Tuesday, July 31, 2012

What I Read Last Week: July 23-29

One of the cool things about science is that there is always something to do, there is always something to learn and there is always something new being discovered and published. One of the big parts of being a scientist is keeping up with the trends. And how do we do that? By reading all the latest news and scientific publications. In an effort to give you an idea of the sorts of things that get published as peer review research I've started this new post - a wrap up of the scientific literature I've read this week. Most of my reading is in my area - human genetics, medical genetics, forensic science but occasionally I find other papers that are weird, wonderful or just downright interesting (yes, I do read papers for fun sometimes!) For extra kicks, I've also included what else I'm currently reading since reading could probably be considered a second profession for me.

This may be an accurate representation of actual piles of currently unread scientific papers on my desk.

The last week's reading is a little light on, because I've been trawling through my own data in the evenings rather than reading. And as you can see, it's a tad dry - lots of method and validation papers, which I've been procrastinating on reading (no guesses why). 

FYI: There's lots of talk of PCR in here - otherwise known as the Polymerase Chain Reaction. For those not playing with DNA day-to-day, here's the wiki page on PCR, which is a good one (lots of descriptions and pictures): A guide to PCR

1. Developmental Validation of the AmpFlSTR Identifiler Plus PCR Amplification Kit: An Established Multiplexed Assay with Improved Performance 
Wang et al. Journal of Forensic Sciences (2012) 57:2 

The official validation study of a new kit from Applied Biosystems which is promising better results with challenging samples. Using known DNA standards the Life Technologies team put a new DNA profiling kit through its paces to demonstrate it is robust and reliable for forensic human identification. Lots of tests were done to demonstrate the accuracy, precision and sensitivity of  the assay is and factors such as how the kit handles degraded DNA and DNA samples that contain inhibitors that make analysis difficult were explored in order to show the expected results for this kit.

2. Choosing Relatives for DNA Identification of Missing Persons
Ge et al. Journal of Forensic Sciences (2011) 56: S1

A study looking at which relatives are best for DNA identifications when only relatives can be used as a reference DNA source; usually in  cases of mass disaster or cold cases. This study gives some statistical weight to common sense - close relatives are best, and parents are more reliable than siblings.  A handy paper especially when many relatives are available and it can be hard to justify choosing or waiting for certain relatives to provide a DNA sample. While it may prove more costly, this study shows the choice of relative can yield better or easier-to-interpret results (thus saving headaches and more cost)

3. Novel Methods of molecular sex identification from skeletal tissue using the amelogenin gene
Gibbon et al. Forensic Science International: Genetics (2009) 3

A few years old now, this paper compared two PCR approaches to amplify the variable regions of the amelogenin gene (which is on both the X and Y chromosomes) for quick and cost-effective sex identification of degraded skeletal remains. Variations exist in this gene between the X and Y chromosomes, including a deletion of genetic sequence which means the same gene region of is a different size between the X and Y chromosome. This size difference and other variations can be used to identify if an individual has two X chromosomes (ie. is female) or an X and Y (ie. is male).  A good way to use DNA to confirm anthropological results especially when skeletal remains are difficult to sex (such is the case with fragmented remains). However this study also highlights the key challenge: sometimes the DNA is too degraded to get a result from PCR to analyse! 

4. Hybridization capture of microsatellites directly from genomic DNA
Refseth et al. Electrophoresis (1997) 18

In terms of modern scientific publication rates, this paper is almost vintage!  A nice easy method paper describing a method to capture microsatellites from genomic DNA. Microsatellites (or Short Tandem Repeats or STRS) are small repetitive sequences of DNA that are usually combinations of two, three, four or five nucleotides repeated a number of times eg. TCA -TCA-TCA-TCA that exist in most genomes. The number of repeats are highly variable from individual to individual, and some markers are more variable than others.  Microsatellites are key in forensic DNA biology, because it is a panel of these markers that are used for human identification. I read this paper because it describes methods to "fish" these types of sequences out of a DNA extract and analyse them without using PCR as a primary method (ie. amplifying the DNA of interest).

5. Stochastic Modeling of Polymerase Chain Rection and Related Biotechnologies
Sun et al (found online)

A short random document I found online which proposes a mathematical method for analysis of stochastic (sporadic) variation associated with amplification of DNA, using Polymerase Chain Reaction (or PCR) a very common method for analysis of DNA.

In the other pile:   The August Edition of "Australian Sky and Telescope" and "Feast' magazines. Haven't had too much of an opportunity to get really into the magazines yet, but first browse on Saturday morning with my coffee put me in a good mood - after all food and astronomy are two of my big interests in life.

Preview to next week's edition: I've started Laurence Krauss's new book, a paper comparing DNA extraction methods, some population genetics and possibly even some new research comparing new DNA sequencing technologies. 

Monday, July 16, 2012


Well that went quickly didn't it?

It's been over TWO months since my last post. Mind you, it's been a pretty trying couple of months and to be honest, I just haven't had the time or the right frame of mind to keep this blog going. However, lots has been happening on all fronts so here's an update on what I've been up to, and a short reflection on some of the recent science news.

 Of course, I can't ignore what probably will be the science breakthrough of the year, if not the decade, and for some physicists, of their lifetime: The results out of the LHC regarding that little particle. All So much has been said already by those far more qualified than I, but what I can say is that even as a biologist I can appreciate the amazing result and what it means for the standard model of particle physics.  There were the usual cries of "But what does it mean for us? How will it cure, fix, or make life better?" Science isn't just about making the world better or life easier, sometimes the beauty in science is finding out something unknown, of adding a new piece of knowledge to what we know. Where a new piece of knowledge can take us in terms of applications is really an open-ended question. It's well known in science when one answer is found, about a thousand more questions simultaneously arise and a scientists work will possibly never be done. When Einstein published the Theories of Relativity, nobody could predict it would enable us to use satellites to track locations in the form of GPS. Finding the Higgs Boson is another piece of the puzzle, and a wonderful demonstration of how global effort can be enacted to improve our understanding of the world.  I listened to the live broadcast announcement of the discovery, and I even understood little parts of it! Despite not understanding all the physics I could hear the excitement, the sheer pride of the chief scientists as they spoke of the result, and this is something that made me proud to be part of the scientific community, and inspired to keep chipping away at my own research questions. The discovery and announcement of this little particle was a wonderful day for scientists of all disciplines, and the result is a shining example of collaborative science at its finest.

I've got some great papers to review for my paper dissection posts including one on how men with wider faces tend to lie, the correlation of size and strength to human formidability and some examples of sci-fi getting real including genes that can be activiated using radiowaves and how methylation of DNA can be linked to memory.  It can be said that like New York, Science never sleeps!

Speaking of unrest, on the PhD front it's been a harrowing couple of months. I waited nine weeks to finally hear that my PhD scholarship has been extended. I didn't think waiting would actually get to me, afterall I had good grounds for an extension, but waiting that long without an answer was hard, and stressful and even at times, quite distressing. The story behind the extension is a good one - it involves a mix of an electricity cut, insurance claims, waiting for orders and a supervisor who went AWOL. Basically I was delayed, and thankfully as slow as the government was, my money was approved.   The lab work also wasn't going so well - it seemed everything I touched turned to rubbish. And I mean everything - even the most basic of procedures were either failing or turning up cruddy results. Thankfully I stuck it out and thankfully I've done the troubleshooting and things seem to be back to working (for now). I've only got three weeks of lab work left, which is pretty crazy. It's getting hard to say goodbye to things I've been doing constantly for almost three years, it is also exciting to know a new adventure is coming and I since I can see that tiny little light at the end of tunnel, the motivation to keep going is probably what will see me through the hard part i.e.finishing all the loose ends and producing a coherent document at the end of it all.

The big news is that I submitted my first paper from my thesis - it is still sitting with a sub-editor waiting to go to review. It was a great feeling to finally press submit, but there was also a touch of trepidation. I've been in the field long enough to know sometimes getting a paper published is like a lottery. Sometimes you get good reviewers, sometimes you don't, sometimes the comments are mean, sometimes they are helpful and sometimes it feels like a merry-go-round. Just when you think you've achieved something, there is a peer reviewer who will bring you right back down to ground with a resounding thump.  It does seem for every 10 steps you make, there is at least one setback - grant rejections, paper rejections, nasty comments, politics, no money, failed experiments. But all the setbacks mean when you do something great, or your paper does get published, it is all the more sweeter.  If I've learnt anything in this PhD (aside from science) is that we are all full of far more fight and passion and endurance than I ever imagined.

So stay tuned, the blog is well and truly back! And I have a new motto especially in times of stress, of which there will be several between now and when I submit the thesis:

I have a funny feeling that in order to keep calm in the next couple of months, I will be baking a lot of cakes.....