danny’s space

It is done. Phew. Up until 4am this morning printing out stuff, and then wake up today to collage, lug it all to uni and hand it in. Unfortunately a few other honours students are still going. I guess it’s okay, you only lose 0.5 marks per day it’s late, not like the crazy 10%/day thing.

So what to do now? Don’t know. Sleep? Who knows. But I think a copy and paste of my acknowledgements page is in order…

I am indebted to many people for their invaluable assistance, helpful advice, and kind guidance rendered this year.

Immense gratitude is owed to my three supervisors, Robyn Overall, Penny Smith, and David Day, who have spent countless hours supporting me in my struggle with biology. Thanks go to Robyn for being, amongst other things, a smiling and reassuring constant with a fantastic ability for lateral thinking; to Penny for her eagerness and vast knowledgebase; and to David for his clever ideas and meticulous appraisals.

Much appreciation is also extended to Angela Ho for her friendship, skilful guidance and eagerness to share, as well as for supplying vectors, competent cells, an Arabidopsis cDNA library, and other lab paraphernalia. I am grateful to Jing Ji, Michelle Barthet and Emilie Cameron for their unceasing and uncomplaining help in vector construction, supplying competent cells, and general lab assistance. Thanks go to Debbie Barton for her patient teaching of tricky immunocytochemistry techniques and for her help and advice on microscopy. Thanks also to Errin Johnson for her self-sacrificial attitude when giving assistance and advice in anything from PCRs to confocal microscopy. I am also indebted to both Errin and Debbie for their highly demanding, last-minute efforts trying to divulge the secrets of protein aggregates using electron microscopy, which was nothing short of heroic. I look forward to studying this in greater detail with them. Christine Faulkner, now living in Scotland, was indispensable in setting up half the project, donating vectors and providing encouragement. I am grateful for the help offered by John Gardiner in searching microarray databases as well as for his kind concern for me. Laurence Cantrill provided much valuable assistance with the Zeiss confocal microscope and other cell biology matters, as well as being open and approachable. I also owe a great debt to Dave Collings from Australian National University for conjuring up half the project and for helpful discussions and encouraging comments on artefacts and over-expression. Thanks to Leila Blackman, also from ANU, for her constructive observations and for vectors. Thanks also to Rosemary White and Craig Wood, both from Canberra, for supplying dyes and vectors. Louise Cole must also be mentioned for her helpful advice. Thanks to Ellie Kable and the Electron Microscopy Unit for allowing the use of the Nikon confocal microscope; to Jan Marc for allowing the use of his particle inflow gun; and to the Skurray/Firth lab for kindly allowing the use of their equipment.

This list would be incomplete without mentioning the rest of the honours students, whose friendship and support have made this year much more enjoyable.

Finally, I am greatly thankful for the support and understanding of my family and Sara, who have undoubtedly borne the majority of my stress this year. Last but not least, I am thankful that God has given me this wonderful opportunity to study this world in such detail and be continuously amazed at the intricacies of biology.

No days left! Just a part of a day. A large part, but still only a part.

Bit of a scare before. The printer stopped working, wasn’t communicating with the computer. *Gasp* But I think it’s a cable fault (what the heck, that never happens) because when I used another USB cable it worked fine. Strange stuff.

Meanwhile, the thesis is at 74 pages now, phew. Just going through a final draft looking for mistakes, of which there are probably a lot.

It’s scream time!

Lessons of the day: learn how to colour-match screen and printer output before crucial printing needs to be done. Also, laptop displays are very bad at reproducing colour. On the Photosmart 3110, the ICC profile that came with the updated printer drivers is the way to go, along with the ‘absolute colorimetric’ setting, whatever that means.

Still waiting for updates from my supervisor but I think she’s called it a day, so will have to wait until tomorrow morning. Then will need to frantically update the thesis with her corrections, send it around to supervisors for them to have a read, and then hopefully make final corrections, print and check over a final draft, and then should be done.

Well, save for all that printing. Publishing four copies of a 150 page thesis on two colour inkjets is quite, erm, interesting.

Oh how I wish it was all over. I’m sure my supervisors feel the same way.

I’m so sick of having to find references for stuff that is like, duh.

Second draft is done. It’s down to 86 pages, so 11 more to cut. Shouldn’t be too hard for my supervisors, they’re very experienced at chopping things.

Another thing I’ve realised much too late is the value of good (electronic) note taking while reading. It makes finding references so much easier. Electronic is good because it’s searchable. I started using EverNote, but it has quite a few limitations including its bodgy search function. It’s built on a good premise but has many user interface issues. Hopefully the new version they put out in the last few weeks is better.

Anyway, need sleep. Argh!

How time flies. Am I having fun? Well, by definition, I must be.

The MMB people hand in today. Mind you, their thesis is substantially shorter and their projects tend to be better executed, just because they’re an, erm, better endowed school.

Anyway, still making changes and cutting out lots of stuff. So much to do, so little time left. Why am I blogging then?

Just when I thought it was smooth sailing…

Went in to uni today to get face-to-face feedback from my supervisors. And was talking to a friend and she mentioned something about double spacing.

DOUBLE SPACING?!

Turns out my thesis as it stands is 25 pages over the limit. Great. I still need to make lots of changes to the expression, also add a fair bit of stuff to the discussion, move things around, and even re-analyse one of my results. Also need to make a new figure or two, change a few existing figures. Plus we need to chop away 25 pages worth of thesis.

It’s going to be a long weekend. And not the good type.

Nearly there. Drafts for chapters 1, 2 and 3 done. Chapter 4 to go, but hopefully this one will be short. Then the abstract, then the acknowledgements. Then the title page. The funnest till last.

74 pages of text so far. 117 pages all up.

And was the purchased article worth it? Not really, they only had one sentence that I wanted, and it was essentially data not shown anyway. Argh! You live, you learn.

- Edit -

Ok no I lie. Still need to do the introduction to chapter 2, argh, I forgot all about that. Nooooooo…

What a rort.

Thank you for purchasing an article through the Nature Publishing Group.

You purchased the following article(s):

Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter

The total cost of the order is: US$ 30.0

The article is three pages long. That’s US$10 per page. But it’s not available on USYD, UNSW or UTS library servers, argh! Which meant I would have had to go into uni just to get a three page article. At this stage in the game I thought it would be worth it. Maybe I’m an idiot for purchasing it. But hey it’s done and I can (perhaps) sleep easier. It’s an article I needed - that’s my excuse. Mind you I haven’t read it yet.

Hmm, that’s almost as much as this server costs a year… I feel so jipped.

Chapter 2 results done. Need to revise chapter 3 with changes that one supervisor sent over. Then need to get a mooove on with chapter 2 discussion. Already 0.75 days behind. But should be on track for finishing. This however leads to laxity.

Making bi-daily updates is fun.

Trying to find a reference to cite for a simple statement like “alpha helices are stable” is not.

The sky is blue (Dog, pers. comm.).

The draft for chapter 2 is done. Chapter 2 has been swapped with chapter 3. Which means chapter 2 (the old chapter 3) still needs work, namely the intro, results and discussion. Eek! But hopefully there’s not that much to do for the intro, nor for the results. Not like the 20 or so colour plates containing a zillion images I had to do for chapter 3 (the old chapter 2). And not to mention me having a brain freeze and accidentally deleting a figure. Actually I overwrote the updated figure with the older, mostly empty backup. Drats!

My eyes have given up on me and now refuse to focus. I think I’ve gone partially cross-eyed from looking at the laptop screen for at least 3 weeks now. That’s waking up at 8, sitting on the computer and typing until 1 or 2 in the morning.

Needless to say, can’t wait till it’s all over.

But, scary as it sounds, I am looking forward to doing chapter 2. A change is as good as a holiday, perhaps. But I also want a holiday.