Project: Students!

"Once a job is fouled up, anything done to improve it only makes it worse" - Murphy's Law perhaps?

9.00 am...

Our eager undergraduate project students arrived today, lab books and calculators in hand.  "Do we get a protocol?" I was asked.  Not exactly, was my response.  Blank stares rapidly turned to fear as I explained the purpose of the following few months. 

Their mission was to produce Matrix Metalloproteinase domains from a DNA construct provided.  I had begun a similar project two years before and was aware of the culture shock.  They would have full ownership of the project, responsibility for outlining the methodology and management of their own time.

9.30 am...

Starting simply, we began with simple buffers and a few concentration calculations.  This in itself generated scratching of heads and a sweaty brow or two.  

10.15 am...

Lumps of Tris Base began dissolving, swirling around on the magnetic stirrer.  Adjust pH with hydrochloric acid I advised.  

11.15 am...

Tris still swirling.

12.00 pm...

LUNCH!!

I have a peek at my old project lab book.  My first experience of making LB bacterial media was traumatic at best.  "Error in calculation, LB re-made" my scribbles shout from the worn pages. 

I'm reminded that we all have to start somewhere and with a little support and some good advise, great things happen.

1.00 pm...

The hustle and bustle in the lab continues.  The Tris solution has been made and labelled, the project students are hunched over their lab books making notes.

I'm feeling positive.
 



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Paper, paper everywhere

"Must get data, must get data".

Muttering my new mantra, I have finally emerged, relatively unscathed, from a mound of paperwork.  

Every spare minute has been spent deciphering the virtually illegible scrawls recording the past year of my PhD adventures!

It is review time and I have been collating data, drawing graphs and sifting through images.  Submission of my report detailing my work is required to continue my studies (and hopefully impress my supervisory team).  I have been beavering away compiling a complete compendium of my research to date, hence my absence from the 'blogosphere'.

Surprisingly, this has not been an easy task.  I am reminded about time.  The past (how little I feel I've achieved), the present (punctuated by repetitive strain injury brought about by vigorous typing) and the future (so much left to do...).  

Report emailed.  


A clear mind yields positive results in the lab.  Cue heavy breathing (not dissimilar to Darth Vader) courtesy of my protective respirator, I add a little dash of APMA to my protein sample.  WOO HOO! With successful protein activation complete I can now focus on getting some tangible data.


Year Two begins...



 
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Chromatography capers!

The general feeling of exhaustion continues but despite that it's been a busy day in the lab, at least for the machines.

While my protein sample sloooooowly travels through the vast capillary network on the chromatography machine I have been glued to a computer screen. Automation rules...well at least it would if I didn't have to keep running into the coldroom to swap over buffers. At 4 degrees it is practically arctic and I left my fur-lined snow boots at home!

I wash the lines through with lashings of salt to disturb the molecular interactions that transiently immobilise my mutant protein. Contaminants removed, all is looking good and more importantly, clean.

Two weeks and two days later I still have to check protein concentration and check purity. Each step in the process makes me increasingly nervous. Time is critical as samples degrade, some of my counterparts have worked around the clock...check under the office desks and you can find a duvet or two!

Tick tock.

A quick run through with ethanol to clean the instrumentation and home time beckons. No lab duvet shenanigans tonight.



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Liquid Life

"Ouch".

The needle pierces my flesh, I can't look.  The throbbing sensation reaches a crescendo.


Approximately 5 litres of blood is traversing my circulatory system at a rapid rate and I'm feeling just a little queasy.  I've never been a huge fan of diagnostic blood letting but deep within my tissues, these biconcave crimson cells may hide the reason for my lethargy.

Distribution of precious oxygen molecules throughout my tissues will eventually contribute to the creation of energy, much needed when chasing after a small (grubby) child.  


Clearly, as highlighted by my continual yawning, my mitochondria are feeling oxygen deprived.  Or perhaps, the little white soldiers that patrol the depths of my insides are overwhelmed by an ambush of viral invaders.


Either way, the tubes of scarlet liquid that line the desk in the phlebotomy clinic are the true essence of life.


Donate today!

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Buzzing Brain

Fluorescent lights glare, fridges hum…I’m back in the lab.

A cursory glance of my laboratory bench suggests a need for fresh reagents. New ecosystems have sprung forth, swirling around within the glass bottles that line my workstation. I have created life and it was somewhat shorter than the usual nine months gestation.

Before diluting chemicals and adjusting pH levels, I decided that I would catch up on a little news.

‘Migraine Risk Linked to Gene’

Investigation of the genetic code of migraine sufferers has identified a region located between two genes (PGCP and MTDH). These particular genes are known to regulate neighbouring gene EAAT2, which instructs cells of the brain to produce a major transporter protein responsible for regulating glutamate levels.

But why is this important?

Glutamate is an important neurotransmitter, a chemical that stimulates synapses, sending signals between the cells of our central nervous system and affecting cognition, memory and learning.

Catastrophe!

Suffer a stroke or head injury ruptures the cellular boundaries, spilling glutamate throughout the cerebral tissues. Brain cells swell and burst in response to over-stimulation by glutamate and so a potentially deadly cascade begins.

I imagine the crescendo of glutamate molecules bubbling within my brain, generating technicolour waves of light and bizarre auditory hallucinations.

Luckily the dull thud within my brain is far from the agonizingly intense storm experienced by migraine sufferers. I reach for my tepid cup of coffee, caffeine surges through my body. Dopamine floods my brain as the caffeine molecules bind to my adenosine receptors.

My brain is buzzing and I’m ready to start the day!





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Bacteria Bashing!

“Thanks Postie!”

I imagine a shiny rotund white building, six stories high and set in fields of luscious green grass. Behind the modern curvaceous walls, the latest whirring and clicking gizmos sit in large fluorescently lit rooms. Devoid of life, huge silver automated machines analyse thousands of samples and churn out reams of data.

I’m somewhat disappointed, because somewhere in Essex, courtesy of Royal Mail, my package is dropping through the letterbox of a small brick-built building. Judging from the photograph, my DNA samples are in a small industrial site located in East England…wait a minute, I’m sure that’s a Renault Megane parked outside!

Ok, my illusions have been shattered somewhat but I know that in a matter of hours the four precisely labelled tubes containing my mutant bacterial DNA, will have been efficiently processed.

I have discovered that saying ‘mutant DNA’ generally raises eyebrows and occasionally a voice of concern. Fear not. When adding, deleting and altering parts of the bacterial genome it’s more likely to harm them, than us. In fact, introducing a human gene into a bacterium is hard work and often produces toxic proteins in the wee little bug. It is by chance/skill/luck (delete as necessary) that your protein is viable. Be assured that protein extraction from the nutritious bacterial soup will result in a swift demise for our sausage-shaped friends.

“PING…you have mail”

Opening the document, I quickly scan the page.

CCCGCCTAC, positive for the mutation I have introduced…let the bacteria bashing begin.

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Demystifying Biology?

"How's things?" 

Surrounded by the buzz of conversation and buoyed up with a dose of caffeine, I found myself explaining the intricacy of protein structure.  With nothing more than a half-eaten chicken salad sandwich and a steaming latte I carefully demonstrated the finer points of matrix metalloproteinase (MMP) structure to my lunchtime companion.  


For friends and family, comprehension of my research often requires a brief science lesson with a variety of props.  Lego, I have found, is particularly good and readily available (Jack usually has a half-constructed T. Rex to hand), sometimes a biro and napkin suffice.


Once upon a time, when asked about my day I would mutter things like "plasmid...protein purification...chromatography".  In return, I'd receive confused head-nodding and blank stares.  A few years ago I was doing the same thing, when getting to grips with university lectures.  I'd furiously take notes, hoping that when I read them later all would become clear.  When it didn't, I used my trusty Collins Biology Dictionary and a GCSE Chemistry book.  I never understood why everything had to be so complicated.  

Strolling back from lunch, past fast-paced strangers, I wondered if ever they thought about the circadian rhythms that contribute to our metabolism and insatiable hunger at noon, or the signalling pathways that detect low glucose levels and remind us its time for feeding.  


For many, their own biology is a mystery...



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