finger update

It still hurts.

!

ten things

1. Life should be a fucking box of chocolates, complete with gold foil casings, an illustrated guide to the contained confectionaries, a sensible eat-by date, list of ingredients (including possible allergens) and a nice secure box that won't let any sweet goodness escape. Not to mention cherry liquer.
2. I propose the formation of a Cholecalciferol Club, the purpose of which is to protect the ongoing bone density of its members. I earnestly believe that this will be most effectively achieved by partaking in extended daily luncheons in the fickle Melbourne sun.
3. How many literature reviews does it take to fill a recycling bin?
4. When I was in grade 3 or 4, we made placemats. The method goes something like this. Firstly, obtain a sheet of canvas. Secondly, paint it, however you wish. Thirdly, cut out random bits of image from wrapping paper, preferably that nauseatingly populated with teddy bears and pastel-coloured balloons. Fourth, slather the whole lot in a layer of Estapol. Fifth, gasp outside after desperately holding your breath in order not to inhale the undoubtedly toxic fumes. Sixth, repeat steps four and five as respiratory and neurological function allows. Seventh, enjoy your placemat (or, as it were, take it home and let it languish in a cupboard until your mother relegates it to that most holy resting place of all school art projects - the bin).
5. My laptop is a machine abused.
6. "Could everybody please check their pockets for the blue keys?"
7. A horrible fatigue has set in - not that I shouldn't be used to this by now.
8. "Ignacio Provencio is the discoverer of melanopsin, a photopigment found in specialized photosensitive ganglion cells of the retina. He is currently an Associate Professor of Biology at the University of Virginia."
9. I don't believe that we have a purpose but I do believe my brain can perceive fun, regardless.
10. I hope you aren't wasting my time like I am. Bloody AMS.

A long time between posts...

Well, it really has been quite a while. I've had my computer back for a week now, but the incompetent service people (some of whom appear to have been sacked) have still not repaired it successfully, and it experiences the veil of death once per day, often at inconvenient times. I cannot bear to be parted from it again so soon, since it is the only way I can get video chat with Australia, but I know that it's going to have to go back in for repairs very soon.

As to what I've been doing for the last few weeks, the answer is really "Not much". Research has been proceding, and I am now mostly working on my own. I haven't done a great deal with my main project yet, since I have been working on a separate project in which my supervisor seems quite interested. It is a more clinically-focussed project than mine, looking to develop a treatment for prostate cancer. I don't hold much hope for it, but we shall see what happens. So far, though, it has not been good. Why? We have previously run a couple of QPCRs looking at the two RNAs of interest in the prostate cancer cell lines we have cultured. The results had been fairly stable. However, I took a look at the literature to see what was expected, and although the data were very scarce, what we had found seemed to be different from what would be expected. Therefore we decided to change from SYBR green (with which we had had some problems) to TAQMAN, which is far more specific, but much more expensive. For comparison, 250 reactions with TAQMAN probes is about £300, whereas a similar amount of SYBR green primers costs only £3 (and arrives from Germany on the same day/next day... shockingly fast post). With the TAQMAN probes, we got the same results as we had had with SYBR green. However, I repeated the experiment in triplicate to have some solid data, and the results were significantly different. We thought that this could be a problem with the cDNA, but the RNA that I looked at at the same time, as well as the housekeeping gene, showed previously validated results. I ran an experiment with the last of the old cDNA alongside some new cDNA, and the results of both were different, and also somewhat different to the previous results. What was interesting was that the results were closer to what would have been expected from the literature.

Yesterday I ran yet another repeat, and the results were different again. Two particular cell lines seem to have results that shoot all over the place, and there is little explanation for it. It still remains to be seen what is the problem...

I have not been doing any cell culture for a few days now, which has been nice because it has given me the last two weekends free. I will have to start doing some culture again soon becuase we have run out of RNA of a number of our cell lines. This means that I'm probably going to be working 7 days for a while as I struggle with 7 cell lines at once. At least I only need RNA and not miRNA and protein at the same time. I am learning transfections, which I have not yet started, but will be doing at some point in the next few months when I have established a decent cell line panel for the SPRED (Sprouty-related Enabled/Vasodilator-stimulated phosphoprotein homology domain 1 Domain-containing protein...) and have good data about the expression levels. I will not begin my culturing this week since it is a bank holiday (=long weekend) this weekend, and I will be visiting my cousin in Kent. She has a place in a fairly rural village, with chickens (yay!), and I am going to visit an English beach. Should be interesting... I will have photos to show.

This will be my first time leaving Cambridge since I arrived here, and one of the things that really shocked me about this was the cost of public transport here. I am travelling a distance of only 82 miles (approximately equivalent to Frankston to Geelong), but the tickets cost me the better part of £40! Just imagine if it cost us $80 (or even $40) to make that trip. For the same price, I can easily fly to Sydney or Brisbane from Melbourne. Oh, and this is after the 1/3 student discount, and the cheap off-peak tickets, and booking well in advance to minimise cost. It is no surprise that everyone here seems to own a car; when a car will pay for itself in 10 trips (yes, cars here are very cheap; a new car can be bought and insured for under £2000, and second-hand cars start around £200-£400 for a reasonable car with low mileage)

The weekend before last, I had some free time, so I decided to visit the Fitzwilliam museum, since I have heard a lot about it and wanted to see it for myself. I was there for a whole day, but was only able to explore a single floor, so I will have to visit it again. It is an huge place, with artifacts from all over the world, and it is well laid-out. Most importantly, it is free entry. While I was there, I was fortunate enough to discover that a recital was going to take place that day, so I was able to hear an excellent violinist play a number of pieces, the only one of which I really cared for was La Campanella. I am looking forward to the early music festival that is approaching, and there are early music recitals every week. I just wish that work finished in time to regularly attend, but even if I could that would certainly reduce the number of dinners I would be able to have each week. Many of the festival recitals will be on weekends and in some of the cathedrals around, so I am quite excited to attend these.

I have posted some new pictures on Flickr. Please look and comment. :) There are still a number that need sorting before posting, so some more will be up in the next few days. Here is a church I discovered while meandering outside of town on my bike.

There is a lot of beautiful rural scenery and nature around here, as well as the ancient buildings. Nature here is interesting, since with Australian eyes it all looks man-made. In many ways, it is; this country has been grazed and farmed for so long that even the forests conform to man's will. However, it's lovely to see wild apple trees, plum trees, and blackberries everywhere, and to be able to pick and eat fruit while riding along (if one can avoid the ever-present wasps). Back home, these plants would be considered evidence of man's presence, but here they are actually native. On certain roads there is the ever-present smell of cider from all the fallen apples fermenting by the roadside.

One of my weekend activities seems to be to fight a war against the wasps. I don't like these insects, but refuse to kill them, and perhaps they realise this and therefore are rather bold in their attempts to eat my food. No matter how much I close my windows (something which I do not like doing), draw the curtains, and trap the wasps in bathtowels, they keep coming back through my window and flying around, looking for my cordial, I think. I close it tightly and wash it vigorously, but the wasps still seem to like elderflower cordial as much as I do. One wasp had the misfortune of becoming trapped under a towel which I must have pressed down slightly too firmly, and was a casualty of war. The rest have, for now, been put off by the slightly cooler weather. I dread the forecast of sun for the weekend, because it means that the war will resume. These wasps are far too ingenious; I trapped one in my bin, put it out in the corridor still trapped in the bin, and closed my door. It managed to eat its way out through the plastic, crawl under my door, and fly around the room again... Very clever for an insect!

Some wasps attacking a cluster of blackberries

I will post some more soon, and certainly after this weekend, when I will have some new scenery and new experiences to provide blog-fodder.

finger pain

On Thursday the mobile blood bank came to RCH. I dropped in to see if they had any appointments and the lady said I could do it right then. I'd had lunch before, and I was bored, so I happily agreed. I filled out all the enrolment and history forms, and proceeded to the cubicle where the Red Cross worker would put me on the system and test my haemoglobin levels.

*Prick*

A quick jab to the side of the tip of my left ring finger. Ouch. I chatted briefly about the glucose test we did in first year uni as she squeezed out a few droplets of bright-red lifejuice, the final drops onto a cute little glass slide.

One to two minutes after the initial prick, it was still very painful, and I told her this. It was then that a foreboding fist of nausea began to burn in my belly. "Oh SHIT," I thought.

"Do you need to lie down?"
"I don't think so."
"Are you sure?"

---

And, naturally, I rise, my vision begins to fuzz over, like TV static, and I'm lowered to the floor, legs elevated, and there are three or four people looking down at me, one pressing a cold towel to my head, the other wiping one around my neck, the other saying "I don't think you should give blood today..."

After a few minutes, I get up, and am directed to "Go! Eat Cheese! Biscuits! Cheese! Eat Cheese!" I do so (well, I eat biscuits but not the cheese... it was that cute little wrapped stuff that I loved when I was a kid).

Sigh.

---

The strange thing is, the pin-prick point is still extremely sensitive when I touch it or fully extend the finger, even 2 days after the event. Explanations, anyone?

It's been a long time since I last posted...

Okay, so I’ve been very, very lazy with blogging... and my crazy hours plus inefficiency doing experiments doesn’t seem to help much. – which I will write about later. First thing first...
Last Wednesday the lab had a feast, because one of our researchers, 4 weeks before her due date, was going on maternity leave – which I kept on making the mistake of calling it a “holiday”, and getting funny looks from her. So we decided we should have a session to feed her and the baby.
So one PhD booked the Teaching Lab room, where we had almost all the Sem 5 pracs, for lunch, and everyone in our lab brought something along. Plates and trays and plastic containers piled with different foods lined up desk/bench in the room, where Sandra used to neatly line up the microscopes and petri dishes. Hmm enticing...
Nonetheless, food was abundant, and mostly interesting and tasting very nice, with a gross oversupply of desserts.
The most interesting dish was probably the some dish called Saaq....something, made by the Iranian PhD. It was long, thin-grained rice (not a familiar species to me since I’m used to the short, oval-grained northern Chinese grown rice) with a spinach/onion puree. The rice is slightly harder and drier than the ones I usually have, and with a different aroma, and the puree was slightly sour tasting.
Then there were Indian , which were brown, pyramid shaped pastry with hard shells and a spicy curry pea and potato filling. Slightly too spicy for my liking. Another PhD student from India bought the Indian version of the spring roll, with exactly the same type of pastry, but curry fillings, and unfortunately I forgot to ask her the name of the dish.
And of course, there were the party pies and sausage rolls brought by the organising PhD student, that everyone seemed to have ignored in the face of all the other delicacies... then there were savoury Chinese pancakes with carrot and radish fillings made by the other Chinese in the lab, who was a senior researcher, and the soup-filled buns that I bought and steamed.
Onto the desserts. Regrettably there were too many varieties... Home-made muffins, yo-yos, coconut biscuits and a DELICIOUS lemon tart (made by our Dutch-born, part-time vet, king-of-structural-immunology; the cooking prowess of this 50yo+ man puts me to shame... but then again, everyone’s cooking would put me to shame) were amongst the favourites. But people also bought chocolate-coated teddy bears biscuits and a custard-filled-chocolate-coated pastry thing (please excuse Hong’s shocking Western culinary vocab), and a very curious “cookie” that resembles a walnut, with hard cookie ball-shaped shell and soft caramel core.
Most bizarre of all was that someone even brought their homegrown lemons, which were tiny and tasted like a crossbreed between lemons and oranges. Despite their looks, they actually proved to be excellent after-meal fruits, especially when everyone was bursting with food. So much for feeding Luda.
A few random amusements took place during the lunch. Not only were people from other labs peering into the room and giving us sad looks when being informed that it was a McCluskey Lab only lunch, but in fact people in the tea room started nibbling our goods while they were heated up in the stove or in transit from the tearoom fridge to the Lab across. Then there was a professor of medicine from WA visiting Jim, our lab head who's originally from WA. So yet another stranger came to enjoy our free feast, and got his clinical judgement quizzed over Luda's "condition" which will prevent her from working. Interestingly, Jim is a double specialist in Pathology and Rheumatology (plus subspecialty in clinical immunology, of course), but he used to work as a Royal Flying Doctor in WA ages ago... Makes me wonder how old this guy really is...

The long journey

So it's been a month into AMS, and the journey to go is still long

Well, for me, it seems that everyday, my journey to AMS is long enough. 1.5 hours there and back is taking a lot out of me.

I'm tired by the time I get to the lab. I sit at the microscope and stare at stains of muscle...and it all looks the same. I stare at genetic sequencing results, and every peak looks like a genetic mutation. I sit in meetings where world-class clinical geneticists and neurologists discuss rare cases of muscular dystrophy without a definite proteomic or genetic diagnosis. And I'm interested, but not much really filters through to that space in my skull called "brain."

So I'm investigating novel proteins and their potential role in muscle disease. Stabbing in the dark and testing patients for abnormalities in proteins that may only have been studied in mouse models or stand alone proteomic assays. I love it as a research topic, I really do.

But what I really love more is sleep.

Stress is getting into everyone

In the last 2 weeks, I started growing accustomed to running around in the lab frantically and confluzzledly trying to accomplish trivial but oddly difficult tasks, such as collecting liquid nitrogen, and purifying DNA. Thankfully my supervisor Nigel had been patient with my painfully overcareful ways many a time, but patience does have its limits. I do recall one time last week when I was fixing a brain for microtome slicing ever so painfully pussilanimously (if there were ever such a way of describing it), that he suddenly reached out and over my fingers, squeezed the fixative forcefully out of the tube in my hands . I gave a yelp of surprise at the time because I thought that was a little forceful of him to do so, and also the brain had shifted slightly away from midline. Well, that's Nigel for you, very paternalistic, fatherly-like, always treating me like a child. Not that I have any problems with being treated like a child :)...

Today after writing down my protocols for RNA extraction, I find myself faced with an entire day of just sitting down and reading papers or facebooking, which is really much appreciated when in need of rest. But, instead, silly me decided to go observe my friend Gabi with the Morris Water Maze test. This behavioural test is pretty cool, because watching a rat swim around in a pool of water and ruffle its wet fur when perched on the platform is just too cute! Well it was cool until you realize that you have to scoop up rat faeces from the bottom of the pool after every 2nd or 3rd swim, plus there are 4 trials altogether per day for 5 days, so if one has 10 rats, that would be in total 40 rat swims to record per day, 200 per 5 days, for just one cohort (note I have 18 rats waiting). I found my interest fading away after the 10th swim or so...

But even for the first day of the water maze behavioural study, Gabi is starting to show signs of stress - the "losing it" stage. At lunchtime, she told us that over the weekend she dreamt of her dog having a seizure, and there was an incision over its head (refer to rat electrode implantation below and you'll get what I mean). And later on, she asked lab coworker Amelia (who is a close friend of hers), what day it was, and laughed to say that the answer was 218 (referring to the age of her rats). It was a joke, of course, but still I adviced her to have some well deserved rest.

Thankfully, my mind is still intact and well functioning. But my brain had been sulking quite a lot lately that today it finally brought upon me this horrible migraine to disable me from doing work. Finally, I had to admit defeat and left during a meeting because my urge to vomit had become quite overwhelming... I'm all better now, after having emptied all my stomach contents into a plastic bag, and having carrots and golden kiwis (all of my week's stock) replace my lost nutrition. Right now, I'm reflecting on how much Rahul was there for me when I needed a shoulder to lie on, on how much my lab mates and supervisor were concerned for me when I was sick today (no, it wasn't the swine flu fear), and so am really thanking God for having such a lovely work environment. :)

Will hopefully be going Go karting and Darkzoning soon with my lab mates in an organized outing soon. Can't wait to destress! :D
















Above is one photo I stole from the lab.Please keep this secret and do not post it elsewhere or they'll murder me! D:

FML

Friday, I moved out of my place in Carlton North to live with my parents for a few months. This is where all hell breaks loose. FML

Saturday, hell decides not only to break loose, but to form a cone around me personally and not burn me but slowly roast me, cooking my insides to a sad, mushy mess. FML

Today, I don't know what to do with myself. FML

Of Weekend Work and Fortune Tellers...

Well, it's been a while since I last posted, and will probably be a while until I post again because I am taking my computer back in for further repairs (I love being able to get every thing fixed for free, so I have a new computer when my warranty expires...) So... on to what happened during my weekend...

On Friday night I went out to a pub with my coworkers, and had a good time watching drunk people and talking, though of course the gradual increase in decibels of the music eventually made talking impossible and my continued inhabitance of the building undesirable. Still, it wasn't a bad way to spend an evening. I ended up spending most of the rest of the night on the phone, which wrote off some of Saturday morning. When I finally got up, it was time to go to work, since I had cell cultures growing that needed to be split and frozen down, and others which needed to be thawed and grown. They're like little chicks, really, constantly needing feeding and attention, regardless of the day. At least there is some ability to control them, since you can plate out very small amounts which will take quite a long time to grow, or large amounts which will grow quickly, but the cells tend to be quite temperamental, and like to grow in particular ways. Therefore there is a range of percentages by which they can be split, and the rate of growth sometimes means that they cannot be delayed for more than 1.5 days.

I finished work at 6, and rode out to the Backs (the backs of the large city-centre colleges), to sit on the bank of the Cam and drink (lemonade in my case) with my coworkers. It was pleasantly sunny and the atmosphere was nice. As we were sitting there and observing people, a strangely-dressed man was observed. He was wearing a patchwork jacket of gaudy fabrics, a jester's hat, torn socks, and loud pants. We were remarking on this apparition, when he decided that our little party looked like an interesting place to visit. He sat down and said something like the following very quickly: "Good evening esteemed sirs and madam I wonder if I would be able to beg the enormous favour of a moment of your time to introduce myself I am appelated Andi Pandi and I have the fascinating and esoteric talent of being able to read everything about you, more than you would ever cogitate or consider credible, simply from the order in which you select these coloured cards I have with me etc etc etc". We decided that it would be amusing to partake of this offer, so he went ahead and laid out his cards. I picked some, repeated the sequence a few times, and when he was happy he began to spout an awful lot about my many layers of feeling. As expected, he said enough that was general so that some things applied, and enough that was specific that he had observed from my interaction with workmates. After he finished, it was such fun to ask him specific questions and watch him wriggle... Particularly when he couldn't work out what my profession was ("something involving scrutinising"), despite a lanyard around my neck saying "Addenbrooks," and a hospital ID and a research ID. Eventually he saw it and pretended to "discover" that my colours meant that I was a doctor working long hours in the ED... not exactly. Anyway, it was quite a lot of fun, and he was a good sport.

Sunday was a bit of a non-day. I went shopping. That's about all that can be said for it. It's funny that even the aforementioned hypermarket is not open for long on a Sunday; only from 10am until 4pm. Still, that was enough. And that was my boring Sunday. I was going to go to someone I don't know's house for dinner, but then his wife was sick, so I ate a lonely meal and slept. Sometimes life here is not very exciting...

This is true procrastination...

So it's about 7 hours until I'm supposed to get up for a brand new AMS day of a brand new AMS week, but I'm still sitting in front of the computer, feeling utterly sluggish and not wanting to do the work that I was supposed to have done on Friday:
Experiment design.
It's a relatively simple antibody workup. But not so simple when there are 4 or 5 antibodies that needs to be done on relatively few samples. We're only harvesting 2 mice spleens and 4 mesenteric lymph nodes. One mouse spleen might yield 10^8 lymphocytes, if my technique can be called "up to scratch". That's not a lot of cells to stain. Another practical difficulty is the selection of fluorochromes for Flow Cytometry. Wouldn't it have been nice to have all the colours in the world? But at most there're only 5 available for our use. Not to mention the cells still need to be stained with the usual anti-CD4 and anti-Valpha/beta to select CD4+ T lymphocytes.
Experiment starts 8:00am tomorrow morning.
I'm sitting here feeling anything but productive. Must be the whether, I think.
Ah well, at least I'll get to have fun searching for little white blobs of Lymph node in the big white fatty mass of the mice mesentery tomorrow. That's always something to look forward to.