A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water

Background: Water and High Purity Water (HPW) distribution systems can be contaminated with human pathogenic microorganisms. This biocontamination may pose a risk to human health as HPW is commonly used in the industrial, pharmaceutical and clinical sectors. Currently, routine microbiological testing of HPW is performed using slow and labour intensive traditional microbiological based techniques. There is a need to develop a rapid culture independent methodology to quantitatively detect and identify biocontamination associated with HPW. Results: A novel internally controlled 5-plex real-time PCR Nucleic Acid Diagnostics assay (NAD), was designed and optimised in accordance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, to rapidly detect, identify and quantify the human pathogenic bacteriaStenotrophomonas maltophilia, Burkholderia species, Pseudomonas aeruginosa and Serratia marcescenswhich are commonly associated with the biocontamination of water and water distribution systems. The specificity of the 5-plex assay was tested against genomic DNA isolated from a panel of 95 microorganisms with no cross reactivity observed. The analytical sensitivities of the S. maltophilia, B. cepacia, P. aeruginosa and the S. marcescens assays are 8.5, 5.7, 3.2 and 7.4 genome equivalents respectively. Subsequently, an analysis of HPW supplied by a Millipore Elix 35 water purification unit performed using standard microbiological methods revealed high levels of naturally occurring microbiological contamination. Five litre water samples from this HPW delivery system were also filtered and genomic DNA was purified directly from these filters. These DNA samples were then tested using the developed multiplex real-time PCR NAD assay and despite the high background microbiological contamination observed, both S. maltophilia andBurkholderia species were quantitatively detected and identified. At both sampling points the levels of both S. maltophilia and Burkholderia species present was above the threshold of 10 cfu/100 ml recommended by both EU and US guidelines. Conclusions: The novel culture independent methodology described in this study allows for rapid (<5 h), quantitative detection and identification of these four human pathogens from biocontaminated water and HPW distribution systems. We propose that the described NAD assay and associated methodology could be applied to routine testing of water and HPW distribution systems to assure microbiological safety and high water quality standards

Interactome comparison of human embryonic stem cell lines with the inner cell mass and trophectoderm

Networks of interacting co-regulated genes distinguish the inner cell mass (ICM) from the differentiated trophectoderm (TE) in the preimplantation blastocyst, in a species specific manner. In mouse the ground state pluripotency of the ICM appears to be maintained in murine embryonic stem cells (ESCs) derived from the ICM. This is not the case for human ESCs. In order to gain insight into this phenomenon, we have used quantitative network analysis to identify how similar human (h)ESCs are to the human ICM. Using the hESC lines MAN1, HUES3 and HUES7 we have shown that all have only a limited overlap with ICM specific gene expression, but that this overlap is enriched for network properties that correspond to key aspects of function including transcription factor activity and the hierarchy of network modules. These analyses provide an important framework which highlights the developmental origins of hESCs

CDP-diacylglycerol phospholipid synthesis in detergent-soluble, non-raft, membrane microdomains of the endoplasmic reticulum

Phosphatidylinositol (PI) is essential for numerous cell functions and is generated by consecutive reactions catalyzed by CDP-diacylglycerol synthase (CDS) and PI synthase. In this study, we investigated the membrane organization of CDP-diacylglycerol synthesis. Separation of mildly disrupted A431 cell membranes on sucrose density gradients revealed cofractionation of CDS and PI synthase activities with cholesterol-poor, endoplasmic reticulum (ER) membranes and partial overlap with plasma membrane caveolae. Cofractionation of CDS activity with caveolae was also observed when low-buoyant density caveolin-enriched membranes were prepared using a carbonate-based method. However, immunoisolation studies determined that CDS activity localized to ER membrane fragments containing calnexin and type III inositol (1,4,5)-trisphosphate receptors but not to caveolae. Membrane fragmentation in neutral pH buffer established that CDP-diacylglycerol and PI syntheses were restricted to a subfraction of the calnexin-positive ER. In contrast to lipid rafts enriched for caveolin, cholesterol, and GM1 glycosphingolipids, the CDS-containing ER membranes were detergent soluble. In cell imaging studies, CDS and calnexin colocalized in microdomain-sized patches of the ER and also unexpectedly at the plasma membrane. These results demonstrate that key components of the PI pathway localize to nonraft, phospholipid-synthesizing microdomains of the ER that are also enriched for calnexin. Copyright © 2011 by the American Society for Biochemistry and Molecular Biology, Inc

Activated vortex lattice transition in a superconductor with combined sixfold and twelvefold anisotropic interactions

Numerical simulations are used to examine the transition dynamics between metastable and ground state vortex lattice phases in a system with combined sixfold and twelvefold contributions to the vortex-vortex interactions. The system is initially annealed using a twelvefold anisotropy, yielding domains of two different orientations and separated by grain boundaries. The vortex-vortex interaction is then suddenly changed to a sixfold anisotropy, rendering the twelvefold state metastable. Applying a drive that mimics an oscillating magnetic field causes the metastable state to decay, indicated by the structure factor that evolves from twelve to six peaks. The results fit the behavior seen in recent small-angle neutron scattering studies of the vortex lattice in MgB2. At higher drive amplitudes, the decay exhibits a two step process in which the initial fast decrease is followed by a slower regime where avalanches or bursts are correlated with dislocation annihilation events. The results are compared to other types of metastable systems with quenched disorder that decay under a periodic external drive.Comment: Accepted for publication, New J. Phy

Pediatric cataracts of different etiologies contain insoluble, calcified particles

Our recent studies in mice suggest that a crucial event for the development of cataracts is the formation of calcium-containing deposits. To examine the generality of pathologic mineralization as a novel mechanism of cataract formation, we analyzed lens material from different human cataract surgeries. Human lens material was obtained from routine cataract surgeries performed on three patients with dense, white cataracts: a 10-month-old with congenital cataracts, a 9-year-old with a uveitic cataract, and a 17-year-old with a traumatic cataract. The aspirated material from the cataract surgeries contained insoluble material that could be isolated by centrifugation. Many particles within the insoluble fraction stained with Alizarin red, a dye that stains insoluble calcified material. The appearance of these human insoluble, Alizarin red-stained particles was similar to some of those detected in homogenates from cataractous mouse lenses. These results support the hypothesis that pathologic mineralization may have a mechanistic role in the formation of cataracts of different etiologies

Phosphatidylinositol 4-kinase IIβ negatively regulates invadopodia formation and suppresses an invasive cellular phenotype

The type II PI 4-kinases enzymes synthesise the lipid phosphatidylinositol 4-phosphate (PI(4)P) which has been detected at the Golgi complex and endosomal compartments, and which recruits clathrin adaptors. Despite common mechanistic similarities between the isoforms, the extent of their redundancy is unclear.We found that depletion of PI4KIIα and PI4KIIβ using siRNA led to actin remodelling. Depletion of PI4KIIβ also induced the formation of invadopodia containing membrane type I matrix metalloproteinase (MT1-MMP).Depletion of PI4KII isoforms also differentially affected TGN pools of PI(4)P and post-TGN traffic. PI4KIIβ depletion caused increased MT1-MMP trafficking to invasive structures at the plasma membrane and was accompanied by reduced colocalisation of MT1-MMP with membranes containing the endosomal markers Rab5 and Rab7, but increased localisation with the exocytic Rab8. Depletion of PI4KIIβ was sufficient to confer an aggressive invasive phenotype on minimally invasive HeLa and MCF-7 cell lines. Mining oncogenomic databases revealed that loss of the PI4K2B allele and underexpression of PI4KIIβ mRNA is associated with human cancers. This finding supports the cell data and suggests that PI4KIIβ may be a clinically significant suppressor of invasion. We propose that PI4KIIβ synthesises a pool of PI(4)P that maintains MT1-MMP traffic in the degradative pathway and suppresses the formation of invadopodia

Bottlenose Dolphins Mom-Calf Interactions over the First and Second Year of Life

As both wild and captive dolphin calves develop, they spend less time with their mothers and more time engaged in independent activities. In this study, the social development of six captive dolphin calves (Tursiops truncatus) were examined over the first and second year of life. Focal animal behavioral ethogram data were collected using a 30 second scan sampling technique. The predominant swim position and individual behaviors were recorded. There were a number of general developmental patterns: (1) an increase in the percentage of time that the calves engaged in solo swimming, (2) a decrease in infant position, and (3) a decrease in echelon position. The shift in primary swim position and increase in independent (solitary) behaviors exhibited over the study is consistent with past research on calf development. The basis for the difference each calf’s behavior could be a result of the experience or type of mother, the unique personalities in the calves, or a combination of both

Beluga Whales Socio-Sexual Interactions and Behaviors (Delphinapterus leucas)

Cetaceans are known for developing social relationships with each other by displaying various social and contact behaviors. Few studies have investigated the social interactions and types of contact behavior between belugas (Delphinapterus leucas). The present study focused on the frequencies of many social behaviors observed among four belugas (three males and one female) in the care of humans and the changes in behavior over an extended period of time. Continuous data were collection via video recordings over a four year period and were coded for social interactions. Preliminary analysis revealed that Male C was the most likely to initiate social interactions in this social group. It appears that the social interactions among the individuals may be somewhat stable over time. The findings of this study have implications for better understanding beluga social interactions of whales that are living under managed care

The Politics of Service Delivery Reform

This article identifies the leaders, the supporters and the resisters of public service reform. It adopts a principal–agent framework, comparing reality with an ‘ideal’ situation in which citizens are the principals over political policy-makers as their agents, and policy-makers are the principals over public service officials as their agents. Reform in most developing countries is complicated by an additional set of external actors — international financial institutions and donors. In practice, international agencies and core government officials usually act as the ‘principals’ in the determination of reforms. The analysis identifies the interests involved in reform, indicating how the balance between them is affected by institutional and sectoral factors. Organizational reforms, particularly in the social sectors, present greater difficulties than first generation economic policy reforms

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology

Biomedical ontologies contain errors. Crowdsourcing, defined as taking a job traditionally performed by a designated agent and outsourcing it to an undefined large group of people, provides scalable access to humans. Therefore, the crowd has the potential overcome the limited accuracy and scalability found in current ontology quality assurance approaches. Crowd-based methods have identified errors in SNOMED CT, a large, clinical ontology, with an accuracy similar to that of experts, suggesting that crowdsourcing is indeed a feasible approach for identifying ontology errors. This work uses that same crowd-based methodology, as well as a panel of experts, to verify a subset of the Gene Ontology (200 relationships). Experts identified 16 errors, generally in relationships referencing acids and metals. The crowd performed poorly in identifying those errors, with an area under the receiver operating characteristic curve ranging from 0.44 to 0.73, depending on the methods configuration. However, when the crowd verified what experts considered to be easy relationships with useful definitions, they performed reasonably well. Notably, there are significantly fewer Google search results for Gene Ontology concepts than SNOMED CT concepts. This disparity may account for the difference in performance – fewer search results indicate a more difficult task for the worker. The number of Internet search results could serve as a method to assess which tasks are appropriate for the crowd. These results suggest that the crowd fits better as an expert assistant, helping experts with their verification by completing the easy tasks and allowing experts to focus on the difficult tasks, rather than an expert replacement