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.