Optimizing PCR: One Scientist’s Not So Fond Memories

primer_tubesThe first time I performed PCR was in 1992. I was finishing my Bachelors in Genetics and had an independent study project in a population genetics laboratory. My task was to try using a new technique, RAPD PCR, to distinguish clonal populations of the sea anemone, Metridium senile. These creatures can reproduce both sexually and asexually, which can make population genetics studies challenging. My professor was looking for a relatively simple method to identify individuals who were genetically identical (i.e., potential clones).

PCR was still in its infancy. No one in my lab had ever tried it before, and the department had one thermal cycler, which was located in a building across the street. We had a paper describing RAPD PCR for population work, so we ordered primers and Taq DNA polymerase and set about grinding up bits of frozen sea anemone to isolate the DNA. [The grinding process had to be done using a mortar and pestle seated in a bath of liquid nitrogen because the tissue had to remain frozen. If it thawed it became a disgusting mass of goo that was useless—but that is a topic for a different blog.] Since I had never done any of the procedures before, my professor and I assembled the first set of reactions together. When we ran our results on a gel, we had all sorts of bands—just what he was hoping to see. Unfortunately, we realized that we had added 10X more Taq DNA polymerase than we should have used. I repeated the amplification with the correct amount of Taq polymerase, and I saw nothing. Continue reading “Optimizing PCR: One Scientist’s Not So Fond Memories”

Selecting the Right Colony: The Answer is There in Blue and White

cloning2Ah, the wonders and frustrations of cloning. We’ve all been there. After careful planning, you have created the cloned plasmid containing your DNA sequence of interest, transformed it into bacterial cells and carefully spread those cells on a plate to grow. Now you stand at your bench gazing down at your master piece: a plate full of tiny bacterial colonies. Somewhere inside those cells is your DNA sequence, happily replicating with its plasmid host. But wait – logic tells you that not ALL of those colonies can contain your plasmid.  There must be hundreds of colonies. Which ones have your plasmid? You begin to panic. Visions of yourself old and grey and still screening colonies flash through your mind. At the next bench, your lab-mate is cheerfully selecting colonies to screen. Although there are hundreds of colonies on her plate as well, some are white and some are blue. She is only picking the white colonies. What does she know that you don’t? Continue reading “Selecting the Right Colony: The Answer is There in Blue and White”

For the Birds: Knitting Nests for Baby Birds Might Just Help Your Health To

It seems that spring has finally come to Southern Wisconsin. The snow has melted. Most days it is warm enough you can go outside without a parka, hat and mittens. The tree buds are starting to swell. And that traditional oracle of spring, the American robin (Turdus migratorius), has been spotted in trees and yards—along with its less friendly cousin, the red winged black bird (Agelaius phoeniceus).

While spring brings the return of migratory birds, it also brings an increase in the number of rescued baby birds flooding into local wildlife rescues and humane societies. When the babies come to these centers, they need a warm, soft, breathable and washable home that resembles the nest they were hatched in.

It turns out that knitted or crocheted nests are a perfect solution. The nests aren’t just used for baby birds; baby rabbits, squirrels, bats, ferrets and racoons are just a few additional animals that benefit. And the best part is, you could be improving your own health while you create those cozy nests. Continue reading “For the Birds: Knitting Nests for Baby Birds Might Just Help Your Health To”

Over 50 million Died in the Pandemic of 1918-A Century Later We are still Searching for a Universal Flu Vaccine

One hundred years ago, the world was taking its first deep breaths as it celebrated the end of World War I. The Armistice of Compiègne, was signed on November 11,1918, officially ending the four-year long conflict, which claimed the lives of more than 8 million soldiers (1). What the world didn’t yet realize was that they had been battling a far deadlier enemy in the hospitals and at home than any army the soldiers faced on the fields of war.

During the last year of the war, a deadly influenza virus rampaged around the globe leaving between 50 and 100 million dead in its wake.

Influenza Ward, France 1918. 


The boys were coming in with colds and a headache and they were dead within two or three days. Great big handsome fellows, healthy men, just came in and died. There was no rejoicing in Lille the night of the Armistice.
Sister Catherine Macfie from her post at casualty clearing station no. 11 at St André near Lille, France (2).

Continue reading “Over 50 million Died in the Pandemic of 1918-A Century Later We are still Searching for a Universal Flu Vaccine”

Learning New Things About mtDNA Inheritance from a Four-Year-Old Boy and a Tenacious Team of Scientists

We inherit our cells’ mitochondria from our mother. These energy-producing organelles are present in large numbers in most cells, meaning that cells can contain thousands of copies of the DNA associated with the mitochondria (mtDNA)—all passed on wholly from our mother. New evidence suggests, however, that this cannon principle of maternal-only inheritance of mtDNA might need to be refined. And it all started with a four-year-old boy.

Continue reading “Learning New Things About mtDNA Inheritance from a Four-Year-Old Boy and a Tenacious Team of Scientists”

The Five Steps to miRNA Profiling

MicroRNAs (miRNAs) are small, non-coding RNAs that play a role in regulating cancer by acting as both tumor suppressors and oncogenes. Ranging in size from 18–25 nucleotides, miRNAs function in feedback mechanisms to regulate many cellular processes including cell proliferation, apoptosis, cell signaling and tumorigenesis (1).

Not surprisingly, dysregulation of miRNA expression can have serious repercussions. For example, miRNAs are dysregulated in almost all human cancers (1). Because of the potential to influence cancer growth and development, there is growing interest in miRNA profiling to identify possible biomarkers for cancer diagnosis or prognosis, as well as potential therapeutic targets (1).

Growing interest in miRNAs as both biomarkers of disease and therapeutic targets drives the need for fast and effective methods for miRNA profiling. Profiling miRNA targets follows a relatively simple workflow: sample selection, RNA extraction, RNA QC and quantitation, RNA profiling and data analysis (2,3). So what happens at each step?

Five steps of miRNA profiling
The Five Steps of miRNA Profiling

Continue reading “The Five Steps to miRNA Profiling”

Fished to the Edge: How DNA Identification Can Help Fight the Illegal Trade of Threatened Shark Species

Whether your first encounter was peering through the thick glass of an aquarium tank or peeking through your fingers in a darkened theater, there is something about sharks that captures our imagination. These fierce, and sometimes fearsome, creatures have existed in our oceans for over 400 million years, and  survived multiple mass extinction events, including the one that killed the dinosaurs. They are not, however, the vicious, vengeful villain that some movies would have us believe. Sharks are apex predators, who play an important role in the world’s ocean ecosystem by regulating the population of prey species below them.  Unfortunately, they are also part of one of the most threatened group of marine fish in the world. Of the more than 400 species of sharks that exist in our oceans today, approximately 15% are considered vulnerable, endangered or critically endangered. Continue reading “Fished to the Edge: How DNA Identification Can Help Fight the Illegal Trade of Threatened Shark Species”

Beneath the Writing: Non-Invasive DNA Sampling from Modern and Historic Writing Surfaces

We can learn a lot about the past and its people from the written records of the time. What people write and how they write it can gives us glimpses into historical events, interpersonal relationships, social standing and even social and cultural norms. From paper to papyrus to clay tablets, the surface that holds the writing can tell us things that the words cannot.

For plant-based writing surfaces, the quality of the surface or even the technique used to make it can give historians and archeologists insight into the people who used them. What more could we learn if we knew what plant, or plants, were used in the production of ancient writing material? Continue reading “Beneath the Writing: Non-Invasive DNA Sampling from Modern and Historic Writing Surfaces”

From Dating Apps to In Vitro Fertilization, the Challenges to Saving the Endangered Northern White Rhino

In April of 2017 a profile appeared on the dating app Tinder. Describing himself as “One of a kind”, the poster was 43 years old, not in great physical shape, and yet so sought after he required around the clock body guards. His name was Sudan, and he was the last living male northern white rhino. His keepers at the Ol Pejeta Conservancy in Kenya weren’t expecting Sudan to find love. They were hoping to raise awareness of the species’ dire situation and money for the research and development of an in vitro fertilization (IVF) method for rhinos.

Northern white rhino
With only two remaining, can we save the northern white rhino? © Matt Caldwell / 123RF Stock Photo.

Northern white rhinos used to range over all or parts of Uganda, Sudan, Chad, the Democratic Republic of the Congo and the Central African Republic. In the 1960s there were an estimated 2,360 northern white rhinos left in the wild (1). Civil unrest in the region made conservation difficult, and by 2003 poaching and other pressures had reduced the number of northern white rhinos living in the wild to four individuals living in the Garamba National Park in the Democratic Republic of the Congo. There has been no sign of that wild population since 2007 (2), and they are considered extinct in the wild as of 2008. Continue reading “From Dating Apps to In Vitro Fertilization, the Challenges to Saving the Endangered Northern White Rhino”

The Amazing, Indestructible—and Cuddly—Tardigrade

Everyone has their favorite microscopic creature—you all do have a favorite, right? Mine is unquestionably the tardigrade. Tardigrades, also called water bears or moss piglets, are microscopic invertebrates that are composed of five segments: one head segment and four body segments, each with a pair of legs. They are 0.1–1.2mm in length, making them easy to see under low magnification, and have a brain and well-developed nervous system. Tardigrades are found in just about every environment on earth. Termed “extremophiles”, they have adapted to survive in even extremely harsh environments. Your neighborhood pond? The Himalayas? Antarctica? Deep sea? Tardigrades live in all those places.

Although many of us fell in love with these microscopic animals the first time we saw them—because there is no denying that they are darn cute— there are other good reasons why scientists are so fascinated by these creatures. Tardigrades are incredibly resilient. And by resilient, I mean almost indestructible. Continue reading “The Amazing, Indestructible—and Cuddly—Tardigrade”