Andrew Porterfield's Profile

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The Ins & Outs of Illumina Sequencing

The future of personalized medicine depends on affordable DNA sequencing. In the race for the $1,000 genome, several sequencer manufacturers are working on making equipment that can sequence DNA and RNA faster and more accurately. But so far, only one company – San Diego, California-based Illumina – has US FDA regulatory approval to use its […]

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In Genomics & Epigenetics 30th of August, 2016
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Southern (blot) exposure remains a useful technique

At a meeting recently, I asked two PhD molecular biologists about the last time they used a Southern blot. After nearly a minute of unrestrained laughter, they asked “Who on earth still does that?” “Maybe for a very, very specific use,” conjectured one of the scientists. When I asked the scientist who taught me the […]

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How Thermophilic Bacteria Survive, Part II: DNA

In part I, I answered the question, “How do proteins in thermophiles survive under high temperatures?” In this part, I’ll look look at how nucleic acids survive -thrive, even- in conditions that are too hot for most of us, but ideal for a number of organisms, including the one that gave us Taq polymerase and […]

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In PCR, qPCR and qRT-PCR 9th of July, 2016
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Catalyzing Through Confusion: Making (Some) Sense of Enzyme Units

On the surface, it would seem easy enough to pick an enzyme (or an amount of enzyme) for an experiment. Just look at the concentration on the label, adjust accordingly, and you’re on your way. Alas, not with enzymes. The number of units used to measure enzymes is dizzying. However, it’s better now than it […]

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All in the Chip: Ion Torrent Sequencers

Ion Torrent technology, when it was introduced in 2010, was one of several machines that promised to revolutionize genetics. These were benchtop machines that showed their prowess in quickly sequencing smaller exomes and other DNA samples (about 10-20 million bases per run, compared to Illumina HiSeq, which could read 250 billion bases in a run). […]

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In Genomics & Epigenetics 9th of July, 2016
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What Is a Ct Value?

When conducting real-time PCR, you’re looking for the exact amount of a target sequence or gene in your sample. During the PCR reaction, you measure its progress by accumulation of a fluorescent signal during amplification. But there’s also a lot of background fluorescence, which you want to bypass in order to glean meaningful information from […]

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In PCR, qPCR and qRT-PCR 16th of July, 2015
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A Guide to Genetic Variants

Perhaps one of the most significant discoveries in modern genetics (after the genetic code was laid out, anyway) is the role of genetic variations in evolution, disease and the creation of plants and animals. While the Human Genome Project (and a lot of other genome projects, for that matter) showed how many genes living things […]

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In Genomics & Epigenetics 15th of May, 2015
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A Quick Guide to pH, pKa and pI

They’re easy numbers to take for granted, so it’s a good exercise once in a while to remind ourselves what pH, pKa and pI stand for: pH—the measure of acidity. It’s the negative logarithm of the proton concentration. pKa—an association constant. It’s the negative logarithm of the ratio of dissociated acid and conjugated base, over […]

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In Basic Lab Skills & Know-how 7th of January, 2015
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How Does BLAST Work?

More than a pun on the explosive growth of sequencing data, BLAST makes annotation and comparisons of similar sequences much easier. Created by a group at the U.S. National Center for Biotechnology Information in 1991, the Basic Local Alignment Search Tool is arguably the most heavily used tool for sequence analysis (that’s available for free, […]

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In Software & Online Tools 23rd of July, 2014
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Ready to commercialise your research? Bioincubators are worth considering

Finding adequate sources of funding is the primary challenge of just about any startup company, and biotechnology is no different. In fact, the regulatory, scientific and logistical requirements of making a new drug or device could easily be the most challenging of any industry. In addition, the global recession of 2007-2009 (combined with austerity measures […]

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In Of Interest 30th of April, 2014