Working with RNA doesn’t have to be a nightmare

We’re all familiar with the Central Dogma of Molecular Biology: DNA is transcribed into RNA, which is translated into proteins. It’s drilled into our heads from the early days of biology classes, and it’s surprisingly useful when we start exploring in our own research projects. For example, if you’re interested in gene expression, you’ll most likely be working with RNA, specifically mRNA. Messenger RNA (mRNA) is transcribed from DNA and is used by ribosomes as a “template” for a specific protein. The total mRNA in a cell represents all of the genes that are actively being transcribed. So, if you want to know whether or not a gene is being transcribed, RNA purification is a great place to start.

When preparing your RNA samples for a downstream assay, there are several roadblocks and pitfalls that could give you quite a headache. Let’s tackle two of the most common.

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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”

High-Throughput Purification with Experts Included

Implementing automated nucleic acid purification or making changes to your high-throughput (HT) workflow can be complicated and time-consuming. There are also many barriers to success such as challenging samples types and maintaining desirable downstream results that can add to the stress, not to mention actually getting the robotic instrumentation to do what you want it to. All of this makes it easy to understand why many labs avoid automating or own expensive instrumentation that goes unused. Continue reading “High-Throughput Purification with Experts Included”

Weird samples? Contact Tech Serv to find the right DNA purification kit for you.

“Dear Tech Serv,
We would like to detect DNA collected from swabs rubbed on the inside thighs of frogs. What would be the best DNA extraction kit to use for this?”

“Hi Tech Serv,
I need to find out a suitable kit for extracting DNA from bird fecal samples. Can I use ReliaPrep™ gDNA Tissue Miniprep System for that?”

These are just some examples of unconventional sample type inquiries that the Promega Technical Services Team receives regularly from scientists around the world. Many of these inquiries land in the hands of Technical Services Scientist, Paraj Mandrekar (a.k.a. “sample type guru”).

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Biotechnology From the Mouths of Babes

As a science writer, much of my day entails reviewing and revising marketing materials and technical literature about complex life science research products. I take for granted the understanding that I, my colleagues and our customers have of how these technologies work. This fact really struck me as I read an article about research to improve provider-patient communication in healthcare settings.

The researchers completed an analysis revealing that patient information materials had an average readability at a high school level, while the average patient reads at a fourth-grade level. These findings inspired the researchers to conduct a study in which they enlisted the help of elementary students to revise the content of the patient literature after giving them a short lesson on the material.

The resulting content did not provide more effective ways to communicate indications, pre- and post-op care, risks or procedures—that wasn’t really the point. Instead, the study underscores the important connection between patient literacy and health outcomes. More specifically, a lack of health literacy is correlated with poor outcomes and increased healthcare costs, prompting action from the US Department of Health & Human Services.

While healthcare information can be complex and full of specific medical terminology, I recognized that a lot of the technical and marketing information we create for our products at Promega has similar features. Wouldn’t it be interesting to find out how descriptions of some of our biggest technologies translate through the eyes and mouths of children?

After enlisting some help from my colleagues, I was able to catch a glimpse of how our complex technologies are understood by the little people in our lives. The parents and I explained a technology and then had our child provide a description or drawing of what they understood.

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Choosing a Better Path for Your NGS Workflow

Imagine you are traveling in your car and must pass through a mountain range to get to your destination. You’ve been following a set of directions when you realize you have a decision to make. Will you stay on your current route, which is many miles shorter but contains a long tunnel that cuts straight through the mountains and obstructs your view? Or will you switch to a longer, more scenic route that bypasses the tunnel ahead and gets you to your destination a bit later than you wanted?

Choosing which route to take illustrates a clear trade-off that has to be considered—which is more valuable, speed or understanding? Yes, the tunnel gets you from one place to another faster. But what are you missing as a result? Is it worth a little extra time to see the majestic landscape that you are passing through?

Considering this trade-off is especially critical for researchers working with human DNA purified from formalin-fixed paraffin-embedded (FFPE) or circulating cell-free DNA (ccfDNA) samples for next-generation sequencing (NGS). These sample types present a few challenges when performing NGS. FFPE samples are prone to degradation, while ccfDNA samples are susceptible to gDNA contamination, and both offer a very limited amount of starting material to work with.

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Elephant Endotheliotropic Herpesvirus—A Tiny Virus Threatens the World’s Elephants

My favorite ice-breaker of all time is: “List one fact about you that no one would guess”. It is my favorite because I have an awesome answer (if I do say so myself). My go-to answer is: I spent a summer working with elephants.

It was the summer before I graduated from college, and it was really only one elephant, a five-year-old African elephant named Connie. Connie was intelligent, curious and mischievous—her favorite game with me was trying to untie my shoelaces (hint: double knotting is important). Working with her was one of the most amazing experiences of my life and left me with an abiding love for these creatures.

African elephant mother and child
Young African elephant touches his mother

Understandably, I was excited last year when one of my fellow bloggers wrote about Promega helping support the work of Virginia Riddle Pearson, who was working to identify and track strains of elephant endotheliotropic herpesvirus (EEHV) in African Elephant populations. EEHV is associated with the lethal elephant hemorrhagic disease (EHD) (1). This disease is a serious threat to the captive breeding programs of these endangered creatures. Between 1962 and 2007, it accounted for 58% of the deaths of North American captive-born Asian elephants between 4 months and 15 years of age (1). These deaths include the first Asian elephant calves born at the National, Oakland and Bronx Zoos. EHD also claimed the first live-born Asian elephant calves conceived by artificial insemination in both North America and Europe.

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Better NGS Size Selection

One of the most critical parts of a Next Generation Sequencing (NGS) workflow is library preparation and nearly all NGS library preparation methods use some type of size-selective purification. This process involves removing unwanted fragment sizes that will interfere with downstream library preparation steps, sequencing or analysis.

Different applications may involve removing undesired enzymes and buffers or removal of nucleotides, primers and adapters for NGS library or PCR sample cleanup. In dual size selection methods, large and small DNA fragments are removed to ensure optimal library sizing prior to final sequencing. In all cases, accurate size selection is key to obtaining optimal downstream performance and NGS sequencing results.

Current methods and chemistries for the purposes listed above have been in use for several years; however, they are utilized at the cost of performance and ease-of-use. Many library preparation methods involve serial purifications which can result in a loss of DNA. Current methods can result in as much as 20-30% loss with each purification step. Ultimately this may necessitate greater starting material, which may not be possible with limited, precious samples, or the incorporation of more PCR cycles which can result in sequencing bias. Sample-to-sample reproducibility is a daily challenge that is also regularly cited as an area for improvement in size-selection.

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How Do I Choose the Right GoTaq® Product to Suit My Needs for EndPoint PCR?

We offer a wide array of GoTaq® DNA Polymerases, Buffers and Master Mixes, so we frequently answer questions about which product would best suit a researcher’s needs. On the Taq Polymerase Page, you can filter the products by clicking the categories on the left hand side of the page to narrow down your search. Here are some guidelines to help you select the match that will best suit your PCR application. Continue reading “How Do I Choose the Right GoTaq® Product to Suit My Needs for EndPoint PCR?”

Six (and a Half) Reasons to Quantitate Your DNA

Knowing how much DNA you have is fundamental to successful experiments. Without a firm number in which you are confident, the DNA input for subsequent experiments can lead you astray. Below are six reasons why you should quantitate your DNA.

6. Saving time by knowing what you have rather than repeating experiments. If you don’t quantitate your DNA, how certain can you be that the same amount of DNA is consistently added? Always using the same volume for every experiment does not guarantee the same DNA amount goes into the assay. Each time there is a new purified DNA sample, the chances that you have the same quantity as before are lessened. Consequently, without knowing the DNA concentration of the sample you are using, the amount of input DNA cannot be guaranteed and experiments may have to be repeated.

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