What is broad-range 16S rDNA PCR?

PCRs have revolutionised the detection of bacteria in clinical samples since their widespread introduction in the 1990s.1 Quantitative PCR (qPCR), also known as specific PCR, involves the targeting of particular bacterial species. The technique uses specific primers (short strands of nucleic acid needed to initiate DNA replication) and fluorescent probes to allow real-time quantification of target bacterial DNA during amplification. The qPCR assay is a mainstay of microbiological diagnostics within the National Health Service (NHS). At our hospital approximately 200 qPCRs are performed per week for the investigation of bacterial infections. Although qPCR is by far the most frequently used molecular technique in bacterial diagnostics, in certain scenarios a broad-range (non-specific) 16S rDNA (ribosomal DNA) PCR is increasingly being used. Broad-range 16S rDNA PCR is also more commonly used in research settings, originally for use in detecting and identifying unusual bacterial species but now more widely used in the rapidly expanding field of microbiome research. This technique provides the initial step in the process of analysing complex microbial communities in human, zoological and even geological settings. In the future, analysis of individualised microbial communities using broad-range 16S rDNA PCR may be a key component of personalised medicine

Wearable Sensors Outperform Behavioral Coding as Valid Marker of Childhood Anxiety and Depression

There is a significant need to develop objective measures for identifying children under the age of 8 who have anxiety and depression. If left untreated, early internalizing symptoms can lead to adolescent and adult internalizing disorders as well as comorbidity which can yield significant health problems later in life including increased risk for suicide. To this end, we propose the use of an instrumented fear induction task for identifying children with internalizing disorders, and demonstrate its efficacy in a sample of 63 children between the ages of 3 and 7. In so doing, we extract objective measures that capture the full six degree-of-freedom movement of a child using data from a belt-worn inertial measurement unit (IMU) and relate them to behavioral fear codes, parent-reported child symptoms and clinician-rated child internalizing diagnoses. We find that IMU motion data, but not behavioral codes, are associated with parent-reported child symptoms and clinician-reported child internalizing diagnosis in this sample. These results demonstrate that IMU motion data are sensitive to behaviors indicative of child psychopathology. Moreover, the proposed IMU-based approach has increased feasibility of collection and processing compared to behavioral codes, and therefore should be explored further in future studies

Simvastatin inhibits TLR8 signaling in primary human monocytes and spontaneous TNF production from rheumatoid synovial membrane cultures

Simvastatin has been shown to have anti-inflammatory effects that are independent of its serum cholesterol lowering action, but the mechanisms by which these anti-inflammatory effects are mediated have not been elucidated. To explore the mechanism involved, the effect of simvastatin on Toll-like receptor (TLR) signalling in primary human monocytes was investigated. A short pre-treatment with simvastatin dose-dependently inhibited the production of tumor necrosis factor-α (TNF) in response to TLR8 (but not TLRs 2, 4, or 5) activation. Statins are known inhibitors of the cholesterol biosynthetic pathway, but intriguingly TLR8 inhibition could not be reversed by addition of mevalonate or geranylgeranyl pyrophosphate; downstream products of cholesterol biosynthesis. TLR8 signalling was examined in HEK 293 cells stably expressing TLR8, where simvastatin inhibited IKKα/β phosphorylation and subsequent NF-κB activation without affecting the pathway to AP-1. Since simvastatin has been reported to have anti-inflammatory effects in RA patients and TLR8 signalling contributes to TNF production in human RA synovial tissue in culture, simvastatin was tested in these cultures. Simvastatin significantly inhibited the spontaneous release of TNF in this model which was not reversed by mevalonate. Together, these results demonstrate a hitherto unrecognized mechanism of simvastatin inhibition of TLR8 signalling that may in part explain its beneficial anti-inflammatory effects

Renal and Splenic Micro-Infarctions Following Bronchial Artery Embolization with Tris-Acryl Microspheres

A bronchial artery embolization (BAE) is an important therapeutic method used to control acute and chronic hemoptysis. We report a case of multiple micro-infarcts involving both the kidneys and spleen, following a BAE with 500-700 µm crossed-linked tris-acryl microspheres (Embospheres) in a patient with bronchial artery pulmonary vein shunts. The superior penetration characteristics of the microspheres may have resulted in the greater tendency to cross the bronchial artery pulmonary vein shunts, which subsequently caused the systemic infarcts in our patient. We propose the use of larger sized microspheres (700-900 µm), which may aid in avoiding this complication

Terahertz Security Image Quality Assessment by No-reference Model Observers

To provide the possibility of developing objective image quality assessment (IQA) algorithms for THz security images, we constructed the THz security image database (THSID) including a total of 181 THz security images with the resolution of 127*380. The main distortion types in THz security images were first analyzed for the design of subjective evaluation criteria to acquire the mean opinion scores. Subsequently, the existing no-reference IQA algorithms, which were 5 opinion-aware approaches viz., NFERM, GMLF, DIIVINE, BRISQUE and BLIINDS2, and 8 opinion-unaware approaches viz., QAC, SISBLIM, NIQE, FISBLIM, CPBD, S3 and Fish_bb, were executed for the evaluation of the THz security image quality. The statistical results demonstrated the superiority of Fish_bb over the other testing IQA approaches for assessing the THz image quality with PLCC (SROCC) values of 0.8925 (-0.8706), and with RMSE value of 0.3993. The linear regression analysis and Bland-Altman plot further verified that the Fish__bb could substitute for the subjective IQA. Nonetheless, for the classification of THz security images, we tended to use S3 as a criterion for ranking THz security image grades because of the relatively low false positive rate in classifying bad THz image quality into acceptable category (24.69%). Interestingly, due to the specific property of THz image, the average pixel intensity gave the best performance than the above complicated IQA algorithms, with the PLCC, SROCC and RMSE of 0.9001, -0.8800 and 0.3857, respectively. This study will help the users such as researchers or security staffs to obtain the THz security images of good quality. Currently, our research group is attempting to make this research more comprehensive.Comment: 13 pages, 8 figures, 4 table

A Novel Unsupervised Method to Identify Genes Important in the Anti-viral Response: Application to Interferon/Ribavirin in Hepatitis C Patients

Background: Treating hepatitis C with interferon/ribavirin results in a varied response in terms of decrease in viral titer and ultimate outcome. Marked responders have a sharp decline in viral titer within a few days of treatment initiation, whereas in other patients there is no effect on the virus (poor responders). Previous studies have shown that combination therapy modifies expression of hundreds of genes in vitro and in vivo. However, identifying which, if any, of these genes have a role in viral clearance remains challenging. Aims: The goal of this paper is to link viral levels with gene expression and thereby identify genes that may be responsible for early decrease in viral titer. Methods: Microarrays were performed on RNA isolated from PBMC of patients undergoing interferon/ribavirin therapy. Samples were collected at pre-treatment (day 0), and 1, 2, 7, 14 and 28 days after initiating treatment. A novel method was applied to identify genes that are linked to a decrease in viral titer during interferon/ribavirin treatment. The method uses the relationship between inter-patient gene expression based proximities and inter-patient viral titer based proximities to define the association between microarray gene expression measurements of each gene and viral-titer measurements. Results: We detected 36 unique genes whose expressions provide a clustering of patients that resembles viral titer based clustering of patients. These genes include IRF7, MX1, OASL and OAS2, viperin and many ISG's of unknown function. Conclusion: The genes identified by this method appear to play a major role in the reduction of hepatitis C virus during the early phase of treatment. The method has broad utility and can be used to analyze response to any group of factors influencing biological outcome such as antiviral drugs or anti-cancer agents where microarray data are available. © 2007 Brodsky et al

A Dimer of the Toll-Like Receptor 4 Cytoplasmic Domain Provides a Specific Scaffold for the Recruitment of Signalling Adaptor Proteins

The Toll-like receptor 4 (TLR4) is a class I transmembrane receptor expressed on the surface of immune system cells. TLR4 is activated by exposure to lipopolysaccharides derived from the outer membrane of Gram negative bacteria and forms part of the innate immune response in mammals. Like other class 1 receptors, TLR4 is activated by ligand induced dimerization, and recent studies suggest that this causes concerted conformational changes in the receptor leading to self association of the cytoplasmic Toll/Interleukin 1 receptor (TIR) signalling domain. This homodimerization event is proposed to provide a new scaffold that is able to bind downstream signalling adaptor proteins. TLR4 uses two different sets of adaptors; TRAM and TRIF, and Mal and MyD88. These adaptor pairs couple two distinct signalling pathways leading to the activation of interferon response factor 3 (IRF-3) and nuclear factor κB (NFκB) respectively. In this paper we have generated a structural model of the TLR4 TIR dimer and used molecular docking to probe for potential sites of interaction between the receptor homodimer and the adaptor molecules. Remarkably, both the Mal and TRAM adaptors are strongly predicted to bind at two symmetry-related sites at the homodimer interface. This model of TLR4 activation is supported by extensive functional studies involving site directed mutagenesis, inhibition by cell permeable peptides and stable protein phosphorylation of receptor and adaptor TIR domains. Our results also suggest a molecular mechanism for two recent findings, the caspase 1 dependence of Mal signalling and the protective effects conferred by the Mal polymorphism Ser180Leu

Balancing the dilution and oddity effects: Decisions depend on body size

Background Grouping behaviour, common across the animal kingdom, is known to reduce an individual's risk of predation; particularly through dilution of individual risk and predator confusion (predator inability to single out an individual for attack). Theory predicts greater risk of predation to individuals more conspicuous to predators by difference in appearance from the group (the ‘oddity’ effect). Thus, animals should choose group mates close in appearance to themselves (eg. similar size), whilst also choosing a large group. Methodology and Principal Findings We used the Trinidadian guppy (Poecilia reticulata), a well known model species of group-living freshwater fish, in a series of binary choice trials investigating the outcome of conflict between preferences for large and phenotypically matched groups along a predation risk gradient. We found body-size dependent differences in the resultant social decisions. Large fish preferred shoaling with size-matched individuals, while small fish demonstrated no preference. There was a trend towards reduced preferences for the matched shoal under increased predation risk. Small fish were more active than large fish, moving between shoals more frequently. Activity levels increased as predation risk decreased. We found no effect of unmatched shoal size on preferences or activity. Conclusions and Significance Our results suggest that predation risk and individual body size act together to influence shoaling decisions. Oddity was more important for large than small fish, reducing in importance at higher predation risks. Dilution was potentially of limited importance at these shoal sizes. Activity levels may relate to how much sampling of each shoal was needed by the test fish during decision making. Predation pressure may select for better decision makers to survive to larger size, or that older, larger fish have learned to make shoaling decisions more efficiently, and this, combined with their size relative to shoal-mates, and attractiveness as prey items influences shoaling decisions