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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.