What is PathoGenetix’s Genome Sequence Scanning technology?

PathoGenetix and the U.S. Department of Agriculture’s Agricultural Research Service (USDA-ARS) have agreed to collaborate on an evaluation of PathoGenetix’s Genome Sequence Scanning technology for use in identifying strains of Shigatoxin-producing E. coli (STECs) and Salmonella enterica, two types of pathogens frequently implicated in foodborne illness outbreaks. The ability to quickly and accurately identify these pathogens, particularly in their most virulent forms, can have significant public health and financial impact for consumers, farmers and ranchers, and the agricultural and food industries.

Under the agreement, USDA-ARS will provide PathoGenetix with genetic information and bacterial strains of E. coli and Salmonella.  USDA-ARS and PathoGenetix researchers will analyze the strains, both as isolates and in mixed cultures, using PathoGenetix’s Genome Sequence Scanning technology, currently in development for commercial use as the RESOLUTION™ Microbial Genotyping System. Results of the joint analysis will assist USDA-ARS in evaluation of the RESOLUTION System as a platform for rapidly identifying pathogenic Salmonella and E. coli in food samples.

PathoGenetix’s GSS technology identifies microbial DNA from complex mixtures or from isolates, and automates the process from sample preparation through data analysis to provide actionable information in five hours. Because GSS scans microbial DNA directly from a mixed culture and does not require a pure culture, it can reduce the time, complexity, skill and cost required for molecular identification and strain typing.

The strain type information provided by GSS is comparable to pulsed field gel electrophoresis (PFGE), the current standard for pathogen typing in foodborne outbreak investigation and response. As a result, GSS may enable quicker decisions affecting food safety and public health.

PathoGenetix has signed an agreement with independent contract testing laboratory

PathoGenetix has signed an agreement with independent contract testing laboratory, Q Laboratories, Inc., to conduct an independent evaluation of the RESOLUTION™ Microbial Genotyping System. Q Laboratories will begin testing the RESOLUTION System in its Cincinnati, Ohio laboratory in April, and provide feedback on ease-of-use, speed and performance in food safety testing

The RESOLUTION Microbial Genotyping System is based on PathoGenetix’s proprietary Genome Sequence Scanning™ (GSS™) technology, a breakthrough in microbial identification with significant advantages for food safety testing. GSS works directly from complex mixtures such as enriched food samples, and automates the identification process from sample preparation to final result to provide actionable information in just five hours, days faster than identification methods currently in use in the food industry.

Q Laboratories, Inc. participated in PathoGenetix’s RESOLUTION Customer Experience Program in November, where it received an initial in-depth, hands-on review of the GSS technology.  PathoGenetix’s first round of evaluations for the RESOLUTION System has focused on leading contract testing laboratories serving the food safety industry. Many food producers worldwide rely on these third party laboratories for all or part of their food quality and safety testing programs.

“We are extremely pleased to be conducting onsite evaluations of the RESOLUTION Systems by highly experienced, industry-leading food contract testing labs such as Q Laboratories,” said John Czajka, PhD, PathoGenetix’s Vice President of Business Development.  “These evaluations are demonstrating the speed and accuracy of the RESOLUTION System, and providing key end-user feedback on its fit and function within high-volume laboratory workflows.”

Additionally, the U.S. Food and Drug Administration (FDA) has recently begun a nine month lease of RESOLUTION System to evaluate the System for use in public health foodborne illness outbreak investigation and response as part of a three year collaboration between the FDA and PathoGenetix.

What is PathoGenetix Delivers Bacterial Identification System?

PathoGenetix, Inc., developer of an automated system for rapid bacterial strain typing, announced today that it has delivered and installed an early commercial version of the RESOLUTION Microbial Genotyping System to MRIGlobal, an independent contract research organization. MRIGlobal has purchased the RESOLUTION System as part of a U.S. government-funded project, and will be evaluating use of the System for identification and strain typing of specific organisms using MRI-developed assays.

The RESOLUTION System is based on PathoGenetix’s proprietary Genome Sequence Scanning (GSS) technology, which enables pathogen serotype identification and strain typing in just five hours, directly from complex mixtures such as environmental, clinical and enriched food samples. Initially developed to detect bio-threat pathogens in environmental samples under a five-year, $50-million contract through the Department of Homeland Security, the breakthrough GSS technology isolates and analyzes DNA direct from complex mixtures—without the need for a pure culture isolate. The strain type information provided by GSS is comparable in resolution to pulsed field gel electrophoresis (PFGE), one of the current gold standards for pathogen identification.

MRIGlobal and PathoGenetix have collaborated for several years in the ongoing evaluation of the GSS technology for biodefense applications. MRIGlobal has purchased a RESOLUTION System as part of a U.S. government-funded project, and will be evaluating the system for use in the rapid identification of specific organisms, using MRIGlobal-developed assays. The RESOLUTION instrument will be used to build a database for identification of select microorganisms. As one of the nation’s leading research institutes, MRIGlobal conducts programs in the areas of national security and defense, life sciences, energy and the environment, agriculture and food safety, and engineering and infrastructure.

What is automated system for rapid bacterial identification

PathoGenetix, Inc., a developer of an automated system for rapid bacterial identification, and Applied Maths, NV, a leader in bioinformatics and analytical solutions for public health and research laboratories, presented a novel study at InFORM 2013 comparing three different genomic methods for typing bacterial pathogens: the new technologies, whole genome sequencing (WGS) and Genome Sequence Scanning™ (GSS™), and the traditional pulsed field gel electrophoresis (PFGE). PFGE is the current standard for pathogen identification in foodborne illness outbreak investigation and response.

The BioNumerics® software suite (Applied Maths) was used to analyze a data set of 190 pathogenic E. coli strains from the Centers for Disease Control and Prevention (CDC). Clustering of related strains was performed using patterns generated by PFGE and whole genome sequence data included in the CDC data set, and GSS fingerprints, PathoGenetix’s proprietary technology used in the RESOLUTION™ Microbial Genotyping System. For the set of E. coli isolates tested, the analysis shows a remarkably high congruence between the GSS groupings and WGS groupings, while maintaining a good concordance with the PFGE groupings. With respect to WGS, the GSS groupings also turn out to be more discriminatory than the PFGE groupings.

The RESOLUTION System can work from a mixed sample and does not require the preparation of a cultured isolate, as is the case with whole genome sequencing and PFGE, and provides strain type and serotype results in less than five hours.

The collaborative research is detailed in a poster presented yesterday at the InFORM 2013 meeting being held this week in San Antonio, Texas. InFORM meetings are designed to coordinate and enhance the work of microbiologists, epidemiologists and environmental health specialists focused on foodborne disease surveillance, outbreak detection and response. The meeting is sponsored by the CDC, the Association of Public Health Laboratories (APHL), the U.S. Department of Agriculture Food Safety and Inspection Service (FSIS), and the Food and Drug Administration (FDA), and integrates the separate PulseNet and OutbreakNet annual meetings held in previous years.

Steps to understand How to prepare biological buffers?

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Buffers are essential to life. They help maintain the proper functioning of cellular systems by resisting rapid changes in pH. In living organisms, the pH of the blood is maintained at a pH of 7.4. A slightly more basic pH (7.7) would result in convulsions and muscle spasms while a slightly acidic pH (6.95) would result in coma and even death.

Most chemical reactions are affected by the acidity of the solution in which they occur. As such, you can maintain a constant concentration of hydrogen ions within the physiological range, manipulate a particular reaction to occur or to proceed at an appropriate rate by controlling the pH of the reaction medium through the use of the appropriate biological buffer system.

Upon the addition of a strong base such as NaOH to the buffer solution, the hydrogen ion will bind with the hydroxide ion to form water. Upon the addition of a strong acid, however, the conjugate base will simply bind with the additional hydrogen ions to form acetic acid. In each case, equilibrium can be maintained.

Note: Weak acids and bases do not dissociate completely in water but exist in solution as a mixture of dissociated and dissociated molecules.

How Do Buffers Work?

All buffers have an optimal pH range over which they can moderate the changes in hydrogen ion concentration. This is generally defined as the pKa or the negative log of the dissociation constant of the acid. The pKa can be determined by using the Henderson-Hasselbalch equation:

pH = pKa + log10 [A-]/[HA]

However, since there are acids that can lose more than one hydrogen ion (polyprotic acids), they can have multiple pKa values. If the pKa values are close together, the optimal pH range will be a continuum determined by the range of pKas.

You know Which non-radioactive assays are used to determine cell cytotoxicity and cell proliferation?

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While there are a number of non-radioactive assays that can help determine cell proliferation and viability as well as cell toxicity, determining the most appropriate assay to use can be very vital in obtaining the right information from the given cell sample. So, how do you know which one to use in each particular case? Here is a guide that can help you accomplish this task.

Measuring Cell Viability, Proliferation and Cytotoxicity

Cell viability and cytoxicity assays are best used in determining the metabolic and proliferative activities of cells within a given sample. As such, they can be used to obtain vital information on the effects of certain experimental stimulus on the proliferation of cells within an in vitro environment.

There are a number of ways by which you can get an accurate indication of the cell vitality within your sample. You can choose to assess plasma membrane integrity, mitochondrial activity and/or metabolic activity to accomplish your purpose.

Membrane integrity can be assessed by monitoring the passage of LDH to the extracellular environment. Since LDH is normally confined inside the cell, its presence in the extracellular environment indicates loss of cell membrane integrity, an occurrence that usually follows apoptosis or necrosis. If you want to measure the amount of LDH in your sample, consider using CytoScan LDH Cytotoxicity and Cytoscan Fluoro Cytotoxoicity Assays.

On the other hand, you may want to use Cytoscan WST-1 Cell Proliferation Assay if you are interested in determining cell cycle regulatory factors. This particular colorimetric assay works on the basic principle that tetrazolium salt WST-1 will be reduced to water-soluble formazan by the action of cellular dehydrogenases. The resulting formazan dye can then be accurately measured by absorbance.

For cell density determination, you can use the Cytoscan SRB Cytotoxicity Assay. This particular assay is based on the quantitative staining of cells with the fluorescent dye Sulforhodamine B, an anionic aminoxanthene dye that forms an electrostatic complex with the basic amino acid residues of proteins under moderately acid conditions. This reaction provides a sensitive linear response that can be readily measured at absorbances between 560 and 580 mm. This method is regarded to be a highly efficient and cost-effective method for screening and has a sensitivity that is comparable to those using fluorimetric methods.

Cytotoxicity Assays, you know How Are They Classified?

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Subjecting cells to cytotoxic compounds may bring different results. Cells may stop growing and dividing actively, lose cell membrane integrity and suffer instantaneous death (necrosis) or initiate a series of events that will lead to programmed cell death (apoptosis). To better understand the effects of toxic compounds on living cells and to measure the level by which they begin to exhibit their harmful effects on biological systems, researchers and pharmaceutical laboratories use cytotoxicity assays to learn what they need to know.

In general, there are three distinct types of cytotoxicity assays. There are assays that determine cell viability by:

Exhibiting a change in the membrane permeability or metabolism (viability assays);

Measuring their absolute long term survival rate and their capacity to regenerate (long term survival assays);

Exhibiting survival in an altered or genetically mutated state (irritancy assays).

Viability Assays