Scientific Walk in Romantic Sintra

I went away last weekend to refocus and refresh before this hectic season. I'm in the process of writing my first year report, but at this moment, I am kinda frozen in time and space. So, as what the trainer of the Graduate School of Life Sciences (GSLS) suggested, I begin a short piece of free writing on some random topic.

Finally, I was in Sintra. After pondering for a few nights on which part of Sintra I should do and how much I was willing to spend, I've decided on Castelo dos Mouros (Moorish Castle) and Parque e Palacio Nacional da Pena (Pena National Palace and Park).

View of Palacio Nacional da Pena from Castelo Dos Mouros at the spot where King Ferdinand II loved as he found it an inspiration for his romantic ideals.

My favourite picture of the Castelo

It was an amazing journey and I did take many excellent shots of the breathtaking views, and plants! I never thought I'd end up in the Dept of Plant Sciences, but since I'm already in it, I should make the best out of it. I may be a ChlamyScientist working on molecular biology/physiology of Chlamydomonas reinhardtii, but my colleagues are great physiologists/ecologists. I'm beginning to see beyond the green and to see each plant as a different species. It will take time, but I hope I can make my way closer to them greenies.

Navelwort I think... also in Parque Nacional da Pena

Sedum sp. in Parque Nacional da Pena

Fascicularia bicolor, a Bromeliad in Castelo Dos Mouros

Failed Experiments are Norms!

I guess I can't help it. For two weeks I've been struggling with the no-results syndrome. It's TOTALLY NORMAL! Yes, I know, and all I need to do is to exhaust all possibilities before I will bow down to the word "defeated". I know many of my fellow scientist readers would feel me, and mentally support me through this "darkness". At least, I'm still doing work. That's something to rejoice for. It's JUST PCR. What wrong can it go, right? Well, it's just probably 101 things which can go wrong in a simple tiny tube with 20 microlitre of PCR reagents. *Laugh ironically*

When I'm in despair, I am automatically brought to reminder of this particular bible verse (2 Corinthians 4:8-9).

Nope, I shan't be crushed, I shan't be in despair, I shan't be abandoned, I shan't be destroyed.

I will come out stronger than ever, because every single moment of failure helps to bulk up the "what not to be done" Pandora box. I was to the point of giving up by telling myself that if it were not meant to be, then it would be okay to give up, but God didn't give up on my intention of completing this PhD. Second chance is received. And so, this is not the time to mope for too long. I'll just whine for another few more seconds and then continue the second part of my day.

Exciting times ahead in June: First year report which will enable my upgrade to proper PhD candidate is due in about two weeks' time (Sorry, not even there yet when it comes to first year report! *sad face*). Then it's the season of viva voce to defend my research and to prove my worth (as much as I don't like to use this as a benchmark of who I am and the potential that I have). And yes, Erasmus+ Students and Alumni Association (ESAA) Kickoff Event in Brussels.

Fingers crossed I'll be ready for the adrenaline-pumping June. I just want to live my life to the fullest, because I only live once, and this God-gifted life I have is not exactly mine but His, given to me freely so that I may live a life of grace and joy.

Now, who says great scientists can't be great believers? I am not a great scientist, nor a great believer. I'm just a trying scientist and a trying believer. If Albert Einstein and Gregory Mendel were great scientists and great lovers of God's own heart, then I can.

Me no want to live a life with excuses, justifying things I did wrong and in regrets all the time.

New Toy: Lenovo Miix 10

This is the first time I used a Windows 8 tablet. Though it was an Amazon Warehouse deal, but to me it is still a new toy nevertheless. In fact, this time round, as much as it is a toy gadget, but I'm justifying its usage as an option to have a "work holiday" when I want to travel, yet still be able to work intermittently. It does help when I draw strength from seeing new stuffs outside Cambridge and then form some new ideas for my experiments.

Enough with the justifications, now back to the toy itself. I spent about £150 on this warehouse deal for a "Used-Very Good" Miix 10 Windows 8 tablet. It comes with original Windows 8, and Microsoft Office 2013 Student package, which helps a lot since I am using a Windows 8.1 laptop with Office 2007. I wanted to install Office 2013, but the product key only allowed ONE single installation *sad face* but I already have Office 2007 so it's pretty much the same.

Let's talk about the operating system (OS). When I purchased my laptop, it was on Windows 8. I wonder how many times I complained about how unfriendly it was. The signature Start button of all previous Windows (95, NT, XP, 7, Vista...) was removed, and I couldn't find my way around for the first few weeks. I sorta got used to it but I didn't like it at all. When Microsoft introduced its update to Windows 8.1, I freely embraced it. The signature Start was back!!! My days from that point forward were great, and are still happy with it. Now, Miix 10 is the first generation to Lenovo's 10.1" Windows tablet, and yes, it is no longer selling on Lenovo's website. Hence, I know it would come with Windows 8. Oh my horror! Then again, I could update it to Windows 8.1 so I didn't worry too much about it.

Though it was mentioned that the hard disk of Miix 10 is 64 GB, the space available was only about 45GB. I got over-excited when I received the tablet, so I started installing my usual need - Mendeley reference manager. Programs eat up disk space like a hungry PacMan. So when I finished with the necessary updates of Windows 8 to enable the upgrade to 8.1, the HDD didn't have enough. Well, finally after numerous uninstallation of unwanted apps,  I finally managed to upgrade to Windows 8.1.  It was as though life returns to the tablet finally.

Other pros and cons of a brand new Miix 10 which I found on the usual tablet review websites - I do agree. So I won't comment much on those aspects, since they'd know better than I do. I would comment on the basis of my current profession as a PhD student in the process of writing up the first year report to be upgraded to a PhD candidate. Since I am writing a lot, so Office 2013 (as I mentioned previously) is an additional bonus so one point for Miix 10. However, the annoying part that the virtual keyboard still pops up though it is docked to the external keyboard will be something I need to address and consider in future.

I'll share the part II of my encounter with this tablet and a possible decision of whether I will be keeping it in the next two weeks or so. My short trip to Lisbon will be an ultimate test for Miix 10 if it is suitable for my use.

Time to return to reality and work on my project. Till then....

Keep Calm and Start Writing!

How apt is this "keep calm" phrase!

Some of my friends have begun writing their theses, some had completed and submitted. As for me, I am just starting my PhD journey (finally!) when I joined this lab (Physiological Ecological Group). Looking at how four months flew off like lightning, I should begin writing the first year report soon since the deadline is on 1st June.

The reluctant mind and body says, "There is still time. Chillax!" But both know better that it is only a lie. One thing would lead to another, and there are thousands, if not millions of papers I need to wade through in order to seek for the knowledge. I have yet to start writing the ONE word needed for me to begin.

It's time to think. It's time to start writing. I shall.. Within this week. Now, I shall give my pair of fatigues eyes a rest. Ciao!

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.

Stupid Fish, Really??

It is hard for me to explain my current situation openly right now, but tonight I shall listen to Einstein. 

Hear ye all my fellow PhD friends out there! Dear Einstein and his wisdom!

Source: http://om.symphonyoflove.net/wp-content/uploads/2014/09/Albert-Einstein-Everybody-is-a-genius.-But-if-you-judge-a-fish-by-its-ability-to-climb-a-tree-it-will-live-its-whole-life-believing-that-it-is-stupid.jpg