Cool New Animation

Check out the cool new animation found on this website:

http://primaxstudio.com/stuff/scale_of_universe/ 

It's very good, but doesn't adequately represent the prokaryotic domains.  Oh well.  Still cool.

For Those of You Studying For Your Micro Midterm...

Good luck! 

Here's a little humour for you (from Gary Larson):

Can Microbes Degrade Continent-Sized Floating Plastic Islands?

Currents in many of the world's oceans, form vortexes (called gyres) that result in the accumulation of floating debris in a specific location.  One such gyre, in the north Pacific, has captured and deposited a mass of plastic covering an area that is said to be twice the area of the entire country of France!  This enormous mass of garbage goes by many names, including the Great Pacific Garbage Patch and the Pacific Trash Vortex. 

Image from: Kid Friendly Organic Life

Researchers at the University of Sheffield, UK are embarking on a major research project to determine factors that can help promote microbial degradation of plastic in ocean environments.  Much like the lab exercise that we started at the beginning of the semester at NAIT, they are examining physical and chemical factors that affect the rate at which plastic is degraded.  While we are studying degradation in a soil environment, they are focusing on a marine environment. 

Some Bacteria Can Stand Up and Walk

A recent article in Science by Gibiansky et al. (2010) reports that Pseudomonas aeruginosa can actually stand upright and use type IV pili (a motility structure we discussed in class the other day) to "walk".  They used a novel method of computational microscopy to track the progress of individual P. aeruginosa cells as they moved across a solid surface within a biofilm. 

This research builds upon earlier research by Orans et al. (2009) who elucidated the crystal structure of the P. aeruginosa type IV pilus in hopes of learning more about how to disrupt twitching motility over solid surfaces. 

Biofilm formation and twitching motility are both essential for the ability of P. aeruginosa to establish infections.  These types of infections are the most common cause of death for people afflicted with cystic fibrosis and they can cause a variety of other problems, such as ear, skin, and eye infections. 

The Rowland Institute at Harvard University collects videos of bacterial motility in action, including a video of twitching by P. aeruginosa from a paper by Skerker and Berg (2001). 


References:
M. L. Gibiansky, J. C. Conrad, F. Jin, V. D. Gordon, D. A. Motto, M. A. Mathewson, W. G. Stopka, D. C. Zelasko, J. D. Shrout, G. C. L. Wong. Bacteria Use Type IV Pili to Walk Upright and Detach from Surfaces. Science, 2010; 330 (6001): 197 DOI: 10.1126/science.1194238

Jillian Orans, Michael D. L. Johnson, Kimberly A. Coggan, Justin R. Sperlazza, Ryan W. Heiniger, Matthew C. Wolfgang, and Matthew R. Redinbo. Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility. Proceedings of the National Academy of Sciences, 2009; DOI: 10.1073/pnas.0911616107

Skerker, J.M. and Berg, H.C. Direct observation of extension and retraction of type IV pili. Proc Natl. Acad. Sci. USA, 98, 6901-6904 (2001).

E. coli Genetically Engineered to Produce Expensive Cancer Drug

In the Oct. 1 issue of the journal "Science", researchers report a major genetic engineering accomplishment.  The potent anti-cancer drug "Taxol" is very expensive (about $10000 per dose), in part due to the high cost of production.  In the past, the drug was extracted from the Pacific Yew tree - it required approximately two to four trees to treat a single patient.  More recently scientists succeeding in producing Taxol from plant tissue culture, but plant tissue culture is still very expensive, and the concentration of Taxol produced was miniscule.  The new genetically engineered E. coli strain is cheaper to grow and maintain, and produces about 1000 times more Taxol than the previous systems. 

For more information, see the original article in Science:
Ajikumar et al. 2010.  Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli.  Science 330:70-74.

Graduates from the NAIT Biological Sciences Technology - Lab and Research program often find work in research labs that do research of this nature - using similar tools and techniques to solve a variety of scientific and technological problems leading to profound benefits to society.  The basic methods used in this study are taught throughout the NAIT program.    

Park Lights Powered by Dog Poop

A dog park in Cambridge, Massachusetts is now using methane gas, produced by methanogenic Archaea from the anaerobic digestion of dog poop, to power the lights in the park (for a summary of the project, see this website). 

People walking their dogs in the park are encouraged to collect their dogs' waste using biodegradable plastic doggie-doo collection bags (like the ones we used for our plastics biodegradation lab).  Then the bags are fed into an anaerobic digester, where a consortium of Bacteria and Archaea digest the waste, producing a mixture of methane (CH4) and carbon dioxide (CO2).  The methane serves as a fuel to power the lights in the park. 

Methanogenic bacteria are used in a wide range of other similar applications, including a sewage treatment plant in Renton, Washington that is entirely powered by fuel cells that use methane. 

In addition to the benefit of generating energy from waste, another benefit is that the methane gets oxidized to CO2.  Methane is more than 20 times more potent as a greenhouse gas than CO2. 

How to RSS

This post isn't about microbiology at all, but rather provides a bit of information on how best to keep up with the world around us (including microbiology).  RSS feeds!

To keep up with all sorts of web content (such as news and blogs), instead of you having to go out and check what's new, RSS feeds bring the new content to you, in one convenient location (such as Google Reader).

To get set up to receive RSS feeds, you need to:

1. Set up a reader for yourself.  I recommend Google Reader.  You'll need to sign up for an account with Google, which is fairly easy and straightforward.
2. In your web browser, such as Mozilla Firefox, Google Chrome, or Internet Explorer, you must be signed into your reader account.
3. Go to your favourite news sites and blogs (such as www.dougs-bugs.blogspot.com) and subscribe to the RSS feeds.  Look for and click on the RSS symbol:

With Mozilla Firefox, any page that is RSS-enabled will have the RSS symbol appear in the address bar, making it very easy to subscribe.

For more information on how to set up RSS-feeds, here is the video that I showed in class: RSS in Plain English.

Researchers Working on a Vaccine Against the Black Plague

The Black Plague?  Why would researchers work on a vaccine against a disease that no one gets anymore?  The plague, caused by the Gram-negative bacterium Yersinia pestis, is best known for the plague pandemic that decimated the population of Europe by a third in the 1300's. 

There is considerable interest in developing a vaccine against Yersinia pestis as it is among the list of "category A", highest priority microorganisms on the bioterrorism watch-list (along with Bacillus anthracis, Clostridium botulinum, Francisella tularensis, smallpox, and hemorrhagic viruses like Ebola).  There is a long history of military research and deployment of the plague as biological weapon.  For example, the former Soviet Union, during the Cold War, produced bombs to deliver Yersinia pestis to major US cities. The Japanese military dropped Yersinia pestis-infected fleas on parts of China during World War II. 

Progress on the vaccine has not been encouraging.  Recent studies still show unpredictable and only partial immunization. 

For a review of the use of plague as a biological weapon, check out this paper.

Ig-Nobel Prize Recognizes the Work of Marine Microbiologists

Everyone has heard of the Nobel Prizes - awarded in recognition of ground-breaking work in scientific research.  Well, the Ig Nobel Prizes recognize strange and unusual research.  From the Ig Nobel website:

The Ig Nobel Prizes honor achievements that first make people laugh, and then make them think. The prizes are intended to celebrate the unusual, honor the imaginative — and spur people's interest in science, medicine, and technology.

One of this year's prizes goes to a team of microbiologists, including Karina Acevedo-Whitehouse of the Zoological Society of London, studying the microflora of cetaceans (whales).  They developed a novel sampling technique involving the use of a remote control helicopter to collect samples from the residue exhaled from whale blow-holes.  They then examine the samples for the presence of possible respiratory pathogens, such as Mycobacterium tuberculosis and Streptococcus pneumoniae.  Their whale-snot research may help conservation efforts to save the huge creatures. 

Check out this website to see a cool video of their helicopter-sampling technique.

A New Approach to Treating Bacterial Infections

The typical treatment for a bacterial infection: antibiotics.  These life-saving chemicals have had an enormously positive impact on human health and longevity, providing treatments for diseases that once killed millions of people.  The problem: antibiotics are becoming less and less useful as bacteria evolve antibiotic resistance.  Diseases once thought to be a thing of the past are re-emerging with antibiotic resistant strains of bacteria causing infections.  For example, the black plague, which decimated the population of Europe back in the 1300's, is re-emerging with the evolution of antibiotic strains of Yersina pestis. 

Antibiotics treat bacterial infections by killing the bacteria or by inhibiting bacterial growth allowing the immune system to eliminate the invading bacterial cells.  Antibiotic resistance mechanisms rapidly evolve due to the selective pressure put on bacterial populations to gain resistance.  Any bacterial cell with a mutation that allows it to survive antibiotic treatment will proliferate, passing on the antibiotic resistance trait to all its descendants, resulting in a population of antibiotic-resistant cells. 

Researchers at Case Western Reserve University in Cleveland, Ohio have recently tried a different approach to treating bacterial infection. 

They are searching for an alternative treatment for Staphylococcus aureus infections.  Methicillin-resistant S. aureus (MRSA) is a serious cause for concern due to a large number of hospital-aquired (nosocomial) infections.  

Instead of using drugs to kill MRSA, they designed a drug that would simply prevent the cells from releasing the toxins that make people sick.  The bacteria are not destroyed by the drug, so there isn't any selective pressure for the bacteria to evolve resistance mechanisms. 

Not a Microbiology Post - Plant Inventory Cuts Number of Recognized Plant Species by 600,000

Although this blog primarily focuses on microbiology, we are currently discussing taxonomy and systematics in class, so this blog post is related to that topic - but in the Plant Kingdom.

Many of the previously recognized plant species were described in times prior to the use of current molecular genetic tools for constructing accurate phylogenies and before the widespread availability of information technologies for maintaining an accurate list of plant species.  Consequently, many plants were described more than once and given multiple distinct species names.

Efforts are now underway to create an accurate and complete inventory of all of the world's plants. To date, there have been 600,000 previously recognized plant species stricken from the list due to redundancies.  It is estimated that the final list will contain only about 400,000 plant species in total.

This article illustrates some of the issues that we discusses in class - difficulties and inaccuracies related to the old system of taxonomy, and it also highlights the improvements made with modern systematics.

An accurate inventory of plant species is thought to be essential for conservation efforts.

New Extremophilic Archean Species Discovered

The first topic in our microbiology class is a "survey of the microbial world" where we are touching upon the vast diversity of microbial life on Earth.  Earlier this month, a new type of extremophile was found dwelling in the depths of the ocean near a deep sea hydrothermal vent.  As might be expected, this barophilic and hyperthermophilic organism is from the domain Archaea.  Thermococcus onnurineus is of particular interest to scientists because it is the first organism found at these light-less underwater ecosystems that have the capability of growing using formate (HCOO-) as their sole "food" source (carbon and energy source).  They are thought to live symbiotically with fermentive bacteria near hydrothermal vents. 

The scientists first hypothesized that T. onnurineus was capable of growth on formate after having sequenced its genome and finding genes that were known to be involved with formate metabolism.  They tested the hypothesis by growing the bug up in culture conditions providing formate as the only available carbon and energy source. 

Discoveries of this nature provide more insight into ongoing development of technologies for biohydrogen production (renewable energy source). 

For more information, see the original paper:
Formate-driven growth coupled with H₂ production, Yun Jae Kim et al., Nature 467 , 352-355 (16 September 2010).
doi:10.1038/nature09375