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. 

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