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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 lulu.com. 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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Rapid detection methods for pathogens

Posted by paustian on Oct 07, 2008 - 12:06 PM


Detecting pathogens in and on food is of great interest, especially considering the amount of ready to eat and processed food that is now consumed in the world. Recent Salmonella enterica and Haemorrhagic E. coli outbreaks have demonstrated the importance of testing food. One drawback to many current methods is that they rely on culturing the microbe from the food, with these procedures taking days to complete. Rapid methods for detecting pathogens are under development and Yamazaki et. al describe a new method, a loop-mediated isothermal amplification assay, for the detection of Vibrio parahaemolyticus. The assay takes 60 minutes or less to complete, in contrast to culturing methods that require several days.

Motility and competitiveness in mutualism and pathogenicity

Posted by paustian on Oct 07, 2008 - 11:50 AM

Photorhabdous luminescens is a pathogen of certain important insects. What is more interesting from a science point of view, is that this microbe has a nematode partner. The nematode attacks the insect larvae and injects P. luminescens into it. The microbe then quickly kills the insect larvae and provides a ready meal for itself, with the nematode happily consuming the feast of microbes generated. In this report, Easom and Clarke demonstrate that while loss of motiliy does not seem to affect either symbiosis (with the insect or the nematode), a motility minus P. luminescens is less fit than wild-type for growth and in nature would be quickly out-competed by its motile brethren.

Working out what an ORF does

Posted by paustian on Oct 02, 2008 - 01:09 PM
ORFs are not a new kind of dolphin. They are Open Reading Frames worked out by DNA annotation programs. Scientists understand the genetic code and have written programs that can scan sequenced DNA and figure out where likely coding regions are. Why likely? Because we never really know if a cell uses that DNA for coding. Programs have gotten pretty good at guessing, and potential protein coding sequences get identified pretty accurately. Problem is, often, its not clear what a protein does. Sometimes the protein coded for has an amino acids sequence that is very similar to a protein thats function is known. If the homology is high, in almost all cases, the unknown protein has the same function. But what about all the other ones? In this paper by Sluijter et. al the authors describe how they determined a potential function of a ORF product and then tested it. The gene was the MPN229 ORF from Mycoplasma pneumoniae. They first detected homology at the DNA sequence and protein sequence level to single-stranded DNA binding (ssb) proteins from other microbes and then demonstrated ssb activity for the purified protein from Mycoplasma pneumoniae. This protein has significance because it may be involved in antigenic variation, a process that helps the microbe avoid attack by the hosts immune system. 

Cancer metastasis may occur earlier than thought

Posted by paustian on Sep 26, 2008 - 07:40 AM
One of the more deadly parts of any cancer, is the ability of cancer to metastasize to other parts of the body. Since this is a difficult process, it was thought that this occurred late in a cancer, when there were many cells to attempt the journey. A report by Podsypanina et. al suggests that this may not be the case and that normal, pre-cancerous cells may be able to metastasize.

LuxS is everywhere, but quorum sensing is not

Posted by paustian on Sep 22, 2008 - 12:30 PM
Rezzonico et al. find that LuxS, part of a mechanisms called quorum sensing, may have a metabolic role in sulfur metabolism in many microbes. A significant number of the bacteria that were thought to use this quorum sensing gene, may actually be using this enzyme in the formation of S-adenosyl-L-methionine only. These authors searched through the genomic databases looking for the receptors that were required for quorum sensing (using LuxPQ of Vibrio harveyi and Lsr ABC-transporter from Salmonella typhimurium). They found that a subset of LuxS containing candidates, also had the receptor for the quorum-sensing system. Without both, it is dubious that quorum sensing can occur. However, quorum-sensing ability cannot be completely ruled out, as they may be using a quorum-sensing receptor that is functionally workable, but not homologous to the two candidates that were used for the search.

A new rapid method for the detection of Salmonella in food

Posted by paustian on Sep 22, 2008 - 12:12 PM
Regan et al. have developed a method to rapidly detect Salmonella in various foods. Classic tests involve selection and identification procedures that take up to 4 days to complete. The method proposed involves a two-step enrichment (requiring about 20 hours) followed by RT-PCR (real time polymerase chain reaction). RT-PCR is a way to rapidly amplify and detect specific DNA fragments in a solution. Primers, little DNA sequences that are compatible with the sequence of interest and flank it, are added to the sample to test. A series of cycles with a DNA polymerase are then run. If the sequence of interest is present, it will be greatly amplified and detected by special equipment. The test developed showed accuracy matching that of the classical method. This may be useful in the tracking of epidemics and the rapid testing of food.

Predicting antibiotic resistance

Posted by paustian on Sep 18, 2008 - 01:08 PM


Predicting antibiotic resistance to novel anitmicrobials would be a neat trick. And with the use of bioinfomatics and the large collection of DNA that has been sequenced, it may be possible. Sanchez et. al. et. al demonstrate a proof of concept experiment. This is a clever, and novel approach and will hopefully better prepare medicine to predict and deal with drug resistance.


Ticks and disease

Posted by paustian on Sep 18, 2008 - 12:13 PM


Francisella tularensis causes a nasty febrile infection that is highly contagious in humans . It is of intense interest because of its prevalence in the environment and its potential as a biological weapon. The natural reservoirs of the microbe and its prevalence are not fully understood, and a study by Zhang et. al. provides some insight into this. The microbe was found in two tick species, Dermacentor silvarum (sheep tick) and Ixodes persulatus, at a rate of 1.98 % in Northern China. So the microbe is reasonably common in the environment.


Ulcers and a Mexican Pre-Columbian Mummy

Posted by paustian on Sep 15, 2008 - 12:37 PM

There is often a debate about what diseases were brought to the America's with the arrival of Europeans and what was was already there. It has been suggested that ulcers, caused by Helicobacter pylori, were also shared with the native population by conquering Europeans. A recent study by Castillo-Rojas et. al. decided to answer this question. Extracts taken from mummies were subject to PCR amplification looking for evidence of Helicobacter pylori. These mummies pre-date the arrival of the Conquistadors. If they are infected with the microbe, then it was already here and not brought in during the 15th century. They found that in fact, some of the mummies were infected and ulcers.

Through the Microscope Second edition is now available

Posted by paustian on Aug 28, 2008 - 07:24 PM
The second edition of Through the Microscope is now complete. The second edition has new figures, improved clarity, updated legends and the removal of many errors and typos. This should make the experience with the book that much better. You can enjoy the book in two ways.
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