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Target length effect on sensitivity and specificity of oligonucleotide microarrays: Advantages of a modified PCR based labelling method over the dendrimer technology.
Abdullah Gibriel1*, Walter Kolch2 and Andrew Pitt1,3

Several methods have been developed for target labelling to enable DNA microarray quantification without taking careful consideration for target length effect. This report highlights the importance of choosing the optimum target length that would ensure specificity without compromising sensitivity of the assay. It also shows the advantages of using the modified PCR method over other methods in generating labelled amplicons of the desired lengths to maximize hybridization efficiency.

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On chip micro-extraction and real-time PCR with integrated SPAD optical fluorescence detection for nucleic acid analysis
Cristina Potrich, Elisa Morganti, Nicola Massari, Lucio Pancher, C. Kostoulas, Laura Pasquardini, Cristian Collini, Andrea Adami, Lorenzo Lunelli, F. Kalatzis, David Stoppa, Cecilia Pederzolli, Leandro Lorenzelli

A PDMS lab-on-a-chip for one step DNA isolation and real time-polymerase chain reaction (RT-PCR) has been designed, fabricated, and characterized for point-of-care clinical diagnostics. In addition, a module for on-chip optical detection based on SPAD - Single-Photon Avalanche Diode - detector has also been developed and used to monitor the presence of specific DNA polymorphisms possibly related to genetic diseases.

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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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Scientific News
Top 10 Life Science Innovations of 2016
2016 has seen the release of some truly innovative products. To help you digest these developments, The Scientist have listed their top picks for the year.
Using Cancer Cells' Mass to Predict Treatment Response
A device has been developed that can detect changes in cell mass at a minute scale.
NVIDIA Awards $400k to Trailblazers in Cancer Research
NVIDIA Foundation furthers research that could lead to new and more targeted treatments with investments.
Malaria Parasite Evades Rapid Test Detection in Children
A study at the University of North Carolina found that gene deletion poses a threat to Malaria eradication efforts.
Working With Advanced Nanoimagers
Oxford Nanoimaging report on the work of early-adopters for their Nanoimager technology at the MRC Centre for Molecular Bacteriology and Infection.
History of Cells Told Through MEMOIR
MEMOIR technique developed by CalTech researchers enables the life history of cells to be read.
Nanoscale ‘Muscles’ Powered by DNA
Scientists have developed nanoscale "muscles" to integrate with custom DNA, that can force the material to bend, curl and flip.
Dissecting Bacterial Infections at the Single-Cell Level
Researchers have used single-cell analysis technology to provide new insight into the Salmonella infection process.
Peer Review is in Crisis, But Should be Fixed, Not Abolished
After the time to get the science done, peer review has become the slowest step in the process of sharing studies, and some scientists have had enough.
Cancer Stem Cells Fuel Tumor Growth
Mass. General, Broad Institute team finds strong evidence that cancer stem cells are important drivers of tumors in patients.
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