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Primeur weekly 2017-02-27

Focus

Square Kilometre Array data crunching will require compute power beyond Moore's Law ...

Exascale supercomputing

ADIOS Version 1.11 moves I/O framework from research to production ...

Focus on Europe

Microsoft researcher tapped for opening keynote at ISC 2017 ...

Atos acquires zData, a premier consulting firm with unparalleled expertise in Big Data solutions ...

HPC5 consortium now registered as official Digital Hub with I4MS ...

Middleware

HPE and Red Hat join forces to give customers greater choice for NFV deployments ...

Hardware

Tokyo Tech supercomputer TSUBAME3.0 scheduled to start operating in summer 2017 ...

NASA saves energy and water with new modular supercomputing facility ...

Mellanox sets new DPDK performance record with ConnectX-5 ...

Mellanox introduces world-leading 6WIND-based router and IPsec Indigo platform at unmatched price/performance ...

Mellanox and ECI smash virtual CPE performance barriers with Indigo-based platform ...

ORNL director moving to new post at Battelle ...

DDN ranks no. 1 as HPC storage market leader and top supplier ...

National Science Foundation funds supercomputer cluster at Penn State ...

Applications

Watson Health Medical Imaging Collaborative expands to 24 members; IBM debuts Watson Imaging Clinical Review, the first cognitive imaging offering ...

3D-e-Chem team develops Virtual Machine for computer-aided drug discovery ...

IBM Research is training Watson to identify eye retina abnormalities ...

Lorentz-eScience competition 2018 to issue Call for Applications ...

Learning how to fine-tune nanofabrication ...

Deep Learning predicts hematopoietic stem cell development ...

New algorithm identifies gene transfers between different bacterial species ...

Artificial intelligence in quantum systems, too ...

ExxonMobil sets record on NCSA's Blue Waters supercomputer ...

The Cloud

eww ITandTEL implements high-performance Platform-as-a-Service environment with Red Hat technologies ...

New algorithm identifies gene transfers between different bacterial species


Mosaic pneumococcal population structure caused by horizontal gene transfer is shown on the left for a subset of genes. Matrix on the right shows a genome-wide summary of the relationships between the bacteria, ranging from blue (distant) to yellow (closely related). Photo: Pekka Marttinen.
24 Feb 2017 Aalto - Gene transfers are particularly common in the antibiotic-resistance genes of Streptococcus pneumoniae bacteria. When mammals breed, the genome of the offspring is a combination of the parents' genomes. Bacteria, by contrast, reproduce through cell division. In theory, this means that the genomes of the offspring are copies of the parent genome. However, the process is not quite as straightforward as this due to horizontal gene transfer through which bacteria can transfer fragments of their genome to each other. As a result of this phenomenon, the genome of an individual bacterium can be a combination of genes from several different donors. Some of the genome fragments may even originate from completely different species.

In a recent study combining machine learning and bioinformatics, a new computational method was developed for modelling gene transfers between different lineages of a bacterial population or even between entirely different bacterial species. The method was used to analyse a collection of 616 whole-genomes of a recombinogenic pathogenStreptococcus pneumoniae.

In the study, several individual genes in which gene transfers were considered particularly common were identified. These genes also included genes causing resistance to antibiotics.

"In the case of antibiotic-resistance genes, the number of gene transfers may be related to how useful these genes are to bacteria and to the resulting selection pressure", stated Academy Research Fellow Pekka Marttinen from the Aalto University Department of Computer Science.

"The study will not provide a direct solution to antibiotic resistance because this would require a profound understanding of how the resistance occurs and spreads. Nevertheless, knowing the extent to which gene transfer occurs between different species and lineages can help in improving this understanding", he explained.

The study was able to show that gene transfer occurs both within species and between several different species. The large number of transfers identified during the study was a surprise to the researchers.

"Previous studies have shown that gene transfers are common in individual genes, but our team was the first to use a computational method to show the extent of gene transfer across the entire genome", Pekka Marttinen stated.

"The method also makes it possible to effectively examine ancestral gene transfers for the first time, which is important in examining transfers between different species."

Molecular Biology and Evolutionpublished the results in February. Rafal Mostowy, Nicholas J. Croucher, Cheryl P. Andam, Jukka Corander, William P. Hanage and Pekka Marttinen are the authors of the article titled " Efficient inference of recent and ancestral recombination within bacterial populations ".

Source: Aalto University

Back to Table of contents

Primeur weekly 2017-02-27

Focus

Square Kilometre Array data crunching will require compute power beyond Moore's Law ...

Exascale supercomputing

ADIOS Version 1.11 moves I/O framework from research to production ...

Focus on Europe

Microsoft researcher tapped for opening keynote at ISC 2017 ...

Atos acquires zData, a premier consulting firm with unparalleled expertise in Big Data solutions ...

HPC5 consortium now registered as official Digital Hub with I4MS ...

Middleware

HPE and Red Hat join forces to give customers greater choice for NFV deployments ...

Hardware

Tokyo Tech supercomputer TSUBAME3.0 scheduled to start operating in summer 2017 ...

NASA saves energy and water with new modular supercomputing facility ...

Mellanox sets new DPDK performance record with ConnectX-5 ...

Mellanox introduces world-leading 6WIND-based router and IPsec Indigo platform at unmatched price/performance ...

Mellanox and ECI smash virtual CPE performance barriers with Indigo-based platform ...

ORNL director moving to new post at Battelle ...

DDN ranks no. 1 as HPC storage market leader and top supplier ...

National Science Foundation funds supercomputer cluster at Penn State ...

Applications

Watson Health Medical Imaging Collaborative expands to 24 members; IBM debuts Watson Imaging Clinical Review, the first cognitive imaging offering ...

3D-e-Chem team develops Virtual Machine for computer-aided drug discovery ...

IBM Research is training Watson to identify eye retina abnormalities ...

Lorentz-eScience competition 2018 to issue Call for Applications ...

Learning how to fine-tune nanofabrication ...

Deep Learning predicts hematopoietic stem cell development ...

New algorithm identifies gene transfers between different bacterial species ...

Artificial intelligence in quantum systems, too ...

ExxonMobil sets record on NCSA's Blue Waters supercomputer ...

The Cloud

eww ITandTEL implements high-performance Platform-as-a-Service environment with Red Hat technologies ...