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. 

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.

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.

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 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.

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.

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.

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.

1. Purchase a subscription to the web site for $30, which gives you access to all the content. Read the directions on how to sign up for a subscription.
2. Purchase the hard copy of the textbook, which also includes a free subscription to the website for $55. The textbook is available for sale at lulu dot com. Click on the button below.

Gary and I have spent the past month combing through the text book looking for errors and clarifying passages that students have had trouble with. Hundreds of errors and typos have been removed and many figures have been clarified or improved. The book is now in a much more polished state than it was just a few weeks ago. In the next week, a new print edition will be sent to the printer and will be ready for order. Look for an announcement soon.

For those who like the website, but would really like a hard copy to be able to take with them, the authors are pleased to present.

Through the Microscope

The website, excluding chapter 26, is available as a book from lulu.com. This is a paperback book and is a faithful rendering of the text. This was made possible by the development of an application to render the entire website as a pdf file that lulu.com can then publish. To keep costs low, the process is nearly automatic (well it does take about a day to get things in order and verify that it is rendered correctly). What this does mean is that the formatting is not beautiful, but the text is completely usable. If you want a hard copy of the web site, you now have an outlet. The price of the text has been set at $55.00