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Attention Subscribers After 5/24/2013

The 5th edition of Through the Microscope is now finished and available as a website subscription, as an ebook and as a hard copy from For subscribers to the 4th edition who are still using it, the book will stay available until May 15th, 2014. At that point, it will be retired. Thank you for all your support. For more information about the 5th edition, check out the latest news


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Edition 5 of Through the Microscope

Posted by paustian on May 23, 2013 - 10:53 AM

The process of creating the 5th edition of Through the Microscope has begun. Unlike typical publishers, the process is completely open and you can watch the book take shape. Here is what is coming in the new edition

  1. Upgrade the backend server software to the latest release of Zikula.
  2. Create a new look for the book
  3. Update Microbial Diversity
  4. Update Microbial Ecology
  5. Update Bacterial Structure

The deadline for the 5th edition is August 2013.

Using Biosensors to detect important molecules

Posted by paustian on Feb 14, 2013 - 08:56 AM

An international team of scienctists has worked out a new biosensor that is able to detect its target molecule over a large concentration range. This will make these sensors more useful in many different applications; drug detection, cancer screenings, cancer treatment, and infectious disease. The method can detect its target in seconds.

Calorie restriction may not lengthen life

Posted by paustian on Sep 13, 2012 - 12:42 PM

The results are in, calorie restriction may not extend your life. Previous studies of rats and mice demonstrated that calorie restriction could extend life span. While human behavior can sometimes be rat-like, there are distinct differences in physiology between rats and humans. A much anticipated calorie restriction study using rhesus monkeys shows that these results do not translate to our close cousins. Being overweight is a tremendously important predictor of life expectancy, but the number of calories you consume, if you are still thin, does not appear to make a difference in this study.

Test taking actually improves comprehension of material

Posted by paustian on Aug 01, 2012 - 03:14 PM

Jeffrey D. Karpicke and Janell R. Blunt report that using tests to measure your comprehension of a subject also has the side benefit of helping you remember the material better. The NY times has an excellent article summarizing the findings.

Through the Microscope has dozens of concept quizzes throughout the text that help you to check your understanding of the material. Each chapter also has an end of chapter quiz to further cement the concepts. As you use this text, make sure you take advantage of theses tools.

Natural gas as a way to reduce climate change?

Posted by paustian on Jul 10, 2012 - 01:03 PM

Cornell Professor Lawrence M. Cathles who studies Earth sciences calculates that switching from coal and oil to natural gas as we move toward renewable energy could decrease carbon emissions significantly. We do need a transition period, but lets make it as short as possible.

A new antimalaria drug: less expensive, simple treatment, easy to produce

Posted by paustian on Jul 09, 2012 - 11:15 AM

Malaria is the most important tropical disease in the world, with over 665,000 deaths worldwide, many of them in children. The malaria parasites, protozoa of the Plasmodium genus, are susceptible to a number of drugs, but have been becoming more resistant the drugs available for treatment. Professor Jonathan Vennerstrom of the University of Nebraska Medical Center College of Pharmacy and his team announce the development of Synriam (a synthetic trioxolane) that has many of the properties of artemisinin, but none of the downsides.

The paper describing the synthesis, toxicology, and effectiveness of this trioxolane is available in Nature. I found it was interesting that this paper was published in 2004, yet the clinical trials took 8 years to complete and bring this drug to market. It demonstrates how careful governments have to be with new drugs being introduced into the market.

Getting the floc out of here

Posted by paustian on Jun 04, 2012 - 01:34 PM

Floc is a real work, even if your spell-checker flags it. In fact, it's a scientific word that describes those little particles of fluff that float in aquatic systems. These little specs floating in the water column have a sinister secret, they harbor antibiotic resistance. Drudge et. al from McMaster University tested four different sites, Hamilton Harbour, impacted by sewer overflow; Sunnyside Beach in Toronto, impacted by wastewater; a rural stream by light agricultural activities; and a remote lake in a natural preserve area in Algonquin Park looking for 54 different known antibiotic resistance genes. As one would expect, the more pollution in the water system, the more antibiotic resistance genes were found. This is yet another reason to keep aquatic environments clean.

Bacteria are your friends

Posted by paustian on Mar 23, 2012 - 10:19 AM

Most people think germs on their bodies are a Bad Thing. If they didn't, hand sanitizers, disinfectant soap and bleach would not sell so well. As we learn more about the microbes that inhabit our bodies, we are realizing that the human being is really a superorganism composed of about a trillion human cells and 10 trillion microorganisms. Rarely a microbe will cause illness, but these are transient residents that the body actively removes. Most other microbes that live on us are benign and a significant number of them are critical to our good health.

In the latest issue of Science magazine, Torsten Olszak et. al describes how the microbes we come in contact with as children stimulate natural killer cells (part of the immune system) assisting in their development. Without this contact, the natural killer cells do not develop tolerance and can precipitate immune-related diseases such as irritable bowel syndrome and asthma. This contact must occur during childhood for tolerance to develop.

Culturing microorganisms

Posted by paustian on Mar 02, 2012 - 03:54 PM

For over 100 years microbiologists have known, to their great consternation, that in any given environment, at least 90% of all microbes are unculturable. In the last few decades, we have developed molecular tools to see these microbes in the environment and determine their presences and number, but we still cannot bring them into culture. There are all sorts of ideas for why this might be true. Many of these microbes may be slow growing, and the fast growing microbes easily outpace them in laboratory medium. Maybe the media we use is "too rich" for many microbes and we need to create media with more dilute nutrients to capture these shy microbes. Maybe the metabolic demands of these microbes were too difficult to replicate in the laboratory and many of them will not grow. Whatever the reason, as of right now, we are nearly blind when it come to these unculturable microbes.

Just this week, what I believe will become a landmark paper, was published in Applied and Environmental Microbiology. Buerger et. al created a simple, elegant experiment to try to capture the slow-growing bacteria. Sediment from the ocean shore of Massachusetts Bay was diluted and then dispensed into wells of a microtiter plate such that each well received only 1 microbe per well. The growth medium used was 0.1x LB medium, a dilution of a common, rich medium. The plates was carefully wrapped and placed in a humidified chamber for 18 months. Yes, that is a 1.5 year experiment! Periodically the plates were checked for growth and any well showing growth was then characterized.

A topoisomerase I mutation is lethal, the definative paper.

Posted by paustian on Feb 28, 2012 - 03:45 PM

Topoisomerase I unwinds the DNA during cell replication and is an enzyme that is found in Archaea, Bacteria, and Eukarya. Most every living thing has a homolog. To everyone's surprise, it is possible to create mutations that completely remove the activity of the enzyme, yet have cells capable of growth. These cells are sick, but they can grow. The latest research by Stockum et al. shows that these deletion mutants of topoisomerase I actually have compensating mutations, and in fact loss of topoisomerase I is lethal. This makes much more sense.

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