Andrew Porterfield's Profile

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Don’t Get Lost in RNA-seq Translation: RNA Sequencing the NGS Way

DNA sequencing (PCR, Sanger or next-generation sequencing (NGS)) is a now familiar part of any molecular biology lab. But ‘RNA-seq’, the so-called “Cinderella of genetics”, is now becoming the belle of the ball, providing new insights into this most central molecule of the ‘central dogma’.  The many flavors of RNA Whilst genomic DNA is the […]

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In Genomics & Epigenetics 27th of March, 2014
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Benchside Matchmaking—Finding the Right Buffer for Your Experiment

Buffers are often taken for granted, but they can make or break an experiment.  In previous posts, we’ve talked about the wide ranges of buffers available for biological research and the characteristics of a “Good” buffer. Organic buffers are not inert! They can interact with your experimental molecule, or change pH due to changes in […]

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In Chemistry for Biologists 24th of March, 2014
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What Makes a “Good” Laboratory Buffer?

Just about any molecular biology experiment will involve the action of enzymes or other active proteins. And when enzymes are involved, the pH of your experimental environment is going to change. This is because most enzymatic reactions involve the loss or gain of hydrogen ions (protons), which modifies the pH of the environment. Biological systems […]

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In Basic Lab Skills & Know-how 22nd of January, 2014
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The Irish Potato Famine: NGS Unearths The Fungus Responsible For Over 1 Million Deaths

The Irish Famine (or ‘Great Potato Famine’ if you live outside the Emerald Isle) killed one million people and forced another million to leave the country between 1845 and 1852. It was caused by a blight on the country’s main food stock- the Irish ‘Lumper’ potato. Now, researchers have identified the genome of the blight […]

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In Genomics & Epigenetics 7th of November, 2013
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Keeping up With the Periodic Table

The periodic table, that ingeniously arranged display of atomic weights, numbers and elements that’s probably posted on a door way in the back of your lab, isn’t a static document. It’s changed a fair amount in its lifetime, largely as weights are refined and new elements added. However in 2011, the International Union of Pure […]

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In History of Biology 16th of October, 2013
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What’s in a Number: Getting the Right Passage in Cell Culture

Getting the Right Passage Number Using an American Type Culture Collection (ATCC) reference strain for every experiment would be great, but not all that practical. So, most labs subculture their cells into a new vessel. This subculture is also known as a “passage.” A passage number is the number of times a cell culture has […]

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Neigh need for NGS for meat testing- in the mane, PCR is enough!

Horsemeat testing is continuing to show that contamination, while lower than when first reported, is still not, well, stable! There’s been horse meat around for donkey’s years..! The UK Food Standards Agency (FSA) showed at the end of March that it’s testing found 352 samples out of 362 contained less than 1% horsemeat. Of the […]

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In Genomics & Epigenetics 28th of March, 2013
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Sifting Detritus—Extracting DNA and RNA Samples from Soil and Feces

The value of PCR to forensics has been known for a long time; but now, getting purified DNA and RNA samples from soil and fecal samples is becoming more important and commonplace as tests for environmental impacts, disease spread, and even biomarkers for colon cancer become more prevalent. And if you thought getting nucleic acids […]

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Big Foot In Mouth Or Tongue In Cheek?! Sasquatch Sequenced.

“Bigfoot is real, according to genetic analysis.” That bold statement appears on the website of a new journal, the sole paper in which presents what it claims is a mitochondrial DNA match and gene sequence of the (still-mythical) creature Sasquatch, or Bigfoot. Taking samples from Sasquatch Melba Ketchum, a veterinarian who runs a DNA testing […]

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In Genomics & Epigenetics 28th of February, 2013
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I Know Who You Are: Using ‘Private’ DNA Sequences To Identify People

Searching for ancestors online is a popular activity. So is having your DNA sequenced. But merging the two has created a problem; it’s very, very easy to use genealogy software and DNA sequence data to identify people who are supposed to be anonymous. A spanner in the works This means all sorts of data, like […]

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In Genomics & Epigenetics 14th of February, 2013