With the advent of genome editing using CRISPR-Cas9, researchers have been excited by the possibilities of precisely placed edits in cellular DNA. Any double-stranded break in DNA, like that induced by CRISPR-Cas9, is repaired by one of two pathways: Non-homologous end joining (NHEJ) or homology-directed repair (HDR). Using the NHEJ pathway results in short insertions or deletions (indels) at the break site, so the HDR pathway is preferred. However, the low efficiency of HDR recombination to insert exogenous sequences into the genome hampers its use. There have been many attempts at boosting HDR frequency, but the methods compromise cell growth and behave differently when used with various cell types and gene targets. The strategy employed by the authors of an article in Communications Biology tethered the DNA donor template to Cas9 complexed with the ribonucleoprotein and guide RNA, increasing the local concentration of the donor template at the break site and enhancing homology-directed repair. Continue reading “All You Need is a Tether: Improving Repair Efficiency for CRISPR-Cas9 Gene Editing”
Nucleic Acid from FFPE Samples: Effects of Pre-Analytical Factors on Downstream Success
Part one of three
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.
Continue reading “Nucleic Acid from FFPE Samples: Effects of Pre-Analytical Factors on Downstream Success”It Takes a Village: Automating Plasmid Purification for iGEM
Today’s blog is guest-written by Wihan Adi, a Master’s student majoring in physics at Justus-Liebig-University in Giessen and team member of iGEM Marburg. Although his background is in nuclear and particle physics, his research interests shifted toward affordable biosensors for point-of-care cancer detection, which is how he ended up doing microbiology for iGEM.
Back in March when the iGEM season had just started, Maurice, a fellow iGEM Marburg team member, told me that he was exchanging emails with Margaretha Schwartz from Promega. Given my background as a physics student, Promega was not a household name for me at the time. “So, are you interested in automating a plasmid purification protocol?” asked Maurice. He told me that Promega was willing to supply the Wizard® MagneSil® Plasmid Purification System for this purpose; that was another name that added to my confusion.
This year, iGEM Marburg is aiming to establish a fast phototrophic organism as a synthetic biology chassis. For this goal we chose Synechococcus elongatus UTEX 2973, with a reported doubling time of 90 minutes. More specifically, we are creating an easy to use toolbox to empower rapid design testing, including genome engineering tools, self-replicating plasmid systems, natural competence and a Golden Gate-based part library. Our team chose to work on phototrophic organisms because we envision accelerating research in this particular field. (Note: Last year, Marburg’s iGEM project won the Grand Prize!)
Continue reading “It Takes a Village: Automating Plasmid Purification for iGEM”The 30th International Symposium on Human Identification: Elevating DNA Forensics
Thirty Years of ISHI
In the fall of 1989, a small group of forensic scientists, law enforcement officials and representatives from Promega Corporation gathered in Madison, Wisconsin, for the very first International Symposium on Human Identification (ISHI). At the time, DNA typing was in its infancy and had not yet been validated as a forensic method. The available technology consisted of two methods: detection of restriction fragment length polymorphisms (RFLPs) and variable number of tandem repeats (VNTRs). Promega had developed products based on both analytical methods, which essentially provide a DNA “fingerprint” or profile for each individual tested.
Among the attendees at that first symposium was Tom Callaghan, then a graduate student. That experience made a significant impact on his career path. Last week, at ISHI 30, he presented a session on rapid DNA testing. Dr. Callaghan currently serves as a Senior Biometric Scientist for the FBI. In 1999, he was instrumental in launching the FBI’s Combined DNA Index System (CODIS) and in 2003, he became the first CODIS Unit Chief.
Continue reading “The 30th International Symposium on Human Identification: Elevating DNA Forensics”NLRP3: The New Hope for Treating Chronic Inflammatory Diseases
Our innate immune system was meant to do good. Up until a century ago, most humans died from infectious diseases like diarrhea, tuberculosis and meningitis. Over millions of years, our immune system has evolved to fight these life-threatening infections from pathogens. As a result, we have developed a highly efficient response to these tiny invaders. But it seems that our immune system may be turning against us.
Continue reading “NLRP3: The New Hope for Treating Chronic Inflammatory Diseases”Sci Comm Tips From An iGEM Judge
Formal judgment in any context is nerve-racking. Scientists, familiar with being judged, rely on others to evaluate (and hopefully accept) everything from a PhD thesis defense to grant proposals and peer-reviewed journal article submissions. The frustrating part is not knowing exactly what the judges are looking for. Sure there are requirements and guidelines to follow—but how are the judges going to interpret them? It would be a whole lot easier if we could just peek into their minds. Unfortunately for most, that fantasy isn’t likely to turn into reality.
But if you are part of an iGEM team, today is your lucky day! Our own Preeta Guptan volunteers as a judge for the iGEM competition, and in today’s article, you will get her insider’s perspective about what iGEM judges look for. You will also get some tips to help you excel in the iGEM competition—and effectively communicate about science in general.
Preeta is an External Innovation Manager at Promega, which means she seeks out and investigates technology that might be valuable for Promega to license or acquire. The opportunity to scout up-and-coming synthetic biology advances was one reason she wanted to be an iGEM judge, but curiosity was at the core of her decision. Preeta and the other judges bring their unique perspectives and experiences to each iGEM project and team they evaluate. Here are some suggestions from Preeta:
Continue reading “Sci Comm Tips From An iGEM Judge”Creating Sonic Sculptures with Artist-in-Residence, Joe Willie Smith
Joe Willie Smith has always been a creator. As a young child growing up in Milwaukee, his mother encouraged him to make art and find beauty in the everyday. Following years of work in printing and graphic design (including posters for Gil-Scott Heron and Chaka Khan), Smith began channeling his inspiration and creativity into building playable “sonic sculptures” out of found objects. “They’re not all considered instruments…sometimes I just make soundscapes out of them,” Smith says.
As the artist-in-residence for the Promega Fall Art Showcase, Smith set out to create a sonic sculpture from collected items from the Promega campus. He planned to perform on the instrument at the opening of the Art Show, but his creative process led to something much more—a collaborative experience in sound and color.
Continue reading “Creating Sonic Sculptures with Artist-in-Residence, Joe Willie Smith”Seeds of Change Award Recognizes Commitment to Local Community
Community Shares of Wisconsin presented Promega with its Seeds of Change award for our workplace giving efforts. The award is presented to a local business that shows innovation, growth, and commitment to Community Shares of Wisconsin. Over the past 15 years Promega and our employees have collectively contributed more than $717,000 to Community Shares work! Our 100% corporate matching helps employee gifts go twice as far to member nonprofits and the community.
Charitable giving programs and paid time off for community service are examples of Promega’s commitment to corporate responsibility. Learn more at https://www.promega.com/responsibility #corporateresponsibility
Nicole Haselwander and Stephanie Shea were on hand at the Community Change-Maker Awards hosted by Community Shares of Wisconsin to accept the Seeds of Change award on behalf of Promega Corporation. “It was an incredibly inspiring and uplifting program,” says Stephanie.
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The Surprising Life of Bones
Standing, walking, running. When was the last time you gave your skeleton a second thought? How about when that car barely missed you in the parking lot? Or a deer ran in front of you? Maybe you just missed a car door opening on your bike ride today?
Your bones were involved in your response to that sudden shock/surprise, but not the way you think.
You may have jumped, swerved or hit the brake pedal (congratulations on the excellent reflexes) and yes, bones were involved in all of those actions. But a new article in Cell Metabolism reveals that bone is the essential component in initiation of that response.
Continue reading “The Surprising Life of Bones”Experimenting with Resilience: Lessons from Grad School
Today’s blog is guest-written by Susanna Harris, a graduate student at the University of North Carolina in Chapel Hill.
It’s one thing to hear that everything is going to be okay. It’s another to know it and make it that way.
Photo provided by Susanna Harris
At the end of a lab meeting where I had outlined my last of six years getting my PhD, my advisor announced she would be moving the lab from North Carolina to Massachusetts in about six months. Just when everything had settled into place, this announcement turned my bookshelf of plans on its side once again. Suddenly, I didn’t know what would happen next.
I chose to go to grad school partly to challenge myself to accept uncertainty. When I started my PhD in Microbiology in 2014, I thought this would mean reading new papers and adjusting experiments accordingly. As it has turned out, the real challenge has been to constantly get back up as life and graduate school knock me flat on my ass. Yes, I needed strength to power through, but even more than that, I needed resilience.
Continue reading “Experimenting with Resilience: Lessons from Grad School”