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Find video protocols related to scientific articles indexed in Pubmed.
Synergistic modulation of cyclobutane pyrimidine dimer photoproduct formation and deamination at a TmCG site over a full helical DNA turn in a nucleosome core particle.
Nucleic Acids Res.
PUBLISHED: 11-13-2014
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Sunlight-induced C to T mutation hotspots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C or 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by DNA polymerase ? and defines a probable mechanism for the origin of UV-induced C to T mutations. We have now determined the photoproduct formation and deamination rates for 10 consecutive T=(m)CG CPDs over a full helical turn at the dyad axis of a nucleosome and find that whereas photoproduct formation and deamination is greatly inhibited for the CPDs closest to the histone surface, it is greatly enhanced for the outermost CPDs. Replacing the G in a T=(m)CG CPD with A greatly decreased the deamination rate. These results show that rotational position and flanking sequence in a nucleosome can significantly and synergistically modulate CPD formation and deamination that contribute to C to T mutations associated with skin cancer induction and may have influenced the evolution of the human genome.
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Undetected oesophageal perforation and feeding-tube misplacement.
Br J Nurs
PUBLISHED: 10-28-2014
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This is a case report of an electromagnetically (EM)-guided Cortrak feeding tube that perforated the lower oesophagus and was not detected by the EM trace or by plain X-ray. Misplacement was diagnosed from computed tomography (CT) following injection of radio-contrast medium down the tube. Recommendations are offered for use of the EM trace in patients at high risk of oesophageal perforation.
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Membrane Inlet Mass Spectrometry for Homeland Security and Forensic Applications.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 08-22-2014
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A man-portable membrane inlet mass spectrometer has been built and tested to detect and monitor characteristic odors emitted from the human body and also from threat substances. In each case, a heated membrane sampling probe was used. During human scent monitoring experiments, data were obtained for inorganic gases and volatile organic compounds emitted from human breath and sweat in a confined space. Volatile emissions were detected from the human body at low ppb concentrations. Experiments with compounds associated with narcotics, explosives, and chemical warfare agents were conducted for a range of membrane types. Test compounds included methyl benzoate (odor signature of cocaine), piperidine (precursor in clandestine phencyclidine manufacturing processes), 2-nitrotoluene (breakdown product of TNT), cyclohexanone (volatile signature of plastic explosives), dimethyl methylphosphonate (used in sarin and soman nerve agent production), and 2-chloroethyl ethyl sulfide (simulant compound for sulfur mustard gas). Gas phase calibration experiments were performed allowing sub-ppb LOD to be established. The results showed excellent linearity versus concentration and rapid membrane response times.
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Organ-based Tube Current Modulation: Are Women's Breasts Positioned in the Reduced-Dose Zone?
Radiology
PUBLISHED: 08-22-2014
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Purpose To retrospectively determine the potential of organ-based tube current modulation (OBTCM) to reduce the radiation dose delivered to breast tissue by computed tomography (CT) by determining breast angular position in relation to the zones of decreased versus increased radiation. Materials and Methods The authors obtained institutional review board approval for this study and patients' written informed consent. In two academic centers (center A: Beth Israel Deaconess Medical Center, Boston, Mass; and center B: Hôpital André Vésale, Montignies-le-Tilleul, Belgium), data were collected from clinical thoracic CT examinations performed in 498 women (mean age, 60 years; age range, 18-95 years) in the supine position and 34 women (mean age, 53 years; age range, 18-84 years) in the prone position. One radiologist in each center determined breast tissue location and measured its inner and outer boundaries with respect to the isocenter of the CT examination. The percentages of women with breast tissue within and those with breast tissue outside the zone of decreased radiation delivered by OBTCM were determined. The location of breast tissue was correlated with patient age and with sagittal and coronal diameters of the thorax by using the Student t test, Fisher exact test, and Pearson correlation. Results None of the women lying in the supine position had the entirety of the breast tissue located within the reduced-dose zone. Breast tissue was located in the increased-dose zone in 99% of women lying supine and in 82% of women lying prone. Conclusion The breast angular position of almost all women was higher than the angular limit of the reduced versus the increased dose in OBTCM. No woman, regardless of supine or prone position, had all breast tissue within the reduced-dose zone. © RSNA, 2014.
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Understanding functional miRNA-target interactions in vivo by site-specific genome engineering.
Nat Commun
PUBLISHED: 08-19-2014
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MicroRNA (miRNA) target recognition is largely dictated by short 'seed' sequences, and single miRNAs therefore have the potential to regulate a large number of genes. Understanding the contribution of specific miRNA-target interactions to the regulation of biological processes in vivo remains challenging. Here we use transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technologies to interrogate the functional relevance of predicted miRNA response elements (MREs) to post-transcriptional silencing in zebrafish and Drosophila. We also demonstrate an effective strategy that uses CRISPR-mediated homology-directed repair with short oligonucleotide donors for the assessment of MRE activity in human cells. These methods facilitate analysis of the direct phenotypic consequences resulting from blocking specific miRNA-MRE interactions at any point during development.
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Brief Report: Complement C5a Promotes Human Embryonic Stem Cell Pluripotency in the Absence of FGF2.
Stem Cells
PUBLISHED: 08-05-2014
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The complement activation product, C5a, is a pivotal member of the innate immune response; however, a diverse number of non-immune functions are now being ascribed to C5a signalling, including roles during embryonic development. Here we identify the expression of the C5a precursor protein, C5, as well as the C5a receptors, C5aR and C5L2, in both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs). We show that administration of a physiologically relevant dose of purified human C5a (1nM) stimulates activation of ERK1/2 and AKT signalling pathways, and is able to promote maintenance of the pluripotent state in the absence of FGF2. C5a also reduced cell loss following dissociation of human pluripotent stem cells. Our results reveal that complement C5a signalling supports human stem cell pluripotency and survival, and thus may play a key role in shaping early human embryonic development. Stem Cells 2014.
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Nasogastric tube depth: the 'NEX' guideline is incorrect.
Br J Nurs
PUBLISHED: 07-22-2014
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Misplacing 17-23% of nasogastric (NG) tubes above the stomach ( Rollins et al, 2012 ; Rayner, 2013 ) represents a serious risk in terms of aspiration, further invasive (tube) procedures, irradiation from failed X-ray confirmation, delay to feed and medication. One causal factor is that in the National Patient Safety Agency (NPSA) guidance to place a tube, length is measured from nose to ear to xiphisternum (NEX) ( NSPA, 2011 ); NEX is incorrect because it only approximates the nose to gastro-oesophageal junction (GOJ) distance and is therefore too short. To overcome this and because the xiphisternum is more difficult to locate, local policy is to measure in the opposite direction; xiphisternum to ear to nose (XEN), then add 10 cm. The authors determined whether external body measurements can be used to estimate the NG tube length to safely reach the gastric body. This involved testing the statistical association of body length, age, sex and XEN in consecutive critically ill patients against internal anatomical landmarks determined from an electromagnetic (EM) trace of the tube path. XEN averaged 50 cm in 71 critically ill patients aged 53±20 years. Tube marking and the EM trace were used to determine mean insertion distances at pre-gastro-oesophageal junction (GOJ) (48 cm), where the tube first turns left towards the stomach and becomes shallow on the trace; gastric body (62 cm), where the tube reaches the left-most part of the stomach; and gastric antrum (73 cm) at the midline on the EM trace. Using body length, age, sex and XEN in a linear regression model, only 25% of variability was predicted, showing that external measurements cannot reliably predict the length of tube required to reach the stomach. A tube length of XEN (or NEX) is too short to guarantee gastric placement and is unsafe. XEN+10 cm or more complex measurements will reach the gastric body (mid-stomach) in most patients, but because of wide variation, external measurements often fail to predict a safe distance. Only the EM trace or possibly direct vision can show in real time whether the tip has safely reached the gastric body.
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A micropixelated ion-imaging detector for mass resolution enhancement of a QMS instrument.
Anal Bioanal Chem
PUBLISHED: 06-26-2014
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An in-vacuum position-sensitive micropixelated detector (Timepix) is used to investigate the time-dependent spatial distribution of different charge state (and hence different mass-to-charge (m/z)) ions exiting an electrospray ionization (ESI)-based quadrupole mass spectrometer (QMS) instrument. Ion images obtained from the Timepix detector provide a detailed insight into the positions of stable and unstable ions of the mass peak as they exit the QMS. With the help of image processing algorithms and by selecting areas on the ion images where more stable ions impact the detector, an improvement in mass resolution by a factor of 5 was obtained for certain operating conditions. Moreover, our experimental approach of mass resolution enhancement was confirmed by in-house-developed novel QMS instrument simulation software. Utilizing the imaging-based mass resolution enhancement approach, the software predicts instrument mass resolution of ?1,0000 for a single-filter QMS instrument with a 210-mm long mass filter and a low operating frequency (880 kHz) of the radio frequency (RF) voltage.
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Fluoroquinolone Resistant Rectal Colonization Predicts Risk of Infectious Complications after Transrectal Prostate Biopsy.
J. Urol.
PUBLISHED: 06-03-2014
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Infection after transrectal prostate biopsy has become an increasing concern due to fluoroquinolone resistant bacteria. We determined whether colonization identified by rectal culture can identify men at high risk for post-transrectal prostate biopsy infection.
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HTML5 PivotViewer: high-throughput visualization and querying of image data on the web.
Bioinformatics
PUBLISHED: 05-21-2014
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Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data.
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Confirming nasogastric tube position with electromagnetic tracking versus pH or X-ray and tube radio-opacity.
Br J Nurs
PUBLISHED: 04-16-2014
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Recent evidence suggests official statistics greatly underestimate the occurrence of complications from misplaced nasogastric (NG) tubes, even when detected. Current methods of confirming tube position do not provide adequate protection from misplacement. In addition, some tubes are inadequately radio-opaque. We prospectively audited placement of Cortrak polyurethane tubes (PUTs) to determine: accuracy of the electromagnetic (EM) trace in confirming tube position, radio-opacity of PUTs compared with previously placed polyvinylchloride (PVC) Ryles tubes and whether 12 French PUTs can be used to aspirate gastric residual volumes (GRVs). A total of 127 PUTs were placed in 113 patients. EM traces accurately confirmed tube position compared with X-ray (100% agreement). A 'gastric' EM trace has been defined for future use by other operators. PUTs were adequately radio-opaque with good agreement between interpreters (>98%) whereas PVC Ryles tubes were insufficiently radio-opaque (57-73%), invisible in 23% of cases and with poor agreement between interpreters leaving risk of error. The alternative of using pH confirmation was not possible in 44%. In these cases subsequent X-ray incurred a 2-hour delay to feed and medicines. In addition, neither post-placement pH testing nor X-ray warn of lung placement and potential trauma, whereas the EM trace warned of lung placement prior to damage in 7% of placements. 12 French, single-port PUTs appear adequate to aspirate large GRVs. EM tracing may be considered a standalone method of confirming NG tube position. Corflo (Cortrak) PUTs are adequately radio-opaque. Use of PVC Ryles and other inadequately radio-opaque tubes should stop.
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Effect of sequence and metal ions on UVB-induced anti cyclobutane pyrimidine dimer formation in human telomeric DNA sequences.
Nucleic Acids Res.
PUBLISHED: 03-04-2014
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Irradiation of G-quadruplex forming human telomeric DNA with ultraviolet B (UVB) light results in the formation of anti cyclobutane pyrimidine dimers (CPDs) between loop 1 and loop 3 in the presence of potassium ions but not sodium ions. This was unexpected because the sequences involved favor the nonphotoreactive hybrid conformations in K(+) solution, whereas a potentially photoreactive basket conformation is favored in Na(+) solution. To account for these contradictory results, it was proposed that the loops are too far apart in the basket conformation in Na(+) solution but close enough in a two G-tetrad basket-like form 3 conformation that can form in K(+) solution. In the current study, Na(+) was still found to inhibit anti CPD formation in sequences designed to stabilize the form 3 conformation. Furthermore, anti CPD formation in K(+) solution was slower for the sequence previously shown to exist primarily in the proposed photoreactive form 3 conformation than the sequence shown to exist primarily in a nonphotoreactive hybrid conformation. These results suggest that the form 3 conformation is not the principal photoreactive conformation, and that G-quadruplexes in K(+) solution are dynamic and able to access photoreactive conformations more easily than in Na(+) solution.
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Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.
Cancer Cell
PUBLISHED: 02-12-2014
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Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.
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Identification of vaccine antigens using integrated proteomic analyses of surface immunogens from serogroup B Neisseria meningitidis.
J Proteomics
PUBLISHED: 02-07-2014
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Meningococcal surface proteins capable of evoking a protective immune response are candidates for inclusion in protein-based vaccines against serogroup B Neisseria meningitidis (NmB). In this study, a 2-dimensional (2-D) gel-based platform integrating surface and immune-proteomics was developed to characterize NmB surface protein antigens. The surface proteome was analyzed by differential 2-D gel electrophoresis following treatment of live bacteria with proteinase K. Alongside, proteins recognized by immune sera from mice challenged with live meningococci were detected using 2-D immunoblots. In combination, seventeen proteins were identified including the well documented antigens PorA, OpcA and factor H-binding protein, previously reported potential antigens and novel potential immunogens. Results were validated for the macrophage infectivity potentiator (MIP), a recently proposed NmB vaccine candidate. MIP-specific antisera bound to meningococci in whole-cell ELISA and facilitated opsonophagocytosis and deposition of complement factors on the surface of meningococcal isolates of different serosubtypes. Cleavage by proteinase K was confirmed in western blots and shown to occur in a fraction of the MIP expressed by meningococci suggesting transient or limited surface exposure. These observations add knowledge for the development of a protein NmB vaccine. The proteomic workflow presented here may be used for the discovery of vaccine candidates against other pathogens.
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Development and evolution of risk assessment for food allergens.
Food Chem. Toxicol.
PUBLISHED: 01-20-2014
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The need to assess the risk from food allergens derives directly from the need to manage effectively this food safety hazard. Work spanning the last two decades dispelled the initial thinking that food allergens were so unique that the risk they posed was not amenable to established risk assessment approaches and methodologies. Food allergens possess some unique characteristics, which make a simple safety assessment approach based on the establishment of absolute population thresholds inadequate. Dose distribution modelling of MEDs permitted the quantification of the risk of reaction at the population level and has been readily integrated with consumption and contamination data through probabilistic risk assessment approaches to generate quantitative risk predictions. This paper discusses the strengths and limitations of this approach and identifies important data gaps, which affect the outcomes of these predictions. These include consumption patterns among allergic individuals, analytical techniques and their application, severity-dose relationships, and the impact of extraneous factors which alter an individual's physiology, such as infection or exercise. Nevertheless, application of these models has provided valuable insights, leading to further refinements and generating testable hypotheses. Their application to estimate the risk posed by the concurrent consumption of two potentially contaminated foods illustrates their power.
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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.
Nat. Genet.
PUBLISHED: 01-12-2014
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Gene expression during development and differentiation is regulated in a cell- and stage-specific manner by complex networks of intergenic and intragenic cis-regulatory elements whose numbers and representation in the genome far exceed those of structural genes. Using chromosome conformation capture, it is now possible to analyze in detail the interaction between enhancers, silencers, boundary elements and promoters at individual loci, but these techniques are not readily scalable. Here we present a high-throughput approach (Capture-C) to analyze cis interactions, interrogating hundreds of specific interactions at high resolution in a single experiment. We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. In addition, we show how Capture-C will expedite identification of the target genes and functional effects of SNPs that are associated with complex diseases, which most frequently lie in intergenic cis-acting regulatory elements.
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Probability of a shockable presenting rhythm as a function of EMS response time.
Prehosp Emerg Care
PUBLISHED: 01-08-2014
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Survival from cardiac arrest is associated with having a shockable presenting rhythm (VF/pulseless VT) upon EMS arrival. A concern is that several studies have reported a decline in the incidence of VF/PVT over the past few decades. One plausible explanation is that contemporary cardiovascular therapies, such as increased use of statin and beta blocker drugs, may shorten the duration of VF/PVT after arrest. As a result, EMS response time would become an increasingly important factor in the likelihood of a shockable presenting rhythm, and consequently, cardiac arrest survival.
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Safe laboratory handling of Neisseria meningitidis.
J. Infect.
PUBLISHED: 01-07-2014
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Transmission of Neisseria meningitidis mainly occurs by formation of aerosols generated in the nasopharynx. Working with meningococci in vitro and performing manipulations where aerosols may be generated may result in laboratory acquired infections if appropriate safety precautions are not taken. This review details the practical aspects and experience of safe working with N. meningitidis in the laboratory. The specific risk factor for laboratory-acquired infection is exposure to aerosols containing meningococci. Prevention should therefore focus on the use of microbiology safety cabinets during manipulation of meningococci and this should be reflected in local risk assessments, supported by safe practices of work appropriate facilities and equipment, training/competency and immunisation policies.
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Precautionary labelling of foods for allergen content: are we ready for a global framework?
World Allergy Organ J
PUBLISHED: 01-01-2014
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Food allergy appears to be on the rise with the current mainstay of treatment centred on allergen avoidance. Mandatory allergen labelling has improved the safety of food for allergic consumers. However an additional form of voluntary labelling (termed precautionary allergen labelling) has evolved on a wide range of packaged goods, in a bid by manufacturers to minimise risk to customers, and the negative impact on business that might result from exposure to trace amounts of food allergen present during cross-contamination during production. This has resulted in near ubiquitous utilisation of a multitude of different precautionary allergen labels with subsequent confusion amongst many consumers as to their significance. The global nature of food production and manufacturing makes harmonisation of allergen labelling regulations across the world a matter of increasing importance. Addressing inconsistencies across countries with regards to labelling legislation, as well as improvement or even banning of precautionary allergy labelling are both likely to be significant steps forward in improved food safety for allergic families. This article outlines the current status of allergen labelling legislation around the world and reviews the value of current existing precautionary allergen labelling for the allergic consumer. We strongly urge for an international framework to be considered to help roadmap a solution to the weaknesses of the current systems, and discuss the role of legislation in facilitating this.
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ATRX dysfunction induces replication defects in primary mouse cells.
PLoS ONE
PUBLISHED: 01-01-2014
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The chromatin remodeling protein ATRX, which targets tandem repetitive DNA, has been shown to be required for expression of the alpha globin genes, for proliferation of a variety of cellular progenitors, for chromosome congression and for the maintenance of telomeres. Mutations in ATRX have recently been identified in tumours which maintain their telomeres by a telomerase independent pathway involving homologous recombination thought to be triggered by DNA damage. It is as yet unknown whether there is a central underlying mechanism associated with ATRX dysfunction which can explain the numerous cellular phenomena observed. There is, however, growing evidence for its role in the replication of various repetitive DNA templates which are thought to have a propensity to form secondary structures. Using a mouse knockout model we demonstrate that ATRX plays a direct role in facilitating DNA replication. Ablation of ATRX alone, although leading to a DNA damage response at telomeres, is not sufficient to trigger the alternative lengthening of telomere pathway in mouse embryonic stem cells.
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Monitoring of human chemical signatures using membrane inlet mass spectrometry.
Anal. Chem.
PUBLISHED: 01-01-2014
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This work is an attempt to assist border security crackdown on illegal human immigration, by providing essential results on human chemical signatures. Data was obtained using a portable quadrupole mass spectrometer coupled with a membrane probe for volunteers of both genders and under different conditions in a container simulator. During experiments, participants were asked to follow various protocols while volatile organic compounds emitted from their breath, sweat, skin, and other biological excretes were continuously being monitored. Experimental setups using different membrane materials (both hydrophilic and hydrophobic) including heating of the sampling probe and sampling flow rates were examined. From our measurements, significant information was obtained for NH3, CO2, water, and volatile organic compounds levels, illustrating a human chemical profile and indicating human presence in a confined space.
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Humanized mice as a model to study human hematopoietic stem cell transplantation.
Stem Cells Dev.
PUBLISHED: 09-25-2013
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Hematopoietic stem cell (HSC) transplantation has the potential to treat a variety of human diseases, including genetic deficiencies, immune disorders, and to restore immunity following cancer treatment. However, there are several obstacles that prevent effective HSC transplantation in humans. These include finding a matched donor, having a sufficient number of cells for the transplant, and the potency of the cells in the transplant. Ethical issues prevent effective research in humans that could provide insight into ways to overcome these obstacles. Highly immunodeficient mice can be transplanted with human HSCs and this process is accompanied by HSC homing to the murine bone marrow. This is followed by stem cell expansion, multilineage hematopoiesis, long-term engraftment, and functional human antibody and cellular immune responses. As such, humanized mice serve as a model for human HSC transplantation. A variety of conditions have been analyzed for their impact on HSC transplantation to produce humanized mice, including the type and source of cells used in the transplant, the number of cells transplanted, the expansion of cells with various protocols, and the route of introduction of cells into the mouse. In this review, we summarize what has been learned about HSC transplantation using humanized mice as a recipient model and we comment on how these models may be useful to future preclinical research to determine more effective ways to expand HSCs and to determine their repopulating potential in vivo.
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Nucleic Acid-directed Self-assembly of Multifunctional Gold Nanoparticle Imaging Agents.
Biomater Sci
PUBLISHED: 09-24-2013
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Gold nanoparticles have attracted much interest as a platform for development of multifunctional imaging and therapeutic agents. Multifunctionalized gold nanoparticles are generally constructed by covalent assembly of a gold core with thiolated ligands. In this study, we have assembled multifunctionalized gold nanoparticles in one step by nucleic acid hybridization of ODN (oligodeoxynucleotide)-derivatized gold nanoparticles with a library of pre-functionalized complementary PNAs (peptide nucleic acids). The PNAs were functionalized by conjugation with DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) for chelating (64)Cu for PET imaging, PEG (polyethylene glycol) for conferring stealth properties, and Cy5 for fluorescent imaging. The resulting nanoparticles showed good stability both in vitro and in vivo showing biodistribution behavior in a mouse that would be expected for a PEGylated gold nanoparticle rather than that for the radiolabelled PNA used in its assembly.
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Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 09-03-2013
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Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NF?B) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.
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A Simple and Efficient Synthesis of an Acid-labile Polyphosphoramidate by Organobase-catalyzed Ring-Opening Polymerization and Transformation to Polyphosphoester Ionomers by Acid Treatment.
Macromolecules
PUBLISHED: 09-03-2013
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The direct synthesis of an acid-labile polyphosphoramidate by organobase-catalyzed ring-opening polymerization and an overall two-step preparation of polyphosphodiester ionomers (PPEI) by acid-assisted cleavage of the phosphoramidate bonds along the backbone of the polyphosphoramidate were developed in this study. The ultrafast organobase-catalyzed ring-opening polymerization of a cyclic phospholane methoxyethyl amidate monomer initiated by benzyl alcohol allowed for the preparation of well-defined polyphosphoramidates (PPA) with predictable molecular weights, narrow molecular weight distributions (PDI<1.10), and well-defined chain ends. Cleavage of the acid-labile phosphoramidate bonds on the polyphosphoramidate repeat units was evaluated under acidic conditions over a pH range of 1-5, and the complete hydrolysis produced polyphosphodiesters. The thermal properties of the resulting polyphosphoester ionomer acid and polyphosphoester ionomer sodium salt exhibited significant thermal stability. The parent PPA and both forms of the PPEIs showed low cytotoxicities toward HeLa cells and RAW 264.7 mouse macrophage cells. The synthetic methodology developed here has enriched the family of water-soluble polymers prepared by rapid and convenient organobase-catalyzed ring-opening polymerizations and straightforward chemical medication reactions, which are designed to be hydrolytically degradable and have promise for numerous biomedical and other applications.
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Between red and yellow: evidence of intermediates in a vapochromic Pt(II) salt.
Chem. Commun. (Camb.)
PUBLISHED: 08-29-2013
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[Pt(tpy)Cl]ClO4·H2O (1·H2O) changes from red to yellow upon dehydration due to increased Pt···Pt distances. Spectroscopic, diffraction, gravimetric and calorimetric data demonstrate the presence of intermediates during hydration and dehydration which signifies surprising mechanistic complexity in the vapochromic response.
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Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors.
Cell Stem Cell
PUBLISHED: 08-06-2013
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We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (1) differential complexity of sequence motifs bound by GATA1, GATA2, and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (3) the potential to predict gene expression trajectories based on global associations between TF-binding data and target gene expression; and (4) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. This rubric exemplifies the utility of this cross-platform resource for deconvoluting the complexity of transcriptional programs controlling stem/progenitor cell fate in hematopoiesis.
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Dysregulation of the complement cascade in the hSOD1G93A transgenic mouse model of amyotrophic lateral sclerosis.
J Neuroinflammation
PUBLISHED: 08-01-2013
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Components of the innate immune complement system have been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS); however, a comprehensive examination of complement expression in this disease has not been performed. This study therefore aimed to determine the expression of complement components (C1qB, C4, factor B, C3/C3b, C5 and CD88) and regulators (CD55 and CD59a) in the lumbar spinal cord of hSOD1(G93A) mice during defined disease stages.
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MIG: Multi-Image Genome viewer.
Bioinformatics
PUBLISHED: 07-10-2013
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Multi-Image Genome (MIG) viewer is a web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. This methodology has been used successfully to analyze ChIP-Seq data and RNA-Seq data and to detect somatic mutations in genome resequencing projects.
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Roles of Free Radicals in Type 1 Phototherapeutic Agents: Aromatic Amines, Sulfenamides, and Sulfenates.
J Phys Chem A
PUBLISHED: 06-24-2013
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Detailed analyses of the electron spin resonance (ESR) spectra, cell viability, and DNA degradation studies are presented for the photolyzed Type I phototherapeutic agents: aromatic amines, sulfenamides, and sulfenates. The ESR studies provided evidence that copious free radicals can be generated from these N-H, N-S, and S-O containing compounds upon photoirradiation with UV/visible light. The analyses of spectral data allowed us to identify the free radical species. The cell viability studies showed that these agents after exposure to light exert cytotoxicity to kill cancer cells (U937 leukemia cell lines HTC11, KB, and HT29 cell lines) in a dosage- and time-dependent manner. We examined a possible pathway of cell death via DNA degradation by a plasmid cleavage assay for several compounds. The effects of photosensitization with benzophenone in the presence of oxygen were examined. The studies indicate that planar tricyclic amines and sulfenamides tend to form ?-electron delocalized aminyl radicals, whereas nonplanar ones tend to yield nitroxide radicals resulting from the recombination of aminyl radicals with oxygen. The ESR studies coupled with the results of cell viability measurements and DNA degradation reveal that planar N-centered radicals can provide higher potency in cell death and allow us to provide some insights on the reaction mechanisms. We also found the formation of azatropylium cations possessing high aromaticity derived from azepines can facilitate secondary electron transfer to form toxic O2(•-) radicals, which can further exert oxidative stress and cause cell death.
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Polyphosphoester-based cationic nanoparticles serendipitously release integral biologically-active components to serve as novel degradable inducible nitric oxide synthase inhibitors.
Adv. Mater. Weinheim
PUBLISHED: 06-22-2013
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A degradable polyphosphoester (PPE)-based cationic nanoparticle (cSCK), which is integrated constructed as a novel degradable drug device, demonstrates surprisingly efficient inhibition of inducible nitric oxide synthase (iNOS) transcription, and eventually inhibits nitric oxide (NO) over-production, without loading of any specific therapeutic drugs. This system may serve as a promising anti-inflammatory agent toward the treatment of acute lung injury.
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Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level.
Nat Commun
PUBLISHED: 06-05-2013
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Haematopoietic stem cells (HSCs) are the founding cells of the adult haematopoietic system, born during ontogeny from a specialized subset of endothelium, the haemogenic endothelium (HE) via an endothelial-to-haematopoietic transition (EHT). Although recently imaged in real time, the underlying mechanism of EHT is still poorly understood. We have generated a Runx1 +23 enhancer-reporter transgenic mouse (23GFP) for the prospective isolation of HE throughout embryonic development. Here we perform functional analysis of over 1,800 and transcriptional analysis of 268 single 23GFP(+) HE cells to explore the onset of EHT at the single-cell level. We show that initiation of the haematopoietic programme occurs in cells still embedded in the endothelial layer, and is accompanied by a previously unrecognized early loss of endothelial potential before HSCs emerge. Our data therefore provide important insights on the timeline of early haematopoietic commitment.
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Mitosis and apoptosis: how is the balance set?
Curr. Opin. Cell Biol.
PUBLISHED: 05-28-2013
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Anti-mitotic agents are used extensively during cancer chemotherapy. These agents target microtubules and thus block mitotic progression by activating the spindle assembly checkpoint. Following a prolonged mitotic arrest, cells either die in mitosis via apoptosis, or exit mitosis without dividing and survive, a process known as slippage. What dictates the balance between these two fates is unclear, but recent advances highlight the importance of the pro-survival Bcl2 family, with Mcl1 degradation emerging as a key determinant of mitotic cell fate. Here we review these advances, with a view towards identifying how the balance between apoptosis and slippage can be tipped in favour of death. This in turn may open up new opportunities to sensitize cancer cells to anti-mitotic agents.
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The receptor for complement component C3a mediates protection from intestinal ischemia-reperfusion injuries by inhibiting neutrophil mobilization.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 05-21-2013
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C3a is a key complement activation fragment, yet its neutrophil-expressed receptor (C3aR) still has no clearly defined role. In this study, we used a neutrophil-dependent mouse model of intestinal ischemia-reperfusion (IR) injury to explore the role of C3aR in acute tissue injuries. C3aR deficiency worsened intestinal injury, which corresponded with increased numbers of tissue-infiltrating neutrophils. Circulating neutrophils were significantly increased in C3aR(-/-) mice after intestinal ischemia, and C3aR(-/-) mice also mobilized more circulating neutrophils after granulocyte colony-stimulating factor infusion compared with WT mice, indicating a specific role for C3aR in constraining neutrophil mobilization in response to intestinal injury. In support of this role, C3aR(-/-) mice reconstituted with WT bone marrow reversed IR pathology back to WT levels. Complement C5a receptor (C5aR) antagonism in C3aR(-/-) mice also rectified the worsened pathology after intestinal IR injury but had no effect on circulating neutrophils, highlighting the opposing roles of C3a and C5a in disease pathogenesis. Finally, we found that using a potent C3a agonist to activate C3aR in vivo reduced neutrophil mobilization and ameliorated intestinal IR pathology in WT, but not C3aR(-/-), mice. This study identifies a role for C3aR in regulating neutrophil mobilization after acute intestinal injury and highlights C3aR agonism as a potential treatment option for acute, neutrophil-driven pathologies.
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Efficient protection and transfection of small interfering RNA by cationic shell-crosslinked knedel-like nanoparticles.
Nucleic Acid Ther
PUBLISHED: 04-06-2013
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Despite the great potential of small interfering RNA (siRNA) as a therapeutic agent, progress in this area has been hampered by a lack of efficient biocompatible transfection agents. Recently, cationic shell-crosslinked knedel-like nanoparticles (cSCKs) were found to possess lower cytotoxicity and better transfection ability for phosphorothioate ODNs and plasmid DNA than the commonly used cationic lipid-based agent Lipofectamine. To determine the usefulness of cSCKs for siRNA transfection, a small library of cSCKs with varying percentage of primary and tertiary amines was assessed for its ability to bind to siRNA, inhibit siRNA degradation in human serum, and to transfect HeLa and mouse macrophage cell lines. The silencing efficiency in HeLa cells was greatest with the cSCK with 100% primary amines (pa100) as determined by their viability following transfection with cytotoxic and non-cytotoxic siRNAs. cSCK-pa100 showed greater silencing efficiency than Lipofectamine 2000 in the HeLa cells, as well in 293T and human bronchial epithelial (HEK) cells, but was comparable in human bronchial epithelial (BEAS-2B) cells and human mammary epithelial (MCF10a) cells. cSCK-pa100 also showed greater silencing of iNOS expression than Lipofectamine 2000 in a mouse macrophage cell line, and provided greater protection from serum degradation, demonstrating its potential usefulness as an siRNA transfection agent. The siRNA silencing of iNOS at lower concentrations of siRNA could be enhanced by complexation with the fusogenic GALA peptide, which was shown to enhance endosomal escape following uptake.
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Imaging mRNA expression levels in living cells with PNA·DNA binary FRET probes delivered by cationic shell-crosslinked nanoparticles.
Org. Biomol. Chem.
PUBLISHED: 03-28-2013
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Optical imaging of gene expression through the use of fluorescent antisense probes targeted to the mRNA has been an area of great interest. The main obstacles to developing highly sensitive antisense fluorescent imaging agents have been the inefficient intracellular delivery of the probes and high background signal from unbound probes. Binary antisense probes have shown great promise as mRNA imaging agents because a signal can only occur if both probes are bound simultaneously to the mRNA target site. Selecting an accessible binding site is made difficult by RNA folding and protein binding in vivo and the need to bind two probes. Even more problematic, has been a lack of methods for efficient cytoplasmic delivery of the probes that would be suitable for eventual applications in vivo in animals. Herein we report the imaging of iNOS mRNA expression in live mouse macrophage cells with PNA·DNA binary FRET probes delivered by a cationic shell crosslinked knedel-like nanoparticle (cSCK). We first demonstrate that FRET can be observed on in vitro transcribed mRNA with both the PNA probes and the PNA·DNA hybrid probes. We then demonstrate that the FRET signal can be observed in live cells when the hybrid probes are transfected with the cSCK, and that the strength of the FRET signal is sequence specific and depends on the mRNA expression level.
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Mapping the stability diagram of a quadrupole mass spectrometer with a static transverse magnetic field applied.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 03-25-2013
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Previous experimental and theoretical work identified that the application of a static magnetic (B) field can improve the resolution of a quadrupole mass spectrometer (QMS) and this simple method of performance enhancement offers advantages for field deployment. Presented here are further data showing the effect of the transverse magnetic field upon the QMS performance. For the first time, the asymmetry in QMS operation with B x and B y is considered and explained in terms of operation in the fourth quadrant of the stability diagram. The results may be explained by considering the additional Lorentz force (v x B) experienced by the ion trajectories in each case. Using our numerical approach, we model not only the individual ion trajectories for a transverse B field applied in x and y but also the mass spectra and the effect of the magnetic field upon the stability diagram. Our theoretical findings, confirmed by experiment, show an improvement in resolution and ion transmission by application of magnetic field for certain operating conditions.
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Quadrupole mass filter: design and performance for operation in stability zone 3.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 03-23-2013
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The predicted performance of a quadrupole mass filter (QMF) operating in Mathieu stability zone 3 is described in detail using computer simulations. The investigation considers the factors that limit the ultimate maximum resolution (Rmax) and percentage transmission (%Tx), which can be obtained for a given QMF for a particular scan line of operation. The performance curve (i.e., the resolution (R) versus number (N) of radio frequency (rf) cycles experienced by the ions in the mass filter) has been modeled for the upper and lower tip of stability zone 3. The saturation behavior of the performance curve observed in practice for zone 3 is explained. Furthermore, new design equations are presented by examining the intersection of the scan line with stability zone 3. Resolution versus transmission characteristics of stability zones 1 and 3 are compared and the dependence of performance for zones 1 and 3 is related to particular instrument operating parameters.
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Neural tube defects, folate, and immune modulation.
Birth Defects Res. Part A Clin. Mol. Teratol.
PUBLISHED: 03-13-2013
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Periconceptional supplementation with folic acid has led to a significant worldwide reduction in the incidence of neural tube defects (NTDs). However, despite increasing awareness of the benefits of folic acid supplementation and the implementation of food fortification programs in many countries, NTDs continue to be a leading cause of perinatal morbidity and mortality worldwide. Furthermore, there exists a significant subgroup of women who appear to be resistant to the protective effects of folic acid supplementation. The following review addresses emerging clinical and experimental evidence for a role of the immune system in the etiopathogenesis of NTDs, with the aim of developing novel preventative strategies to further reduce the incidence of NTD-affected pregnancies. In particular, recent studies demonstrating novel roles and interactions between innate immune factors such as the complement cascade, neurulation, and folate metabolism are explored.
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SCIMITAR: Subject-carried implant monitoring inductive telemetric ambulatory reader for remote data acquisition from implanted orthopaedic prostheses.
Med Eng Phys
PUBLISHED: 03-10-2013
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This work describes the functions of the external, portable part of a telemetry system for powering and interrogating implantable electrical devices built within orthopaedic implants for real-time data acquisition of strain, load, temperature, humidity and other relevant data (e.g. from inertial sensors). The system contains a battery powered inductive energiser and demodulator to remotely power the implant electronics and demodulate the signals transmitted from the implanted device. Due to the housing of the internal coil, sufficient inductive coupling is obtained between the external and internal tuned circuits to enable simultaneous power and data transmission over the same inductive link. The actual performance of this system when used with one specific implant was studied, and some correspondence made to the relevant theory. Performance factors relating to both power efficiency and data reconstruction were identified.
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A high-throughput and quantitative method to assess the mutagenic potential of translesion DNA synthesis.
Nucleic Acids Res.
PUBLISHED: 03-06-2013
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Cellular genomes are constantly damaged by endogenous and exogenous agents that covalently and structurally modify DNA to produce DNA lesions. Although most lesions are mended by various DNA repair pathways in vivo, a significant number of damage sites persist during genomic replication. Our understanding of the mutagenic outcomes derived from these unrepaired DNA lesions has been hindered by the low throughput of existing sequencing methods. Therefore, we have developed a cost-effective high-throughput short oligonucleotide sequencing assay that uses next-generation DNA sequencing technology for the assessment of the mutagenic profiles of translesion DNA synthesis catalyzed by any error-prone DNA polymerase. The vast amount of sequencing data produced were aligned and quantified by using our novel software. As an example, the high-throughput short oligonucleotide sequencing assay was used to analyze the types and frequencies of mutations upstream, downstream and at a site-specifically placed cis-syn thymidine-thymidine dimer generated individually by three lesion-bypass human Y-family DNA polymerases.
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Ciprofloxacin resistance in the faecal carriage of patients undergoing transrectal ultrasound guided prostate biopsy.
BJU Int.
PUBLISHED: 03-06-2013
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WHATS KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Transrectal ultrasound guided prostate biopsies (TRUSBx) are associated with a spectrum of complications, including most significantly infection, which affects up to 5% of patients. In the most severe cases, infection leads to sepsis, a life-threatening complication. Escherichia coli is the primary responsible pathogen. Although antibiotic prophylaxis with fluoroquinolones is routinely used, there is evidence that the infection rate after TRUSBx is increasing, and this appears to be due to an increasing prevalence of ciprofloxacin-resistant rectal flora. This is the largest prospective clinical trial to date analysing the rectal flora of men undergoing prostate biopsies. We determined the microbial and antibiotic sensitivity profiles from 849 patients. Ciprofloxacin-resistant Gram-negative organisms were identified in the rectal flora of 19.0% of men. Furthermore, fluoroquinolone use within 6 months preceding a TRUSBx and the presence of a prosthetic heart valve were significant predictors of ciprofloxacin resistance on rectal swab. Determining the prevalence of rectal fluoroquinolone resistance has important implications in evaluation of the suitability of prophylactic regimens. Antimicrobial profiles derived from rectal swabs pre-biopsy may prove useful in guiding targeted antibiotic prophylaxis.
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C5a receptor signaling prevents folate deficiency-induced neural tube defects in mice.
J. Immunol.
PUBLISHED: 02-18-2013
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The complement system is involved in a range of diverse developmental processes, including cell survival, growth, differentiation, and regeneration. However, little is known about the role of complement in embryogenesis. In this study, we demonstrate a novel role for the canonical complement 5a receptor (C5aR) in the development of the mammalian neural tube under conditions of maternal dietary folic acid deficiency. Specifically, we found C5aR and C5 to be expressed throughout the period of neurulation in wild-type mice and localized the expression to the cephalic regions of the developing neural tube. C5aR was also found to be expressed in the neuroepithelium of early human embryos. Ablation of the C5ar1 gene or the administration of a specific C5aR peptide antagonist to folic acid-deficient pregnant mice resulted in a high prevalence of severe anterior neural tube defect-associated congenital malformations. These findings provide a new and compelling insight into the role of the complement system during mammalian embryonic development.
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Elevated complement factor C5a in maternal and umbilical cord plasma in preeclampsia.
J. Reprod. Immunol.
PUBLISHED: 02-14-2013
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Preeclampsia is a leading cause of morbidity and mortality worldwide, encompassing significant short- and long-term health sequelae. Recently, there has been accumulating evidence for a role of the complement system in the pathogenesis of numerous complications of pregnancy, including preeclampsia. The present cross-sectional study compared the plasma concentrations of complement factors C3a and C5a between normotensive pregnancies and pregnancies complicated with either preeclampsia or gestational hypertension alone. We found that maternal plasma C5a concentration was significantly higher in preeclamptic pregnancy than in pregnancy affected by gestational hypertension alone or normotensive pregnancy. Umbilical cord plasma C5a concentrations were also higher in pregnancies complicated by preeclampsia compared to gestational hypertension or normotensive pregnancy. Maternal and cord plasma C5a concentrations were significantly correlated, suggesting that C5a can freely diffuse between maternal and fetal circulation. There were no significant differences in C3a concentrations in maternal or cord plasma between any groups. These results support the hypothesis that C5a may play a role in preeclampsia, but not in gestational hypertension.
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Development of a large scale human complement source for use in bacterial immunoassays.
J. Immunol. Methods
PUBLISHED: 02-08-2013
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The serum bactericidal assay is the correlate of protection for meningococcal disease but the use and comparison of functional immunological assays for the assessment of meningococcal vaccines is complicated by the sourcing of human complement. This is due to high levels of immunity in the population acquired through natural meningococcal carriage and means that many individuals must be screened to find donors with suitably low bactericidal titres against the target strain. The use of different donors for each meningococcal strain means that comparisons of assay responses between strains and between laboratories is difficult. We have developed a method for IgG-depletion of 300 ml batches of pooled human lepirudin-derived plasma using Protein G sepharose affinity chromatography that retains complement activity. However, IgG-depletion also removed C1q. This was also eluted from the affinity matrix, concentrated and added to the complement source. The final complement source retained mean alternative pathway activity of 96.8% and total haemolytic activity of 84.2% in four batches. Complement components C3, C5, properdin and factor H were retained following the process and the IgG-depleted complement was shown to be suitable for use in antibody-mediated complement deposition and serum bactericidal activity assays against serogroup B meningococci. The generation of large IgG-depleted batches of pooled human plasma allows for the comparison of immunological responses to diverse meningococcal strain panels in large clinical trials.
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Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes.
Hum. Mol. Genet.
PUBLISHED: 01-17-2013
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Craniofrontonasal syndrome (CFNS), an X-linked disorder caused by loss-of-function mutations of EFNB1, exhibits a paradoxical sex reversal in phenotypic severity: females characteristically have frontonasal dysplasia, craniosynostosis and additional minor malformations, but males are usually more mildly affected with hypertelorism as the only feature. X-inactivation is proposed to explain the more severe outcome in heterozygous females, as this leads to functional mosaicism for cells with differing expression of EPHRIN-B1, generating abnormal tissue boundaries-a process that cannot occur in hemizygous males. Apparently challenging this model, males occasionally present with a more severe female-like CFNS phenotype. We hypothesized that such individuals might be mosaic for EFNB1 mutations and investigated this possibility in multiple tissue samples from six sporadically presenting males. Using denaturing high performance liquid chromatography, massively parallel sequencing and multiplex-ligation-dependent probe amplification (MLPA) to increase sensitivity above standard dideoxy sequencing, we identified mosaic mutations of EFNB1 in all cases, comprising three missense changes, two gene deletions and a novel point mutation within the 5 untranslated region (UTR). Quantification by Pyrosequencing and MLPA demonstrated levels of mutant cells between 15 and 69%. The 5 UTR variant mutates the stop codon of a small upstream open reading frame that, using a dual-luciferase reporter construct, was demonstrated to exacerbate interference with translation of the wild-type protein. These results demonstrate a more severe outcome in mosaic than in constitutionally deficient males in an X-linked dominant disorder and provide further support for the cellular interference mechanism, normally related to X-inactivation in females.
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Reduced dosage of ERF causes complex craniosynostosis in humans and mice and links ERK1/2 signaling to regulation of osteogenesis.
Nat. Genet.
PUBLISHED: 01-03-2013
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The extracellular signal-related kinases 1 and 2 (ERK1/2) are key proteins mediating mitogen-activated protein kinase signaling downstream of RAS: phosphorylation of ERK1/2 leads to nuclear uptake and modulation of multiple targets. Here, we show that reduced dosage of ERF, which encodes an inhibitory ETS transcription factor directly bound by ERK1/2 (refs. 2,3,4,5,6,7), causes complex craniosynostosis (premature fusion of the cranial sutures) in humans and mice. Features of this newly recognized clinical disorder include multiple-suture synostosis, craniofacial dysmorphism, Chiari malformation and language delay. Mice with functional Erf levels reduced to ?30% of normal exhibit postnatal multiple-suture synostosis; by contrast, embryonic calvarial development appears mildly delayed. Using chromatin immunoprecipitation in mouse embryonic fibroblasts and high-throughput sequencing, we find that ERF binds preferentially to elements away from promoters that contain RUNX or AP-1 motifs. This work identifies ERF as a novel regulator of osteogenic stimulation by RAS-ERK signaling, potentially by competing with activating ETS factors in multifactor transcriptional complexes.
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High-resolution analysis of cis-acting regulatory networks at the ?-globin locus.
Philos. Trans. R. Soc. Lond., B, Biol. Sci.
PUBLISHED: 01-01-2013
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We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human ?-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the ?-globin cluster.
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BubR1 blocks substrate recruitment to the APC/C in a KEN-box-dependent manner.
J. Cell. Sci.
PUBLISHED: 12-22-2011
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The spindle assembly checkpoint (SAC) is a signalling network that delays anaphase onset until all the chromosomes are attached to the mitotic spindle through their kinetochores. The downstream target of the spindle checkpoint is the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase that targets several anaphase inhibitors for proteolysis, including securin and cyclin B1. In the presence of unattached kinetochores, the APC/C is inhibited by the mitotic checkpoint complex (MCC), a tetrameric complex composed of three SAC components, namely BubR1, Bub3 and Mad2, and the APC/C co-activator Cdc20. The molecular mechanisms underlying exactly how unattached kinetochores catalyse MCC formation and how the MCC then inhibits the APC/C remain obscure. Here, using RNAi complementation and in vitro ubiquitylation assays, we investigate the domains in BubR1 required for APC/C inhibition. We observe that kinetochore localisation of BubR1 is required for efficient MCC assembly and SAC response. Furthermore, in contrast to previous studies, we show that the N-terminal domain of BubR1 is the only domain involved in binding to Cdc20-Mad2 and the APC/C. Within this region, an N-terminal KEN box (KEN1) is essential for these interactions. By contrast, mutation of the second KEN box (KEN2) of BubR1 does not interfere with MCC assembly or APC/C binding. However, both in cells and in vitro, the KEN2 box is required for inhibition of APC/C when activated by Cdc20 (APC/C(Cdc20)). Indeed, we show that this second KEN box promotes SAC function by blocking the recruitment of substrates to the APC/C. Thus, we propose a model in which the BubR1 KEN boxes play two very different roles, the first to promote MCC assembly and the second to block substrate recruitment to APC/C(Cdc20).
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Once daily maraviroc 300 mg or 150 mg in combination with ritonavir-boosted darunavir 800/100 mg.
J. Antimicrob. Chemother.
PUBLISHED: 12-15-2011
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To describe the pharmacokinetics of maraviroc when dosed at 150 or 300 mg once daily with 800/100 mg of darunavir/ritonavir.
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Lopinavir/ritonavir single agent therapy as a universal combination antiretroviral therapy stopping strategy: results from the STOP 1 and STOP 2 studies.
J. Antimicrob. Chemother.
PUBLISHED: 12-14-2011
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We designed two different studies to evaluate two different combination antiretroviral therapy (cART) stopping strategies namely a staggered stop approach (STOP 1 study) and a protected stop approach (STOP 2 study) to find the best universal stop strategy.
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Pharmacokinetics of antiretroviral drugs in anatomical sanctuary sites: the male and female genital tract.
Antivir. Ther. (Lond.)
PUBLISHED: 12-14-2011
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HIV resides within anatomical sanctuary sites, where local drug exposure and viral dynamics may differ significantly from the systemic compartment. Suboptimal antiretroviral concentrations in the genital tract may result in compartmentalized viral replication, selection of resistant mutations and possible re-entry of wild-type/resistant virus into the systemic circulation. Therefore, achieving adequate antiretroviral exposure in the genital tract has implications for the prevention of sexual and vertical transmission of HIV. Penetration of antiretrovirals in the genital tract is expressed by accumulation ratios derived from the measurement of drug concentrations in time-matched seminal plasma/cervicovaginal fluid and plasma samples. Penetration varies by gender and may be drug (as opposed to class) specific with high interindividual variability. Concentrations in seminal plasma are highest for nucleoside analogues and lowest for protease inhibitors and efavirenz. Seminal accumulation of newer agents, raltegravir and maraviroc, is moderate (rank order of accumulation is nucleoside/nucleotide reverse transcriptase inhibitors [lamivudine/zidovudine/tenofovir/didanosine > stavudine/abacavir] > raltegravir > indinavir/maraviroc/nevirapine > efavirenz/protease inhibitors [amprenavir/atazanavir/darunavir > lopinavir/ritonavir > saquinavir] > enfuvirtide). In the female genital tract, the nucleoside analogues exhibit high accumulation ratios, whereas protease inhibitors have limited penetration; however, substantial variability exists between individuals and study centres. Second generation non-nucleoside reverse transcriptase inhibitor etravirine, and maraviroc and raltegravir, demonstrate effective accumulation in cervicovaginal secretions (rank order of accumulation is nucleoside/nucleotide reverse transcriptase inhibitor [zidovudine/lamivudine/didanosine > emtricitabine/tenofovir] > indinavir > maraviroc/raltegravir/darunavir/etravirine > nevirapine/abacavir > protease inhibitors [amprenavir/atazanavir/ritonavir] > lopinavir/stavudine/efavirenz > saquinavir).
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Pharmacokinetics of antiretroviral drugs in anatomical sanctuary sites: the fetal compartment (placenta and amniotic fluid).
Antivir. Ther. (Lond.)
PUBLISHED: 12-14-2011
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HIV resides within anatomical sanctuary sites where local drug exposure and viral dynamics may differ significantly from the systemic compartment. Widespread implementation of antiretroviral therapy has seen a significant decline in the incidence of mother-to-child transmission (MTCT) of HIV. In addition to suppression of maternal plasma/genital viral loads, antiretroviral agents that cross the placenta and achieve adequate concentrations in the fetal compartment may exert a greater prophylactic effect. Penetration of antiretrovirals in the fetal compartment is expressed by accumulation ratios derived from the measurement of drug concentrations in paired maternal plasma and umbilical cord samples. The nucleoside analogues and nevirapine accumulate extensively in cord blood and in the surrounding amniotic fluid, whereas the protease inhibitors (PIs) exhibit low-to-moderate placental accumulation. Early data suggest that high placental/neonatal concentrations are achieved with raltegravir, but to a lesser extent with etravirine and maraviroc (rank order of accumulation: raltegravir/nucleoside reverse transcriptase inhibitor [tenofovir > zidovudine/lamivudine/emtricitabine/stavudine/abacavir] > non-nucleoside reverse transcriptase inhibitor [nevirapine > etravirine] > PI > maraviroc/enfuvirtide). More comprehensive in vivo pharmacokinetic data are required to justify the potential use of these agents as safe and effective options during pregnancy.
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p31comet-mediated extraction of Mad2 from the MCC promotes efficient mitotic exit.
J. Cell. Sci.
PUBLISHED: 11-18-2011
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Accurate chromosome segregation requires the spindle assembly checkpoint to be active at the onset of mitosis, before being silenced following chromosome alignment. p31(comet) is a checkpoint antagonist in that its inhibition delays mitotic exit, whereas its overexpression overrides the checkpoint. How exactly p31(comet) antagonises the checkpoint is unclear. A prevalent model is that p31(comet) acts as a cap by inhibiting recruitment of the open conformation form of Mad2 (O-Mad2) to the kinetochore-bound complex of Mad1-C-Mad2 (closed conformation Mad2), an essential step that is required for checkpoint activation. Here, we show that although p31(comet) localises to kinetochores in mitosis, modulation of its activity has no effect on recruitment of O-Mad2 to kinetochores. Rather, our observations support a checkpoint-silencing role for p31(comet) downstream of kinetochores. We show that p31(comet) binds Mad2 when it is bound to the mitotic checkpoint complex (MCC) components BubR1 and Cdc20. Furthermore, RNAi-mediated inhibition of p31(comet) results in more Mad2 bound to BubR1-Cdc20, and conversely, overexpression of p31(comet) results in less Mad2 bound to BubR1-Cdc20. Addition of recombinant p31(comet) to checkpoint-arrested extracts removes Mad2 from the MCC, whereas a p31(comet) mutant that cannot bind Mad2 has no effect. Significantly, expression of a Mad2 mutant that cannot bind p31(comet) prolongs the metaphase to anaphase transition. Taken together, our data support the notion that p31(comet) negatively regulates the spindle assembly checkpoint by extracting Mad2 from the MCC.
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Inhibition of heat shock transcription factor binding by a linear polyamide binding in an unusual 1:1 mode.
Chembiochem
PUBLISHED: 08-17-2011
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Heat shock proteins (HSPs) are known to protect cells from heat, oxidative stress, and the cytotoxic effects of drugs, and thus can enhance cancer cell survival. As a result, HSPs are a newly emerging class of protein targets for chemotherapy. Among the various HSPs, the HSP70 family is the most highly conserved and prevalent. Herein we describe the development of a ?-alanine rich linear polyamide that binds the GGA heat shock elements (HSEs) 3 and 4 in the HSP70 promoter in an unusual 1:1 mode and inhibits heat shock transcription factor 1 (HSF1) binding in vitro.
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Structural characterisation, stability and antibody recognition of chimeric NHBA-GNA1030: an investigational vaccine component against Neisseria meningitidis.
Vaccine
PUBLISHED: 08-09-2011
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A new generation multi-component vaccine, principally directed against serogroup B Neisseria meningitidis (4CMenB), has recently been developed. One of its components, identified through reverse vaccinology, is the neisserial heparin-binding antigen (NHBA) which is included in the formulation as a novel NHBA-GNA1030 fusion protein (NHBA-FP). We describe here the biophysical characteristics of this vaccine antigen to understand better its structural properties in solution and concurrent immunogenicity prior to formulation. By deliberately stressing the protein to lose its immune responses, we were able to study the proteins structural changes at the molecular level. The unmodified NHBA-FP was found to be mainly monomeric with mass of 67kDa and secondary structure dominated by ?-sheets and turns (57% average). The antigen was very stable in storage buffer. It could be forced to unfold in a low-salt buffer resulting in the exposure of one of its two tryptophan residues at 50°C. Long-term stress studies (10-15 days at 37°C) showed modification in the chromatographic and electrophoretic profiles with progressive degradation and aggregation. Since there was little change in secondary structure (as monitored by circular dichroism and tryptophan fluorescence spectroscopy), the loss of functional immunogenicity of the thermal stressed protein could be mainly attributed to the observed fragmentation and aggregation. We therefore conclude that the maintenance of the intact, non-fragmented state of the NHBA-FP is important to preserve its functional immunogenicity. This may thus be utilised as an assay for the control testing of the protein.
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The cost-effectiveness of early access to HIV services and starting cART in the UK 1996-2008.
PLoS ONE
PUBLISHED: 08-02-2011
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To calculate use, cost and cost-effectiveness of people living with HIV (PLHIV) starting routine treatment and care before starting combination antiretroviral therapy (cART) and PLHIV starting first-line 2NRTIs+NNRTI or 2NRTIs+PI(boosted), comparing PLHIV with CD4?200 cells/mm3 and CD4>200 cells/mm3. Few studies have calculated the use, cost and cost-effectiveness of routine treatment and care before starting cART and starting cART above and below CD4 200 cells/mm3.
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Oil-in-water monitoring using membrane inlet mass spectrometry.
Anal. Chem.
PUBLISHED: 07-19-2011
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A membrane inlet mass spectrometry (MIMS) system has been used for detection and analysis of two types of North Sea crude oil. The system was installed on-field on the Flotta Oil Terminal (Orkney, UK). It consisted of a quadrupole mass spectrometer (QMS) connected to the capillary probe with a silicone-based membrane. The produced mass spectra and calibration plots from the MIMS instrument showed the capability to measure levels of individual hydrocarbons within crude oil in seawater. The generated mass spectra from the field tests also showed the ability to distinguish between different types of oil and to determine concentrations of toxic hydrocarbons in oil (e.g., benzene, toluene, and xylene (BTX)). The performance of the instrument at different temperatures of seawater and oil droplet sizes was also investigated. The results showed that the QMS-based MIMS system has a potential to complement existing oil-in-water (OiW) monitors by being able to detect different oil types and specific hydrocarbon concentrations with high accuracy, which are currently not supported in commercially available OiW monitors.
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Inhibition of inflammation and fibrosis by a complement C5a receptor antagonist in DOCA-salt hypertensive rats.
J. Cardiovasc. Pharmacol.
PUBLISHED: 07-15-2011
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The anaphylatoxin C5a generated by activation of the innate immunity complement system is a potent inflammatory peptide mediator through the G-protein-coupled receptor C5aR (CD88) present in immune-inflammatory cells, including monocytes, macrophages, neutrophils, T cells, and mast cells. Inflammatory cells infiltrate and initiate the development of fibrosis in the chronically hypertensive heart. In this study, we have investigated whether treatment with a selective C5aR antagonist prevents cardiovascular remodeling in deoxycorticosterone acetate (DOCA)-salt hypertensive rats. Control and DOCA-salt rats were treated with PMX53 (AcF-[OPdChaWR], 1 mg·kg·d oral gavage) for 32 days; structural and functional changes in cardiovascular system were determined. DOCA-salt hypertension increased leukocyte extravasation into ventricular tissue, increasing collagen deposition and ventricular stiffness; PMX53 treatment attenuated these changes, thereby improving cardiac function. Further, treatment with PMX53 suppressed an increased expression of C5aR in the left ventricle from DOCA-salt rats, consistent with the reduced infiltration of inflammatory cells. Vascular endothelial dysfunction in thoracic aortic rings was attenuated by PMX53 treatment, but systolic blood pressure was unchanged in DOCA-salt rats. In the heart, PMX53 treatment attenuated inflammatory cell infiltration, fibrosis, and ventricular stiffness, indicating that C5aR is critically involved in ventricular remodeling by regulating inflammatory responses in the hypertensive heart.
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Strain response of an instrumented intramedullary nail to three-point bending.
J Med Eng Technol
PUBLISHED: 06-04-2011
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An experimental biomechanical evaluation of an instrumented intramedullary nail (TriGen® META Nail, Smith&Nephew®) was undertaken. The objectives were two-fold. The first was to identify the most sensitive strain gauge positions and orientations on the nail, and the second was to demonstrate that the nail was capable of detecting changes in stiffness of the nail-bone composite. The function of the instrumented nail is to quantify fracture healing objectively and directly, and so to predict delayed repair or non-union 2 months before current methods.
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Genome sequence of Rhodobacter sphaeroides Strain WS8N.
J. Bacteriol.
PUBLISHED: 05-27-2011
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Rhodobacter sphaeroides is a metabolically diverse photosynthetic alphaproteobacterium found ubiquitously in soil and freshwater habitats. Here we present the annotated genome sequence of R. sphaeroides WS8N.
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Biotinylated quercetin as an intrinsic photoaffinity proteomics probe for the identification of quercetin target proteins.
Bioorg. Med. Chem.
PUBLISHED: 05-05-2011
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Quercetin is a flavonoid natural product, that is, found in many foods and has been found to have a wide range of medicinal effects. Though a number of quercetin binding proteins have been identified, there has been no systematic approach to identifying all potential targets of quercetin. We describe an O7-biotinylated derivative of quercetin (BioQ) that can act as a photoaffinity proteomics reagent for capturing quercetin binding proteins, which can then be identified by LC-MS/MS. BioQ was shown to inhibit heat induction of HSP70 with almost the same efficiency as quercetin, and to both inhibit and photocrosslink to CK2 kinase, a known target of quercetin involved in activation of the heat shock transcription factor. BioQ was also able to pull down a number of proteins from unheated and heated Jurkat cells following UV irradiation that could be detected by both silver staining and Western blot analysis with an anti-biotin antibody. Analysis of the protein bands by trypsinization and LC-MS/MS led to the identification of heat shock proteins HSP70 and HSP90 as possible quercetin target proteins, along with ubiquitin-activating enzyme, a spliceosomal protein, RuvB-like 2 ATPases, and eukaryotic translation initiation factor 3. In addition, a mitochondrial ATPase was identified that has been previously shown to be a target of quercetin. Most of the proteins identified have also been previously suggested to be potential anticancer targets, suggesting that quercetins antitumor activity may be due to its ability to inhibit multiple target proteins.
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An experimental glenoid rim strain analysis for an improved reverse anatomy shoulder implant fixation.
J. Orthop. Res.
PUBLISHED: 04-28-2011
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Loosening of glenoid components in TSA is a main cause of failure. In reverse anatomy TSA designs used for unstable joints, fixation is particularly demanding. Strains developed around the glenoid rim of biomechanical sawbone scapulae implanted with (a) the original fixed-fulcrum Bayley-Walker glenoid prosthesis in current clinical use, and (b) a revised version with conical cross-section, were compared. The conical shape of the revised design was hypothesized to produce greater strains in the glenoid rim than the original tapered screw design. The 2D strain field at three accessible locations around the rim of each scapula was measured with three-element rosette strain gauges for two types of simulated cancellous bone fill under applied physiologically relevant loads. The average strain energy densities around the rim for the conical design were greater than for the original design by a factor of 1.55-2.25 for all loading conditions. Results indicate that a significantly greater proportion of load was directed toward cortical bone in the conical design, thus promoting cortical bone loading.
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Modelling real-time simultaneous saccharification and fermentation of lignocellulosic biomass and organic acid accumulation using dielectric spectroscopy.
Bioresour. Technol.
PUBLISHED: 04-28-2011
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Dielectric spectroscopy (DS) is routinely used in yeast and mammalian fermentations to quantitatively monitor viable biomass through the inherent capacitance of live cells; however, the use of DS to monitor the enzymatic break down of lignocellulosic biomass has not been reported. The aim of the current study was to examine the application of DS in monitoring the enzymatic saccharification of high sugar perennial ryegrass (HS-PRG) fibre and to relate the data to changes in chemical composition. DS was capable of both monitoring the on-line decrease in PRG fibre capacitance (C=580 kHz) during enzymatic hydrolysis, together with the subsequent increase in conductivity (G=580 kHz) resulting from the production of organic acids during microbial growth. Analysis of the fibre fractions revealed >50% of HS-PRG lignocellulose had undergone enzymatic hydrolysis. These data demonstrated the utility of DS biomass probes for on-line monitoring of simultaneous saccharification and fermentation (SSF).
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Complement C5a inhibition reduces atherosclerosis in ApoE-/- mice.
FASEB J.
PUBLISHED: 04-13-2011
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The complement C5a receptor, CD88, is present on many of the cells found within human atherosclerotic plaques, but little is known about the role of C5a in atherogenesis. Using real-time PCR, we determined that ApoE(-/-) mice fed a normal diet express more aortic CD88 mRNA compared with controls, and this increase coincides with atherosclerotic lesion development (P<0.001 for 3- vs. 25-wk-old animals). Conversely, mRNA expression of the alternative C5a receptor, C5L2, in aortas of ApoE(-/-) mice, was lower than controls at all time points. Using immunohistochemistry, we confirmed the presence of CD88 on macrophages, smooth muscle cells, and activated endothelial cells in plaques from brachiocephalic arteries. Treatment of ApoE(-/-) mice with a CD88 antagonist (PMX53; 3 mg/kg s.c. 3 ×/wk plus 1 mg/kg/d p.o.) for 25 wk reduced lesion size and lipid content in the plaque by ? 40% (P<0.05). Our study provides evidence for a proatherogenic role for C5a and identifies the CD88 antagonist PMX53 as a potential antiatherosclerotic drug.
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Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors.
J. Virol.
PUBLISHED: 04-06-2011
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HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of env compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing in vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1 env intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence in vivo.
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Generation of bivalent chromatin domains during cell fate decisions.
Epigenetics Chromatin
PUBLISHED: 03-18-2011
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In self-renewing, pluripotent cells, bivalent chromatin modification is thought to silence (H3K27me3) lineage control genes while poising (H3K4me3) them for subsequent activation during differentiation, implying an important role for epigenetic modification in directing cell fate decisions. However, rather than representing an equivalently balanced epigenetic mark, the patterns and levels of histone modifications at bivalent genes can vary widely and the criteria for identifying this chromatin signature are poorly defined.
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QMS in the third stability zone with a transverse magnetic field applied.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 02-22-2011
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We report here a study using a quadrupole mass spectrometer (QMS) in which a static magnetic field is applied transversely to the body of the mass filter operating in stability zone 3. Significant improvement in QMS performance was obtained under certain magnetic field conditions, and these have been explained in terms of our theoretical model. The theoretical approach assumed in the model is that the QMS contains hyperbolic rods as electrodes and that the magnetic field acts over the full length of the mass filter assembly. Our latest analysis also predicts for what values of operating parameters an enhancement of the quadrupole resolution is achieved when a transverse magnetic field is applied. The model predicts instrument resolution R?>?5000 for Ar with a 100 mm long mass filter and R?>?3500 for a HT and D(2) mixture with a 200 mm long mass filter via application of a transverse magnetic field.
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Phenotypic characterization of HIV-specific CD8+ T cells during early and chronic infant HIV-1 infection.
PLoS ONE
PUBLISHED: 02-21-2011
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Although CD8(+) T cells play an important role in the containment of adult HIV-1 replication, their role in infant HIV-1 infection is not as well understood. Impaired HIV-specific CD8(+) T cell responses may underlie the persistently high viral loads observed in infants. We examined the frequency and phenotype of infant HIV-specific CD8(+) T cells in 7 HIV-infected antiretroviral therapy-naïve infants during the first 2 years of life, using class I HLA tetramers and IFN-?-ELISPOT. The frequency (0.088-3.9% of CD3(+)CD8(+) cells) and phenotype (CD27(+)CD28(-), CD45RA(+/-), CD57(+/-), HLA-DR(+), CD95(+)) of infant HIV-specific CD8(+) T cells were similar to reports in adults undergoing early infection. Unlike adults, at 23-24 months post-infection a high frequency of HIV-specific CD8(+) T cells expressed HLA-DR (mean 80%, range 68-85%) and CD95 (mean 88%, range 79-96%), suggesting sustained activation and vulnerability to apoptosis. Despite comparable expansion of HIV-specific CD8(+) T cells of a similar phenotype to adults during early infection, infant T cells failed to contain HIV-1 replication, and remained persistently activated and vulnerable to apoptosis during chronic infection.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.