The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria

The identification of mycobacteria is essential because tuberculosis (TB) and mycobacteriosis are clinically indistinguishable and require different therapeutic regimens. The traditional phenotypic method is time consuming and may last up to 60 days. Indeed, rapid, affordable, specific and easy-to-perform identification methods are needed. We have previously described a polymerase chain reaction-based method called a mycobacteria mobility shift assay (MMSA) that was designed for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) species identification. The aim of this study was to assess the MMSA for the identification of MTC and NTM clinical isolates and to compare its performance with that of the PRA-hsp65 method. A total of 204 clinical isolates (102 NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing fragments of the 16S rRNA and hsp65 genes. Both methods correctly identified all MTC isolates. Among the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement was observed for the 94 NTM isolates identified by both methods. The MMSA provided correct identification for 96.8% of the NTM isolates compared with 94.7% for PRA-hsp65. The MMSA is a suitable auxiliary method for routine use for the rapid identification of mycobacteria

RAP1 GTPase Overexpression is Associated with Cervical Intraepithelial Neoplasia

<div><p>RAP1 (RAS proximate 1), a small GTP-binding protein of the <i>RAS</i> superfamily, is a putative oncogene that is highly expressed in several malignant cell lines and types of cancers, including some types of squamous cell carcinoma. However, the participation of RAP1 in cervical carcinogenesis is unknown. We conducted a cross-sectional study of paraffin-embedded cervical biopsies to determine the association of RAP1 with cervical intraepithelial neoplasia (CIN). Standard and quantitative immunohistochemistry assessment of RAP1 expression in fixed tissue was performed on 183 paraffin-embedded cervical biopsies that were classified as normal or non-dysplastic mucosa (NDM) (n = 33); CIN grade 1 (n = 84) and CIN grade 2/3 (n = 66). A gradual increase in RAP1 expression in NDM < CIN 1 < CIN 2/3 (<i>p<0</i>.<i>001</i>) specimens was observed and was in agreement with the histopathologic diagnosis. A progressive increase in the RAP1 expression levels increased the risk of CIN 1 [odds ratio (OR) = 3.50; 95% confidence interval (CI) 1.30-10.64] 3.5 fold and the risk of CIN 2/3 (OR = 19.86, 95% CI 6.40-70.79) nearly 20 fold when compared to NDM. In addition, stereotype ordinal regression analysis showed that this progressive increase in RAP1 expression more strongly impacted CIN 2/3 than CIN 1. Our findings suggest that RAP1 may be a useful biomarker for the diagnosis of CIN.</p></div

Immunohistochemical staining of RAP1.

<p>Left—Squamocolumnar junction of non-dysplastic cervical mucosa (NDM) showing very weak immunostaining for RAP1 in the cytoplasm of basal cells and no staining in the intermediate and superficial cells. Middle—CIN 1 showing moderate staining for RAP1 in cells distributed in the basal third of the epithelium and showing RAP1 expression in neutrophils. Right- CIN 2/3 showing strong staining for RAP1 in cells diffusely distributed throughout the entire epithelial thickness, with nuclear translocation of RAP1.</p

Morphometric analysis of RAP1 and p16^INK4A immunohistochemical staining.

<p>Relative Intensity (RI) data of RAP1 anfd p16^INK4A expression in NDM, CIN 1, and CIN 2/3 samples are expressed in box plot format, with boxes stretching from the 25^th percentile to the 75^th percentile and the line across the box representing the median values. Statistically significant differences (p <0.05) are shown by dotted lines.</p

Estimated coefficients, standard errors, z-scores, and two-tailed <i>p</i>-values for the fitted stereotype regression model.

<p>Log-likelihood: -136.46</p><p>Abbreviations: SE—Standard error; NDM—non-dysplastic mucosa; CIN—cervical intraepithelial neoplasia.</p><p>* Identifiability constraints proposed proposed by Anderson [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123531#pone.0123531.ref026" target="_blank">26</a>].</p><p>Estimated coefficients, standard errors, z-scores, and two-tailed <i>p</i>-values for the fitted stereotype regression model.</p

Associations between RAP1 expression and risk of CIN progression.

<p>Abbreviations: OR—Odds ratio; NDM—non-dysplastic mucosa; CIN—cervical intraepithelial neoplasia.</p><p>Associations between RAP1 expression and risk of CIN progression.</p

Scores of RAP1 and p16^INK4A immunohistochemical expression in precursor lesions of cervical neoplasia.

<p>Abbreviations: NDM—non-dysplastic mucosa; CIN—cervical intraepithelial neoplasia.</p><p>Scores of RAP1 and p16^INK4A immunohistochemical expression in precursor lesions of cervical neoplasia.</p