The Xanthophyll Cycle in Photosystem II

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 !

Wednesday, 18 June 2014

A Super Long Day: BBY Spinach Protocol

So today was an extremely long day in the lab. I was in from 8am-6.30pm...

The length of the BBY spinach protocol is why we started off with the isolation of stacked thylakoid preparation first, to see if it yielded high amounts of PSII super complexes. However, no matter what, the PSII super complexes were not pure in the sense that the PSI was still always attached onto them, which is not what we wanted. We only wanted PSII super complexes to analyse the pigments in the Xanthophyll cycle under light stress. Therefore, we took the the protocol of BBY spinach, which involves more steps, but the isolation of ONLY PSII super complexes is the final outcome- an outcome which we desire.

Due to the fact today was a  long day, I took many photos to keep me going & the 2 shots of coffee I took at 7am! (Warning you, there are many photos to follow, to the end of the page!)

Preparing the muslin filter ate for the grinded  slushy spinach leaves via the polytron. The protocol of BBY spinach starts off identical to isolation of stacked thylakoids.

Irina & Petra walking down the fourth floor corridor. Irina is a 2nd year biochemistry student from Queen Mary. She is doing her third year project with Ruban and basically is shadowing/ learning techniques before the start of her project! So glad she is here, more people in the lab more fun, as she is quite social so there's always something to talk about. Labs are always so fun in our team: Me, Irina, Petra and Erica. We have good chemistry, chemistry is so important. Can't imagine how my studentship would be like if it wasn't like this....

Fourth floor corridor, offices and labs ~

Walking up the stairs~

Irina university grown peas! Her 3rd year project will be involving peas so she has to grow them! It's quite nice how she can grow hers and see her material from start to end.  Due to the fact that my material is spinach and we buy from Whitechapel market, I have no control over the conditions the spinach are grown in! Obviously, every factor matters in science and we like to control as much as we can :)

Such a fine day on Fogg's rooftop ! Love the colour of the sky.

A fig tree grown by Anna, phd student at Ruban's Lab. Quite impressive right? Looks so healthy ;)

Adding the spinach leaves from the freezing cold icy water into the glass square cylindrical column, getting it ready for grinding with the polytron!

OH GOSH THE GREEN IS JUST SO LUSH! Love this photo, its ever so vivid ;) So yes filtering.

Squeezing the filtrate to get all the liquid out, you can only do this in the first filtrate as the second time filtering, you just let it filter drip.

#2 filtering 

Helping each other with the filtrate.

Adding solution in a filtering system. Later you will see how we filter the solution with pumping air outwards using a pump attached onto the de gaser equipment. Which rapidly forces the liquid to filter through the pores.

Measuring the O/D. Allowing us to calculate the chorophyll A: B ratio with such measurement. 

The blue slot is for the reference, acetone, what we added to our solutions extra.

Keypad for the spectrometer.

Pouring our solutions into the glass columns after centrifugation.

Nicely drawn table for recording the O/D of my solutions.

Moved labs where we shall be de gasing the solution so it will filter through rapidly. Petra is sorting out the pipes for vaccum out the air.

Me holding onto the pipe which vaccums out the air. As you can tell already the liquid on the top has rapidly filtered all the way through.
We have to do this knee tapping technique to get rid of the bubbles at the bottom of the flask. Alot of bubbles are attached to the magnetic stirrer which is required when we are making the buffer solution, adding all the powders.

Here is Ruban's dark lab! Instrumental !

Here is where all Ruban's researchers are placed. Erica, Petra, all the phd students: Anna & Max.

Biochemistry lab~ one which i've talked about already. I so prefer being in the biochemical lab there usually some form of light coming through compared to the dark lab. The dark lab just makes me feel sleepy during the day, as its pretty much blackout in there!

 Lunch time has arrived! So here is how my lunch is usually spent!

Finally I have manage to take a picture of the Fogg Building, which is Queen Mary's School of Biological and Chemical Sciences department. Yes completely lego, have to abit its one of the coolest buildings, or at least striking of that on campus ;) 

So we walked to the opposite side of the canal by the university to have lunch. What you observe: the blue building is student accommodation. Loving the hole in the middle of the building, in chinese feng shui terms its very good for a building to have a structured hole like that in the middle~ This is most of QM most expensive halls~ think its £180, but they get a bath tub ensuite! Posh! My first year halls is the brown halls right next to it on this right hand side of this photo. It's called Pooley house~ ensuite~ have fun memories there. Oh gosh how first year seems so ever long ago, but yet has passed so recently! 

By the canal, see this pretty canal boat with flowers on the top. Have to admit this area is a pretty nice area to relax and go for lunch on a hot summers day :)

My packed lunch bag. Yes it is abit childish, but I'm quite into all the cute things :) You are never too old, haha! Also, because I'm small and orential I can probably get away with it. Also, I brought a Costa (there is a Costa opposite my university) ice coffee to keep me going after lunch, especially because we have been in for so long, and had even more hours to do after ! 

Peak into my lunch box. Love siesta lunchboxes very clever designs! Healthy food = healthy mind :) good motto!

 Back to the labs!
Really love the labs timer. Its magnetic and fits nicely into my small hands. So need one for my oven as it doesn't have a timer, this piece of tech would be extremely useful!

This is a larger centrifuge, which can spin to max speeds of 30,000 rpm! Looks like a japanese washing machine to me :P

Because the large centrifuge doesn't have a pre cool setting, we keep the inner disc parts in the fridge to pre cool them that way!

Oh how UK weather changes so rapidly. Now it is gloomy! But the nice lego architecture of Fogg building always brightens any day!

This looks like it could be part of a canon! It is where we place out test tubes for centrifugation.

Massive microwave! Well looks like this, this moves whatever you put in it in a square motion!

Placing in the fridge already pre cool disc part of the centrifuge.

Fixing on the lid.

Seriously looks like a japanese washing machine...

Adjusting the settings.

Here is is in lab.

Ruban's office is very close to the large centrifuge, so I thought to take a photo :) Where all the meetings are!

Very concentrated material!

Me using a 5ml pipette, look so ready in action.

Inverting the tube to ensure uniformity in solution.

take #2 : smiles :D

Counter balance of water, checking via eye that it is roughly the same in level. Obviously, we measured it out before hand in weight to ensure it is correctly balanced.

Placing the tubes in!

Signing in that we used the centrifuge last. 

Using a paint brush and added H20 to re suspend the pellet obtained from the large centrifuge, important to keep in icy temperatures as mentioned before!

Using a syringe to filter through the material through a mini filter placed on top of the ependorf tube.

 End of the day: Autoclave time:

So there is a trolley outside the autoclave room which all the labs on the fourth floor place their equipment on, which they desired to be autoclaved.

Placing all the equipment in the trolley in the autoclave! 

Autoclave in a different position. Seriously looks like a massive pizza oven! I swear I always think that everything in the lab looks like something else in life, haha.

The instructions for which setting to set for what you are autoclaving. Pretty self explanatory.

Everything set. READY TO GO.

Finally, the end of the day: What a long a day! 
And also a blog post too! Haha hope you enjoyed it :)