Tag Archives: Biotechnology

Bioenergy Trees – Meeting Summary for a New Phytologist Symposium

I already mentioned (here and here) the New Phytologist Symposium on Bioenergy Trees, but I’d like to let you know that my meeting commentary has been published in the journal.  I highly recommend attending one of the many New Phytologist Symposia based on their intimate size and the excellent quality of speakers.

Conference on the Progress of the “1000 Plant & Animal Reference Genomes Project”

The organizers of the “Second International Conference on the Progress of the “1000 Plant & Animal Reference Genomes Project” have again announced a call for abstracts for the meeting, which will be held from the 10th to 12th of July in Shenzhen, China.  I’ve noticed a large increase in the number of meetings in China (see here) and this meeting is also sponsored by the Beijing Genomics Institute (BGI).

As you can gather from the name, the “100 Plant and Animal Reference Genome Project” seeks to provide a total of 1000 plant and animal genomes for the use of researchers (For more information on the “1000 Plant and Animal Reference Genomes Project” see here).

This meeting seeks to increase the number of collaborators, particularly from a global perspective, to this project.  To register for this meeting see here, and stay connected to this meeting and the BGI by following them on Twitter (@BGI-Events).  You can even enter yourself in a drawing to win a gift (a soft-drink soda!) when you provide proof you have re-tweeted meeting notices from the BGI.  The meeting with have two sessions: one on the progress and prospects of the 1000 plant and animal reference genome project and another on new developments in sequencing and bioinformatics technology.  There will be five workshops: crop genomics and breeding, aquaculture genomics, vegetable and flower genomics, forest and fruit tree genomics, and rare animal genomics (I’m not really sure what “rare” means in this sense).

Beijing Genomics Institute’s International Conference on Genomics 6

Seems like there are a whole series of symposia right now proclaiming to be the international conference on genomics and I do not know who holds the rights to the title.  I figure more meetings in this research area can’t hurt the state of the science.  The Beijing Genomics Institute has been sponsoring an annual series, The International Conference on Genomics, now on its 6th year, and, despite the name of “international conference”, it’s always held in or around Beijing.

This year’s meeting, The International Conference on Genomics 6 (ICG-VI) aims to promote research in basic and applied genomics by sponsoring a series of presentations focused on new sequencing techniques and bioinformatic strategies.  There will be sessions centered on new sequencing techniques, transcriptomics, epigenomics, metagenomics, proteomics, bioinformatics and data mining, and social issues relating to new genomic information.  Registration for the meeting can be found here.

High-Throughput Synthesis

The chemical synthesis of oligonucleotides – argurably the cornerstone of modern gene and genome research – creates DNA segments used as primers and probes in experimental studies.  Oligonucleotide synthesis has employed two techniques over the last few decades, first utilizing a modified version of Sanger nucleotide sequencing, and, predominantly in the last decade, automated microarray technologies modified to engineer sequences.

Despite a decrease in cost and increase in throughput over the last decade, the chemical synthesis of oligonucleotides is still subject to error rates contributing to inaccuracies in scientific experiments and financial costs that significantly reduce research budgets.  Methods for generating long nucleotides have recently been in the public news as the basis for the creation of really large synthetic genomes (for commentary on this see here, here, and here).

Two recent papers originating from George Church’s lab (link) at Harvard have introduced new methods for oligonucleotide synthesis that improve cost per base and appreciably reduce synthesis error rates (commentary on these papers can be found here, here, and here).  The techniques developed by Church’s research group have led to an impressive reduction in error rates of nucleotide synthesis as well as a drastic reduction in the cost of nucleotide synthesis (image link here).  Whether or not these new techniques can be developed commercially has yet to be determined, but they represent a reduction in the cost and improvement in the quality of oligonucleotide synthesis.

In the journal Nature Biotechnology, Matzas et al report (“High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing”) the use of next-generation sequencing techniques to synthesize oligonucleotides increasing both quality and throughput.  The research group selected sequencing beads from the 454 sequencing platform with the desired sequences of interest, physically separated the beads, and used them for further nucleotide synthesis.  By using the high-throughput nature of pyrosequencing, the authors were able to synthesize orders of magnitude more oligonucleotides than traditional synthesis methods.

The research paper by Kosuri et al (“Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips”) addressed the issues of cost and accuracy of oligonucleotide synthesis.  The research group used specific primers to amplify pre-designed nucleotides using pyrosequencing methods and then used PCR to amplify error free oligonucleotides.  Most importantly, the group showed that they could synthesize oligonucleotides for approximately one cent ($) per base pair improving on the current cost of about 20 cents ($) per basepair.