PLOS Synthetic Biology Event: Interview with Dr. Fuzhong Zhang

There's an event coming up this afternoon, 4pm UK time - an interview by Dr. Steven Burgess (Department of Plant Sciences, University of Cambridge) with Dr. Fuzhong Zhang (University of Washington, St Louis) on the role of cyanobacteria in space (and more!). Dr. Zhang's research is currently funded by NASA and it'll be cool to join them in the discussion on NASA research.

Click here to join the Google Hangout session

If you guys have watched the Martian, you probably know what this movie is one of the few which featured a botanist as a hero in a film. Dr. Zhang is researching on growing cyanobacteria in space. There are other research going around the world - including growing plants in soil from Mars, etc.

Your job will be to ask questions during the interview!

Just in case you wonder how does cyanobacteria looks like. Here's an image of it!

http://www.waterboards.ca.gov/water_issues/programs/bluegreen_algae/docs/cyanobacteria_microscope_big.jpg

Enjoy yourselves!

#syntheticbiology #PLOSSynbio #livestream #interview #cyanobacteria's role in #space #research #NASA today 4pm BST
https://plus.google.com/u/0/events/c2gnundras37n5c08pvst80cgj8

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).

Guest Blogger

I've invited someone to write a couple of entries for my blog. I read something he wrote recently and thought it'd be nice if he could join me to make my blog more interesting.

First a scientist, a scholar, and a sincere individual. The sunshine in my life too! I look forward to host his writings!

Re: http://bloggingtips.moneyreigninc.netdna-cdn.com/wp-content/uploads/2012/06/how-to-attract-guest-bloggers-297x300.jpg

Never Leave Experiments Alone...

It's norm in research life that we leave something over the weekend to grow, incubate, etc. so that we could have a good start for the week ahead. Likewise, I also did the same most of the time.

The last weekend of August happened to be the last bank holiday of the year in the UK so my boyfriend invited me to visit his family up north. It was a good weekend, and a long one too. We went to the Peak District which is relatively close to his hometown. I wished I brought my proper walking boots so that I could try walking up to Mam Tor. Unfortunately, a pair of simple sneakers was my companion for the weekend. Let's just say, I still savoured the beauty of Peak District from afar where heather bloomed.

View from Mam Tor

Why did I mention such a nice weekend? Oh well, in order for me to not freak myself out after a good weekend, I did set up some cells to grow over the weekend. I ensured the cultures were bubbling with carbon dioxide before I left the lab on Friday. Little did I know what awaited me on Tuesday was a huge shock that some kind individual had turned off my CO2 supply over the weekend! Yes, the conditions of my cell growth was compromised, so I had to subculture them and waited for another day or so before I continued my experiment. I did cry like a sad kitten abandoned by its mother in my boyfriend's lab out of shock, surprise and anger. I couldn't understand why it happened, to the point of questioning my memory if I did turn it on. Thinking back, I was and am very certain I did turn it on and the cultures were bubbling before I left.

Something took me by surprise again on Saturday evening. As you know, recently I am running some experiments which involved electron microscopy. Usually, I do fixing and embedding myself. I started the process of fixation and embedding on Thursday, which meant I had to return during the weekend to refresh the epoxy resin twice a day. I had prepared fresh resin for the day on Saturday morning and then left for a short visit to Burwell to meet up a German friend of mine. An overzealous individual roaming in the imaging center over the weekend had decided to clean up anything that had my name written, so when we returned to the imaging center for the final refresh of resin, I was totally appalled that my resin had gone missing from the stirrer. More upsetting was to find my pot sitting in the oven with so much of waste in it. I felt so sick when I saw the covers which I labeled with my name sitting in the oven covering pots filled with so much of waste. I didn't have my phone with me, else I would have taken a photos of it. I am helping my boyfriend to fix some of his samples which he needs for his publication. So he was with me when I performed the fixation/ embedding process. I'm glad he was with me to witness all these. We had to prepare fresh resin for the evening. I'm saddened by the fact someone is so inconsiderate, especially we sort of knew who was the other person roaming in the imaging center that weekend. I'm not pointing anyone because I can't be sure, but this raises my alarm once again that someone is out to get rid of me.

A threat had been delivered to me verbally on the evening when the outcome of my first year report was out:
"You can either exit gracefully with an MPhil, or if they let you stay, you will lose all your freedom and they'll observe you like a hawk and the slight mistake that you make, they'll show you the door".

The same individual who delivered such statement also told someone in the department that my cakes tasted horrible and he wished a previous PhD student was still there because her cakes were great. Apparently my cakes tasted alright and people do love it. It was vicious and mean to say things like that to a mutual co-worker, especially when this person ate the cakes I made. Unless, of course, he pretended to ingest it but secretly had been throwing them away. That, I wouldn't know.

I am worried. I am appalled. I am helpless. I am in the dark. I am getting depressed and paranoid.

Yet I know, I am not wrong to fight for something I know I can do and to fight against those who had been messing with my potential of doing a PhD for the past one year. And I am receiving help from the University Counselling Services to ensure I remain sane. I am still producing results despite all my health issues and weird things which are going on around me.

Here's an article published on Nature 467, 516-518 (2010) about Research Integrity. Have fun reading!

Living with Depression While Doing a PhD

I stumbled into this blog post on PhD(isabled) accidentally, and found it very relevant to PhD students nowadays. I feel deeply for the PhD student who wrote the article... This part of the article hit me harder because I am going through similar hurdle, though it didn't start off with having depression.

Any form of health problem could slow us down in PhD progression. But it shouldn't be a reason why we are being told we are not capable of doing a PhD just because our health isn't great or that we take longer time than average to complete a task. If one has dyslexia, one will be given special aid so that they can do a PhD. But if one has hormonal problem or depression which slows us down, one is told by those normal, healthy people that we're incapable of doing a PhD. Academia has become such a sorry state at the moment. Equality? What's that? Until I see justice in my case, I don't believe there isn't discrimination...

An excerpt from the blog post I found interesting:
My own experience is that it takes time for medications to kick in, and only with the right medication can I start to do any kind of working through the issues causing the depression. My last severe episode was mostly spent sitting around waiting for things to get slightly better. That sounds a hell of a lot more fun than it was. I don’t know if people who haven’t been there can know how it feels. It really is a fight to get through one day at a time. Depression impairs your thinking. It is harder to reason like usual, or be creative, or whatever it is you’re normally good at. My memory goes completely to pot. I get times and dates muddled up, miss appointments and stand up friends, which is mortifying. So if you start trying to create a new model of some important theory or other when you’re under par, its going to be even tougher than normal.

Is there a problem with people (supervisors and students) seeing that as a sign they’re not actually capable of doing the PhD work when in fact its just a sign your health isn’t great just now? Can it magnify the anxiety if you think if you can’t think yourself well then you’re also not capable of doing the PhD? I wonder if blogs like this one have an important role in getting this crucial, fundamental message across to supervisors, departments and funding bodies.

I’ve tried to get involved with causes like this before. I found I didn’t have the resources to keep up.

I’ve seen friends take on enormous responsibility for campaigns and causes at the cost of their health.

I had serious doubts about writing anything about this. I can only claim to speak from my own experience. I worry enormously about anyone reading this and feeling misrepresented, but at the same time it feels right to say something.

In the end my constant mantra is to put my health first because everything else depends on that.

I can only be politically active within the limits of my health.

I can only be a researcher within the limits of my health, and not even the PhD comes before it.

Excerpt taken from https://phdisabled.wordpress.com/2013/11/15/living-with-depression-while-doing-a-phd/comment-page-1/#comment-1159

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!

Immunogold Labelling

Today I've got some peace by chilling at the imaging centre to run some immunogold labelling (IgL). My samples had been fixed in epoxy resin (I'll show you guys some pics in action when I'm running it next week). For now, I'm using older ones, mounted on nickel grids. I'm using a modified protocol from Skepper (2000), J. Microscopy 199, 1-36. (I'll link it later)

I'm having research fun and I think research should be fun. Science is mind blowing and fun. Unfortunately some people have very distorted and disillusioned vision of what "fun" and professionalism in science means.

Right now I'm battling a birdman who wants to kick me out because he's totally disapproving my idea of fun in science. Calling me unprofessional, unproductive and unknowledgeable is low if not bitchy. Telling untruths and causing me this much of troubles at this point only caused me to find him disgusting, and crazy. Stalking me under the disguise of taking my attendance without me knowing is mental harassment.

Maybe some would think that I'm wasting my time battling against a silent but dangerous birdman but if I don't fight until the last drop of my blood runs dry, I'd do myself the biggest harm. As much as I'd like to live in peace to do a PhD, the evil birdman thinks he can show me the door easily. Making my research life difficult is only making the birdman's life worse. I'm a resilient wild grass. Have always been that way.

The birdman said he'd not help with carrying of gas cylinders for me from now on. I'm perfectly happy that he refuses to help me, though I'm totally pissed with his unprofessional and childish behaviour. Thanks to this behaviour I have more conviction that I should fight till the end.

St. Paul mentioned about him running his race till the end. I need to put up a good fight too. If not, I'll be disappointing myself in the end.

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?

Festival of Plants 2015

Yet another of my free writing :)

I went to the Festival of Plants in Cambridge University Botanic Garden last Saturday. A nice sunny day to be out there among the beautiful spring plants. Our first stop was the canopy where there were stalls with interactive games and explanations provided by volunteers of Festival of Plants. One thing which attracted me was the booth on algae and biofuel. I work with Chlamydomonas reinhardtii, one of the few algae studied widely on its ability to produce biofuel, and I do like the idea of this animal-like single-cell lower plant being such a useful tool to study various aspects. We created a furry cartoonish ChlamyBaby (look below). There are some other activities which I didn't stay long enough to gather info. However, it seemed to me that people were enjoying themselves. We passed by the glasshouse and there was an interactive concert going on. Nice vocal for sure!

There were tours around the gardens, according to my friend, it was very beneficial as the guide told the stories of many of the trees around the garden. There was a talk tent where various talks were conducted. Apparently they were good too.

ChlamyBaby wading on the grass

I managed to capture a few nice shots - thanks to the lovely afternoon sun!

Moor hen feeding her chick

Colourful tulips

Peony?

Iris

I had a great time that afternoon. Discovered it was my friend's birthday, which was nice. Since the weather was great! :)

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!