Safety First (and Sensitivity too!): Diamond™ Nucleic Acid Dye

diamond_dyeGel electrophoresis and gel staining are common lab tasks that you may not think too much about.  It’s a fairly routine part of your day…purify DNA or RNA, check it on a gel.  As you probably know, interchelating agents like ethidium bromide can be used to visualize your nucleic acids on a gel for relatively low cost. The problem with ethidium bromide is that it’s highly mutagenic, making it less than ideal to work with and disposal of ethidium bromide can be quite costly. There are other commercially available alternatives to ethidium bromide that use fluorescent-based dyes to detect nucleic acids in gels. Some of these are touted to be safer than ethidium bromide; others are marketed as more sensitive.  If you are going to switch from an interchelating agent to something safer, you certainly don’t want to lose out on sensitivity.

To make your gel staining safer, more convenient, and more cost-effective, we’ve developed the Diamond™ Nucleic Acid Dye. The Diamond™ Nucleic Acid Dye is not detectably genotoxic or cytotoxic at the 1:10,000 dilution recommended for gel staining, as determined by the Ames MPF™ Assay, is more sensitive than competing fluorescent-type “safe” dyes, and, in its concentrated form, is room-temperature stable for 90 days (1, 2).   If you are looking to switch to a safer, more sensitive way to stain your polyacrylamide or agarose gels to visualize your DNA or RNA, you may want to give the Diamond™ Nucleic Acid Dye a try.

  1.  Schagat, T. and Hendricksen, A. Diamond™ Nucleic Acid Dye is a Safe and Economical Alternative to Ethidium Bromide. [Internet] July 2013; tpub 125. [cited: 2013, July, 29]. Available from: http://www.promega.com/resources/articles/pubhub/diamond-nucleic-acid-dye-is-a-safe-and-economical-alternative-to-ethidium-bromide/
  2. Truman, A., Hook, B. and Hendricksen, A. Diamond™ Nucleic Acid Dye: A Sensitive Alternative to SYBR® Dyes. [Internet] June 2013; tpub 121. [cited: 2013, July, 29]. Available from: http://www.promega.com/resources/articles/pubhub/diamond-nucleic-acid-dye/

The Price for Convenience May Not Be That Pricey After All

Hour glass

I was having a discussion with my mother just the other day about cleaning products (lively topic, I know). She showed me her newest time saver…prediluted bleach. Huh, I thought. I guess that does save a bit of time, but I couldn’t resist telling her that she was paying triple the price for a whole lot of water. She said, without pause, that it was worth it to her to not have to splash fully concentrated bleach around. A convenience worth paying for, in her words.

I don’t know why this struck me as odd. I pay for convenience all the time as I get older. When I started running gels back in college, I wouldn’t have dreamed of buying a precast gel, but several years into my lab life I found myself running more than 15 gels a week, so precast was really a convenient alternative. When I was a grad student, I poured all of my own plates (and most of the plates for older students, too!). Fast forward a few years, and I running upwards of 300 microbial selective cultures per week. The switch to prepoured plates was a no brainer.

When put in the context of what our time is worth, would you rather be thawing and mixing loading dyes, buffers, stains, reagents, etc., or are you better of grabbing a premixed, room-temp stable dye or ladder/loading dye mix off the shelf and getting on with your research? I think most scientists would agree that these small conveniences allow you to free up a little more time to do the important work you should be doing.

I’m curious…what time savers or convenience items do you find that make your day a little easier in the lab?

A New Edge in Bisulfite Conversion

methyledge_featureproduct_280x140I’ve talked quite a bit about bisulfite conversion and DNA methylation analysis in  past posts. Aberrant methylation events have significant impacts in terms of incidence of cancer and development disregulation. Researchers studying DNA methylation are often working with DNA from “difficult” tissues such as formalin-fixed, paraffin embedded tissues, which characteristically yield DNA that is more fragmented than that purified from fresh tissue. Traditional methods for bisulfite conversion involve a long protocol, harsh chemicals, and generally yield highly fragmented DNA. The DNA fragmentation may significantly impact the utility of the converted DNA in downstream applications such as bisulfite-specific PCR or bisulfite sequencing.

An ideal bisulfite conversion system would allow for complete conversion of a DNA sample in a short period of time, provide high yield of DNA, minimally fragment the DNA, work on a wide range of input DNA amounts (from a wide variety of sample types), and, while we’re at it, be easy to use and to store. Whew! That’s quite the list. Continue reading

eClutter No More!

A nice clean desktop and organized inboxes for the new year...

A nice clean desktop and organized inboxes for the new year…

As each year draws to a close, I find myself making a mental list of everything that I want to change for the new year. I’m going to work out more often, I’m going to eat less starch (goodbye, my dear French bread), I am going to declutter my closets…the list goes on and on.  Unfortunately, my list looks very similar year over year, so I think I’m going to make one, true resolution and stick with it this year. I am going to do a big, fat, clean sweep of my computer. It doesn’t sound like a big task, but I have a veritable electronic war zone in front of me and I am feeling the need to purge.  Having this amount of eClutter is just as disruptive to my productivity as is having a messy house.

I was completely embarrassed a few days ago when I was having some computer issues at work.  The wonderful staff at the help desk logged into my computer remotely and saw the roughly 90 bajillion icons and shortcuts on my desktop. This was, electronically speaking, akin to having your in-laws over for dinner and having them see a pile of laundry laying in the middle of the livingroom floor. There is nothing suspect or devious about the material on there, but the sheer mess of it was embarrassing. My personal email accounts are also a terrifying disaster. I have, over the the years, subscribed to way to many newsletters and newsfeeds. It’s to the point that I have roughly 3000 unread personal email messages that are all old newsletters, promotions, and offers that have long-since expired. I am electronically suffocating under all the mess.

So here’s my plan for 2013:

  1. I am going to clean up my shortcuts and delete all the stuff that I don’t need.
  2. I am going to clean my gmail inbox, and
  3. I am going on a unsubscribe extravaganza.

If I can manage to get all of that cleaned, I just may have time to hit the gym!

Choosing the Right Reverse Transcriptase for Your Project

There are a lot of choices when it comes to reverse transcriptases.  Choosing the correct one for your cDNA synthesis and RT-PCR project is important.    Here are a few questions that will lead you to right RT for your application: Continue reading

American Society for Human Genetics Meeting

To everyone who stopped by the Promega booth at the ASHG meeting last week, thank you! We had some great conversations about science, life in the lab, and the projects you are all working on. I enjoy this meeting every year. I enjoy speaking with the graduate students, the post-docs, the clinicians, bioinformaticians, and genetic counselors. I did not have a chance to go to any of the talks this year, but the discussions that happened within the Promega booth were fascinating! It is heartening to see the tools that Promega provides helping scientists to unravel some mysteries about the human genome and human disease. I am proud to be a collaborator in this effort, and I look forward to next year’s meeting. The next chapter of each of your research stories will be, no doubt, as interesting as the last.

It’s the crunchy bits I like the best

I was supremely lucky this past fall to get six delicious fresh figs. It’s a rare treat for me since figs have such a short season and an even shorter shelf life. This year, I nearly had to leg wrestle my way to the bin at the store to score some of these fresh beauties. I had commented to another patron at the store that I couldn’t wait to get these little fellas home, stuff them with some goat cheese, wrap them in a bit of bacon, give them a quick balsamic and honey glaze, and pop them into the oven. Now, tender, sweet figs stuffed with rich, herbed goat cheese and wrapped with what is, quite possibly, the world’s most perfect meat makes me weak in the knees. The bacon, of course, is sublime, but the sweetness of the figs with the delicate crunch of those seeds really sells it.

My fellow shopper replied with “Well, good for you. I couldn’t possibly eat any of that. I’m vegan.”  Fair enough. In a past life, I worked as a personal chef and did a tremendous amount of work with vegetarians and vegans alike. Although I may never personally understand a life without cheese, I can respect it and I can certainly cook in that fashion.

One portion of that exchange, however, didn’t quite seem right. I actually followed Mr. Vegan (I didn’t ask his name) into the next aisle and asked for some clarification. “I’m sorry,” I continued, “but what did you mean by you couldn’t eat any of it? Cheese and bacon are out, but who could ever turn down a looker like this?” I asked, tapping my fresh figs ever so gently.

He just smiled and told me to look it up. Harrumph. Continue reading

Cancer research yields unexpected results

Louis Pasteur once said “Chance favors the prepared mind”. Surely any scientist can attest to this. Discoveries of things  like artificial sweeteners, Teflon, and penicillin were all unintended products of unrelated research. Recently, scientists at the Duke Cancer Institute studying the microevolution of enzymes involved in cancer happened upon a missing enzymatic link in a very unrelated area of research that has less to do with cancer than with the production of carpeting, apparel, and auto parts(1).

Nylon is a critical component in all of those products, any many, many more. Production nylon requires a compound called adipic acid. This intermediary, one of the most widely used chemicals in the world,  is produced from fossil fuels and pollution released from its refinement process is a leading contributor to global warming. To date, there hasn’t been a “green” way of producing adipic acid because there is one critical enzyme in the synthesis pathway that isn’t available: 2-hydroxyadipate dehydrogenase.

Biochemical engineering on its own had not produced a sufficient dehydrogenase to do the job. Enter the cancer researchers.   Cancer involves the microevolution of cells which offer benefits to the cells, sometimes including gain-of-function mutations in metabolic enzymes. Duke researchers identified a  mutation in glioblastomas that alters the function of isocitrate dehydrogenase. The Duke team applied their knowledge of how enzymes change during cancer to lay the blueprints on a new method for producing  clean, green, adipic acid. By using the same mutation framework, the scientist found that they could create enzymes from homoisocitrate dehydrogenase found in yeasts and bacteria that were capable of producing adipic acid from inexpensive sugars. The group still needs to scale up their production, a process that will still require a tremendous amount of work.

1.  Reitman, Z. et al. (2012) Enzyme redesign guided by cancer-derived IDH1 mutations.  Nat. Chem. Biol.  Available online.

Nanotechnology Goes Green

Wouldn’t it be nice to have a renewable, inexpensive replacement for metals, non-organic plastics, and electrical components?  Less mining, less petrochemicals, less environmental stress— it’s not a far fetched, pie-in-the-sky idea anymore.  And the source for a super-substitute material is right in your back yard.

Nanocrystalline cellulose (NCC), a product of wood pulp, have been touted as a “wonder material” whose tensile strength—214 megapascals—is eight times that of stainless steel, almost twice as strong as cast iron, and nearly equal the strength of structural steel.  NCC is produced by gently removing hemicellulose and lignin from the wood which, incidentally, can be scrap wood such as twigs and sawdust.  The purified wood is milled and hydrolyzed to remove impurities.  What’s left is cellulose fibers suspended in water.  When the water is removed, the resulting paste of fibers that can be molded or spread into sheets and freeze dried.  As they dry, the approximately 200 nanometer long fibers join together by hydrogen bonds and create a super strong material that has also is very conductive.  These properties make NCC very attractive to the electronics and computing industries as well as defense.  The United States army is using NCC to make lightweight body armor and has tested it in applications such as ballistics.

Given the abundance of starting material and the incredibly physical properties of NCC, the interest in further developing the manufacturing base is huge.  On July 26th, the U.S. Forest Service Forest Products Laboratory opened a $1.7 million dollar nanocrystalline cellulose production facility right here in Madison, Wisconsin.  The intent of the facility is ramp up production quickly and, hopefully in a few years, be able to sell NCC for a few dollars a kilogram.

Up, Up, and Away…..

Who doesn’t love a good party? One thing that surely signals a party is that telltale cluster of balloons, tugging cheerfully from the mailbox at the end of the driveway, almost chanting “Party over here!”. Think twice, however, before making that next helium balloon purchase.

Helium, that lighter than air element which is responsible for giving helium balloons their gravity-defying loft, is the second most common element in the universe, is non-reactive, and turns into a liquid at very cold temperatures without freezing solid. All of these properties have made helium a useful tool in medicine, space exploration, electronics, and manufacturing. The supplies of helium are dwindling and experts estimate that reserves of this  natural resource could be gone within the next 25-50 years or so. There are ways to reclaim helium from the atmosphere, but they are very expensive and will certainly drive up the cost of products and services that require helium, such as MRIs and LCD televisions.

It may seem like a small contribution, but choosing air filled balloons for your next festivity can help.  Try air inflated balloons hung or draped from the ceiling or arranged as centerpieces. Or skip those balloons all together and spend your money on something your guests will really appreciate…like a bigger cake!