Peeking Inside the Chrysalis: Metamorphosis in 3-D

Metamorphosis. In the case of butterflies, it is nature’s version of the great makeover. A plump and slow caterpillar transforms itself into a chrysalis and, tucked snuggly away from the curious prying eyes of the world, metamorphoses into a colorful, graceful butterfly.

Growing up in Iowa, my sister and I had a summer tradition of stalking the milkweed plants in search of Monarch caterpillars. Once we captured our prey, we brought our new acquisitions home and placed them in lovingly crated Mason jar containers filled with milkweed leaves and sticks.  Over the next few days these lucky caterpillars lived in the lap of luxury with a constant supply of milkweed leaves. Once the time came for the caterpillar to transform into a chrysalis, we waited with baited breath for the butterfly to emerge.

As a child, those ten or so days I spent watching the unchanging chrysalis were filled with breathless speculation about what must be happening inside. Years later in biology class I learned all about the stages of butterfly development and what was really happening inside the shell of the chrysalis. This knowledge came with a little kernel of sadness though, because there was only one way for science to have figured out what was happening inside the chrysalis, and that way did not end well for the butterfly-to-be.

Wouldn’t it have been nice if we could take pictures of what was happening inside the chrysalis without disturbing nature’s makeover mid cycle?

The Buzz About Akkermansia muciniphila: It’s More Than Just Weight Loss

The bacterium Akkermansia muciniphila is creating quite a stir in science news, with people calling it the “weight loss bacterium”. While it’s exciting to think about a bacterium that has the ability to reduce body weight with no change in food intake, there’s another reason to get excited: The potential to treat obesity-related metabolic disorders such as type-2 diabetes and perhaps even diseases related to intestinal inflammation.

There are hundreds of bacterial species that colonize the gut. Why has this bacterium been dubbed the “weight loss bacterium”, and why do researchers have such lofty goals for this simple unicellular organism?

Optimizing a DNA Methylation Analysis Workflow

When Aristotle compared epigenetics to a net (1), he could not have predicted how right he was.  Recent research has revealed that mechanisms underlying epigenetic effects are numerous and interdependent as are the knots in a net. Each epigenetic mechanism has its players: enzymes, functional groups, substrates etc.  The most important aspect of an epigenetic trait is its reversibility. Methylation of DNA was the first epigenetic modification to be discovered, and 5-cytosine methylation was the first to be linked with gene expression status. Currently, the most popular method for measuring  CpG island methylation status is a bisulfite treatment of DNA followed by PCR or sequencing.

In this week’s webinar, Promega R&D scientist, Karen Reece focused on a workflow from DNA purification to analysis. She described the best methods for DNA isolation, quantification, bisulfite conversion, PCR and sequencing.

Dietary Analysis, DNA Style

DNA testing methods are being used to solve problems in an ever-increasing number of fields. From crime scene analysis to tissue typing, from mammoths to Neanderthals, and from Thutmose I to Richard III, both modern mysteries and age-old secrets are being revealed. The availability of fast, accurate, and convenient DNA amplification and sequencing methods has made DNA analysis a viable option for many types of investigation. Now it is even being applied to solve such mundane mysteries as the precise ingredients used in a sausage recipe, and to answer that most difficult of questions “what exactly is in a doner kebab?”

Easy Science Experiments You Can Do At Home

Image from CSIRO, the Commonwealth Scientific and Industrial Research Organisation in Australia. Find more experiments in their Science By Email program, http://www.csiro.au

If you’re looking for activities to get the young people in your life to step away from the TV or computer, consider teaching them some science! Now, I understand that most young people probably will not jump at the opportunity to learn when they are “playing” online with their friends, but once they see how cool science can be, maybe they will change their minds.

A great resource is Scifun.org created by Chemistry Professor Bassem Shakhashiri at the University of Wisconsin – Madison.  This website is packed with information, but one of my favorite parts is the first option in the “Explore” section: Experiments You Can Do At Home.

Cold-War Bunkers Enlisted in the Fight Against Cold-Loving Fungus: More on the White-Nose Syndrome Story

Bunkers at Aroostook National Wildlife Refuge. photo credit: USFWS/Steve Agius

A lot has happened since I first wrote about White-Nose Syndrome, the fungal disease that has devastated bat populations in North America. The disease, caused by the cold-loving fungus Geomyces destructans, has been identified in many more places, including most recently confirmed cases in Georgia, South Carolina, Illinois and Missouri in the United States and Prince Edward Island, Canada.

Controlling the spread of this disease is a tremendous problem, because as I indicated in a previous blog post, keeping a hardy fungus from spreading among a population of densely packed small animals in tiny, cold damp areas is not a simple task.

This problem is going to require creative solutions, and scientists at the U.S. Fish and Wildlife Service may have come up with a great idea that answers two questions: How do you control the spread of White-Nose Syndrome and what do you do with 43 unused Air Force bunkers?

Compound Screening Using Cell-Free Protein Expression Systems

A protein chain being produced from a ribosome.

Both prokaryotic and eukaryotic cell-free protein expression systems have found great utility in efforts to screen organic compounds for inhibition of the basic cellular functions of transcription and translation, common targets for antibiotic compounds.

Cell-free systems can provide some advantages over cell-based systems for screening purposes. Cell-free systems allow exact manipulation of compound concentrations. This is an important parameter when evaluating the potential potency of the lead compound.

There is no need for cellular uptake to evaluate the effect of the compounds. While uptake evaluation is important for determining the eventual efficacy of the drug, it can unnecessarily eliminate valuable lead compounds in an initial screen. The interpretation of results in living cells is complicated by the large number of intertwined biochemical pathways and the ever-changing landscape of the growing cell. Cell-free systems allow the dissection of effects in a static system for simpler interpretation of results and the ability to specifically monitor individual processes such as transcription or translation. Individual targets not normally present, or found at low concentrations, can be added in controlled amounts.

The following references illustrate this application:

• Buurman, E. T. et al. (2012) Novel rapidly diversifiable antimicrobial RNA polymerase switch region inhibitors with confirmed mode of action in Haemophilus influenzae. J. Bacteriology 194, 5504–12.

• Zhang, Y. and Inouye, M (2009) The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin. J. Biol. Chem. 284, 6627–38.

• Jayasekera, M.M. et al. (2005) Identification of novel inhibitors of bacterial translation elongation factors Antimicrob. Agents Chemother. 49, 131-36.