Some updates

Hi there! Yes I'm still alive and the best news is I've submitted my thesis!!! This is a quick update as I'm currently testing out blogging by email. So I finally submitted my thesis last Thursday. After 3.5 years of lab work and 6 months of full-on thesis writing, it's in folks. It's almost over. I have to wait a few more months to get results and then I can graduate. Meanwhile I got a job. No time wasted. I went for interviews in April as I was finishing up my thesis and got offered two positions. I'm now working at a new environmental institute within another university. Even though my role is more technical support than research, I'm happy to have a permanent full time position. At the end of the day, job security trumps all. I think it would be nice to take a break from research for now. Anyways now that I no longer have my PhD to worry about, I hope to do more crafting. I would love to improve my sewing skills and make clothes. I have started a few new projects this year (to keep my sanity while writing) but I'll share more about that later. Thanks for reading!

Thesis update

This is for my family and friends who are interested in where I am with thesis writing. I'm almost done...with my first draft! You like numbers? I'll show you numbers!

	pages	words
thesis intro.	11	2097
chapter 1	39	6996
chapter 2	27	5325
chp3 intro.	9	1997
chp3 M&M	20	4090
chp3 results	19	2309
chp3 discussion	7	1615
final conclusions	0	0
TOTAL	132	24429

So I still have my final conclusions to write. About 2-4 pages to sum up the significances of my research. I already got feedback on my first draft of thesis intro and chapter 1 so I'll be fixing that up. Hopefully the rest of the chapters won't require too much work to fix up. I'm really hoping to submit by end of March so keep me accountable and please keep praying for me. Thanks I love youse all!

Last experiment?

Time for a little PhD update...this experiment above is brought to you fresh from the lab today. I have good news and bad news. Since my last update (August), I have been able to successfully clone and express my protein of interest. The cloning part was the rate limiting step since it took me like 4 attempts to get positive clones. I tested out this protein with its substrate and behold it has activity! I was so happy I screamed and screamed like a crazy woman. The next step was to add this protein to my cometabolism supernatants and see if my mystery metabolite is indeed the substrate of this protein. Lo and behold! it is! well at least for one of my chlorinated compounds. Above is the repeat experiment to confirm my result, the colour correspond to how much chloride is in the solution. Finally! after all these years I am finally able to identify at least one of the break down products. This work is now done and I can write it up in my thesis!

Now the bad news, despite all my attempts at making cell plugs and running PFGE these last few months, I have no good results. Well it depends on how you look at it. A wise scientist once said "there is no such thing as a failed experiment just undesired or unexpected results". I haven't been able to see plasmids in my transconjugant no matter how I optimize the protocols. The result is both undesired and unexpected! but what if this is the real deal? I can only speculate why this is the case and suggest further experiments. I'm out of time to do any more experiments. So I'm just gonna tell my supervisor I give up and pray he'll just accept it.

In terms of thesis writing, I haven't made that much progress - a page here and a page there. I can see it coming together though. According to my associate supervisor at my recent progress interview, I have a few good stories to tell in my thesis. I'll be so happy when my supervisor finally say I don't have to do any more experiments, fingers crossed as I hunt him down to talk. I can just see myself writing from home full time and feeling really hopeful that I can submit on time too.

***EDIT: right after I posted this I found my supervisor and had a chat with him. He was very encouraged by the result above and after some more talking he said "right I'm not going to lie to you, you definitely have enough for a thesis. That's it, no more experiments, you're done congratulations". That was like music to my ear, the sweet sound of no more lab work. Hooray!!!

I'm back!

Hi there! I've been back from my trip for about a month now but haven't had time to blog. I've been busy getting right back into lab work again and thesis writing on the side. I haven't made as much progress as I would've liked but like my Supervisor always say "as long as the net progress is in the forward direction" lol. Hubby and I had an amazing time seeing the US of A! I will upload some photos and tell you about our trip soon enough I promise!

Crochet coin purse & update

I made this pouch some time back when I was sick at home for a week. I couldn't stand not doing anything so there I was in bed either crocheting or reading (when I'm not sleeping that is). I managed to read Life of Pi which was an interesting book and definitely worth a read. I am all better now, that week off put a dent in my progress but I figure if I didn't rest then, I'd never find the time to actually rest. So sad, I know.

Anyways time for an update. I don't know who actually read this blog anymore but it looks like I've got a few new visitors - hello there! So at the moment I'm preparing my progress presentation for labchat tomorrow. It's been 3 months since my last one and boy have I made progress! Not to get ahead of myself but I have worked extra hard these last few months. It wasn't all smooth sailing though, just last week my third attempt at an experiment actually worked. These transconjugants are so tempermental! I was so stressed out and wasn't a very nice person to be around (I yelled at bickering honours students and almost burnt down the lab!). I'm usually a calm and collected person so my outburst really shocked some people lol. I have mellowed down again so don't worry. Thanks to those who have been praying for me during this stressful time! God has been faithful in answering prayers for progress and teaching me patience as well as perseverence.

So how long to go? I hear you ask. My original plan was to be done by October this year (thesis submitted and all) but that ain't gonna happen. I have two more final experiments left to do before I can stay out of the lab for good. One experiment is to detect the plasmid in my transconjugants using pulse field gel electrophoresis (if it all goes well, it'll only take 1 week). The other experiment is to make (clone and express) a certain protein that I need in order to analyse my metabolites. I give this 3 weeks if all goes accordingly. However this is never the case in biological research, things are bound to stuff up along the way so let's multiply the time I need by 2, which means 2 months to wrap this up! So I'm giving myself til October to finish these experiments. That is also when my scholarship money finish (fair enough they've supported me for 3.5 years already!). I've taken up teaching a class for first year molecular biology this semester so that means some extra income to get me over the line. After that we'll just have to live on husband's income alone until I finish and get a job.

My supervisor seem to think I can write my thesis in 3 months! 150-300 pages or 40-80 000 words in 3 months! That's just crazy! But I guess I need that kind of pressure to get me going. I do have until March next year to submit so that actually allow for 6 months of writing time from October if both of my experiments work. So far I've written about 1/3 of my thesis (assumming I aim for 150 pages), very rough draft of mainly Materials/Methods and Results. This also include my paper (we submitted it in June but still haven't heard back from reviewers) being transposed into thesis format. Having written the paper really helps me with the writing process becasue I no longer see it as one big daunting unachievable task.

Sounds all busy and no play right? wrong! In the midst of all this I'm actually going to take some time off to go on a holiday. See! I'm being kind to myself lol. Husband and I have been planning our epic trip to the US of A for over a year now! It revolves around a conference I'm attending call the 13th International Symposium on Microbial Ecology (ISME13): Stewards of a changing world. I will be presenting a poster on my research there. So our itinerary is San Fransisco (~1 week)> Seattle (conference, 1 week)> NYC/ Washington DC (~1 week)> Los Angeles (3 days)> home. We are quite fortunate to have family and friends in most of these places to host us and or show us around. This is my first time to the US so I'm really excited about not knowing what to expect lol. We fly out on the 16th August which is in 12 days!!! I probably won't post anything until after I come back so until then take care!

The view from here

I realised that most of my posts this year has been about my research or PhD-related! lol Thanks for reading all the nerdiness as I enter the final stages of being a glorified student. Really, special thanks to you my family and close friends who are forever supportive, encouraging and generally putting up with my babblings on the awesomeness of NBB4.
The last 3 months has been like a dream, I'm just amazed at the progress of my research. Those many late nights in the lab was worth it yielding lots of thesis and publication worthy data. I know all this is only possible by the grace of God, so praise Him! Research is so unpredictable, you can be stuck in a doldrum for months and then be hit with waves upon waves of data. You can say I am on a data high at the moment lol. I still have a few more experiments to do for my last chapter (transconjugants) and tie up some loose ends (metabolites) before I can fully concentrate on writing my thesis. I have started writing nonetheless (the view above is from my home office where I've been writing). I've decided to dedicate at least one day a week to writing. That way I'll be able to ease into it while experiments are dying down.
As for my paper, I finished writing the first draft back in early April and handed it in to my supervisor. I was quite nervous about it so I asked him to be kind since this is my first paper. We are currently in the process of editing the final manuscript before submitting it to the journal. So exciting! I hope it gets accepted before I submit my thesis. Also exciting is that a part of my work will be in a major publication currently being written up by my associate supervisor.
Apart from experiments and writing, I'll be attending a conference in August in Seattle, USA!!! So excited as I'll be taking a break and doing some travelling with Tan while I'm there as well. This will be my incentive for finishing up my PhD. Until then keep me accountable with the thesis writing ok?

Life's a feast

Hello friends! I hope this post finds you well. I for one am well just busy as a bee so popping in to say hello. Things have been so hectic for me that I haven't had the time to cook (or craft but that's for another day). Tan has been taking good care of me and of dinners. The lovely feast above consists of BBQ chicken (with garlic sauce) from our local kebab place, fresh focaccia from the local bakery and a simple garden salad. Life is good here in Fairfield!
So the major source of busyness is of course my PhD. I've got so much on my mind I think it might explode! I've had a couple of months stressing over wacky data but that has now been solved. The whole time I thought with much anxiety that I had done something wrong (experimentally or in the processing of the data) but it turned out to be a real phenomenon. NBB4 is such an amazing bacteria! I'm happy to say there has been some progress since that ordeal. Just last week I had a major break through. The molecular constructs I've been developing since last year has finally worked. I was finally able to heterologously express my NBB4-proteins in another host and the amazing thing was they have activity! Now I am trying to confirm this activity in order to do further experiments. Hopefully after this I can achieve my aims and write up this section of my thesis. As for my mating experiment, this is my third attempt. I'm waiting on growth of transconjugants and donors so I could calculate the transfer frequency. I won't know for another month. After that, there are lots I wanna do with the transconjugants. I also have to contact a certain Chemist who can help me detect and identify break down products in my biodegradation experiments. On top of all this, my draft paper is due to my Supervisor by the end of the month along with abstracts for the various conferences I wanna attend this year. So much to do, so little time! but you know what? in the midst of this craziness I feel a deep sense of peace that's beyond myself. I am trusting in God's sovereignty and his providence over my life. He is always near so I have nothing to fear really. What's the worst that could happen? I don't submit on time. Ok off to work on those experiements now ciao!

I have a plan!

Just some of the food consumed by moi this week. I feel so blessed to have beautiful friends who are also great cooks! We celebrated Australia Day this week with a BBQ lunch (as you would) with David and Jo. It was also David's birthday so Jo made that scrumptious cake there. They're off in a few weeks to serve Jesus in Lightning Ridge so we'll definitely miss them. For dinner, we had lovely home-made meat pies at Dave and Jane's place. Jane also made apple pie for dessert so we were spoilt not to mention stuffed! Thanks guys!
This week, we also celebrated our dear friend Susan's birthday at Madam Fling Flong (this gorgeous venue in Newtown filled with lots of beautiful vintage lounges). Yep we've been quite sociable this month.

Ok so the title of this post says I have a plan. Indeed I do, a thesis chapter plan that is! Believe it or not I can see a glimpse of 'light at the end of the tunnel'. God has been so good to me in answering my prayers for results. I must always remind myself that He is sovereign even over my experiments. So I was able to confirm my results from the last post which is a relief. Actually it's more of a scientific breakthrough! Something I've been working on for months (and others probably for years) has finally worked. Although I will need more results to expand on this part of the story. Even though I have a plan, it's still very hard to get the actual writing going. I have so many experiments to do and so little time left in the lab! I would like to write full time for 6 months and submit by October this year. Anyways I've still got my paper to finish up and hopefully this will help with the thesis writing process. I'll leave you with a funny conversation I had with my Supervisor with regard to writing my thesis...

me: what if I get writer's block?

Supervisor: that only happens to people who write fiction, you know when they're trying to make up stuff...
[looks at me apprehensively] I hope you're not making stuff up?!

A flower from NBB4

I went to check on my mating plates on the first day back and this is what I found! One of my NBB4 colony is shaped like a flower! These little mounds are streptomycin spontaneous mutants growing on top of each other. They appeared on my donor plate which is supposed to be negative. Anyways I have potentially exciting results with one of my mating pairs so fingers crossed that I can confirm this.

It's just another manic Monday...not!

Despite being sick since last Thursday I had quite an eventful weekend - will blog about it later I promise. Mondays are usually slow for me at uni, with trying to remember what I did last week and planning what I'm going to do this week. It's morning tea right now and I'm enjoying my first cuppa ('Marvin' was a gift from my big little brother who thinks I like all things alien) with a strange Halloween looking muffin baked by my Supervisor (yeah he caught the baking bug alright). Hope you're having a good start to the week :o)

Our lab on TV!

The most random thing happened this week, our lab was on TV! A Current Affairs to be exact (should I even be proud?!). The segment had nothing to do with our research but it was Microbiology nonetheless. It was on different laundry powders so if you missed it, you can watch it here. Yeah that's my Supervisor doing the experiment and talking about those 'nasty microbes' hehehe. This totally reminds me of that PHD comic with the film crew:

BTW you might've caught glimpse of the 'back of my head' at about 3:48/5:49 hahaha

Another sticky one!

This is what I baked for labchat (our weekly lab meeting) today. We have this roster whereby the person who presented either their research progress or journal club one week has to bring in baked goods the following week. This ensure that there is always baked goods at labchat (not that we don't consume baked goods on the other weekdays e.g. just this Tues we had choc fondue and profiterol cake for Mia/Vicky's birthdays!).

Sticky banana, pecan and date loaf

1 1/4 cup (185g) plain flour
1 tsp bicarbonate of soda
1 tsp ground cinnamon
1/2 tsp salt
120g roasted pecan, roughly chopped
220g pitted dates, roughly chopped
1 cup (220g) castor sugar
2 eggs
1/2 c (125mL) light olive oil
3 very ripe bananas, mashed (about 310mL)
1 1/2 tsp vanilla extract
Sunflower seed or pepitas (pumpkin seed) or both for topping

1. Preheat oven to 180 degree C. Butter a large loaf tin (23x13x6cm) and dust with flour. Set aside.

2. Put flour, bicarbonate of soda, cinnamon and salt into medium mixing bowl and whisk together for 45 sec. Add nuts and dates and toss them about to thoroughly coat in flour mixture.

3. Put the sugar, eggs and oil into another bowl and whisk together for 1-2 min or until light and creamy. Add mashed banana and vanilla extract and whisk together until mixture is fairly smooth (it's ok to still have lumpy banana bits).

4. Stir the dry ingredients into banana mixture until it form a sloppy batter. Scrape into the prepared tin and sprinkle some seeds on top.

5. Bake for 1 hr or until a fine skewer inserted comes out clean. Cool loaf in tin on wire rack for 10 min before turning out onto rack to cool completely. It will keep well in the fridge for up to 5 days otherwise freeze well for up to 3 months.

Result: Everyone enjoyed it and some had seconds - way to gladden a cook's heart! For me personally it was too sweet, will cut back the sugar next time but I guess it's still pretty healthy stuff!

Have a great weekend!

Mini sticky date puddings & smelly undergrads

This is what my sisters and I baked on the weekend. It was a nice day just hanging out with them shopping, baking and crafting. My brothers contributed by playing loud music and making me sew up loose buttons on their jackets. Not that I minded of course! I love them all dearly :o)

Mini Sticky Date Puddings with Hot Butterscotch Sauce

1 1/4 cups chopped stoned dates
1 1/4 cups water
1 teaspoon bicarbonate of soda
3 tablespoons softened butter (60g)
3/4 cup castor sugar
2 eggs, lightly beaten
1 cup self-raising flour

Sauce
1/2 cup cream
100g butter
1/2 cup brown sugar

1. Preheat the oven to 180 degree C. Lightly grease a 6-cup jumbo muffin tin (or regular 12-cup tin).

2. Place the dates and water in a saucepan and bring to boil, simmering for ~5min or until the dates are softened. Remove from heat and stir in bicarbonate of soda.

3. Cream the butter and sugar until light and fluffy. Add the eggs a little at a time, beating after each addition to make a smooth batter. Fold in the sifted flour and then stir in the date-and-water mixture until well combined.

4. Spoon into the prepared muffin cups and bake for ~20min (~15min for 12-cup tin) or until firm and springy to touch.

5. To make the butterscotch sauce, combine all the ingredients in a saucepan and stir over a low heat until the butter is melted. Simmer for ~10min or until thickened. Turn the puddings out and serve warm on individual plates with hot butterscotch sauce poured over the top.

Results: mmm we all quite enjoyed it but be warned that it is sickeningly sweet! Enjoy!

I'm supposed to be writing my paper right now but I'm stuck! I'm about halfway and the draft is due to my Supervisor by the end of this month! Keep me accountable? On top of writing and lab work I've got teaching this semester - a 5 hour prac class every second week...

The lab rat part of me

This is a photograph of DNA under UV light - it represents RFLPs of my clone library.

At the moment I'm supposed to be looking for duplicate profiles and selecting only the unique ones for sequencing (something a software can do but not without some of my own tweaking!). Other things on my tasks list includes annotating small chunks of genome sequences, microcosm survival study of my bacteria (after it has finished breaking down pollutants), metabolites detection on the GC-MS, looking for mega plasmids in my strains using PFGE, enzyme kinetics experiments and finally write my paper! I love science and I love that my project involve techniques from so many different discipline incl. microbiology, chemistry, biochemistry, molecular biology etc. Ok so maybe I should go and actually do these experiments instead of blogging about it ha!

Failed!

Today we had our monthly postgrad bible study lunch at Golden Fang. As part of the planning committee, I was in charge of organizing a 'get-to-know-you' game for the group (since there are many new people this year). I played this candy icebreaker game once before so I thought it was a safe option. Basically you get an assortment of candy in this case M&M's and the colour corresponds to what question you have to ask/answer with the person sitting next to you. I made the little colour-code cards and bought a big packet of M&M's on my way to the restaurant. When it was time to play, I opened the packet and to my astonishment there were only GREEN M&M's! hahaha I didn't read the packet "...now sold as separate colours" because if it's mixed then you'd actually win a prize hahaha needless to say we all had a good laugh out of it!

Campus life

I haven't been crafting much lately. I've just been so busy with lab work and just life in general. I guess it's a good thing - it means I've been productive in my research and living life. I can't believe I'm starting my 3rd year! time sure does fly! I remember the early days of not knowing what to do... oh the tears and joy of research. God has been so gracious to me in providing an on-campus network of post-grad Christians who've been so supportive and encouraging. I guess we're all in the same boat after all. Two of my closest friends on campus are Liz and Jenni who are also Christians, married and doing their PhD! Apart from bible study, we meet up for coffee once a week at The Den aka Azzuri's (the above shot of my fav corner). They have the best shinny Chai on campus! It's so nice to unwind, relax and chat about things beside research.