Exploring the Land of the Silver Fern—Part II

In 2014, Promega created a special incentive to reward field science consultants who help the scientific community take advantage of our on-site stocking program. The winners had to meet ambitious criteria to receive 2 round-trip tickets to anywhere in the world, a week of paid vacation and spending money. Our four winners from 2014 will share photos and stories about their journeys in a semi-regular Friday feature on the Promega Connections Blog.

Today’s travelogue is Part II of the adventures of Sarah Theos, a client support consultant, who used her award to travel to New Zealand. You can read Part I here.

Day 7: Queenstown to Te Anau

My husband surprised me that morning by booking a massage appointment at the spa to soothe my aching muscles. It was a rainy morning and we had a long drive ahead of us to the town of Te Anau, the stopover town on the way to the Fiordland National Park and Milford Sound.  We also saw that we had lucked out on our itinerary as it was supposed to be a beautiful day in Milford the next day (a place that gets over 300 days of rain each year).  Therefore, we didn’t mind one more day of rain if it meant the next day would be amazing.  We drove through the Canterbury plains, passing tons of sheep and dairy farms along the way.  We also found it interesting that they farm deer in NZ.  We drove past a lot of deer farms.  When we arrived in Te Anau, we grabbed some food and went to the local grocery store to stock up on snacks and more wine.  New Zealand has a booming wine industry and we thought that it was worth sampling as many wines as we could.  The day was gray and cold but we decided to walk along Lake Te Anau anyway.  It is a beautiful, massive lake but we didn’t see very much of the surrounding mountains because of the fog.  We stopped briefly at the bird sanctuary to see the Kaka, the Crested Grebe, and other beautiful birds.  That evening, we had the most amazing 5 star dinner at the Redcliff Café and loved it so much that we booked a table there for the next evening!  Since we were getting up super early the next day to drive to Milford, we went to bed early.

Day 8:  Drive through the Fiordland to Milford Soundnew-zealand1a

This had to be my most favorite day of the entire trip.  Not only was the weather amazing, the entire drive to and from Milford Sound was mind blowing.  The New Zealanders call Milford the 8th Natural Wonder of the World and it is easy to see why.  It is in a remote part of the island and 99% of the Fiordland will never see a human.  The Fiordland has waterfalls aplenty, sweeping, colorful landscapes with millions of gorgeous lupin flowers and gigantic, snow covered mountains.  It truly feels as though you have entered another world.  We left early so we would avoid the dreaded crowds and tour buses that clog the two lane road from 10am-4pm. We stopped constantly as the views just kept getting better and better around every twist and turn.  One notable stop was The Chasm.  The Chasm is where the raging Cleddau River has worn a path straight through the mountain so it virtually disappears into the rock.  There are many massive, perfectly round pothole formations in the limestone where pebbles have worn their way through the rocks.  We were the only two people there at that time of the morning.  It felt majestic just to stand there and listen to the tremendous sound of the powerful river disappearing into the mountain and reappearing on the other side. Continue reading

Protein:DNA Interactions—High-Throughput Analysis

Protein-DNA interactions are fundamental processes in gene regulation in a living cells. These interactions affect a wide variety of cellular processes including DNA replication, repair, and recombination. In vivo methods such as chromatin immunoprecipitation (1) and in vitro electrophoretic mobility shift assays (2) have been used for several years in the characterization of protein-DNA interactions. However, these methods lack the throughput required for answering genome-wide questions and do not measure absolute binding affinities. To address these issues a recent publication (3) presented a high-throughput micro fluidic platform for Quantitative Protein Interaction with DNA (QPID). QPID is an microfluidic-based assay that cam perform up to 4096 parallel measurements on a single device.

The basic elements of each experiment includes oligonucleotides that were synthesized and hybridized to a Cy5-labeled primer and extended using Klenow. All transcription factors that were evaluated contained a 3’HIS and 5’ cMyc tag and were expressed in rabbit reticulocyte coupled transcription and translation reaction (TNT® Promega). Expressed proteins are loaded onto to the QIPD device and immobilized. In the DNA binding assay the fluorescent DNA oligonucleotides are incubated with the immobilized transcription factors and fluorescent images taken. To validate this concept the binding of four different transcription factor complexes to 32 oligonucleotides at 32 different concentrations was characterized in a single experiment. In a second application, the binding of ATF1 and ATF3 to 128 different DNA sequences at different concentrations were analyzed on a single device.

Literature Cited

  1. Ren, B. et al. (2007) Genome-wide mapping of in vivo protein-DNA binding proteins. Science 316, 1497–502.
  2. Garner, M.M. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions. Nuc. Acids. Res. 9, 3047-60.
  3. Glick,Y et al. (2016) Integrated microfluidic approach for quantitative high throughput measurements of transcription factor binding affinities. Nuc. Acid Res. 44, e51.

Catching a Child Abuser in Five Days

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Next week, forensic analysts from all over the world will gather in Minneapolis for the 27th  International Symposium on Human Identification (ISHI). So today, we’d like to share one story from a forensics lab that highlights the importance of collaboration, knowledge-sharing and technology development–since that is what ISHI is all about. 

Crimes against children are especially heinous, and it is vitally important that the offenders are removed from the streets as soon as possible. In today’s blog, Sarah Chenoweth from the Anne Arundel County Crime Lab in Maryland describes a sexual assault case that was solved in just five days. Key to this speed were the collaboration between lab staff and state police, and the ability to quickly and reliably amplify DNA profiles from low-DNA samples. Thanks to the efforts of the investigators involved, parents in Maryland, and possibly nationwide, can sleep a little easier.

On Friday, February 5th, the Anne Arundel County Crime Lab was notified of a sex offense involving a 7-year-old victim. With our efficient DNA workflow, including use of the Fusion amplification kit with our 3500 Genetic Analyzer, we were able to identify the perpetrator in only five days. Continue reading

Science Is Not a Wet Blanket: A Marketing Plan for Antibacterial Soap

The relationship between science and marketing usually has great chemistry: effective marketing evokes an emotional response that compels people to buy something, which enables companies to research and develop new products. Let’s call this the honeymoon phase: things seem pretty great on the surface, yet they really need to sort out some uncomfortable truths. For example, don’t these two advertisements make you feel shocked that you aren’t sanitizing your hands before you eat? While cleverly executed, they are a little misleading because they paint a very stark picture of hygiene.

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Ad text: “Rock, Paper, Scissors.” Protex worked with the agency Y&R in Brazil to create this ad in 2012.

Lifebuoy worked with the agency Lowe in Indonesia to create this ad in 2009.

Ad text: “You eat what you touch.” Lifebuoy worked with the agency Lowe in Indonesia to create this ad in 2009.

These ads were created before scientific consensus was reached on the safety of 19 antibacterials. An earlier review of 27 relevant studies found that antibacterial soap was no more effective than regular soap and increases the risk of antibacterial resistance. Has science effectively put an end to antibacterial soap? What should a company that makes both regular and antibiotic soap do to comply with the new FDA ruling without losing revenue?

Identifying Marketing Opportunities

Adhering to good science doesn’t mean stomping out the creativity of your marketing team. Instead, marketers can gain inspiration from the diverse impact bacteria have on human health and present their products in the right context. Continue reading

iGEM: Building Living Machines

Life forms are often compared to machines, whether you are referring to a single cell or a complex organism. This concept is the basis for the International Genetically Engineered Machine (iGEM) Competition. Each year, high school and university students around the world assemble teams that create genetically engineered systems. In addition to the building work, teams document their process and progress through wikis that are assessed by judges at the end of the competition.

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Some members of iGEM 2016 Team Duesseldorf.

In order to synthesize these living machines, iGEM teams use standard biological parts called biobricks—each biobrick is a sequence of DNA encoding a particular biological function. Teams receive a kit of standard biobricks and work over the summer to build and test biological systems in living cells. These basic units are put together to make more complex parts which can then be grouped together to make “devices” that can function within living cells. Continue reading

To Quilt, Perchance to Discover

What is it about Quilting?

Not yet a quilt, this is a stock photo image.

Not yet a quilt, this is a stock photo image.

There is a really big quilt show going on in town right now. The annual Wisconsin Quilt Expo runs Thursday through Saturday, September 8–10, 2016 here in Madison, WI.

This quilt expo is the State Fair for quilters. It is to quilters, what Summerfest, or a Lollapalooza festival is to music fans. It is the Stitch-Stitch fest for those with thimbles (and fabric, of course).

To give you another idea of the size of Quilt Expo, busloads of quilters and quilt fans come to this expo, and there are awards for the best quilt in each of ten categories. Can you imagine the time it takes to judge quilts in 10 different categories?

Quilt Expo is sponsored by Wisconsin Public Television and quilter-in-chief Nancy Zieman, host of the popular public television show “Sewing with Nancy”. Her store, Nancy’s Notions is a destination quilting shop in Beaver Dam, WI. I’ve been to this store twice, both times with dedicated quilters. Each time, my quilter counterpart stopped talking immediately upon entering the store. They looked around once, took a cart and went deep into shopping. I gave up on attempts at conversation, due to a lack of response. Continue reading

Almost As Good As the Expert Down the Hall: The Citations Database

database_1When you are faced with a new research challenge or are troubleshooting in the lab, nothing replaces the wisdom of the lab tech down the hall who has 20 years experience doing the very technique you need to try.

But, sometimes there isn’t a local expert handy.

The Citations Database on the Promega website provides another source of expertise for you. We curate peer-reviewed publications that cite the use of Promega products so that you can see what people have done and how they have done it. We include links to PubMed for articles that are in indexed journals, and we also include brief notes about how the Promega products were used in the research.

Whether you are working with a new sample type, troubleshooting nucleic acid isolation, or trying a completely new assay, see how the Citations Database can help you in the laboratory. Continue reading

The Cell Line Identity Crisis: Old problems, new concerns

If you work with cell lines you may have paid attention to the dramatic headline published last month in the online journal STAT, Thousands of studies used the wrong cells, and journals are doing 29981164-Whistlenothing.” In their column The Watchdogs (“Keeping an eye on misconduct, fraud, and scientific integrity”), Ivan Oransky and Adam Marcus call out the fact that scientists continue to publish research using cell lines that are contaminated or misidentified. Recent estimates have found that the percentage of misidentified cell lines used by scientists is as high as 20 to 36. The blame here is being placed on the peer reviewed journals for not blowing the whistle. The authors call for journals to put some “kind of disclaimer on the thousands of studies affected.”

This is not a new claim. The continuing problem of cell line misidentification, of lack of authentication, has been covered before in various channels. It’s easy to find news publicizing yet another retracted publication. Promega Connections has published a number of blog posts addressing this, one as recently as last year: Do You #Authenticate? This post describes the bold move by the journal Nature to adopt a new policy around cell line authentication. Beginning in May 2015 the journal required authors of all submitted manuscripts to confirm the identity of cell lines used in their studies and provide details about the source and testing of their cell lines. Continue reading

The Unforgettable Experience of Traveling: Beyond the Formal Learning Experience

CTPGE students (l to r): Anna Facchetti, Anqi Fu, Pureum Jeon, and Hajeong Sim; Anna and Anqi are UW-Madison graduate students.

CTPGE students (l to r): Anna Facchetti, Anqi Fu, Pureum Jeon, and Hajeong Sim;
Anna and Anqi are UW-Madison graduate students.

Last fall, I blogged about our partnership with Promega-Hannam BTCI at Hannam University in Daejeon, Korea , providing an overview of the ways in which we have collaborated over the years.

This year, 2016,  included the participation of two Hannam students, Pureum Jeon and Hajeong Sim, in one of our advanced courses, Core Techniques in Protein and Genetic Engineering (CTPGE), which offers graduate credits through the University of Wisconsin-Madison. UW-Madison is a bustling campus with a large international student, staff and faculty population, and Promega Corporation is a global company with a diverse workforce that brings a steady stream of international visitors to its main campus in Fitchburg. My sense is that sometimes those of us who live and work in environments like this, who also regularly tap into global news, can lose touch with what it’s like to leave home and travel to a completely new place, perhaps somewhere far away where the language spoken is not your own.

Our experience with Pureum and Hajeong this summer was a reminder of how important these experiences can be for those who make these journeys. Their participation in the course provided them with valuable training, but the small things, like walking around the UW campus, having dinner with one of us, driving through rural Wisconsin and feeling welcomed at the hotel, also meant so much.

In their own words, here are a few of their thoughts: Continue reading

Meet Marty Ensenberger, Senior Research Scientist on the Spectrum CE System

29160613_lPromega will soon introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines—from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Marty Ensenberger, Senior Research Scientist on the Spectrum CE System. Continue reading