Improving metagenomics efforts
Nature Methods
A novel technique for simplifying the study of important ecosystems is described in the January issue of Nature Methods.
Shotgun sequencing methods used by metagenomics efforts to study microbial communities produce massive collections of sequence fragments that are very difficult to analyze. A number of methods have been used to attempt to assemble and classify these sequences but they generally fail for highly complex samples and short fragments. Isidore Rigoutsos and colleagues describe a new sequence classification method that uses information from 340 completed genomes to classify and assemble sequence fragments from complex communities that have been resistant to previous efforts.
CONTACT
Isidore Rigoutsos (IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA)
Tel: 914 945 1384; E-mail: rigoutso@us.ibm.com
Fast 3D imaging of brain cell networks
Nature Methods
A method of fast scanning microscopy that allows in vivo imaging of signalling in neuronal and glial cell networks is reported in the January issue of Nature Methods. This opens the way to studies of the complex cellular networks involved in information processing in the brain.
Processing of information in the brain involves complex patterns of communication between neural cells within large interconnected groups. Recent research has also highlighted the possible importance of brain support cells, or glia, in regulating this process. Technological limitations, however, have previously made the study of these complex interconnected signalling networks difficult.
Fritjof Helmchen and colleagues describe a method of fast three-dimensional scanning fluorescence microscopy that detects signals from cells in the entire scanned volume over a very short period of time. They were able to achieve such fast scanning by vibrating the microscope lens up and down very quickly while scanning the illumination beam back and forth in a defined pattern at the same time. The authors verified the performance of the method by imaging calcium signals in neuronal and glial cell networks in the brain of anaesthetized rats.
CONTACT
Fritjof Helmchen (University of Zurich, Zurich, Germany)
Tel: +41 (0) 44 635 33 40; E-mail: Helmchen@hifo.unizh.ch
A new tool to analyze bacteria in the gut
Nature Methods
A new technique for analyzing bacterial genetic information is outlined in the January issue of Nature Methods, opening the door for a comprehensive study of all bacteria in our guts. The technique allows researchers to capture and analyze the genetic hitchhikers of the bacterial world, small bits of bacterial genetic information that usually escape scrutiny.
For many organisms once the genome is sequenced all the information needed to determine functionally important genes becomes available. This is not the case for bacteria however. Many bacteria possess hitchhiker genes in the form of small circular DNA molecules called plasmids. Not only do the plasmids contain genes that provide new abilities to the bacteria but copies of these plasmids can also be transferred to other bacteria.
Most large-scale sequencing efforts to characterize all the microorganisms in an ecosystem are unsuitable for analyzing the complex population of plasmids that provides extra-genomic genes. Julian Marchesi and colleagues describe a method to selectively capture these bacterial hitchhikers so they can be sequenced. They tested their method on the bacterial ecosystem living in the human gut and discovered plasmids containing genes of known and unknown function. This method should help determine just how important these small hitchhikers are and what effect they have on microbial ecosystems.
CONTACT
Julian R. Marchesi (University College Cork, Cork, Ireland)
Tel: +353 21 4902820; E-mail: j.marchesi@ucc.ie
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