AMPorterfield

I'm a writer, editor, and communications consultant, specializing in biotech, life sciences and healthcare. I've worked for the Salk Institute, Life Technologies, Amgen, Pfizer, academic institutions, startups, non-profits and consulting firms. I've got a BA from the University of Pennsylvania, and a MS in biotech management from the University of Maryland.

Articles by AMPorterfield:

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…

30 Aug 2016 Genomics & Epigenetics

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…

09 Jul 2016 DNA / RNA Manipulation and Analysis&History of Biology

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…

09 Jul 2016 Basic Lab Skills & Know-how

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…

09 Jul 2016 PCR, qPCR and qRT-PCR

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).…

09 Jul 2016 Genomics & Epigenetics

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…

16 Jul 2015 PCR, qPCR and qRT-PCR

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…

15 May 2015 Genomics & Epigenetics

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…

07 Jan 2015 Basic Lab Skills & Know-how

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,…

23 Jul 2014 Software & Online Tools

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…

30 Apr 2014 Of Interest

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…

27 Mar 2014 Genomics & Epigenetics

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…

24 Mar 2014 Chemistry for Biologists

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…

22 Jan 2014 Basic Lab Skills & Know-how

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…

07 Nov 2013 Genomics & Epigenetics

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…

16 Oct 2013 History of Biology

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…

01 May 2013 Cells and Model Organisms

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…

28 Mar 2013 Genomics & Epigenetics

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…

26 Mar 2013 DNA / RNA Manipulation and Analysis

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…

28 Feb 2013 Genomics & Epigenetics

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…

14 Feb 2013 Genomics & Epigenetics