Researchers at DSMZ Develop Innovative Software for Biolog Inc. Phenotypic Analyses to Improve Our Understanding of the Metabolic Processes of Microorganisms and Other Cells
Published: Apr 27, 2012
HAYWARD, CA--(Marketwire - April 27, 2012) - An interdisciplinary team of microbiologists, plant bioengineers and bioinformatics experts of the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures in Braunschweig has developed an application-oriented software package for the analysis of Biolog high-throughput phenotypic data. The 'opm' (OmniLog Phenotype MicroArray) package, which is based on the free software environment R, allows comprehensive statistical analyses on quantitative data of energy production curves and a better graphic presentation. The new software can provide a valuable contribution toward the greater understanding of physiological interactions in the metabolism of diverse cells, from microorganisms to cancer cells. The initial findings are published in the current issue of the scientific journal PLoS ONE.
Which properties do bacteria, fungi, yeasts or even cancer cell lines have? This question is commonly just as important in basic research as in applied biology. The determination of these properties in the laboratory is often laborious and time consuming. Automatic high-throughput screening such as the Phenotype MicroArray System of the company Biolog, Inc. provides the solution. Here the response of bacteria, yeasts, fungi and animal cells can be tested in parallel for nearly 2,000 physiological assays.
"With the use of a redox dye that forms a violet pigment, up to 96 chemical substances are tested on a single microtitre plate at the same time. One can test whether these substances provide an energy source for microorganisms or cell lines, or have possible antibiotic effects," says microbiologist Dr. Johannes Sikorski. "Changes in the intensity of the pigment formation is measured at frequent intervals of 15 minutes. As a result, highly informative so-called 'respiration kinetics' appear as kinetic graphs, similar to a typical growth curve of bacteria. By measuring over the course of four days, just under 2,000 curves, each with around 380 measured values, can be recorded in a single experiment. Valuable biological information can be derived from the curve, such as the inception, strength and intensity of a physiological reaction."
In order to mine this data, an interdisciplinary team of microbiologists, plant bioengineers and bioinformatics experts of the Leibniz Institute DSMZ has developed a novel software package based on the free software environment R (www.r-project.org). "Until now the analysis software from the manufacturer Biolog was only partially suitable to graphical and statistical evaluation of this wealth of high dimensional data," explains Dr. Markus Göker, an expert in bioinformatics who was responsible for programming the 'opm' package. "Until now most users have analysed data based upon whether a reaction takes place or not. As a result, much valuable data, and therefore significant information, was discarded."
"The new 'opm' package allows for a comprehensive evaluation of curve kinetics with numerous high-resolution forms of graphical analyses. Through the so-called 'bootstrapping technique' one can also test the extent to which individual curves vary significantly from one another. The real strengths of 'opm' lie, however, in that we have enabled all desired analyses for all parts of the comprehensive data record," says Dr. Markus Göker.
"The user can add metadata on the organisms tested or annotate the experimental conditions applied virtually without restriction. Diverse search and selection functions for raw data, curve parameters and metadata allow it to work on specific questions on each data record," explains Lea Vaas, plant bioengineer. "Therefore, with the 'opm' software package, there will be diverse opportunities for innovative test design: tests on metabolism and gene function of microorganisms, such as gene defects coding for regulatory enzymes or even the reaction of cancer cells to anti-cancer agents. All of these can now be analysed at a substantially more detailed level with the OmniLog Phenotype MicroArray system."
Barry Bochner, Ph.D., CEO & CSO of the manufacturer, Biolog, is pleased about the successful cooperation with the Leibniz Institute DSMZ. He explains that: "The newly developed 'opm' package from the researchers of the Leibniz Institute DSMZ can clearly expand and improve the application parameters and significance of Biolog tests and thus offer our users decisive advantages in their research."
Further background information on the 'opm' software and free download can be found at http://www.dsmz.de/research/microorganisms/projects/analysis-of-omnilog-phenotype-microarray-data.html
About the Leibniz Institute DSMZ:
The Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures is an institution of the Leibniz Corporation, and with its comprehensive scientific services and a wide spectrum of biological materials, it has become a worldwide partner for research and industry for decades. As one of the largest biological resource centres of its kind, the DSMZ has been certified to the quality standard ISO 9001:2008 valid worldwide. Alongside the scientific service, the collection-related research forms the second pillar of DSMZ. The collection based in Braunschweig has existed for 42 years and accommodates more than 30,000 cultures and biomaterials. The DSMZ is the most diverse collection worldwide: alongside fungi, yeasts, bacteria and archaea, human and animal cell cultures, as well as plant viruses and plant cell cultures are explored and archived there as well.
Biolog is a privately held company based in Hayward, CA, that continues to lead in the development of powerful new cell analysis tools for solving critical problems in biological, pharmaceutical, and biotechnological research and development. It is the world leader in phenotypic cell profiling. Biolog's products allow scientists to study the growth properties and culture condition responses of bacterial, fungal, and even human cells. As such it is becoming a core technology for many cellular studies. Further information can be obtained at Biolog's website, www.biolog.com.
You can also find a copy of this press release on the DSMZ website www.dsmz.de.
PLoS ONE 7(4): e34846, 2012; http://dx.plos.org/10.1371/journal.pone.0034846
Dr. Johannes Sikorski
Dr. Markus Göker
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