The publication of the complete genome sequence for Mycobacterium tuberculosis H37Rv in 1998 has had a great impact on the research community. Nonetheless, it is suspected that genetic differences have arisen in stocks of H37Rv that are maintained in different laboratories. In order to assess the consistency of the genome sequences among H37Rv strains in use and the extent to which they have diverged from the original strain sequenced, we carried out whole-genome sequencing on six strains of H37Rv from different laboratories. Polymorphisms at 73 sites were observed, which were shared among the lab strains, though 72 of these were also shared with H37Ra and are likely to be due to sequencing errors in the original H37Rv reference sequence. An updated H37Rv genome sequence should be valuable to the tuberculosis research community as well as the broader microbial research community. In addition, several polymorphisms unique to individual strains and several shared polymorphisms were identified and shown to be consistent with the known provenance of these strains. Aside from nucleotide substitutions and insertion/deletions, multiple IS6110 transposition events were observed, supporting the theory that they play a significant role in plasticity of the M. tuberculosis genome. This genome-wide catalog of genetic differences can help explain any phenotypic differences that might be found, including a frameshift mutation in the mycocerosic acid synthase gene which causes two of the strains to be deficient in biosynthesis of the surface glycolipid phthiocerol dimycocerosate (PDIM). The resequencing of these six lab strains represents a fortuitous "in vitro evolution" experiment that demonstrates how the M. tuberculosis genome continues to evolve even in a controlled environment.Publication of the whole genome sequence of the H37Rv strain of Mycobacterium tuberculosis by Stewart Cole and colleagues in 1998 provided a breakthrough in tuberculosis (TB) research (8), leading to insights into the biology, metabolism, and evolution of this infectious pathogen. Large protein families related to fatty acid and polyketide biosynthesis, regulation (e.g., sigma factors and two-component sensor systems), drug efflux pumps and transporters, and the PE_PGRS proteins (a large duplicated family unique to the M. tuberculosis group of mycobacteria) were identified. In addition, transposons, prophage-like elements, and other repetitive and/or mobile genetic elements were identified (18). This genomic information has played an essential role in interpreting gene expression studies, modeling persistence, and identifying essential proteins as putative targets for drug discovery. However, to date the functions of only half of the genes (1,756/ 4,066) have been determined or predicted, and the rest remain annotated as "hypothetical proteins" (6).The H37Rv strain was initially selected for sequencing because it is a widely used laboratory strain that has retained its virulence. H37Rv was initially derived from a clinical isolate, H37, obtained fr...

The lone CX3C chemokine, fractalkine (FK), is expressed in a membrane‐bound form on activated endothelial cells and mediates attachment and firm adhesion of T cells, monocytes and NK cells. We now show that FK is associated with dendritic cells (DC) in epidermis and lymphoid organs. In normal human skin, dual‐color fluorescence microscopy co‐localized FK expression with Langerhans cells expressing CD1a. In tonsil, FK‐positive DC expressed CD83, a marker for mature DC. Human and murine cultured DC up‐regulated FK mRNA expression with maturation. Furthermore, CD40 ligation, but not TNF‐α or lipopolysaccharide treatment, of activated, migratory DC that had migrated from skin explants resulted in a 2.5‐fold increase of surface expression of FK without significant alterations of expression of CD80, CD86, CD54 or MHC class II. Since FK mediates adhesion of T cells to activated endothelial cells, the increased expression of FK during DC maturation (and particularly by CD40 ligation) may play a role in the ability of T cells and mature DC to form conjugates and engage in cell‐cell communication.

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Microsymposia C62to determine the optical constants in a depth dependent manner. By modeling the reflectivity spectra, in combination with angular resolved reflectivity, we show that it is possible to extract accurate optical constants in cases intractable with current techniques. Due to the large number of parameters inherent in such free-form modeling, we use the maximum entropy method to refine the underlying model in fitting the measured reflectivity data. There is an abundance of data on protein interactions and protein complexes, both from conventional small-scale experiments collected over the decades, including three-dimensional structures, and more recently by large-scale functional genomics experiments. We can draw on this information to ask whether (i) non-functional protein interactions constrain protein sequences and (ii) whether protein structures harbor information about conformational changes upon binding to each other. KeywordsIn order to answer the first question, we project evolutionary and systems information onto 397, 196, and 701 proteins of known structure from E. coli, S. cerevisiae and H. sapiens respectively. We find that the propensity of proteins to interact in a non-specific manner with other proteins is inversely correlated with their abundance in E. coli and S. cerevisiae. This tendency is most pronounced at surface residues, suggesting that high abundance proteins have evolved to have a less sticky surface. In E. coli and S. cerevisiae, we also find that the evolutionary conservation of an amino acid is positively correlated with the stickiness of the surface environment around it. Thus, residues in sticky surface patches are evolutionarily more constrained, possibly because they are more likely to trigger non-functional interactions if they mutate. Although significant, the impact of protein stickiness is comparatively small in shaping the physico-chemical properties and evolution of H. sapiens proteins. This suggests that promiscuous protein-protein interactions are freer to accumulate in species with a small effective population size; a phenomenon akin to junk DNA accumulation.While non-functional interactions shape protein sequence and structure, functional protein interactions require not just sequence but also structural complementarity, which often involves conformational changes. We have analyzed the relationships between the structures of proteins and the conformational changes that they undergo upon binding. We find that the relative solvent accessible surface area of both free and bound subunits can be used to predict the magnitude of binding-induced conformational changes. We demonstrate that the relative solvent accessible surface area of monomeric proteins is useful as a simple proxy for intrinsic flexibility and for predicting conformational changes upon binding. In addition to the predictive power of this correlation, it reveals a strong connection between the flexibility of unbound proteins and their binding-induced conformational changes, consistent with the conf...

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