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Primeur weekly 2015-02-02

The Cloud

Shinra Technologies partners with NTT and Techorus and announces launch date of Japanese technical beta ...

UTSA and Indiana University partner on $6.6 million NSF Cloud-based advanced computing systems grant ...

Independent research firm ranks HP private Cloud a leader in China ...

Desktop Grids

Grant for Nerdalize for heating houses with computing power ...

EuroFlash

Business Secretary Cable announces partners in the Alan Turing Institute in the UK ...

Schools in Wales challenged to break the world land speed record of 1,000mph ...

PUZZLECLUSTER: The first reuse application of the PUZZLEPHONE ...

Chemists control structure to unlock magnetization and polarization simultaneously ...

MEP Awards 2015 - Shortlisted nominees for ICT announced ...

DIADEMS - finding the sensor behind the sparkle ...

Entanglement on a chip: Breakthrough promises secure communications and faster computers ...

USFlash

NERSC seeks industry partners for collaborative research ...

Exascale Hearing Testimony in Congress highlights CS research accomplishments ...

D-Wave Systems raises an additional $29 million, closing 2014 financing at $62 million ...

MAGMA MIC 1.3.1 for Intel Xeon Phi coprocessors released ...

Dot Hill announces general availability of the Ultra56 AssuredSAN Hybrid storage array ...

New climate change projections for Australia ...

SGI reports financial results for the second quarter of fiscal 2015 ...

Researchers identify materials to improve biofuel and petroleum processing ...

Supercomputing the evolution of a model flower ...

Obsidian unveils plans for 400G-capable enhanced InfiniBand services platform at EmTech Singapore 2015 ...

New supercomputer allows for massive data analysis in less time ...

IBM Research to lead company's advanced computer chip R&D at SUNY Polytechnic Institute ...

Building trustworthy Big Data algorithms ...

Parallelizing common algorithms ...

New pathway to valleytronics ...

Nanoscale mirrored cavities amplify, connect quantum memories ...

Supercomputing the evolution of a model flower


Juenger Lab
26 Jan 2015 Austin - Scientists using supercomputers found genes sensitive to cold and drought in a plant help it survive climate change. These findings increase basic understanding of plant adaptation and can be applied to improve crops. The computational biology study on the flowering mustard weed Arabidopsis thaliana appeared in the journalMolecular Biology Evolutionin September 2014. The iPlant Collaborative and the supercomputers Stampede, Lonestar and Ranger of the Texas Advanced Computing Center aided in the research. Study funding came from the National Science Foundation (NSF) and the U.S. Department of Agriculture.

"We found pretty good evidence, certainly the best evidence to date, that the evolution of gene expression is an important way that plant populations adapt to local environments", stated study co-author Jesse Lasky, an Earth Institute fellow at Columbia University.

Thomas Juenger is another co-author and a faculty member in the Department of Integrative biology of The University of Texas at Austin. The Juenger Lab has studied Arabidopsis thaliana for over a decade. "It's one of the model plants that biologists study", Thomas Juenger stated. Arabidopsis has one of the smallest genomes of any plant, and in 2000 it was the first plant genome to be completely sequenced.

Plant biologists consider Arabidopsis to be like the fruit fly of their genetic research. But instead of knocking out or ramping up genes with genetic engineering, Thomas Juenger studies natural variation in genes. "We want to understand how they've evolved in response to the processes of natural selection and gene flow and mutation in the field", he stated.

To date, plants have stumped scientists' understanding of how life adapts to climate, specifically the details of gene expression, which can vary wildly in a hardy plant species like Arabidopsis that thrives in environments as diverse as Scandinavia, North Africa, and Central Asia. Genes, or snippets of the four-letter DNA molecule, carry not only the code for which proteins make for its survival but also the instructions for how many to make, or express. Gene expression "... is the part of the organism that we show here is strongly involved in local adaptation to environment", Jesse Lasky stated.

Because plants are rooted, they have to stand their ground against changes in temperature, soil moisture, and insect attacks to name a few. Thomas Juenger explained that one way they cope with environmental change is to change their gene expression.

"As a plant starts to sense dropping temperatures, a cascade of gene expression can allow the plant to acclimatize to cold temperatures, and in effect prepare itself for the coming freezing conditions", Thomas Juenger stated. So his science team used prior lab work that exposed seedlings of Arabidopsis to artificial cold and drought stress to measure changes in gene expression across the entire genome.

Thomas Juenger described the problem of finding the right gene like finding a needle in a haystack. Arabidopsis' relatively tiny genome still contains over 25,000 genes. The needle Thomas Juenger's team sought was what's called a SNP polymorphism, a single letter difference in the over 100 million DNA base pairs that comprise the genes of Arabidopsis. "This is a fundamental challenge in biology", Thomas Juenger stated. "We're looking through tens of thousands of genes to find the right ones, the few that might actually matter."

The scientists took the genes they found and compared them with genomic data from previous studies that sampled Arabidopsis from populations throughout Europe and Asia. They narrowed that reference data to 1,003 strains of the flowering mustard weed. Of those genes that showed changes in their response to their environment, the scientists needed to know if they also showed changes in DNA along environmental gradients. Such a pattern "suggests that there are changes in the DNA sequence that are adapted to those local conditions and that are associated with changes in gene expression", Jesse Lasky stated.

The research team statistically tested for associations between climate and SNP polymorphism by making the hypothesis null, or assuming no association. They did that by shuffling the data and doing permutation testing. "We can randomize climatic variation with respect to SNP polymorphism variation and do that thousands and thousands of times and ask, what sort of test statistic might we observe by chance alone", Thomas Juenger stated. "We can compare that to our real, empirical data."

The computational challenges were daunting, involving thousands of individual strains of Arabidopsis with hundreds of thousands of markers across the genome and testing for a dozen environmental variables. "It's impossible to do this on a standard desktop computer, and it requires some of the throughput that we can have on a cluster like Stampede or Lonestar", Thomas Juenger stated. "The computational time on the clusters at TACC allowed us to evaluate the hypothesis that generated from the SNP data."

Jesse Lasky added that "to run these models across the genome, you quickly run out of time. It's really just a problem where you do lots of little things many, many times. It's much easier to accomplish that when you can run that problem on many cores across a cluster. That was the challenge."

"I didn't have any experience with high performance computing before this", Jesse Lasky confided.

Jesse Lasky called on Weijia Xu, the group lead for the Data Mining and Statistics Group at TACC. "He helped me orient myself to what kind of problem I had and how to scale that up to run it on some of the clusters", Jesse Lasky stated. Weijia Xu also helped by writing a parametric job launcher, which allowed Lasky to get his separate runs across the genome started more easily.

"It was a code I developed to launch multiple R jobs in parallel using an MPI interface", Weijia Xu stated of the launcher. Scientists commonly use the R statistical programming language; and MPI is short for Message Passing Interface, which is a software library that breaks up large computing jobs into smaller ones to run in parallel on the nodes of a cluster.

The NSF-funded iPlant Collaborative helps life scientists use high performance computers. Thomas Juenger remarked that "iPlant, associated with TACC, has certainly been developing lots of new tools, simplifying computational tools for biologists, and giving us access to data storage as well as service units through high performance computing clusters like those at TACC. It's a helpful, timely program that's impacting plant biologists in individual labs around the country."

Jesse Lasky noted that while the results of the experiment with Arabidopsis are promising, more confirmation is needed. "We have experimental work here, but we haven't experimentally shown that the genes that we identified are causing localized adaptations."
Source: University of Texas at Austin - Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2015-02-02

The Cloud

Shinra Technologies partners with NTT and Techorus and announces launch date of Japanese technical beta ...

UTSA and Indiana University partner on $6.6 million NSF Cloud-based advanced computing systems grant ...

Independent research firm ranks HP private Cloud a leader in China ...

Desktop Grids

Grant for Nerdalize for heating houses with computing power ...

EuroFlash

Business Secretary Cable announces partners in the Alan Turing Institute in the UK ...

Schools in Wales challenged to break the world land speed record of 1,000mph ...

PUZZLECLUSTER: The first reuse application of the PUZZLEPHONE ...

Chemists control structure to unlock magnetization and polarization simultaneously ...

MEP Awards 2015 - Shortlisted nominees for ICT announced ...

DIADEMS - finding the sensor behind the sparkle ...

Entanglement on a chip: Breakthrough promises secure communications and faster computers ...

USFlash

NERSC seeks industry partners for collaborative research ...

Exascale Hearing Testimony in Congress highlights CS research accomplishments ...

D-Wave Systems raises an additional $29 million, closing 2014 financing at $62 million ...

MAGMA MIC 1.3.1 for Intel Xeon Phi coprocessors released ...

Dot Hill announces general availability of the Ultra56 AssuredSAN Hybrid storage array ...

New climate change projections for Australia ...

SGI reports financial results for the second quarter of fiscal 2015 ...

Researchers identify materials to improve biofuel and petroleum processing ...

Supercomputing the evolution of a model flower ...

Obsidian unveils plans for 400G-capable enhanced InfiniBand services platform at EmTech Singapore 2015 ...

New supercomputer allows for massive data analysis in less time ...

IBM Research to lead company's advanced computer chip R&D at SUNY Polytechnic Institute ...

Building trustworthy Big Data algorithms ...

Parallelizing common algorithms ...

New pathway to valleytronics ...

Nanoscale mirrored cavities amplify, connect quantum memories ...