Microorganisms: Infectious Disease and Ecology
Blog entries about bacteria, viruses, fungi and other microorganisms.
About the Wild Life in Our Homes (at least the single-celled kind)
Back in the fall, I received a sampling kit, an Informed Consent form and instructions for collecting samples for the Wild Life In Our Homes citizen science project. I carefully swabbed the requested surfaces: exterior and interior door trim, kitchen counter tops, pillowcases, etc., and sent my samples in. I later received confirmation that my samples had been received and again later confirmation that they were being analyzed.
The first paper from this project has been published by Dunn et al. in PLOS ONE (Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes). This initial report covers the first 40 homes sampled, all from the Raleigh-Durham, NC, USA area. Volunteers sampled their homes in the Fall of 2011, collecting specimens from nine areas: cutting boards, kitchen counters, refrigerator, toilet seat, pillowcase, door handle, TV screen, and interior and exterior door trim. The scientists used direct PCR and high-throughput sequencing to sequence the bacterial 16S rRNA gene from the submitted samples. By doing this they were able to estimate the diversity within each sample—they did not distinguish between live and dead organisms, and they did not sequence anything other than the bacterial 16SrRNA, so this study is limited to bacteria. Continue reading “About the Wild Life in Our Homes (at least the single-celled kind)”
Cold-War Bunkers Enlisted in the Fight Against Cold-Loving Fungus: More on the White-Nose Syndrome Story
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 (now renamed Psuedogymnoascus 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? Continue reading “Cold-War Bunkers Enlisted in the Fight Against Cold-Loving Fungus: More on the White-Nose Syndrome Story”
Compound Screening Using Cell-Free Protein Expression Systems
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.
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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.
Rats to the Rescue! From Landmines to Tuberculosis, These Rats Have a Nose to Help
A little over a year ago, I wrote about many of the characteristics of the domestic rat that made them an unexpectedly good choice for a family pet. Since I wrote that blog, my family has welcomed three very personable rats into our home.
To my family, rats are funny, playful, treat-stealing companions. However, in other areas of the world, some distant cousins to our mischievous threesome have become real-world heroes. These rats help clear fields of landmines and, as if that were not heroic enough, significantly increase the number of diagnosed tuberculosis infections. Continue reading “Rats to the Rescue! From Landmines to Tuberculosis, These Rats Have a Nose to Help”
Now Available for Purchase: Promega Colony Counter App
Do you count colonies on agar plates? Do you often need to average counts over a series of plates? The Promega Colony Counter app for iPhone® (3GS, 4S, and 5) and iPod® Touch (4th and 5th generation) allows you to take a picture of your plate, obtain a good first-guess count and refine it quickly by marking additional colonies and masking areas where the app may have over-counted.
The app is available for purchase for 3.99 USD from the iTunes store in North America and Europe.
Antibiotics and Honey–An Old Solution for a New Problem
This month saw the publication of a UK Department of Health report on the growing problem of antimicrobial resistance, which included the shocking recommendation that antimicrobial resistance be added to the UK government list of threats to national security alongside terrorism and pandemic flu. In this report, Professor Dame Sally Davies, Chief Medical Officer for the UK, focused on the increasing problem of multidrug resistant organisms–raising the profile of an important issue that many scientists and health-care professionals have warned us about before. A March 12 Nature editorial welcomed the recommendations as a sign that policy makers in the UK are taking the threat of antimicrobial resistance seriously and are prepared to take more steps to address the problem of multidrug-resistant organisms. Continue reading “Antibiotics and Honey–An Old Solution for a New Problem”
Copper Containing Surfaces and Their Potential for Reducing the Spread of Infection and Antibiotic Resistant Gene Transfer
As a scientist and a jewelry artist, there are not that many occasions when my two passions overlap. As a geneticist, I find the evolution and spread of antibiotic resistant microbes to be fascinating in a “this is really cool and utterly terrifying” sort of way. As a jewelry artist, I love experimenting with new and different metals. Some of my current favorites are stainless steel, copper and bronze, which is an alloy of copper and tin. So you might be able to imagine my excitement when I came across an article in mBio discussing the public health implications of horizontal gene transfer (HGT) of antibiotic resistance genes on clinical and public touch surfaces made from copper alloys compared to those made of stainless steel (1).
Stainless steel: The unexpected, gene-transferring truth
Stainless steel is often used in clinical and public settings as work surfaces as well as other surfaces that are touched and cleaned often. Stainless steel is used in these applications for many of the same reasons I like it for jewelry: it is strong, resilient, relatively inexpensive, stain- and corrosion-resistant and will weather regular cleaning/exposure to moisture well. There is something about a gleaming stainless steel work surface that looks, well, sterile. But is it? Continue reading “Copper Containing Surfaces and Their Potential for Reducing the Spread of Infection and Antibiotic Resistant Gene Transfer”
Mummies are a Reservoir of Viral History
Smallpox was a disease caused by infection with one of two strains of Variola virus (Variola major and Variola minor) and a worldwide scourge that killed up 35% of the people it infected. Luckily, a vaccine was developed when Edward Jenner noticed milkmaids infected with cowpox did not contract smallpox. While Jenner was not the first to vaccinate against smallpox, his discovery and testing were spread to a wide audience and thus became the basis for the vaccination efforts that have eradicated the virus in our lifetime. Despite all the research on smallpox, not much is known about the evolution of the virus. Sequence data for the virus only span the last 50–60 years. However, recent efforts published in the New England Journal of Medicine uncovered a new source for examining the history of smallpox infection: mummies.
Continue reading “Mummies are a Reservoir of Viral History”My Microbiome Made Me Do It
When I was in school I learned that there were two different kinds of bacteria, the nasty ones (pathogens) that could make you sick and the nice ones (commensals), which simply colonized you and did nothing much except occupy a spot that could otherwise be taken up by a pathogen. Any role for those commensal bacteria in health and disease was assumed to be no more than that of a harmless squatter. In recent years, studies of this benign microbial population (microbiome studies) have begun to reveal many more intriguing details about how they affect our health and wellbeing. Maybe it’s not so surprising that “good” bacteria could be good for our health—but could they actually affect how we behave? A review in Science summarized findings that indicate that this is indeed the case—at least for certain animal populations. Could it be true for humans as well? Could our colonizing organisms actually influence how we feel and what we do?
Continue reading “My Microbiome Made Me Do It”