Comparison of PCR ribotyping and multilocus variable-number tandem-repeat analysis (MLVA) for improved detection of Clostridium difficile

<p>Abstract</p> <p>Background</p> <p>Polymerase chain reaction (PCR) ribotyping is one of the globally accepted techniques for defining epidemic clones of <it>Clostridium difficile </it>and tracing virulence-related strains. However, the ambiguous data generated by this technique makes it difficult to compare data attained from different laboratories; therefore, a portable technique that could supersede or supplement PCR ribotyping should be developed. The current study attempted to use a new multilocus variable-number tandem-repeat analysis (MLVA) panel to detect PCR-ribotype groups. In addition, various MLVA panels using different numbers of variable-number tandem-repeat (VNTR) loci were evaluated for their power to discriminate <it>C. difficile </it>clinical isolates.</p> <p>Results</p> <p>At first, 40 VNTR loci from the <it>C. difficile </it>genome were used to screen for the most suitable MLVA panel. MLVA and PCR ribotyping were implemented to identify 142 <it>C. difficile </it>isolates. Groupings of serial MLVA panels with different allelic diversity were compared with 47 PCR-ribotype groups. A MLVA panel using ten VNTR loci with limited allelic diversity (0.54-0.83), designated MLVA10, generated groups highly congruent (98%) with the PCR-ribotype groups. For comparison of discriminatory power, a MLVA panel using only four highly variable VNTR loci (allelic diversity: 0.94-0.96), designated MLVA4, was found to be the simplest MLVA panel that retained high discriminatory power. The MLVA10 and MLVA4 were combined and used to detect genetically closely related <it>C. difficile </it>strains.</p> <p>Conclusions</p> <p>For the epidemiological investigations of <it>C. difficile</it>, we recommend that MLVA10 be used in coordination with the PCR-ribotype groups to detect epidemic clones, and that the MLVA4 could be used to detect outbreak strains. MLVA10 and MLVA4 could be combined in four multiplex PCR reactions to save time and obtain distinguishable data.</p

Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii)

<p>Abstract</p> <p>Background</p> <p>The subtropical island of Taiwan is an area of high endemism and a complex topographic environment. Phylogeographic studies indicate that vicariance caused by Taiwan's mountains has subdivided many taxa into genetic phylogroups. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the evolutionary history of an endemic montane bird, Steere's Liocichla (<it>Liocichla steerii</it>), fit the general vicariant paradigm for a montane organism.</p> <p>Results</p> <p>We found that while mountains appear to channel gene flow they are not a significant barrier for Steere's Liocichla. Recent demographic expansion was evident, and genetic diversity was relatively high across the island, suggesting expansion from multiple areas rather than a few isolated refugia. Ecological niche modeling corroborated the molecular results and suggested that populations of Steere's Liocichla are connected by climatically suitable habitat and that there was less suitable habitat during the Last Glacial Maximum.</p> <p>Conclusions</p> <p>Genetic and ecological niche modeling data corroborate a single history--Steere's Liocichla was at lower density during the Last Glacial Maximum and has subsequently expanded in population density. We suggest that such a range-wide density expansion might be an overlooked cause for the genetic patterns of demographic expansion that are regularly reported. We find significant differences among some populations in <it>F</it>_{<it>ST </it>}indices and an admixture analysis. Though both of these results are often used to suggest conservation action, we affirm that statistically significant results are not necessarily biologically meaningful and we urge caution when interpreting highly polymorphic data such as microsatellites.</p

Functional interaction between Env oncogene from Jaagsiekte sheep retrovirus and tumor suppressor Sprouty2

<p>Abstract</p> <p>Background</p> <p>Jaagsiekte sheep retrovirus (JSRV) is a type D retrovirus capable of transforming target cells <it>in vitro </it>and <it>in vivo</it>. The Envelope <it>(Env) </it>gene from JSRV and from related retroviruses can induce oncogenic transformation, although the detailed mechanism is yet to be clearly understood. Host cell factors are envisaged to play a critical determining role in the regulation of <it>Env</it>-mediated cell transformation.</p> <p>Results</p> <p>JSRV <it>Env</it>-mediated transformation of a lung adenocarcinoma cell line induced rapid proliferation, anchorage-independent growth and tumor formation, but completely abrogated the migration ability. An analysis of the signaling scenario in the transformed cells suggested the involvement of the ERK pathway regulated by Sprouty2 in cell migration, and the PI3K-Akt and STAT3 pathways in proliferation and anchorage-independence. On the other hand, in a normal lung epithelial cell line, <it>Env</it>-mediated transformation only decreased the migration potential while the other functions remained unaltered. We observed that <it>Env </it>induced the expression of a tumor suppressor, Sprouty2, suggesting a correlation between <it>Env</it>-effect and Sprouty2 expression. Overexpression of Sprouty2 <it>per se </it>not only decreased the migratory potential and tumor formation potential of the target cells but also made them resistant to subsequent <it>Env</it>-mediated transformation. On the other hand, over expression of the functional mutants of Sprouty2 had no inhibitory effect, confirming the role of Sprouty2 as a tumor suppressor.</p> <p>Conclusions</p> <p>Our studies demonstrate that <it>Env </it>and Sprouty2 have a functional relationship, probably through shared signaling network. Sprouty2 functions as a tumor suppressor regulating oncogenic transformation of cells, and it therefore has the potential to be exploited as a therapeutic anti-cancer agent.</p

Ultradeep Ks Imaging in the GOODS-N

We present an ultradeep Ks-band image that covers 0.5*0.5 deg^2 centered on the Great Observatories Origins Deep Survey-North (GOODS-N). The image reaches a 5 \sigma depth of Ks(AB) = 24.45 in the GOODS-N region, which is as deep as the GOODS-N Spitzer Infrared Array Camera (IRAC) 3.6 \mu m image. We present a new method of constructing IRAC catalogs that uses the higher spatial resolution Ks image and catalog as priors and iteratively subtracts fluxes from the IRAC images to estimate the IRAC fluxes. Our iterative method is different from the \chi^2 approach adopted by other groups. We verified our results using data taken in two different epochs of observations, as well as by comparing our colors with the colors of stars and with the colors derived from model spectral energy distributions (SEDs) of galaxies at various redshifts. We make available to the community our WIRCam Ks-band image and catalog (94951 objects in 0.25 deg^2), the Interactive Data Language (IDL) pipeline used for reducing the WIRCam images, and our IRAC 3.6 to 8.0 \mu m catalog (16950 objects in 0.06 deg^2 at 3.6 \mu m). With this improved Ks and IRAC catalog and a large spectroscopic sample from our previous work, we study the color-magnitude and color-color diagrams of galaxies. We compare the effectiveness of using Ks and IRAC colors to select active galactic nuclei (AGNs) and galaxies at various redshifts. We also study a color selection of z = 0.65--1.2 galaxies using the Ks, 3.6 \mu m, and 4.5 \mu m bands.Comment: Accepted for publication on ApJS. Online data are availabl

VH1-44 gene usage defines a subset of canine B-cell lymphomas associated with better patient survival

The use of specific immunoglobulin heavy chain variable region (VH) genes has been associated with increased patient survival in human B-cell lymphomas (hBCL). Given the similarity of human and canine BCL (cBCL) in morphology and clinical treatment, we examined the choice of VH in cBCL and determined whether VH gene selection was a distinct feature associated with survival time in dogs. VH gene selection and mutational status in 52 cBCL, including 29 diffuse large B-cell lymphomas (cDLBCL, the most common subtype of cBCL), were analyzed by comparison with the 80 published canine germline VH gene sequences. We further examined the prognostic impact of the subgroups defined by these features on canine survival. We found that VH1-44 was preferentially expressed in the majority of the 52 cBCLs (60%) as well as in the majority of the cDLBCL subset (59%). VH1-44 gene expression was associated with a statistically better overall survival (p=0.039) in cBCL patients, as well as in the cDLBCL subset of patients (p=0.038). These findings suggest that VH gene selection in cBCL is not random and may therefore have functional implications for cBCL lymphomagenesis, in addition to being a useful prognostic biomarker

Frequency distribution of TATA Box and extension sequences on human promoters

BACKGROUND: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. RESULTS: In this study, we conduct a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from the TATA Box motif, TATAWAWN, are classified into three distribution patterns: peak, bottom-peak, and bottom. Fourteen TATA extension sequences are predicted to be the new TATA Box elements due to their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mice, zebrafish and drosophila melanogaster verifies seven of these elements. It is also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human. CONCLUSION: The dedicated statistical analysis on TATA box and its extension sequences yields new TATA elements. The statistical significance of these elements has been verified on random data sets by calculating their p values

On Pseudorandom Encodings

We initiate a study of pseudorandom encodings: efficiently computable and decodable encoding functions that map messages from a given distribution to a random-looking distribution. For instance, every distribution that can be perfectly and efficiently compressed admits such a pseudorandom encoding. Pseudorandom encodings are motivated by a variety of cryptographic applications, including password-authenticated key exchange, “honey encryption” and steganography. The main question we ask is whether every efficiently samplable distribution admits a pseudorandom encoding. Under different cryptographic assumptions, we obtain positive and negative answers for different flavors of pseudorandom encodings, and relate this question to problems in other areas of cryptography. In particular, by establishing a twoway relation between pseudorandom encoding schemes and efficient invertible sampling algorithms, we reveal a connection between adaptively secure multiparty computation for randomized functionalities and questions in the domain of steganography

Estrogen receptor-α polymorphism in a Taiwanese clinical breast cancer population: a case–control study

INTRODUCTION: Receptor-mediated estrogen activation participates in the development and progression of breast cancer. Estrogen receptor (ER)-α polymorphism has been found to be associated with breast cancer and clinical features of the disease in Caucasians. Epidemiologic studies have revealed that age–incidence patterns of breast cancer in Asians differ from those in Caucasians. Genomic data for ER-α in either population is therefore of value in the clinical setting for that ethnic group. METHODS: A case–control study was conducted to establish a database of ER-α polymorphisms in a Taiwanese population in order to compare Western and Taiwanese (Asian) distributions and to evaluate ER-α polymorphism as an indicator of clinical outcome. The ER-α gene was scanned in a Taiwanese clinical breast cancer group (189 patients) and in healthy individuals (177 healthy control individuals). PCR single-strand conformation polymorphism technology was employed and real-time PCR melting curve analysis was performed. RESULTS: Three sites of silent single nucleotide polymorphism (SNPs) were found, as reported previously in Western studies, but at significantly different frequencies. Among the three SNPs, the frequency of allele 1 (TCT → TCC) in codon 10 was significantly lower in breast cancer patients (32.0%) than in control individuals (40.4%; P = 0.018). We found that allele 1 (ACG → ACA) in codon 594 was less common in breast cancer patients with a family history of breast cancer (5.9%) than in those without such a history (19.6%; P = 0.049). Individually, both allele 1 in codon 325 (CCC → CCG) and allele 1 in codon 594 exhibited a reverse association with the occurrence of lymph node metastasis. Furthermore, incorporation of both SNP markers further increased predictive accuracy. CONCLUSIONS: Our data suggest that ER-α polymorphisms are correlated with various aspects of breast cancer in Taiwan. ER-α genotype, as determined during presurgical evaluation, might represent a surrogate marker for predicting breast cancer lymph node metastasis