New features for the textbook have been added over the last month. The back end code that creates glossary entries have been completely redone. Pages from the textbook now load much faster and the authors or administrators can define new words, whose definitions automatically become available to the entire textbook. If you mouse over highlighted words (that appear green like this) a popup glossary entry will be shown to you. This joins other nice features of the textbook including...

• A search function
• The ability to highlight text and then call it back during study time.
• Concept quizzes that test your comprehension of material you just read.
• Animations and videos that bring microbiology alive.

To make the best use of the textbook, don't treat it as you would a conventional hardcover book. Take advantage of the web sites many features.

This website and its accompany book at lulu is a small shot across the bow of the publishing houses that charge ridiculous fees for student textbooks. A similar and related battle is brewing in the journal publishing racket. Nature is proposing a more than 400% increase in the subscription fee they charge the University of California. And we are not talking chump change. The current fee is $4,465 and Nature wants to raise its feel to $17,479 per journal. That amounts to over $1 million dollars a year in subscription fees for the campus.

Subscription processing from PayPal used to involve manual authorization of each user by staff at Textbook Consortia. As of May 2010, a robust implementation of the instant payment notification system has been installed. With this new system, the potential subscriber clicks on the PayPal button and fills out a simple form for payment. Once payment is verified, PayPal sends a notification back to the Through the Microscope site and the subscriber is granted access. Authorization should take just a few minutes. As always, if you are having trouble, contact Textbook Consortia using the contact form.

If you purchase a hard copy of the book from lulu, you are entitled to a free subscription to the website as part of the purchase price. In this case you need to contact Textbook Consortia using the contact form.

The upgrade to the site is finished. I will be adding new features now that I have moved to the latest software.

To those that are signing up for the book. Once you purchase your subscription to the textbook, it can take up to 24 hours for approval. Therefore, please be patient. Orders are processed quickly and in most cases it is only a few hours before you get access to the book.

Betancor et al. examine 266 isolates of Salmonella enterica serovar Enteritidis comparing their genomes and looking for genetic variability in the strains that have been causing a Salmonellosis epidemic in Uruguay. An important take home message from this study was that much of the genetic variability of these isolates has come from phage infection and excision. Phage may turn out to be a major mechanisms of genetic change and may be involved in modulating virulence.

Cohen et. al report, in Nature Microbiology, that the addition of ampicillin, cephalexin or pipericillin will cause E. coli to induce the SOS response. The SOS response is an emergency repair system microbes will turn on when the surrounding environment turns ugly. There are a number of signals that will turn on the SOS response, but the classic inducer is DNA damage. It is now clear that antibiotics will also turn on this response and prevent the cell from dividing and growing. This in turn will make them better able to withstand the harmful effects of the drug they are facing. With this knowledge it may be possible to create effective drugs that inhibit the SOS response, making E. coli and other microbes more susceptible to antibiotics.

Science Magazine has a nice recap of where we are and where we are going with swine flu. It traces the epidemic and gives more information on the origin of the various genes of the virus. It turns out this influenza has ancestry containing human, swine and avian influenza genes. While so for it seems like this virus is causing mild disease, I think it is too early to tell how serious it is going to be. We will learn more as it spreads across the southern hemisphere, as they are approaching winter in that region. One part of this epidemic that has been impressive is the quick reaction of the Mexican, United States and Canadian governments and WHO to this outbreak. Their cooperation likely kept this outbreak from being more severe. Mexico deserves special mention, as they took the extraordinary step of keeping everyone home for a week to greatly slow the rate of transmission in the country. The availability of antiviral drugs and rapid development of a vaccine should help mitigate the damage this virus can cause.

Recent work by the CDC in analyzing new cases of H1N1 in two residents of San Diego indicate that a novel flu strain has developed and this strain is capable of human-to-human transmission. Influenza has been reported in Mexico, Canada, the U.S. and around world. It is becoming more and more likely that a pandemic of influenza is about to occur. Note that these things are extremely difficult to predict, but all the elements are now in line.

Chavos, Posner and Hedtcke compared the profitability of various forms of farming in Southern Wisconsin. The13 year study (1993-2006) found that organic farming is as profitable as conventional farming which uses synthetic pesticides and fertilizers. In fact, when the price premium that organic food goes for is factored in, organically grown food is more profitable.

In the old days. If you wanted to know what a gene did, you made a mutation in it and then tested its growth characteristics in some way to see what it could not do. In some cases, this would tell you something, but sometimes, it would not. If you did not have the growth conditions right, or your gene did something subtle, its phenotype would remain a mystery. Often, you needed to know something about your gene before you could learn anything else. A chicken or the egg conundrum that kept geneticists tearing their hair out.

In today's world, this is no longer the case. With the use of a microarray that can look at the gene expression of an entire genome of a microbe in one experiment, it becomes relatively easy to learn a large amount about a gene of interest. Merighi et al. describe experiments to determine the role of preA and preB in virulence and find that this two-component regulatory system does in fact turn on genes that change the behavior of cells. However, they do not find overt virulence factor influences, but they do trace down what genes are affected by PreA the response regulator of the system.

We are in a constant battle against the microbes around us. To them, we are a very attractive food source. Many microbes live on our bodies in peaceful coexistence, in fact they provide us many benefits, especially protection from pathogens. These are the normal flora and you can read about them in Host-Microbe Interactions. However, other organisms are too disruptive and cause damage to the host, creating a disease state. The article by El-Sharoud et al. describes an emerging pathogen of milk products, Chronobacter, and the author's efforts to survey it source and abundance in the environment.

Using phage to stop bacterial infections has a long history and was gaining popularity in the early 20th century until the discovery of antibiotics. Now that antibiotic-resistant strains of microbes are starting to appear, phage treatments may make a come back. Dabrowska et al describe some experiments with phage and their impact on cancer cell migration. I find this an odd property for phage to have, but who knows?

Biological research is changing in interesting ways due to the advent of a number of new technologies. One such technology is microarrays. The problem at hand was figuring out what genes were being affected by a change in iron concentration in the microbe Pseudomonas syringae, an important pathogen of tomatoes. The relative absence of iron (Fe) is a signal for the microbe that it is now in its host.

Francisella tularensis is a deadly pathogen that when infecting humans, creates an illness that is similar to anthrax. Because of its widespread distribution, it has the potential to be a potent bioweapon. Little is known about the pathology of the disease and the initial studies by Ojeda et al. demonstrate the dissemination of the pathogen depending upon its method of infection. In it they find that pulmonary infection, is a particularly deadly method of infection, resulting in rapid spread throughout the body and frequently death in untreated individuals.

When E. coli encounters a stressful environment, such as the acidic stomach, it will use Dps (DNA-binding protein in starved cells) to protect its DNA. In this study Jeong et al. demonstrate the protective effect of this protein. Mutants lacking Dps are created and shown to have lower acid tolerance than wild-type. Various other experiments also show that without Dps, significant DNA damage takes place in an acidic environment. Charles Kaspar is a faculty member at UW-Madison.

Stabler et. al describe a microarray that is a conglomeration of many of the virulence factors from various species. In their words, "[The] microarray consists of 4958 reporters from 151 bacterial species and include genes for the identification of individual bacterial species as well as mobile genetic elements (transposons, plasmid and phage), virulence genes and antibiotic resistance genes." They infer that a microbe having any collection of these genes is a potential problem. Also, a suspect pathogen can be identified, since each one will have a distinctive footprint on the microarray. This is a clever idea and should have great utility in tracking pathogens, bioterrorism and diagnosing illness.

Avian influenza, while out of the news, is still of great concern to the health community. A pandemic will occur at some point, but it is impossible to predict when. The CDC estimates that we are closer to having a pandemic now than at any time since the last one, 40 years ago. In this recent article, Mills et. al discuss the possibility of a pandemic emerging in multiple areas at once, and how to contain it.

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.

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.

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.