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Andrew Porterfield

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 Andrew Porterfield:

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 and Epigenetics

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 and 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 and 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

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 and 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 and 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 and 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 and 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 and 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 and 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 and 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 and 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 and Epigenetics

Do Bad Genes Beget Disease? Hey, Not So Fast!

The purpose of genetic testing is to find altered genes that could cause disease. Consequently, people could be treated, or prospective parents can make decisions about having children. However, scientists are finding that having a gene which causes disease doesn’t necessarily cause that disease! We are all mutants Researchers at Cambridge and Cardiff universities found that a…

07 Feb 2013 Genomics and Epigenetics

Do Your Homework to Find Good Reference Genes

Comparing and measuring gene expression is certainly an integral part of research—gene expression patterns continue to show us how different cell networks are regulated, and point to new biological pathways and possible treatments for disease. But one crucial part of gene expression lies in making sure that differences in gene expression are due to gene…

28 Jan 2013 PCR, qPCR and qRT-PCR

We Learn a Wee Bit More about Proteins—from Wii

About thirteen years ago, a group of science journalists gathered in a darkened lab at Rice University in Houston, Texas. The lights went off, and the participants took turns donning a clunky helmet with darkened visor. By moving the right thumb, each helmet-wearing reporter suddenly was whisked down the middle of protein ribbon, twisted through…

19 Dec 2012 Fun Stuff

NHS uses NGS to combat MRSA!

Methicillin-resistant Staphylococcus aureus (MRSA) persistently plagues hospitals worldwide. Until now, hospital (or healthcare) MRSA (HA-MRSA) was of a different lineage from MRSA found in the community. Since HA-MRSA could not survive in a non-hospital setting, this made things rather convenient. Testing for HA-MRSA was routine and the isolates, in particular one called ST22, could easily…

22 Nov 2012 Genomics and Epigenetics

Who Found the First Plasmid?

Plasmids—the loops of DNA in bacteria that form the original foundation of biotechnology—were being discovered constantly in the 1940s and 1950s. The only problem was, they were called everything but. Series of scientists found bacteriophages and other strange loops of somatic DNA, and gave them a series of names, including: pangenes, bioblasts, plasmagenes, plastogenes, choncriogenes,…

09 Nov 2012 DNA / RNA Manipulation and Analysis

Genomes on cell phones- there’s no app for that…yet!

A long, long time ago- before the human genome sequence was announced, a cancer specialist friend wrote a whimsical essay in a university newsletter. He predicted that future patients would drive to a clinical data center, plug a flash drive into a computer and have their genomes scanned for current and potential disease. The reaction…

08 Nov 2012 Genomics and Epigenetics

You’re Closer to the Clinic Than You Think: NGS and Clinical Trials

A decade or so ago, the phrase ‘translational research’ began making its rounds through laboratories- it was supposed to take molecular biology results and apply them directly to patients. It brought about things like gene therapy, stem cell therapy, and so forth. You get the idea- valuable research, but not immediately injectable. Valuable and cheap…

18 Oct 2012 Genomics and Epigenetics

Book Review: Flatland, by Edwin A. Abbott

Finishing Flatland, a novella published by British mathematician and teacher Edwin Abbott a good 20 years before Einstein’s General Theory of Relativity and the growth of quantum mechanics, leaves the reader wondering what Abbott could possibly have known about these later figures and events. But the book’s very existence underscores just how fundamental those 20th…

10 Sep 2012 Inspiring and Thought Provoking

How the Ion Torrent Sequencer works

Just before Life Technologies purchased the start-up company Ion Torrent, the fledgling company was dealing with a torrent of another kind—worldwide media interest in its new sequencing technology, which promised to bring the price of next-generation, massively parallel sequencing down to $1,000 per run. Since that dramatic announcement in the summer of 2011, Life Technologies…

06 Sep 2012 Genomics and Epigenetics

How to Save Our Science—a Case Study

Mentioning the abbreviation “GMO” yields one of two reactions: fascination with the biotechnology of creating food and other organisms that thrive despite pests or bad weather, or horror at the idea of creating an unknown, dangerous monster in the laboratory. Rothamsted Research, in Harpenden, England, was yet another biotechnology lab faced with the latter reaction…

27 Aug 2012 Inspiring and Thought Provoking

This Is Your Brain On NGS

Neuroscience presents unique genetics challenges. Genetics of the brain means studying an enormous number of mutations. In addition, many loci encode proteins that interact with each other, so a mutation that affects one protein could, in fact, affect the function of other proteins in a given pathway, even if the other proteins are not mutated.…

23 Aug 2012 Genomics and Epigenetics

How Pure is Your Cell Culture Broth? Comparing Mycoplasma Detection Kits

Mycoplasmas are the most difficult-to-detect organisms in your eukaryotic cell culture. And they can be the most dangerous; they can disrupt cell growth and differentiation and even apoptotic patterns without you even knowing what’s going on until it’s too late. Traditional cell culture methods can take up to a month to yield results, which means…

01 Aug 2012 Cells and Model Organisms

What’s THAT Doing in My Culture?

A young laboratory technician was puzzled by his plates when he pulled them out of the warm room. They never looked that cloudy and fuzzy before. He brought them to his lab director, who shook her head sadly; together, they threw the plates away. Does this story sound familiar? What probably happened was an all-too…

28 May 2012 Cells and Model Organisms

The Invisible Horde: Attacking Mycoplasma Infections

Mycoplasma infections are very, very bad news; these special prokaryotes can rapidly spread through your cell culture and inhibit cell proliferation, induce apoptosis, cytokines and radicals, and otherwise transform your cells. Worst of all, since contamination is not easy to spot, you may not realize your culture is contaminated until it’s too late. The 100…

21 May 2012 Cells and Model Organisms

How Do Buffers Work?

A former colleague and friend of mine worked in technical support, taking calls from scientists. Most of the calls came from life science researchers frustrated by failed experiments. My friend would listen for a bit, then almost always exclaim in very charming but booming Russian-accented English, “No! You must add buffer to the experiment! It…

16 Apr 2012 Basic Lab Skills and Know-how

What Memories Are Made Of

It’s not even noon and you’ve already misplaced your car keys, snuck a peak at the molarity conversion figures you wrote on a sticky note on your lab bench, and reminded yourself to button your lab coat before working under the hood. All of these activities are the work of memory, and each of them…

09 Mar 2012 Inspiring and Thought Provoking

The Secrets of Thermophile Survival: Part I

In response to my last article, The Taq behind PCR, one of our readers, Bonnie Barrilleaux, asked whether DNA could naturally survive at temperatures that would denature it. It also begged the question; how do proteins stay intact and functioning at these high (55°C and up) temperatures? It turns out, cells do a lot of…

13 Jul 2009 PCR, qPCR and qRT-PCR

The Taq behind PCR

Nobel Laureate Kary Mullis is generally credited with inventing the polymerase chain reaction, but his discovery owes a lot to a microbiologist who loved to travel, some refuted assumptions of what can live in hot springs, and a now-closed field station in Yellowstone National Park. Here’s the story. In the 1960s, Thomas Brock was a…

10 Jun 2009 PCR, qPCR and qRT-PCR
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