me recently, what is the point in saving so many people dying from disease, if we just simply do not have the food and energy supply to aid their lifestyles? I like to think about the future generations, some people say global warming is just a natural phenomenon, but I truly believe because of extra carbon emissions in the world, we have severely increased the global temperatures and sea levels, causing devastating effects to the world- such as freak weather and the extinction of animals. I want children in the future and I’m sure the cycle of them wanting children will continue for generations. I want the human race to survive and not be wiped out because we were foolish with damaging the world generations before. Hence, one of the reasons why I’m undertaking a project in photosynthesis, particularly relating to photosystem 2 and the pigments related in light stress. If I can understand the fundamental mechanisms behind photosynthesis, this will aid me in my future research plans in artificial photosynthesis or generations of biofuel energy by genetic modification of plants? 

Friday, 23 May 2014

First blog, little introduction to photosyn-this!

So here it is, my first blog J

In this blog I will mainly be talking about my feelings towards the whole studentship and science issues which are relatable to my areas of interest in research. The two main themes will be upon artificial photosynthesis & synthetic biology. I really feel that synthetic biology is the way forward in life! I will try and write it in a simplistic way so even non-scientific aware readers can easily pick up on this!

 Anyways, let’s start from the beginning. I remember when I got my acceptance letter for the Biochemical Society Studentship. It was during the start of my exam season, which is never fun. However, I did remember being very joyous at the time. Not trying to be arrogant or egotistic in anyways, but I kind of always knew I would get it, not because I am a role student, but because I really put my heart into writing the whole personal statement for this studentship. I truly believe if you put your entire soul and heart into something, the outcome should always be positive, unless it was never meant to be.

The overwhelming happiness that came from this email, WOOHOO!! I GOT IT :D

The whole reason why I applied for the studentship was because while searching for options after graduation and generally reading about science newspapers/ books. I stumbled upon a book called “Regenesis: How synthetic biology will reinvent ourselves and nature.” It was from reading this book that I discovered my true inner interests in synthetic biology. I finally found something that was innovative enough and a science that could really offer big change in the world. I’ve always been really into the whole “energy and sustainable living” themes in life. I think it arose from GCSE geography. I think I just appreciate energy because I know without it I would not have the lifestyle that I enjoy to live, such as being able to Whatsapp my friends and use the internet to read upcoming news, being able to travel to other countries and explore- something I love so dearly. So basically after I just searched in my school department for a professor perfectly suited to my future goals in life, and I found him. Professor Alexander Ruban. Gosh, wasn’t I lucky to find him, he is such an expertise in his field and regularly publishes papers *o*. Obviously at the time I didn’t know this, but once I knocked on his door I knew he was the supervisor to pick because he was so passionate about his research and it seemed like he would be helpful if I ever got confused with the studentship. Call me lucky, as he was the first one I approached and was so willing to take me on. Maybe some things were destined? Ha.

In ways I believe I am an activist in character, I want change. I want to see change in this world. I think ever since University and the whole maturity and aging process, I have stopped turning a blind eye to these modern day issues, which no one really actually genuinely worries/ cares about. Seriously, ask your friends or family members, when do they ever think about how the energy resources are rapidly depleting in this world? How would such depletion affect the way the modern day world turns? You won’t have your laptops, I-phones or cars….we would basically revolt back to the stone ages (I know that such happenings are very unlikely to happen, but it could!) Things that I really think need to be tackled in the energy problem. Yes, I know there are many researchers already working on this issue, but I think the 21st century, energy really should be in the form of renewable, nontoxic and non-harmful source. This is why I think artificial photosynthesis is the way forward, already there has been a developing prototype of a “leaf” which can use the sunlight, to convert CO₂ and H₂O into O₂ and H₂, which H₂ can be used for fission to create energy. It is eventually hoped that the “leaf” will be stored in homes, being able to generate energy for the entire household. So how cool is that? Having a device which acts like a leaf attached to your house, generating energy spontaneously when there is sunlight, then storing it for night time use? You would never even need to pay an electricity bill ever again as you are basically taking energy directly from the no.1 source in the world: the potent sun! Think how much money you could save and how much better the world would be, because we would no longer need pylons for the national grid… Obviously, the leaf device itself will not be cheap, but like most good things in life, investments need to be made in order to get good returns. It is true for anything in life.

Anyways, I shall end with nice, easy to watch videos about artifical photosynthesis. I love watching educational videos like these on youtube. For me it's always easier to learn when watching a video than just plain reading~ I'm a visual learner :)

Here is the artificial photosynthetic leaf that I've been on about in this blog. Love it! Think if most of you watch this video you will probably understand my enthusiasm for this area of research. It's just so exciting :) Alot of my friends who I tell them about this, get a really wow reaction too!

This is another one of my favourite videos, which made me really get into artificial photosynthesis. When I find a research area that I like I always youtube it first for a overall easy overview on the topic! This video clearly highlights the fact that artificial photosynthesis could help reduce carbon emissions and global warming; hence a probably decrease in freak weather, while also generating energy! Also researchers are from Panasonic! Find it really cool how Panasonic are investing into this research :) Having being to Japan myself and absolutely love their culture, it's cool to know that a country I love so much I could possible work in the future, if I plan to specialise into artificial photosynthesis. Especially, puts my Japanese skills that I've been learning at night class over my entire 2nd year to use :)