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Periodontal Pockets Microbiota qPCR Analysis at Different Stages of Periodontitis
Oksana Zorina and Denis Rebrikov

Six major periodontal pathogens were quantified (with standardization to human gDNA) in periodontal pockets of periodontitis patients and healthy subjects by original qPCR assay. Relative amount of pathogens to total bacterial mass increased for P.gingivalis (100-fold), P.intermedia (10-fold) and T.forsythensis (10-fold).

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Low-volume on-chip single sperm cell analysis
Pickrahn I. E. ,Schmidt-Gann G., Kroneis T.

We performed low-volume on-chip DNA typing of single sperm cells isolated by means of laser microdissection. 16plex PCR was successful in 39 of 40 single cell samples yielding a mean PCR efficiency of 62.8%. In addition, we were able to identify a single-cell sample containing more than one cell enabling us to monitor the quality of the whole procedure, and hence, exclude “contaminated” samples from further analysis.

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Development and NDA-Level Validation of a Real-Time PCR Procedure for Detection and Quantification of Residual E.coli DNA Contamination of Biopharmaceutical Products
Dan Papa, Pedro J. Morales and Michael D. Sadick

Escherichia coli (E. coli) has been commonly used for the production of biopharmaceuticals. Among the impurities that must be monitored in biopharmaceuticals is residual host-cell DNA (HCD). This study describes the development and subsequent NDA-level validation of a real time PCR procedure developed in response to a client’s need to improve the sensitivity of detection and quantification of residual E. coli HCD in their drug product.

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Chemically Modified Primers for PCR and Ligation Applications
Elena Hidalgo Ashrafi, Sabrina Shore, Tony Le, Victor Timoshchuk, Natasha Paul, Richard Hogrefe, Inna Koukhareva, Alexandre Lebedev

PCR is an essential tool with utility in a variety of advanced applications. To improve the specificity of PCR, a unique approach to "Hot Start" PCR employing primers containing thermolabile modifications has been developed. These modified primers, named CleanAmp™ Primers, are amenable for use in Hot Start activation schemes as the modification is released after an initial denaturation step.

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Development of a Test Battery for Epigenetic Non-genotoxic Carcinogens
Haroon Rashid

The main objective of this sudy is to obtain an increased insight into the mechanisms of action of epigenetic carcinogens. Although the expected number of non-genotoxic carcinogens among newly registered compounds is unknown, there is a growing concern that when numbers of 2-year cancer bioassays are significantly reduced, non-genotoxic carcinogens may go undetected. Therefore there is a need for the development of alternative methods for their detection.

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Chemically Modified Primers for Improved Multiplex PCR
Elena Hidalgo Ashrafi, Tony Le, Alexandre Lebedev, Richard Hogrefe, Victor Timoshchuk, Sabrina Shore, Inna Koukhareva and Natasha Paul

Multiplex PCR is an advantageous technique used in PCR applications to amplify multiple targets in a single reaction. As useful as it is, this technique presents a new set of challenges that further complicates PCR setup. For example, reactions are more prone to off-target amplifications such as mis-priming and primer dimer due to the increased number of primer pairs.

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Hot Start dNTPs - Novel Chemistries for Use in Advanced PCR Applications
Tony Le, Elena Hidalgo Ashrafi, Sabrina Shore, Victor Timoshchuk, Natasha Paul, Richard Hogrefe, Inna Koukhareva, Alexandre Lebedev

PCR is a widely used scientific tool whose specificity can be increased by the use of Hot Start technologies. Although many Hot Start technologies exist, recently developed CleanAmp™ dNTPs are a distinct approach that employs modified nucleoside triphosphates with a thermolabile protecting group at the 3´-hydroxyl.

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ROLE OF IRF-8 IN THE INTERFACE OF MELANOMA TUMOR CELL-IMMUNE SYSTEM INTERACTION.
Fabrizio Mattei, Giovanna Schiavoni, Massimo Spada, Francesca Spadaro and Lucia Gabriele

Interferon-regulatory factor-8 is essential for differentiation and function of dendritic cells and thus for the induction of competent immune responses. Here, we investigated the role of IRF-8 in affecting immune response against melanoma. Our results reveal a critical role of IRF-8 in controlling melanoma growth and suggest that IRF-8-mediated antitumor activity is the result of a coordinated action between DC-mediated immune response and the tumor suppressor function of IRF-8.

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NEW TECHNOLOGIES FOR FFPE SAMPLES: Improved RNA Isolation and novel cDNA priming for qPCR and for universal mRNA amplification
G Krupp1; R Jaggi2; D Englert3, DJ Wilson3, S Laken3, S, ES Quabius4

Improved FFPE RNA isolation, novel TR priming for complete recovery of FFPE mRNA fragments. Differential expression defines Scores for tumor classification: comparing fresh-frozen with FFPE. Novel flow-through Ziplex microarray platform demonstrates MAQC performance level of data obtained with FFPE samples.

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Scientific News
Surprising Mechanism Behind Antibiotic-Resistant Bacteria Uncovered
Now, scientists at TSRI have discovered that the important human pathogen Staphylococcus aureus, develops resistance to this drug by “switching on” a previously uncharacterized set of genes.
Researchers Develop qPCR Prognosis Test for NSCLC Patients
A nine-gene molecular prognostic index (MPI) for patients with early-stage non-small cell lung cancer (NSCLC) was able to provide accurate survival stratification and could potentially inform the use of adjuvant therapy in patients struggling with the disease.
Genome Wide Annotation of Primary miRNAs Reveals Novel Mechanisms
Researchers have devised a strategy for genome-wide annotation of primary miRNA transcripts, providing extensive new annotations in human and mouse, and shedding light on mechanisms of regulation of microRNA gene expression.
‘Fishing Expedition’ Nets Nearly Tenfold Increase in Number of Sequenced Virus Genomes
Newly developed computational tool finds 12,500 genomes of viruses that infect microbes.
First Gene that Causes Mitral Valve Prolapse Identified
An international research collaboration led by MGH investigators has identified the first gene in which mutations cause the common form of mitral valve prolapse, a heart valve disorder that affects almost 2.5 percent of the population.
Automation Abound at AACC in Atlanta
Discover the latest breakthroughs, trends and products from the AACC Annual Meeting & Clinical Lab Expo.
Ultrafast DNA Diagnostics
New technology developed by UC Berkeley bioengineers promises to make a workhorse lab tool cheaper, more portable and many times faster by accelerating the heating and cooling of genetic samples with the switch of a light.
The Genetic Roots of Adolescent Scoliosis
Scientists at the RIKEN Center for Integrative Medical Sciences in collaboration with Keio University in Japan have discovered a gene that is linked to susceptibility of Scoliosis.
Diagnostic Test Developed for Enterovirus D68
researchers at Washington University School of Medicine in St. Louis have developed a diagnostic test to quickly detect enterovirus D68 (EV-D68), a respiratory virus that caused unusually severe illness in children last year.
Simple Technology Makes CRISPR Gene Editing Cheaper
University of California, Berkeley, researchers have discovered a much cheaper and easier way to target a hot new gene editing tool, CRISPR-Cas9, to cut or label DNA.
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