The Xanthophyll Cycle in Photosystem II

Wednesday, 9 July 2014

Let's buy spinach!!!!

Really quick blog post about the purchasing of spinach for my experiments. The key place to go is the market just down the road from Ruban's Lab, Whitechapel market. The reason why we prefer to purchase market spinach compared to supermarket is often the fact that spinach in the market appears more leafy and rich in a mossy green colour, rich mossy green = rich in chloroplast, exactly what we need for this experiment! 

Whitechapel, for those who don't know it is a vibrant, very vivid, diverse part of London. It is the home to Queen Mary's, Bart's and the London Medical & Dental school, it's a place where I sometimes find myself due to lectures. Anyways, this area had a huge migration of Bangladeshi migrants back in the day, so this area has a huge influence with Bangladeshi culture and various of these market stalls are ran my people of Bangladeshi decent. Here are a few pictures, pardon me these pictures are quite terrible, as I tried to take photos without making it obvious that I was actually taking photos:




Yeah an ordinary main road with market stalls running along the sides.

The only problem I have of this market is that most of the stalls don't stock spinach throughout the day and there are set times which spinach is actually available. When the actual availability time for spinach is, no one ever knows exactly, so sometimes you ask for spinach, the stall vendor says an hour, you come back in an hour and there is still no spinach....It's basically playing the waiting game for spinach.

Monday, 7 July 2014

Start Week 7: Buffer Prep

Starting the week preparing my own set of BBY buffers. Oh the joy! *sarcasm*

Don't get me wrong, I do enjoy the lab but preparing buffers for your actual protocol can be quite mundane. The whole process is essentially weighing and measuring accurately the certain amount of chemicals you need in your buffers etc. A process you compare to actually conducting BBY or results analysis, just doesn't compare with the excitement driven adrenaline levels. Nevertheless, this whole process of buffer prep is crucial to the success of the actual protocol- to yield the desired results as predicted. So no matter how mundane this task may appear to be, disarray the entire buffer preparation and goodbye to your hard work you may spend on your protocol. Every gram, pH set for the buffer could honestly severely disrupt your results.

In short words, every single step matters in science.

Sometimes you may be lucky and a mistake could actually lead to a publication! However, only the ones who are prepared will ever find a success ridden mistake! One of my favourite quotes, clearly portraying such matter belongs to the wise words spoken by Louis Pasteur. Louis Pasteur being famously known for his discovery of vaccination~~~

True, wise words❤ 

Anyways here are some pictures from the day:

Following the instructions for buffer prep. My nice little printed out booklet stuck into my lab book, with the always needed concentration x volume calculation equations !

Cleaning the balance as indicated with the sign, the paint bush really gets to all the nook and cranny

The pH meter, an apparatus which I absolutely dislike using. It's quite slow with detecting the change in pH, so after you've added in your acid/alkali solution it may take like 5 minutes to actually reach it's real pH on the meter. It's definately the part of the buffer preparation which slows me down the most. All the other apparatus, I've gained a technique for being fast and efficient in using them :)

All my buffers completed, labeled and dated, proud to see completion :D

More labels~

MgCl2, used in the buffer prep to aid the further stacking of the thylakoids, to gain a large amount of PSII for analysis.

When normal purified water just won't do. There is always PURELAB! An ultra purified water dispenser. Looks very modern and fancy ;D

PURELAB homescreen. Literally all you need to do is press the bottom which my index finger is pressing.

Saturday, 5 July 2014

Browsing at the science museum

This little blog entry will be about the innovative products which I merrily discovered in the science museum.

I love the science museum in South Kensington. It's actually the museum connected and really close to my boyfriend's university, Imperial College London. So I'm always in there or end up taking a friend coming down to London for the day :)

Anyways was waiting for a friend this saturday as we planned to meet for dim sum in South Kensington. She was late so I just wondered into the science museum browsing the shop. There's always cool gimmicks to be found there! Here are the few things I thought were very querky and innovative; products that really caught my attention!

It's a 3 in 1! Chopsticks, fork, knife. This is such a brilliant idea, as many students in the U.K who are constantly saving. Especially with the cost of living as a London student. I'm always trying my best to pack lunch! Something like this would mean I wouldn't have to bring separate metal knifes and fork for when I make salads, sushi, noodles etc. I'm always loving the idea of compact travel items ;)

Another innovative packed lunch product. Brighten up any plain drinking water with a zing of citrus. Citrus fruits being rich in vitamin C, benefits such as strengthen bones and antioxidants; helping you to reduce the development of cancers and certain disease. A good source of nutrients such as fibre and calcium! :)

Think this lunchbox is designed by the same company as the two products above. I always wanted a lunchbox like this, as at home I often cook alot of salads but salads are quite messy to put in ordinary lunchboxes and once inside such lunchboxes, they no longer look appetizing to eat. However, this lunchbox has a green and white healthy theme going on it which would really complement the rich vibrant colours in salads. Also, the little salad sauce area is great addition, no longer would you need to add your dressing immediately when you make packed lunch. So no wet, awful salads for lunch no more! :3

Element cups !!!!:3

Periodic table, think everyone in a biochemistry lab should have one of these. Even if you don't drink hot drinks could be a nice pencil holder? ;D

Salt and pepper shakers.... OMG I LOVE THIS!!! ITS SOOO FUNKY!!! Haha i think anyone who uses conical flasks everyday would find these querky, or maybe find these disgusting in ways? For me I think they're so radical ;D

So these water stones left on your soiled plants will water your homegrown plants. No need to worry about the watering can again! Looks really cool as well, like a massive contact lense on the soil :O

I'm a big fan of stationary and as you can tell from my labbook blog from before I'm really into colour everywhere. These are just too cute with the pill theme going on. Love it <3

Something I probably would buy my child as an aspiring plant scientist :) Even to me this looks very fun as a 20 year old <3

This looks sooo funky!!! When I move house I'll probably buy something like this to put on my desk. I just like looking at plants its just ever so refreshing and part of our natural life :)

Awr, i thought this looked very adorable<3

A t shirt with all the % of elements inside the human body. Pretty nerdy to be honest but I would be impressed at anyone who wore such a thing. I would personally make friends :P

Thursday, 3 July 2014

Week 6 quick update!

Quick Blog update: Had meeting with Professor Ruban himself on Thursday and discovered how to further proceed with my project. He wanted me to run HPLC on my B4 fraction from BBY spinach preparation obtained from FPLC. The de epxodiation I yielded in my A9 fractions, containing PSII supercomplex, was sufficiently lower than expected, lower than that of my isolation of stacked thylakoids, which should not be the case. This means something wasn't right with the prep. He told me to check the HPLC on the B4 fractions (Where the Light harvesting II complexes were situated.) De epoxidation in B4 fractions should be 100%. However, with out HPLC analysis we found values much of 70%, therefore we clearly knew something was wrong with the preparation. 

Now I know for next time: That I must always run HPLC on my B4 fractions, fractions contianing LHCII supercomplexes to see if it is worth the continuation of the BBY spinach preparation past the steps which are identical in protocol to that of isolation of stacked thylakoids.

Furthermore, the increasing the time of stacking time in the BBY medium. Allow the stacking of thylakoids allows more PSII supercomplexes to be present in the preparation as PSII is mainly found in the stacked thylakoids, compared to that of PSII found mainly in the lamellae of the chloroplast.

Anyways enough science talk, some nice pictures taken over the week
Irina's healthy growing Peas, wow from 3 weeks they have grown so much! Check earlier blogs to see how they looked at the start! We are just  putting wooden sticks in to ensure they grow upright and not tangled :) Happy gardening !

Supervising Irina on HPLC analysis~ teaching her the ways!

This is how HPLC data analysis usually goes by. We check each peak and compare with the reference spectra for the pigment, which we know due to the position in eluting time in HPLC. This bit is my favourite part of the entire experiment procedure, analysis and interpreting results. So fun! :)

Bit of the side stuff!

Here is Petra grinding up ivy leaves using  liquid nitrogen. Yes the steam coming off the ivy is liquid nitrogen that Petra has poured on the leaves, freezing them, making them into crystals, easier to grind into pieces.

Petra adding the ivy crystals into a test tube ready for it to be grinded by hand. Everything done under iced conditions again.

Let the grinding games begin! Apparently Petra hates working with Ivy because they are so hard to grind up and get material from. Did you know Ivy is an incredible plant as they can pretty much grow in any light condition possible. Amazing I love ivy now, like the animal elephant, Ivy is my favourite plant now :) Although i must say spinach is more useful in a sense I can eat them and leafy vegetables are great for the eyes! 

Monday, 30 June 2014

Let's talk about lighting, artifical lighting

Any form of light is always relevant to this blog, especially because my entire project is about light stress on plants, photosynthesis related. Anyways, this is what today's blog will be about! LIGHT! :)

It was in the first year of University that I realised the importance of light to the human body. I use to wake up in the winter term feeling all gloomy and depressed, which is quite strange as usually I'm like fully of energy and bursting with happiness. I guess they call it the winter blues ? Anyways, this lead me to discover the condition of SAD, aka. the seasonal defective disorder, which is basically seasonal depression thought to be related to reduce exposure of sunlight. SAD is believed to cause depression by the disruption to the production of important chemicals in the brain's hypothalamus, chemicals of serotonin and melatonin, made from the amino acid Tryptophan. These chemicals are responsible for regulating the sleep/wake cycle, appetite and mood. No wonder the disruption to the normal sleeping cycle, lack of motivation, lack of libido all start to kick in for many of us in in the UK's winter. So it was from such lunch time google session that I discovered the importance of lighting to the human body. I immediately requested a SAD light to be purchased as a gift from my boyfriend. Sadly, I never received the SAD light and spring came eventually~ I moved on with life.

Skip a year and abit on, to my 2014 exam period, I noticed that using different types of lighting in my room really affected my mood/ how long I could actually study for. Traditionally, I have always used an orange yellow emitting light bulb, I never thought much of it till I realised it wasn't my chair that made me feel feel grouchy over a period of time, nor was it the module I was revising. It hit me again that lighting was a big factor in concentration time for me! It sparked back memories to that winter lunch time google session where I found out SAD lighting really helped SAD individuals!

So I immediately thought brighter and whiter the light the better for concentration, because that is essentially what SAD lights are made of. Especially, because my room has very high ceiling, for the fact it is an old Victorian house and frantically the room is very large in size. Light does not easily reach the far end of my room where my study is place!

So I immediately went out and brought this ecozone bright white light to exchange for the yellow warm tinged study light! I even read reviews before hand how people used this to cure their own SAD in winter.

Super bright Ecozone light bulb huh?
Literally don't even need to switch on the main bedroom light, this was enough. LOOK AT THE GLEAM, how it lights up the entire room~
So initially it was great, for a week I really felt a difference and was studying for long periods of time. Well longer than with the yellow warm tinge light bulb! I even considered changing the entire house to white light bulbs, the change for me was revolutionary! It made me feel more awake and energised, essentially it felt like being outside, but indoors. Text on my lecture printouts were very crisps as well thank to the lighting, everything was great.

BUT.... there is always a but to everything. Nothing is a happy ending like fairy tales I guess.

I slowly felt a bit sick with the white light intensity. Yes it could of been due to the fact I was constantly studying all the time and revision eventually makes you feel a bit sick, but I took breaks and coming back I still felt sick. It wasn't like a mental I feel sick of revision because I revised too much today. I generally have quite strong will and I knew I had to study hard for good grades, so I would always be consciously aware about such thought. No, I felt physically sick, that was when I knew artificial white light must be bad for you. SO there I went, with my usual, exquisite mind, eager to find out proof for any theories I connect together....Is white light bad for you?

Reading from site to site, paper to paper. I came to the conclude it actually was...

Turns out exposure to white light, suppresses your melatonin production by x5 than that to the normal yellow warm tinge light bulbs! This is due to the fact that white light bulbs emit a shorter wavelength than that of ordinary warm yellow tinge bulbs! Gosh I was shocked! Apparently, the U.S government are aware of this and make sure that excessive amounts of light pollution are not introduced in public areas.

Melatonin as expressed above is very important for the body's biological clock. In addition, it has anti cancerous and anti oxidant properties too. I immediately changed back to my yellow warm tinged light bulb and to be honest I didn't feel physical sick anymore. Yes I couldn't study as long, but sometimes it is better to take more breaks really. It's actually been proven that interval learning will aid your memory more likely than that of mass training. Something I learnt in my neuroscience module this year.

Here is the link to the paper itself, explaining why interval learning is better than mass, just in case you are intrigued :)

Click here:  A functional MRI study on associative memory

Saturday, 28 June 2014

Back to Sheffield!

Home visit, yet again! Always need to go back and see the folks! In fact this time it was my brother's birthday so I went back for that reason. Anyways, so some photosynthetic related products while shopping at Meadowhall (It's sheffield massive shopping centre, really good place to go shopping, everything under one rooft! Totally recommend it :)) I'm not sure if it is the fact I'm sciencey that I see these project related products when I go out. Or maybe it's the law of attraction, because I'm always thinking about my studentship in the back of my head, so it just brings me closer to these things? Signs from god? :P

Oh look these could almost pass as spinach leaves, but in rubber form! So cute :3  Quite refreshing to see such a rubber to be honest. Yeah this stationary shop sold all types of rubbers! 

This is a product I observed in Red5 the shop. Love this shop! It is not just for guys, its for girls too, especially girls like me! I'm really into future tech stuff,  especially if it aids in sustainable living or makes your life easier ;D

 Here is a product description & link


The Sun. A massive ball of fire burning hydrogen in to helium about 93,000,000 miles away. It roughly takes 8 minutes for light to travel here and it seems a shame for it to come all that way and not get used to its full potential! That's why we were really excited about the 6 in 1 Solar Robot.
This 'do it yourself kit' is a great beginners introduction to solar power technology and the end result is your very own little robot. There are 6 different ways to build it, so you could have a robot dog one minute, or a boat for your bath the next! If either of those don't do anything for you then why not build your own little plane (moving or still), windmill or solar powered car!
The good news is that you don't need a degree in robotics to start with, or have to try and figure out which screw is A678b and how part D456 slots into F9097a!! The diagrams are big and very easy to follow, there are only 37 parts and no screws are involved!
Sounds great so far, but what if you live in the UK, like us, which hardly ever see's the sun? Well, this eco friendly robot can also be powered by a 50 halogen bulb (or brighter).

Another cute solar product! Maybe one day these products will be developed so people can actually purchase them to generate  massive amounts of energy via the sunlight (probably never in the UK as we don't get enough sun, but places like Egypt & India! ^^)
 Here is a product description & link

It’s time to peel your kids (and own) faces from the TV screens and get them playing back in the real world. This cool building set not only increases creativity and brain development but also has a high impact on fun levels and planet saving power.
All you need to build an exciting new toy is this kit, a fair bit of sunlight and a few pieces of rubbish. Not only are you helping the planet by using its natural solar power but you can recycle old cans, CD’s and plastic bottles. Not a single battery is needed to build the six fun models, just eco-friendly solar power. Inside your kit is a set of easy to follow instructions and diagrams explaining clearly how to install and utilize recycled materials. Turn your old CD’s into a speedy race car, make a used bottle into a flying bird or convert an empty can into the ultimate drumming robot.
The Solar Recycler 6 in 1 Kit is a fantastic way to enjoy learning about the science of renewable energy and gives the imagination a huge boost.

So going to buy my children these when I get around having children somewhere in the far future. Or anything that is remotely similar in the future :) Why give your children Barbie or Cars? When you can give them science experimental kits and Lego for creativity development in the mind ;) 

Thursday, 19 June 2014

HPLC 2nd run!

So today we did HPLC runs on our BBY spinach collected fractions from FPLC performed yesterday, to analyse the pigments in PSII supercomplexes.

This is a microconcentrator which we place our medium in to aid concentrating it, by using a centrifuge. 

HPLC machine again :)

My favourite part is adding the labels to the vials for HPLC, its so intricate task, love it!

Pipetting our medium into the microconcentrator!

The white lids placed on the top of the ependorf tubes are filters, as discussed before we use syrines to inject our sample into the ependorf tube, this technique allows us to filter our medium! 
Went home and stuck in my results from HPLC from today's session. I wanted to edit the files to nicely fit in my lab book and the fact that the windows 2000 interface is just SO slow on the lab computer, makes more sense to do it at home.

Love my Pritt stick, its what makes my lab book so informative, sticking in all the files!

Results from #2 run of HPLC :)

I absolutely love my beloved red canon printer. Scans, copies, prints, duplex. Duplex is a big for me for lecture notes and it's ecofriendly to, save paper! I absolutely adore my printer to bits, haha !