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.