Yersinia pestis, the causative agent of plague, has caused several pandemics throughout history and remains endemic in the rodent populations of the western United States. More recently, Y. pestis is one of several bacterial pathogens considered to be a potential agent of bioterrorism. Thus, elucidating potential mechanisms of survival and persistence in the environment would be important in the event of an intentional release of the organism. One such mechanism is entry into the viable but non-culturable (VBNC) state, as has been demonstrated for several other bacterial pathogens. In this study, we showed that Y. pestis became nonculturable by normal laboratory methods after 21 days in a low-temperature tap water microcosm. We further show evidence that, after the loss of culturability, the cells remained viable by using a variety of criteria, including cellular membrane integrity, uptake and incorporation of radiolabeled amino acids, and protection of genomic DNA from DNase I digestion. Additionally, we identified morphological and ultrastructural characteristics of Y. pestis VBNC cells, such as cell rounding and large periplasmic spaces, by electron microscopy, which are consistent with entry into the VBNC state in other bacteria. Finally, we demonstrated resuscitation of a small number of the non-culturable cells. This study provides compelling evidence that Y. pestis persists in a low-temperature tap water microcosm in a viable state yet is unable to be cultured under normal laboratory conditions, which may prove useful in risk assessment and remediation efforts, particularly in the event of an intentional release of this organism.

The sequence of non-contacted bases at the center of the 434 repressor binding site affects the strength of the repressor-DNA complex by influencing the structure and flexibility of DNA (Koudelka, G. B., and Carlson, P. (1992) Nature 355, 89 -91). We synthesized 434 repressor binding sites that differ in their central sequence base composition to test the importance of minor groove substituents and/or the number of base pair hydrogen bonds between these base pairs on DNA structure and strength of the repressor-DNA complex. We show here that the number of base pair H-bonds between the central bases apparently has no role in determining the relative affinity of a DNA site for repressor. Instead we find that the affinity of DNA for repressor depends on the absence or presence the N2-NH 2 group on the purine bases at the binding site center. The N2-NH 2 group on bases at the center of the 434 binding site appears to destabilize 434 repressor-DNA complexes by decreasing the intimacy of the specific repressor-DNA contacts, while increasing the reliance on protein contacts to the DNA phosphate backbone. Thus, the presence of an N2-NH 2 group on the purines at the center of a binding site globally alters the precise conformation of the protein-DNA interface.It is well established that the sequence-specific binding of proteins to DNA involves specific contacts between DNA bases and protein side chains in a process known as "direct-readout." The precise alignment of DNA and protein can be specifically modulated by the sequence of DNA bases in the binding site that are not directly contacted by the protein. This phenomenon is known as indirect readout. In indirect readout, the affinity or specificity of a protein-DNA complex depends on sequence-dependent alterations in the conformation and/or conformational flexibility of the noncontacted bases in the DNA site.Since sequence-dependent DNA structural differences play a role in mediating protein-DNA complex formation, this implies that a protein binds only to a distorted DNA conformation. Noncontacted bases may be envisioned to affect the formation of a protein DNA complex in any of three ways: 1) altering the deformability of DNA; 2) altering the structure of the DNA in the bound complex, thereby changing the strength of particular protein-DNA contacts; or 3) altering the structure of the unbound DNA, thereby eliminating or requiring the imposition of energetically costly large-scale DNA conformational changes. Although indirect readout is part of the sequence recognition mechanism of many sequence-specific DNA binding proteins, little is known about the physical basis of how base sequence and/or the functional groups on the bases contribute to the sequence dependence of such DNA deformations. In addition, the mechanisms by which sequence-dependent differences in DNA conformation influence the strength or specificity of protein-DNA complexes is also unclear.434 repressor does not contact the functional groups on bases at the center of its binding site (1, 2; see also Fig. 1...

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Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratorybased identification, common in the United States, is unavailable 1 . The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment 2 . The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-ofcare platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis.Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters 3

Inactivation of the lambdoid phage repressor protein is necessary to induce lytic growth of a lambdoid prophage. Activated RecA, the mediator of the host SOS response to DNA damage, causes inactivation of the repressor by stimulating the repressor's nascent autocleavage activity. The repressor of bacteriophage lambda and its homolog, LexA, preferentially undergo RecA-stimulated autocleavage as free monomers, which requires that each monomer mediates its own (intramolecular) cleavage. The cI repressor of bacteriophage 434 preferentially undergoes autocleavage as a dimer specifically bound to DNA, opening the possibility that one 434 repressor subunit may catalyze proteolysis of its partner subunit (intermolecular cleavage) in the DNAbound dimer. Here, we first identified and mutagenized the residues at the cleavage and active sites of 434 repressor. We utilized the mutant repressors to show that the DNA-bound 434 repressor dimer overwhelmingly prefers to use an intramolecular mechanism of autocleavage. Our data suggest that the 434 repressor cannot be forced to use an intermolecular cleavage mechanism. Based on these data, we propose a model in which the cleavage-competent conformation of the repressor is stabilized by operator binding.

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Theiler's murine encephalomyelitis virus (TMEV) is a naturally occurring enteric infection, easily passed from mouse to mouse in communal housing. However, TMEV is often inoculated intracerebrally (IC) to produce a mouse model of multiple sclerosis (MS). It has long been accepted that maintaining colonies of IC-infected mice within laboratory animal facilities poses a risk of spreading infection from mouse to mouse via the fecal-oral route as well as contaminated equipment or personnel. Interestingly, the extent of virus shedding from IC-inoculated mice has not been investigated, although several publications have remarked on the lack of virus in the peripheral body of this MS mouse model. Viral shedding, thus infectivity, would require that TMEV escape the central nervous system (CNS) and be found in bodily secretions. We hypothesized that if the virus can escape the CNS, it would be found circulating within blood or other secretions postinjection (PI), after the blood-brain barrier has been experimentally breached. The data presented show no TMEV RNA was found in the serum, saliva, or feces during the acute and chronic infection stages, although all subjects were positive for TMEV RNA in the CNS. These results, in conjunction with published anecdotal evidence, suggest that mice IC-inoculated with TMEV are not contagious, and thus a relaxation of containment methods is warranted. This report is an example of a collaborative effort between biosafety and research professionals to identify and collect scientifically relevant data to inform a risk assessment.