Nucleic Acid Analysis

The Future of Synthetic Biology: A Recap of iGEM 2019

Posted on by Darcia Schweitzer

After attending the iGEM Giant Jamboree last year and being completely blown away by the projects presented (check out this article or this one), I didn’t think I’d be as astonished this year. I attributed part of the awe I felt over the caliber and quality of the projects to my wide-eyed naiveté, having never attended the event before. The second time around, the “first-time” novelty long worn off, I didn’t expect to feel that same level of amazement.

I couldn’t have been more wrong.

After three days of impressive presentations, I once again felt that same astonishment as I prepared to watch the presentations of the 6 finalists. With good reason—the projects presented by the six finalists completely blew my mind!

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How should I evaluate DNA isolated from FFPE samples to ensure success?

Posted on by Eric Vincent

Part two of three. You can read part 1 here.

Formalin-Fixed Paraffin embedded (FFPE) samples are being used in increasing numbers of molecular assays. In my last blog I discussed some of the pre-analytical variables that can affect results obtained when using FFPE samples. Laboratories can increase the quality of downstream results by controlling variables where possible. While exacting control over the sample acquisition and fixation process can improve results, quality testing of incoming samples is a crucial step in assuring optimal results. There are numerous methods that can be used to evaluate the quality of samples and they can provide different information that can be used to assess sample integrity and suitability for different applications.

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A Diamond in the Rough: New Applications of Diamond Nucleic Acid Dye

Posted on by Leah Cronan

Diamond™ Nucleic Acid Dye (Cat# H1181) is a safe, inexpensive and sensitive fluorescent dye option that binds to single-stranded and double-stranded DNA and RNA. Diamond™ Dye typically is used for staining electrophoresis gels to visualize nucleic acids in a similar to its carcinogenic counterpart, ethidium bromide. However Diamond™ Dye has several advantages: gels stained with Diamond™ Dye can be visualized using either UV or blue-light transilluminators. Also, a wash step after staining is not necessary when using Diamond™ Dye, unlike what is typically recommended for ethidium bromide.

Besides staining electrophoresis gels, there are other applications for this diamond in the rough. Highlighted below are two fascinating uses of this multifaceted tool: touch DNA localization and qPCR detection.

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Discussing the Future of Gene Editing at CRISPRcon Midwest

Posted on by Mariel Mohns
crisprcon_banner
Walking in to the first session at CRISPRcon Midwest.

Last week, a diverse group of stakeholders attended CRISPRcon Midwest, hosted by the Keystone Policy Center and the University of Wisconsin–Madison. The goal of the day-long conference was to emphasize the importance and value of gene editing technology, and how it must be communicated deliberately between scientists, the public, policymakers, and other stakeholders.

Julie Shapiro, Senior Policy Director of Keystone Policy Center, acted as Emcee for the event. Given the diverse group of attendees, she mentioned in her opening remarks that the event organizers were “seeking conversation, not consensus” and emphasized the “power of respectful dialogue.” A slide overhead showcased the ground rules for the day, which included statements such as “dare to listen, dare to share, and dare to disagree.”

crisprcon_poll_word_cloud
Word cloud generated from live polling results at CRISPRcon Midwest.

CRISPRcon aimed to included voices beyond those represented by keynote speakers and panelists, so they incorporated live polling through an online app to keep the audience engaged and an active participant in the conversations throughout the day. From the opening remarks, it was clear that this conference would not just deliver on its promise of thoughtful conversation about the science, but build further understanding about the societal impacts of a rapidly advancing technology.

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Nucleic Acid from FFPE Samples: Effects of Pre-Analytical Factors on Downstream Success

Posted on by Eric Vincent

Part one of three

Peer-reviewed publications containing data dervived from analysis of nucleic acids isolated from FFPE samples have increased dramatically since 2006.

Formalin Fixed Paraffin Embedded samples (FFPE) have been a mainstay of the pathology lab for over 100 years. Initially FFPE blocks were sectioned, stained with simple dyes and used for studying morphology, but now a variety of biomolecules can be analyzed in these samples. Over the past 10 years we have discovered that there is a treasure trove of genomics data waiting to be unearthed in FFPE tissue. While viral RNAs and miRNA were some of the first molecules found to be present and accessible for analysis starting in the 1990s, improvements to DNA and RNA extraction methods have demonstrated that PCR, qPCR, SNP genotyping, Exome and WGS are possible. This has resulted scientific publications of DNA and RNA data generated from FFPE samples starting in 2006, and today we see immense amounts of data generated from FFPE—with nearly 2000 citations in 2018 reporting sequencing of FFPE samples.

Depending on the type of project, prospective or retrospective, the genomics scientist has an opportunity to affect the probability of success by better understanding the fixation process. The challenge with FFPE is the host of variables that have the potential to negatively affect downstream assays.

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Think Restriction Enzymes are so last decade? Not so fast!

Posted on by Leah Cronan
Ribbon diagram of EcoRI homodimer bound to doublestranded DNA
Ribbon diagram of EcoRI homodimer bound to doublestranded DNA

Restriction enzymes sometimes get a lot of flak. In the not-so-distant past, they were the workhorses of molecular biology. Restriction enzymes played a huge role in developing early DNA sequencing techniques. They chop DNA in a predictable manner, which makes cutting and pasting genes of interest manageable and relatively easy, enabling the development of  genetic engineering and recombination technologies. These technologies are now moving beyond restriction enzymes toward more modern methods, with the most talked-about method being CRISPR /Cas9. As technology continues to advance at such a rapid pace, restriction analysis  and other “ancient” technologies feel antiquated. But this is not necessarily the case.

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A Quick Method for A Tailing PCR Products

Posted on by Isobel Maciver
PCR experiment and products, pipette tip, tube in researcher's hand.
PCR is a common technique used in research labs to amplify DNA.

Some thermostable DNA polymerases, including Taq, add a single nucleotide base extension to the 3′ end of amplified DNA fragments. These polymerases usually add an adenine, leaving an “A” overhang. There are several approaches to overcome the cloning difficulties presented by the presence of A overhangs on PCR products. One method involves treating the product with Klenow to create a blunt-ended fragment for subcloning. Another choice is to add restriction sites to the ends of your PCR fragments. You can do this by incorporating the desired restriction sites into the PCR primers. After amplification, the PCR product is digested and subcloned into the cloning vector. Take care when using this method, as not all restriction enzymes efficiently cleave at the ends of DNA fragments, and you may not be able to use every restriction enzyme you desire. There is some useful information about cutting with restriction sites close to the end of linear fragments in the Restriction Enzyme Resource Guide. Also, some restriction enzymes require extra bases outside the recognition site, adding further expense to the PCR primers as well as risk of priming to unrelated sequences in the genome.

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Curiosity and Collaboration: A PhD Journey

Posted on by Mariel Mohns

Concepcion Sanchez-Cid didn’t know she wanted to be a scientist when she was older. She grew up with a love of music and played the violin, but her curiosity and eagerness to learn drove her down the path for a career in biomedical research.

Hear more of Concepcion’s story:

As a Master’s student at the University of Granada, Concepcion studied biotechnology and landed an internship at the Promega Europe Training and Application Lab (PETAL) in France. She worked with the Applications Team to develop protocols for DNA and RNA extraction from soil. When she decided to pursue a PhD, she received a sponsorship from Promega and enrolled as a student at the University of Lyon while also remaining an employee at PETAL.

Concepcion says that the balance between both worlds—academia and industry—provide her with technical skills and a unique support network that has helped shape her PhD thesis work. “Working at a university and a company at the same time…you get very different feedback from people that are very specialized, and they really know what they’re doing, so at the end you integrate everything,” she says. “It’s one of the things I appreciate most about my PhD.”

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Research-Based Training for Sustainable Use and Management of Marine Ecosystems in Namibia

Posted on by Kari Kenefick

In my science blog research/writing, news reports are usually pulled from US sources. But interesting scientific research is obviously being conducted in many places around the globe. When this story from Namibia came along, there was so much I didn’t know. It was time to catch up.

relief map of Namibia
Relief map of Namibia. Image by Natural Earth and Kbh3rd with permission under Wikimedia commons.

Namibia is Exactly Where in Africa?

Namibia is one of the world’s youngest countries, having gained independence from South Africa in 1990. Situated northwest of the country of South Africa on the Atlantic Ocean, Namibia is arid, composed largely of desert.

This blog is about research conducted at the Sam Nujoma Research Center, University of Namibia, on Henties Bay. Henties Bay (not shown on this map) is in the region of Erongo, located in the center of Namibia along the coast. Henties Bay has become a tourist destination in part due to the abundance of fish and marine life found there.

Sam Nujoma Research center.
The Sam Nujoma Research Center of University of Namibia, located near Henties Bay.

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Studying Autophagy in Flies Using CRISPR

Posted on by Leah Cronan

Transcribed RNA can be used to study RNA structure and how it relates to function or how proteins and RNA interact. It can also be used for gene silencing using RNAi (studied more often as a possible therapeutic option) or simply serve as a molecular standard in Real-time RT-PCR. Transcribed RNA is also used in Class 2 Clustered Regularly Interspaced Short Palindromic Repeat systems, or CRISPR.

The CRISPR system, which is naturally occurring in bacteria, has been manipulated to perform gene editing in a laboratory environment. To perform CRISPR in the laboratory environment, you need two main reagents:

  1. The Brains: Guide RNA (gRNA or sgRNA) – Small piece of RNA containing a nucleotide sequence that is capable of binding the chosen Cas Protein, and contains a portion of the sequence that can bind the DNA the researcher intends to modify – the target DNA.
  2. The Brawn: CRISPR-associated endonuclease (Cas Protein) – The protein that cleaves the target DNA; the most popular Cas protein is called Cas9. The Cas protein is guided by the (gRNA).

Guo et al. used Promega’s RiboMAX™ Large-Scale RNA Production System to produce gRNA to be used in CRISPR for their study to determine the effects of the loss of, or mutations in, a specific gene in fruit flies (1).  Atg101 is a gene that plays an important role in autophagy, an intracellular pathway for removing toxins or damaged parts of cells.

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