I’ve been following Fringe on tv, a sorta sci-fi/crime show featuring a former Dawson’s Creeker. Last episode aired in these parts was about a GMO that was ‘freed’ by some PETA people. Subsequently, it ate them because it was a hungry hybrid between a tiger, a bat, a wasp and a lizard. um..no wonder science & GMOs get such a bad rap? Next thing I knew I heard some hysterical laughter coming out of my throat. If only genetics were actually that easy so that you could cross two mammals with a reptile AND an insect.

As of yet, cloning has been kicking my ass. and then some. I’ve been trying to put a gene that expresses a fluorescent green jelly fish protein into my plants (along with other plant genes). Now I’m at the stage where I’m examining my mutant plants. GFP is used regularly in some molecular labs to signal where a gene they’ve inserted into an organism is expressed, in a reporter gene system. It’s a tad bit like how the incredible hulk works (mutant human that turns green when angry?), excepting that plants with GFP don’t get angry (although this could all change if we could make a plant-tiger-lizard hybrid). But from what i’ve now learned, they do turn green if you throw them under certain wavelengths of light whether you want them to..or not. Some wild type tissue naturally fluoresce green, so even if the GFP jelly fish gene isn’t there, it will still act like it is. Technically speaking, it’s considered autofluorescence. And it’s a nightmare for people like me who are trying to use engineered fluorescence to flag down a result.

Can you spot the difference?

(The red is Chlorophyll, which can potentially mask any fluorescence, and make life that much harder. in the top picture, the seedlings were grown in the dark and so have no chlorophyll to block the green fluorescence. So, usually green plants are red under a filter for GFP fluorescence, however, if the protein is present in the tissue it will be green. But, some tissues naturally give off the green instead of the red anyways…)

There are ways of possibly separating out the natural autofluorescence from the engineered fluorescence, simply by experimenting with different filters of light. (As some helpful microscope techs have pointed out to me. one also observed how beautiful autofluorescing plants are, but that’s its probably a frustrating nightmare for me..) Unfortunately the filter I was using lets in loads of different wavelengths. Oh wellz, trying narrower filters soon, as well as a hand-held GFP/UV lamp (fancy) and hoping my luck changes..

and now my anthem of the past two days..
so tired..must..get..out..of..the lab.

Summer’s in full throttle in Oz, meanwhile it’s winter in other parts :P

It’s also magpie mating season, in which the native birds renact Alfred Hitchcock’s endearing movie, the Birds

Weather’s beginning to get scorching…again. Vic’s on bushfire alert. but despite this, the world’s inaugural naked bike race took place in Adelaide

In lab meetings we begin discussing protocols that require being in the cold room for copious amounts of time. And what to do about the growth cabinets (with controlled light and temps) in the growth room, which is always blissfully 35 C in the summer. Causing our plants to suffer heat shock if we leave them out for more than 2 mins.

And then, well, no one says it better than PhD Comics…

A bummer post :(
Cheers to the recession.

In another link I received from the vine, was the headline: PhD holder now a cabby

In a stunning true story, a PI in cell bio and genetics of 16 years, who also holds a PhD from Stanford, was recently released from his contract from a research institute in Singapore. Although he made numerous applications to other research centres, government agencies and universities he didn’t get any takers. :S

Hence, it was time for a career change. Taxi-cab driving in the far east.

*gulps.

I got this link randomly sent to me one day in the lab from one of the PhDs, who owns a fat orange kitty…

poor kitty.

I’m just killing time in the lab with my hunky dorky plants and bacteria, while waiting for a gel to run it’s course.

It’s late. The possums are out, they look like these huge fuzzy cats or really fat racoons without the stripes. They also sound like bats from hell.

There’s a new PhD student coming to the lab sometime this year (?). From Thailand. Has the coolest name ever…“Beer”.

Also, intermittently listening to TheSixtyOne.

I caught a couple of monkeywrenches in my projects, (i.e. getting the one in the million mutation in a pcr product from a high fidelity enzyme, plants that are supposed to stain blue, but don’t…). I figure Murphy’s law is a given in the lab, or at least, for the unfortunate grad students. (what can go wrong, will go wrong. har har).

While at my casual/PT job at the “vitamin store”, which is really a corporate monstrosity I will not name for fear of libel one of my co-workers mentions that he got a customer who had lots of piercings, including one thru the septum of his nose (resembling a bull…). ironically the customer works at a slaughterhouse for cattle, and had been working there 2 years but is now desperately looking for another job. he was so affected by his job that he’s now completely turned off meat and animal products. He came into the store looking for any vegan vitamins, soy protein powder etc. I re-told the story at lunch in the BaMBi tea room to other grads. It lead into a discussion of how we don’t really compute how cows get processed into beef (and other dimensions, like lab “pets” and medical research). And the whole idea of how ignorance is bliss.

Thought it was great to know Australia’s on the cusp of certain things, like research on a vaccine for a world wide pandemic.

As Reported by the Sydney Herald
and the report by CNN

The current trial is testing out the appropriate dosages of the vaccine, which aussie pharamaceutical company CSL believes will produce immunity to the virus. 240 adults were injected with in late July, another 400 children were injected in early August. Results of the trial are expected to come out next month (it takes about 6 weeks to complete).

According to Reuters a representive of the WHO commented that the vaccine should be approved and ready for use come September.

The vaccine will be like a regular flu vaccine, only it will protect against one strain of flu—the swine flu, H1N1.

Sometimes it feels as though the answer is right there, you can’t see it but it’s just beyond your grasp. So elusive, and yet obviously out there…somewhere.

I wonder how many scientists have felt this way.
(I lost track of how many times i’ve felt like that, anyways).

I recently read an old review (from 2002, heh) on how a string of seemingly unconnected discoveries led to one mammoth discovery in plant RNAi, a mother of si/miRNA processing proteins: DICER-LIKE1 (DCL1)

The reviewer likened the circumstances leading up to it as how six blind men standing at different locations would describe an elephant, if it was before them. Eventually, someone realized they were all describing the characteristics of one huge beast.

(It was six men of Indostan,
To learning much inclined,
Who went to see the Elephant
(Though all of them were blind),
that each by observation
Might satisfy his mind…

‘God bless me! but the Elephant
Is very like a wall!’ ‘…a spear!’
‘…a snake!’ ‘…a tree!’
‘…a fan!’ ‘…a rope!’

And so these men of Indostan
Disputed loud and long…
Though each was partly in the right,
And all were in the wrong!"
(Schauer et al., 2002) )

But, going back to the point…
Months ago a visiting tech gave us a tutorial on some supersonic mindblowing machine high tech phenotyping machine. He likened the lot of us grad students and postdocs to pioneers at the forefront of the field. We go where no one has gone before, to make discoveries built on past discoveries. Really though, it feels like we’re the antennae of some huge slow moving, blind snail, reaching out into space.

It’s daunting sometimes, especialy with “high risk” experiments where the outcome could be anything (nothing even). You can expect certain outcomes…but there are always unforetold results that could mean anything, and could open a can of worms (too many leads in too many different directions and too many possible explanations). Or it could be something altogether paranormal.

And there are the small strokes of unexpected genius.
In 1993 one C. elegans knock out group thought they found some small genetic anomaly that was specific only to the species of C. elegans. Then the same “anomaly” or genetic phenomenon began appearing in other organisms and kingdoms. More and more labs began to notice there was something intriguing about these 21-22 nucleotide long genes, with the ability to regulate specific proteins based on their antisense complementarity to sequences on the protein’s mRNA strands. Eventually Fire & Mello observed that double stranded RNAs were the products of the transcription of the unusual genes, and was subsequently the trigger of RNAi gene silencing. One huge can of worms that turned into a gold mine. That aberrant form of gene regulation by miRNAs/siRNAs helped Fire & Mello win the nobel in 2006 and it’s now on the forefront of genetic, stem cell and cancer research.

But, there’s still so much to RNAi we don’t know.
And they’re rather huge questions people have been trying to find the answers to for years, like what exactly is the mechanisms behind a small 19-22 nucleotide long RNA strand inhibiting the synthesis of specific proteins in translational repression?

Still though, like the 6 blind men of Indostan, together I suppose we use our other senses and tools (*ahem, our biological and biochemical experiments) and call out to other, in our jargon filled articles, conferences and seminars.

(I really do think it would be so much cooler, if we could actually see things happening at the molecular level..eg. if we can see the Taq polymerase tack on the dNTPs to new strands of DNA in during PCR in the thermocycler…)

…to groove to when you’re at home or in the lab.
There are so many different ways to connect to friends and potential friends now, online or otherwise. All you need to do is find a hobby, get online and start surfing for networks and groups all about bringing together like-minded ppl. One prime example might be NN itself. lol.

Me and my friends are always looking for new songs and artists to listen to, and not just the same old top 40 songs that the radio pumps out over and over again. Nowadays it’s really easy to just find a fav tune to listen to on youtube or a fav group on MySpace, but you really have to know what you’re looking for. Previously, for a brief moment in time, there was the website Pandora.com, a music streaming site that could put together a playlist of songs with musical similarities to an artist or track you’re interested in. However, now it’s only available in the US due to copyright infringement…

however, other sites have cropped up recently. I have no idea how they found it, but my sources recommend the following:

Grooveshark
LastFm
and TheSixtyOne, an indie music player and my personal fav.

These new sites are something of a cross b/t pandora and myspace. You can search for and stream songs, and then save them into a profile you create to stream again the next time you login. Lastfm and theSixtyOne require free registration and profiles, where you can also list music preferences and add/invite friends. they also come complete with msg boards etc.

On a similar line, there’s also aNobii, a social networking site that revolves around books and lit. It’s an easy way of sharing titles with friends and the rest of the world. Each user profile contains “shelves”, that houses a list of book titles that users put up with their rating and comments. An added bonus of the site is that it tells you if there are other users with similar tastes based on the number of titles you have in common. Subsequently, you can easily browse through their shelves and dig up some other books you might enjoy, with their recommendations.

To cut directly to the chase and find social groups to hang out with in person, Meetup.com allows you to join and create groups based on common hobbies. Group admins can then list a time and place to meet up. All you have to do is sign up for free, list what city in the world you happen to be in, and what you’d be interested in doing with other groups of ppl living near by. It’s also a way of meeting people if you’re new in town.

_~~
I guess this would be my break in my hiatus from blogging. the next few posts I make will probably cover a few humourous (or not) milestones I’ve experienced in the lab in the last coupla months and short vacation in China, where I had a tour of a couple of biotechnology labs there.

For now, I sign off with Le Chloroplast

and i’m off to cater to my mutant “cooks”….

It’s autumn in Australia, while it’s spring in other parts. The recession finally hit us last month, and swine flu has landed as well, threatening to infect millions. Sometimes I’m reminded that over here, we’re essentially living on a large island, a bit more isolated from the rest of the world. Most days, it just feels more and more like home.

The leaves are changing their colour.
Mainly I think of the death in the leaves, the destruction of the chlorophyll and revelation of the other pigments—the carotenoids—that we rarely see in leaves, except when they perish and die. It’s a natural, programmed death.

In the lab one of the Ph.Ds is finishing up his thesis, and the Post Doc is close to submitting a paper to a journal. It’s exciting to see the process, hear about the progress in lab meetings. For the Post Doc, it’s mainly a discussion now, about what journal her research is most suitable for publishing, which reviewers to request and which to avoid. It seems at break neck speed, she and the PI are reviewing, writing and re-writing what they’ve put together. I marvel at how much she’s accomplished, even more so because within the time she’s been here (1-2 years?) she’s had her first baby, who’s now just a year old. The PI also has a baby at home, an energetic 2 year old, the PI next door to us has two kids under 5. I have no idea how they manage it, with teaching courses, superivising projects in the lab.

In some small ways I’m envious, I wonder what it’s like to be settled somewhere, close to people you love and who love you (although I still feel very young, restless sometimes). I broke up with my boyfriend yesterday, after a few weeks of tensions. I knew it was coming, but when it finally ended it still felt like a huge, stunning blow. Mostly…i think it was timing. He’d just gotten his B.Sc. and has no idea what to do now, or what he wants to do. I was too far away to be of any help, but I could feel him slip away, into himself with his own internal struggles. Or maybe the chemicals had run out, the bouquets of love chemicals had run their course (norepinephrine, dopamine…), all the feelings we thought we once had slipped away. And in a way, perhaps they faded to reveal our true selves to each other. Some feelings linger, small threads of attachment holding onto the past, our past. Humans release oxytocin and endorphins when they’re together, somehow they bind the relationship. The more you’re together the more you release. Sadly I think, we’ve been apart more than we have been together. I’d left him behind in Canada, when I came here.