Showing posts with label bacterium. Show all posts
Showing posts with label bacterium. Show all posts

Thursday, March 15, 2012

Bioinformatics Bacterial Identification Tool

    BIBI automates DNA sequence analysis for bacterial identification in
    the clinical field. BIBI relies on the use of BLAST and CLUSTAL W
    programs applied to different subsets of sequences extracted from
    GenBank. These sequences are filtered and stored in a new database,
    which is adapted to bacterial identification.

    For further details refer :http://umr5558-sud-str1.univ-lyon1.fr/ lebibi/lebibi.cgi

Monday, September 19, 2011

Algorithm tailored for short-read data from single cells that improves assembly

Abstract

Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single Escherichia coli and Staphylococcus aureus cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many E. coli cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies.

Figures at a glance








Thursday, December 23, 2010

New programming language will drive DNA

This is no Sci-Fi but reel to real! Yes we can in deed program the DNA for real Now! 

Bioinformatics scientists have built two logic gates for what they hope will become a new programming language for drug design as well as chemical and agricultural product engineering. The accomplishment seems hardly noteworthy except that these logic gates are made of E. coli. The two computational switches are based on two strains of the common bacterium. Researchers are now working to assemble them to perform computations.

This genetic programming software would resemble any other programming language, says Kevin Clancy, senior staff scientist for bioinformatics at Life Technologies Corp. The Carlsbad, CA, company is funding the work, which is being done by researchers at the UC San Francisco School of Pharmacy. Life Tech plans to commercialize the technology.

The software would convert instructions into a DNA sequence to be inserted into a bacterial, yeast or mammal cell. "It allows you to access and rewire biological systems on a scale that hasn't been possible in genetic engineering to date," says Christopher Voigt, UCSF associate professor.


Monday, August 18, 2008

Now a new computer system has been used to map out the metabolism of Nitrogen Fixation by Nostoc

Scientists at the University of Sheffield have shown how bacteria could be used as a future fuel. The research, published in the journal Bioinformatics, could have significant implications for the environment and the way we produce sustainable fuels in the future.

Like all living creatures, bacteria sustain themselves through their metabolism, a huge sequence of chemical reactions that transform nutrients into energy and waste. Using mathematical computer models, the Sheffield team have mapped the metabolism of a type of bacteria called Nostoc. Nostoc fixes nitrogen and, in doing so, releases hydrogen that can then potentially be used as fuel. Fixing nitrogen is an energy intensive process and it wasn´t entirely clear exactly how the bacterium produces the energy it needs in order to perform. Now the new computer system has been used to map out how this happens.

Until now, scientists have had difficulties identifying bacteria metabolic pathways. The bacterial metabolism is a huge network of chemical reactions, and even the most sophisticated techniques can only measure a small fraction of its activity. Dr Guido Sanguinetti, from the University´s Department of Computer Science, who led the study, said: "The research uncovered a previously unknown link between the energy machinery of the Nostoc bacterium and its core nitrogen metabolism. Further investigation of this pathway might lead to understanding and improvement of the hydrogen production mechanism of these bacteria. It will certainly be some time before a pool of bacteria powers your car, but this research is yet another small step towards sustainable fuels."

He added: " The next step for us will be further investigation into hydrogen production, as well as constructing more mathematical models capable of integrating various sources of biological data."

The Sheffield research is the result of an interdisciplinary collaboration of computer scientists and chemical engineers in a new discipline called Synthetic Biology. A major goal of Synthetic Biology is to understand which pathways of the bacterial metabolism are responsible for important functions, and then genetically engineer organisms that can perform the desired function more effectively.

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Tuesday, May 20, 2008

Scientists characterize protein structure of environmentally friendly bacteria

Scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory have determined the structure of a key protein domain in a bacterium that could help with bioremediation of uranium-contaminated land sites.

The researchers, led by Argonne senior biophysicist Marianne Schiffer, characterized the structure of one of the principal domains in a protein responsible for certain types of movement exhibited by the bacterium Geobacter sulfurreducens.

Geobacter
lives in predominantly low oxygen environments and generates energy by transferring electrons to various metallic electron-accepting atoms such as iron or uranium. This ability suggests that Geobacter might be used for remediation of certain types of hazardous waste. For example, when uranium is reduced by this process to its insoluble form, it no longer leaks into groundwater and engineers can inexpensively remove the precipitated uranium.

Do you want to know more?