PhD: A Decision in Life (. or ?)

A last minute plea from a fellow Malaysian to fill in the slot for another PhD student who was supposed to share his/her PhD experience brought me to an eye-opener PhD event by the Cambridge University Biological Society (BioSoc). It was interesting how the event was designed - where types of PhDs available in UK and US were discussed, how to get into a PhD programme, what are the requirements, how PhD is linked to industries (thus no longer confined to academia alone) and finally some form of sharing by a graduate student about the Cambridge graduate experience (that's where I came in).

What I thought was interesting in my talk, of which my boyfriend found it amusing as well is this:
"PhD is not a bed of roses; it is more like walking through the rose bushes where the thorns are poking at us but we'll end up looking at the roses one we get through the bushes".

Other than that, a work-life balance is crucial to stay sane and keep going with our PhD battle. We're all warriors, but remember, we're already first a champion in our lives, when the strongest sperm met the ovum and created us.

I wanted to discuss a bit about the "full stop" and the "question mark" in the opening slide but somehow I didn't. Some people are questioning if they should do a PhD, and some have already decided to do a PhD no matter what happened. Life is full of twists and turns. Ten years down the road, I may not be doing what I'm doing now. But, it is still something I won't regret doing..

So, hang in there, people!



I've attached my slides here (with some info on the deadlines of application for Cambridge).

Electron Microscopy

Just some brief updates of my latest muse - electron microscopy and immunogold labelling (of which I started last Thursday). Perhaps the antibody I probed was abundantly available, so it's pretty awesome to see that the results was as expected for the wild type. As much as I was disappointed that none of the mutants I'm currently looking at has different phenotype when compared to wild type, the data is definitely useful to form future questions for my work. Exciting times ahead!

IgL of my protein of interest - yay!

TEM image of my Chlamybaby - pweeety!!

Here's the paper which I mentioned about the techniques used for IgL. Jeremy is an excellent adviser to me when it comes to imaging techniques. I do my own fixing and cell embedding, so it's always great to have Jeremy around in CAIC whenever I go over. Thanks a lot, Jeremy! :)


Hope you guys find this post helpful :) Cheers!

Quantitative Western Blotting

I've been recently introduced to infrared fluorescence Western blotting and the video embedded is helpful to understand the differences between IR fluorescence Western blotting and the conventional chemiluminescence method. I'd have to work more on this method before I can be conclusive on its potential and usage but so far, it seems amazing and more cost-, labour- and time-effective. I discovered more from the video of its other functions which I would like to explore further, if given the opportunity to do so.

Two of my samples from the LICOR Odyssey system for the infrared fluorescence Western blot I did this afternoon. 

Does anyone know why there's a red band below the green band when I only use one IRdye?

Mating Chlamydomonas reinhardtii

I find this paper by Jiang, X. and Stern, D (2009) published in Journal of Visualized Experiments super cool. It's about mating and separation of Chlamy's tetrad. It's laborious, obviously, but it seems to be something fun to pick up for my PhD. Let's see if it's possible... *chuckles*

Briefly, Chlamydomonas usually exist in haploid single cells, formed by the "mating" of two strains of opposite mating type (plus and minus). An explanation of the diagrammatic representation of the Chlamydomonas life cycle shown below is taken from Zhao H et al., Genes Dev. 2001;15:2767-2777 (click on the link for the full paper). Gametes are formed when vegetative mt+ and mt− cells undergo gametogenesis induced by nitrogen deprivation (middle left). When gametes of opposite mating type (or sex) are mixed together, they adhere to each other via mating type specific adhesion molecules (agglutinins) on their flagella to form large collections of agglutinating cells (upper center). Flagellar adhesion induces gamete activation that leads to release of cell walls, erection of mating structures at the apical ends of the gamete cell bodies (upper right), and several other cellular and biochemical changes that prepare the gametes for cell fusion. All of the events associated with gamete activation can be induced in gametes of a single mating type by incubating them in dibutyryl cAMP (Pan and Snell 2000b). The tips of the mating structures fuse to establish cytoplasmic continuity, and soon thereafter the two gametes merge completely to become a zygote (lower right). Zygote formation can be extremely rapid, and within 5–10 min after gametes are mixed together, 70%–90% of the cells fuse. Immediately after cell fusion, the zygote developmental pathway is initiated and at 2–4 h after fusion, the zygotes form large aggregates of tightly adherent cells (lower center) as a consequence of synthesis of zygote-specific extracellular matrix molecules and cell body adhesion molecules. At about the same time, the mt− chloroplast DNA is degraded. After an obligatory several days in the dark and upon return to nutrient-rich medium, meiosis and germination occur, and each zygote forms four progeny, two mt+ and two mt− vegetative cells (lower right). Vegetative cells undergo mitotic divisions until the nitrogen is depleted from their medium and the cycle begins again. Diagram modified and adapted from Figure 1 of Pan and Snell 2000b.

Source: http://genesdev.cshlp.org/content/15/20/2767/F1.large.jpg

Sounds fun. Enjoy watching the almost 10-minute long video. I found it rather exciting! *Thinking cap ON*

Introduction to Chlamydomonas reinhardtii

I need to write a 5-page proposal today, so I'm getting myself acclimated by doing some free writing here.

An explanation - I'm switching department and supervisor for the rest of my PhD. A difficult decision to make after spending (almost with futile effort) almost 10 months in BioAnth. It's not that I hate human evolutionary genetics, but it's not my cup of tea. So, upon discussion with various people, especially with my current supervisor and college graduate tutor, I embarked on the search for a new project, new supervisor, new department... Hard to bid goodbye, but it's better for everyone, especially for myself. I've nothing to lose in the first place, except some loss of time, but it's for the better.

If the official approval is granted, then I will be joining Professor Howard Griffiths' lab to work on Chlamydomonas reinhardtii together with an awesome team to eventually contribute to the CAPP (Combining Algal and Plant Photosynthesis) project.

An brief introduction of this species which we work on - the Chlamy:

Source: http://upload.wikimedia.org/wikipedia/commons/1/19/Chlamydomonas_TEM_04.jpg

If you could see the area which is densest in the TEM photo, that's our group's interest. The pyrenoid story. There are various aspects which we are looking into, but for now, it shall be a suspense, as it's time for me to run back to the proposal.

Yes, I'm a happier me after the 10 months of struggles, though I'd have tonnes of work to be completed in lesser time than others. Yet, I am still happy and glad. I am thankful to God for answering my prayers and to St. Jude for interceding for me. Miracles do happen, if we also work in tandem with Him.