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Chemical Variant of 7-deaza-dGTP for Improved CG-rich PCR Amplification
E. H. Ashrafi, S. Shore, T. Le, V. Timoshchuk, N. Paul, R. Hogrefe, G. Zon, I. Koukhareva, A. Lebedev

PCR amplification of nucleic acids is a fundamental technique used in many molecular biology laboratories. Despite its wide use, certain GC-rich regions of DNA, such as mycobacterial disease targets, still remain a challenge for amplification. Sequences high in GC content are associated with the formation of secondary structure, which prevents adequate strand separation and DNA polymerase amplification. As a consequence, mispriming is prominent, complicating specific product formation.

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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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Scientific News
Monovar Drills Down Into Cancer Genome
Rice, MD Anderson develop program to ID mutations in single cancer cells.
Biomarkers for Profiling Prostate Cancer Patients
Exiqon A/S has announced the publication of validation of prognostic microRNA biomarkers for the aggressiveness of prostate cancer in independent cohorts.
Gene Analysis System Could Accelerate Pace of Research on the Space Station
The WetLab-2 system will enable spaceflight genomic studies involving a wide variety of biospecimen types in the unique microgravity environment of space.
Liquid Biopsy for NSCLC
'Liquid biopsy' blood test accurately detects key genetic mutations in most common form of lung cancer, study finds.
Rare DNA Will Have Nowhere To Hide
Two National Institutes of Health grants back Rice University effort to develop new diagnostics.
Seeing Cell to Cell Differences
Seeing differences between individual cells for first time explains symptoms of rare genetic disorders, finds penn study.
Circular RNAs Implicated in Cancer
Circular RNAs – like their protein counterparts – are also affected by genomic rearrangements in cancer, resulting in abnormal fusions.
Know Thy Helicobacter pylori
Non-invasive method for genotyping H.pylori developed.
Zika Test Authorized for Emergency Use
n response to a request from the CDC, the FDA has issued an Emergency Use Authorization (EUA) for a diagnostic tool for Zika virus that will be distributed to qualified laboratories.
Lighting Up Disease-Carrying Mosquitoes
Sandia’s QUASR enables speedy, accurate detection of West Nile and other viruses.
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