Do you want to build a snowman? Developing and optimizing a qPCR assay to detect ice-nucleating activity

Snowflakes---MA-400x600Over the last few months we have published several blogs about qPCR—from basic pointers on avoiding contamination in these sensitive reactions to a collection of tips for successful qPCR. Today we look in depth at a paper that describes the design and and optimization of a qPCR assay, and in keeping with the season of winter in the Northern hemisphere, it is only fitting that the assay tests for the abundance and identity of ice-nucleating bacteria.

Ice-nucleating bacteria are gram-negative bacteria that occur in the environment and are able to “catalyze” the formation ice crystals at warmer temperatures because of the expression of specific, ice-nucleating proteins on their outer membrane. Ice-nucleating bacteria are found in abundance on crop plants, especially grains, and are estimated to cause one-billion dollars in crop damage from frost in the United States alone.

In addition to their abundance on crop plants, ice-nucleating bacteria are also found on natural vegetation and have been isolated from soil, snow, hail, cloud water, in the air above crops under dry conditions and during rain fall. They have even been isolated from soil, seedlings and snow in remote locations in Antarctica. For the bacteria, ice nucleation may be a method to promote dissemination through rain and snow.

Although ice-nucleating bacteria have been isolated from clouds, ice and rain, little is known about their true contribution to precipitation or other events such as glaciation. Are such bacteria the only source of warm-temperature (above temperatures at which ice crystals form without a catalyst) ice nucleation? Can they trigger precipitation directly? What are the factors that trigger their release from vegetation into the atmosphere? Can we determine their abundance and variety in the environment? Continue reading “Do you want to build a snowman? Developing and optimizing a qPCR assay to detect ice-nucleating activity”

Methods for Quantitating Your Nucleic Acid Sample

Nucleic acid quanitation webinarFor most molecular biology applications, knowing the amount of nucleic acid present in your purified sample is important. However, one quantitation method might serve better than another, depending on your situation, or you may need to weigh the benefits of a second method to assess the information from the first. Our webinar “To NanoDrop® or Not to NanoDrop®: Choosing the Most Appropriate Method for Nucleic Acid Quantitation” given by Doug Wieczorek, one of our Applications Scientists, discussed three methods for quantitating nucleic acid and outlined their strengths and weaknesses. Continue reading “Methods for Quantitating Your Nucleic Acid Sample”

DNA Purification, Quantitation and Analysis Explained

WebinarsYesterday I listened in on the Webinar “Getting the Most Out of Your DNA Analysis from Purification to Downstream Assays”, presented by Eric Vincent–a Product Manager in the Promega Genomics group.

This is the webinar for you if you have ever wondered about the relative advantages and disadvantages of the many methods available for DNA purification, quantitation and analysis, or if you are comparing options for low- to high-throughput DNA purification. Eric presents a clear analyses of each of the steps in a basic DNA workflow: Purification, Quantitation, Quality Determination, and Downstream Analysis, providing key considerations and detailing the potential limitations of the methods commonly used at each step.

The DNA purification method chosen has an affect on the quality and integrity of the DNA isolated, and can therefore affect performance in downstream assays. Accuracy of quantitation also affects success, and the various downstream assays themselves (such as end-point PCR, qPCR, and sequencing) each have different sensitivities to factors such as DNA yield, quality, and integrity, and the presence of inhibitors. Continue reading “DNA Purification, Quantitation and Analysis Explained”

How to Choose a Good Reference Gene?

A Researcher’s work is never easy but it is even harder when relative data are to be interpreted. This is especially true for Real-Time PCR. It is one of the most accurate ways to evaluate gene expression. However, despite it being such a powerful technique, it still carries many pitfalls which can lead a scientist to the wrong conclusion. Often a new user does not have thorough sample/RNA preparation, equipment or knowledge. So what are the considerations and aspects that the researcher should pay attention to? Continue reading “How to Choose a Good Reference Gene?”

Nanoparticles – Workhorses That Bring Tremendous Benefit

Tiny particles found in clothing, cosmetics, food, electronics or furniture enter our bodies and behave in unexpected (sometimes unwanted) ways. However, in the realm of medicine another type of particle called the nanoparticle can bring untold potential. We can load them with drugs, for example, and deliver them precisely to a diseased organ or cell. Mark Davis from the California Institute of Technology has created nanoparticles that deliver siRNA specifically into melanomas. Davis and his colleagues have not shied away from making bold claims about the therapeutic potential of their work.  They write:

“When taken together, the data presented here provide the first, to our knowledge, mechanistic evidence of RNAi in a human from an administered siRNA. Moreover, these data demonstrate the first example of dose-dependent accumulation of targeted nanoparticles in human tumours. ….These data demonstrate that RNAi can occur in a human from a systemically delivered siRNA, and that siRNA can be used as a gene-specific therapeutic.” Davis et al. 2010. Continue reading “Nanoparticles – Workhorses That Bring Tremendous Benefit”

PCR Protocols for Android

Over the years we have produced several articles and technical resources on PCR. One of the most widely used is a chapter on PCR in the Protocols and Applications guide, featuring an explanation of the techniques involved, tips for reaction optimization, and example protocols for routine PCR, qPCR and RT-PCR. The protocols and applications guide is part of the Promega App, available on the web site, and as an iPhone/iPad and Android App.

Recently, we released an update to the Android app that includes customizable PCR protocols. Right now, three protocols are available in this format (Basic PCR, Hot-Start PCR and qPCR). These custom protocols allow you to input specific values for your experiment, such as concentration of stock solutions, desired number of reactions, etc. These values are used to calculate the volumes required at each step in the procedure, and a customized protocol is generated with the volumes of each reagent calculated and incorporated. Once generated, protocols can be saved for re-use, or emailed to an account for subsequent printing or incorporation into a lab notebook. Continue reading “PCR Protocols for Android”