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Find video protocols related to scientific articles indexed in Pubmed.
Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis.
J R Soc Interface
PUBLISHED: 08-01-2014
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There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In this paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurring in areas where wall shear stress (WSS) gradients exist. We propose two possible mechanisms to account for the observed increase in velocity and WSS between P5 and P6: (i) the measured reduction in typical vessel diameter between both time points and (ii) the reduction in network density triggered by the pruning process. The methodology developed herein is applicable to other biomedical domains where microvasculature can be imaged but experimental flow measurements are unavailable or difficult to obtain.
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The necrophagous fly anthrax transmission pathway: empirical and genetic evidence from wildlife epizootics.
Vector Borne Zoonotic Dis.
PUBLISHED: 07-30-2014
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Early studies confirmed Bacillus anthracis in emesis and feces of flies under laboratory conditions, but there is little empirical field evidence supporting the roles of flies in anthrax transmission. We collected samples during outbreaks of anthrax affecting livestock and native and exotic wildlife on two ranches in West Texas (2009-2010). Sampling included animal carcasses, maggots, adult flies feeding on or within several meters of carcasses, and leaves from surrounding vegetation. Microbiology and PCR were used to detect B. anthracis in the samples. Viable B. anthracis and/or PCR-positive results were obtained from all represented sample types. Genetic analysis of B. anthracis samples using multilocus variable number tandem repeat analysis (MLVA) confirmed that each ranch represented a distinct genetic lineage. Within each ranch, we detected the same genotype of B. anthracis from carcasses, maggots, and adult flies. The results of this study provide evidence supporting a transmission cycle in which blowflies contaminate vegetation near carcasses that may then infect additional browsing animals during anthrax outbreaks in the shrubland environment of West Texas.
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Understanding composition-property relationships in Ti-Cr-V-Mo alloys for optimisation of hydrogen storage in pressurised tanks.
Phys Chem Chem Phys
PUBLISHED: 07-03-2014
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The location of hydrogen within Ti-Cr-V-Mo alloys has been investigated during hydrogen absorption and desorption using in situ neutron powder diffraction and inelastic neutron scattering. Neutron powder diffraction identifies a low hydrogen equilibration pressure body-centred tetragonal phase that undergoes a martensitic phase transition to a face-centred cubic phase at high hydrogen equilibration pressures. The average location of the hydrogen in each phase has been identified from the neutron powder diffraction data although inelastic neutron scattering combined with density functional theory calculations show that the local structure is more complex than it appears from the average structure. Furthermore the origin of the change in dissociation pressure and hydrogen trapping on cycling in Ti-Cr-V-Mo alloys is discussed.
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Classification and management of animal anthrax outbreaks based on the source of infection.
Ann. Ist. Super. Sanita
PUBLISHED: 06-28-2014
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Anthrax is a non-contagious infectious disease; it primarily affects herbivores, but all mammals, including humans, can be affected. Humans may contract anthrax directly or indirectly from infected animals. Veterinary surveillance systems, providing information about animal and human cases, should increase the efficacy of the animal anthrax management in order to protect population. Any aspect of the disease should be carefully monitored to implement effective prevention and control strategies. In this paper we propose a new, detailed classification of anthrax outbreaks, based on the source of the infection and the risk level for humans. We describe three different types of animal outbreaks and suggest the most effective procedures for their management and prevention.
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Hydrogen production from ammonia using sodium amide.
J. Am. Chem. Soc.
PUBLISHED: 06-22-2014
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This paper presents a new type of process for the cracking of ammonia (NH3) that is an alternative to the use of rare or transition metal catalysts. Effecting the decomposition of NH3 using the concurrent stoichiometric decomposition and regeneration of sodium amide (NaNH2) via sodium metal (Na), this represents a significant departure in reaction mechanism compared with traditional surface catalysts. In variable-temperature NH3 decomposition experiments, using a simple flow reactor, the Na/NaNH2 system shows superior performance to supported nickel and ruthenium catalysts, reaching 99.2% decomposition efficiency with 0.5 g of NaNH2 in a 60 sccm NH3 flow at 530 °C. As an abundant and inexpensive material, the development of NaNH2-based NH3 cracking systems may promote the utilization of NH3 for sustainable energy storage purposes.
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Presentation of Mycobacterium abscessus infection following rhytidectomy to a UK plastic surgery unit.
BMJ Case Rep
PUBLISHED: 05-30-2014
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We report the presentation of a patient to a UK plastic surgery unit with Mycobacterium abscessus infection following a facelift surgery in Southern India. Treatment was protracted requiring surgical debridement and 6?months of antibiotics including a 3-week hospital admission for intravenous antibiotic therapy. We describe the clinical presentation, diagnosis and treatment of this unusual microorganism with reference to more familiar pyogenic infections.
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Change of plans: an evaluation of the effectiveness and underlying mechanisms of successful talent transfer.
J Sports Sci
PUBLISHED: 05-12-2014
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Talent transfer (TT) is a recently formalised process used to identify and develop talented athletes by selecting individuals who have already succeeded in one sport and transferring them to another. Despite the increasing popularity of TT amongst national organisations and sport governing body professionals, however, there is little empirical evidence as to its efficacy or how it may be most efficiently employed. Accordingly, this investigation was designed to gain a deeper understanding of the effectiveness and underlying mechanisms of TT, achieved through a two-part study. Stage 1 provided a quantitative analysis of the incidence and distribution or, in this respect, epidemiology of TT, finding the most popular transfer to be sprinting to bobsleigh, with an average transfer age of 19 years. Stage 2 scrutinised the TT process and explored the specific cases revealed in stage 1 by examining the perceptions of four sport science support specialists who had worked in TT settings, finding several emergent themes which, they felt, could explain the TT processes. The most prominent theme was the psychosocial mechanism of TT, an aspect currently missing from TT initiatives, suggesting that current TT systems are poorly structured and should redress their approach to develop a more integrated scheme that encompasses all potential mechanisms of transfer.
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Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum.
J. Exp. Bot.
PUBLISHED: 04-10-2014
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Panicum miliaceum (broomcorn millet) is a tetraploid cereal, which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of this species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in this species and its ancestors.
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The role of differential VE-cadherin dynamics in cell rearrangement during angiogenesis.
Nat. Cell Biol.
PUBLISHED: 01-30-2014
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Endothelial cells show surprising cell rearrangement behaviour during angiogenic sprouting; however, the underlying mechanisms and functional importance remain unclear. By combining computational modelling with experimentation, we identify that Notch/VEGFR-regulated differential dynamics of VE-cadherin junctions drive functional endothelial cell rearrangements during sprouting. We propose that continual flux in Notch signalling levels in individual cells results in differential VE-cadherin turnover and junctional-cortex protrusions, which powers differential cell movement. In cultured endothelial cells, Notch signalling quantitatively reduced junctional VE-cadherin mobility. In simulations, only differential adhesion dynamics generated long-range position changes, required for tip cell competition and stalk cell intercalation. Simulation and quantitative image analysis on VE-cadherin junctional patterning in vivo identified that differential VE-cadherin mobility is lost under pathological high VEGF conditions, in retinopathy and tumour vessels. Our results provide a mechanistic concept for how cells rearrange during normal sprouting and how rearrangement switches to generate abnormal vessels in pathologies.
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Successful delayed nose replantation following a dogbite: arterial and venous microanastomosis using interpositional vein grafts.
J Plast Reconstr Aesthet Surg
PUBLISHED: 01-26-2014
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The nose is one of the most important aesthetic units of the face. Following traumatic amputation, although technically very challenging, replantation is undoubtedly the procedure of choice. We present the first successful replantation of a partially amputated nose subjected to an ischaemic time of over 12 h. The injury was sustained following a dog-bite and inter-positional vein grafts were used to re-establish both arterial and venous blood flow.
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In situ X-ray powder diffraction studies of hydrogen storage and release in the Li-N-H system.
Phys Chem Chem Phys
PUBLISHED: 01-23-2014
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We report the experimental investigation of hydrogen storage and release in the lithium amide-lithium hydride composite (Li-N-H) system. Investigation of hydrogenation and dehydrogenation reactions of the system through in situ synchrotron X-ray powder diffraction experiments allowed for the observation of the formation and evolution of non-stoichiometric intermediate species of the form Li1+xNH2-x. This result is consistent with the proposed Frenkel-defect mechanism for these reactions. We observed capacity loss with decreasing temperature through decreased levels of lithium-rich (0.7 ? x ? 1.0) non-stoichiometric phases in the dehydrogenated material, but only minor changes due to multiple cycles at the same temperature. Annealing of dehydrogenated samples reveals the reduced stability of intermediate stoichiometry values (0.4 ? x ? 0.7) compared with the end member species: lithium amide (LiNH2) and lithium imide (Li2NH). Our results highlight the central role of ionic mobility in understanding temperature limitations, capacity loss and facile reversibility of the Li-N-H system.
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Wheat in the Mediterranean revisited--tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers.
BMC Genet.
PUBLISHED: 01-20-2014
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Single Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat.
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The structure of human apolipoprotein A-IV as revealed by stable isotope-assisted cross-linking, molecular dynamics, and small angle x-ray scattering.
J. Biol. Chem.
PUBLISHED: 01-14-2014
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Apolipoprotein (apo)A-IV plays important roles in dietary lipid and glucose metabolism, and knowledge of its structure is required to fully understand the molecular basis of these functions. However, typical of the entire class of exchangeable apolipoproteins, its dynamic nature and affinity for lipid has posed challenges to traditional high resolution structural approaches. We previously reported an x-ray crystal structure of a dimeric truncation mutant of apoA-IV, which showed a unique helix-swapping molecular interface. Unfortunately, the structures of the N and C termini that are important for lipid binding were not visualized. To build a more complete model, we used chemical cross-linking to derive distance constraints across the full-length protein. The approach was enhanced with stable isotope labeling to overcome ambiguities in determining molecular span of the cross-links given the remarkable similarities in the monomeric and dimeric apoA-IV structures. Using 51 distance constraints, we created a starting model for full-length monomeric apoA-IV and then subjected it to two modeling approaches: (i) molecular dynamics simulations and (ii) fitting to small angle x-ray scattering data. This resulted in the most detailed models yet for lipid-free monomeric or dimeric apoA-IV. Importantly, these models were of sufficient detail to direct the experimental identification of new functional residues that participate in a "clasp" mechanism to modulate apoA-IV lipid affinity. The isotope-assisted cross-linking approach should prove useful for further study of this family of apolipoproteins in both the lipid-free and -bound states.
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Kinetic parameters for nutrient enhanced crude oil biodegradation in intertidal marine sediments.
Front Microbiol
PUBLISHED: 01-01-2014
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Availability of inorganic nutrients, particularly nitrogen and phosphorous, is often a primary control on crude oil hydrocarbon degradation in marine systems. Many studies have empirically determined optimum levels of inorganic N and P for stimulation of hydrocarbon degradation. Nevertheless, there is a paucity of information on fundamental kinetic parameters for nutrient enhanced crude oil biodegradation that can be used to model the fate of crude oil in bioremediation programmes that use inorganic nutrient addition to stimulate oil biodegradation. Here we report fundamental kinetic parameters (Ks and qmax) for nitrate- and phosphate-stimulated crude oil biodegradation under nutrient limited conditions and with respect to crude oil, under conditions where N and P are not limiting. In the marine sediments studied, crude oil degradation was limited by both N and P availability. In sediments treated with 12.5 mg/g of oil but with no addition of N and P, hydrocarbon degradation rates, assessed on the basis of CO2 production, were 1.10 ± 0.03 ?mol CO2/g wet sediment/day which were comparable to rates of CO2 production in sediments to which no oil was added (1.05 ± 0.27 ?mol CO2/g wet sediment/day). When inorganic nitrogen was added alone maximum rates of CO2 production measured were 4.25 ± 0.91 ?mol CO2/g wet sediment/day. However, when the same levels of inorganic nitrogen were added in the presence of 0.5% P w/w of oil (1.6 ?mol P/g wet sediment) maximum rates of measured CO2 production increased more than four-fold to 18.40 ± 1.04 ?mol CO2/g wet sediment/day. Ks and qmax estimates for inorganic N (in the form of sodium nitrate) when P was not limiting were 1.99 ± 0.86 ?mol/g wet sediment and 16.16 ± 1.28 ?mol CO2/g wet sediment/day respectively. The corresponding values for P were 63 ± 95 nmol/g wet sediment and 12.05 ± 1.31 ?mol CO2/g wet sediment/day. The qmax values with respect to N and P were not significantly different (P < 0.05). When N and P were not limiting Ks and qmax for crude oil were 4.52 ± 1.51 mg oil/g wet sediment and 16.89 ± 1.25 ?mol CO2/g wet sediment/day. At concentrations of inorganic N above 45 ?mol/g wet sediment inhibition of CO2 production from hydrocarbon degradation was evident. Analysis of bacterial 16S rRNA genes indicated that Alcanivorax spp. were selected in these marine sediments with increasing inorganic nutrient concentration, whereas Cycloclasticus spp. were more prevalent at lower inorganic nutrient concentrations. These data suggest that simple empirical estimates of the proportion of nutrients added relative to crude oil concentrations may not be sufficient to guarantee successful crude oil bioremediation in oxic beach sediments. The data we present also help define the maximum rates and hence timescales required for bioremediation of beach sediments.
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Volatile hydrocarbons inhibit methanogenic crude oil degradation.
Front Microbiol
PUBLISHED: 01-01-2014
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Methanogenic degradation of crude oil in subsurface sediments occurs slowly, but without the need for exogenous electron acceptors, is sustained for long periods and has enormous economic and environmental consequences. Here we show that volatile hydrocarbons are inhibitory to methanogenic oil biodegradation by comparing degradation of an artificially weathered crude oil with volatile hydrocarbons removed, with the same oil that was not weathered. Volatile hydrocarbons (nC5-nC10, methylcyclohexane, benzene, toluene, and xylenes) were quantified in the headspace of microcosms. Aliphatic (n-alkanes nC12-nC34) and aromatic hydrocarbons (4-methylbiphenyl, 3-methylbiphenyl, 2-methylnaphthalene, 1-methylnaphthalene) were quantified in the total hydrocarbon fraction extracted from the microcosms. 16S rRNA genes from key microorganisms known to play an important role in methanogenic alkane degradation (Smithella and Methanomicrobiales) were quantified by quantitative PCR. Methane production from degradation of weathered oil in microcosms was rapid (1.1 ± 0.1 ?mol CH4/g sediment/day) with stoichiometric yields consistent with degradation of heavier n-alkanes (nC12-nC34). For non-weathered oil, degradation rates in microcosms were significantly lower (0.4 ± 0.3 ?mol CH4/g sediment/day). This indicated that volatile hydrocarbons present in the non-weathered oil inhibit, but do not completely halt, methanogenic alkane biodegradation. These findings are significant with respect to rates of biodegradation of crude oils with abundant volatile hydrocarbons in anoxic, sulphate-depleted subsurface environments, such as contaminated marine sediments which have been entrained below the sulfate-reduction zone, as well as crude oil biodegradation in petroleum reservoirs and contaminated aquifers.
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afterParty: turning raw transcriptomes into permanent resources.
BMC Bioinformatics
PUBLISHED: 10-03-2013
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Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new transcriptome is greater than the effort required to sequence it. Often, following publication, details of the annotation effort are only available in summary form, hindering subsequent exploitation of the data. To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser.
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Structural basis for distinct functions of the naturally occurring Cys mutants of human apolipoprotein A-I.
J. Lipid Res.
PUBLISHED: 09-13-2013
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HDL removes cell cholesterol and protects against atherosclerosis. ApoA-I provides a flexible structural scaffold and an important functional ligand on the HDL surface. We propose structural models for apoA-I(Milano) (R173C) and apoA-I(Paris) (R151C) mutants that show high cardioprotection despite low HDL levels. Previous studies established that two apoA-I molecules encircle HDL in an antiparallel, helical double-belt conformation. Recently, we solved the atomic structure of lipid-free ?(185-243)apoA-I and proposed a conformational ensemble for apoA-I(WT) on HDL. Here we modify this ensemble to understand how intermolecular disulfides involving C173 or C151 influence protein conformation. The double-belt conformations are modified by belt rotation, main-chain unhinging around Gly, and Pro-induced helical bending, and they are verified by comparison with previous experimental studies and by molecular dynamics simulations of apoA-I(Milano) homodimer. In our models, the molecular termini repack on various-sized HDL, while packing around helix-5 in apoA-I(WT), helix-6 in apoA-I(Paris), or helix-7 in apoA-I(Milano) homodimer is largely conserved. We propose how the disulfide-induced constraints alter the protein conformation and facilitate dissociation of the C-terminal segment from HDL to recruit additional lipid. Our models unify previous studies of apoA-I(Milano) and demonstrate how the mutational effects propagate to the molecular termini, altering their conformations, dynamics, and function.
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Multielement NMR studies of the liquid-liquid phase separation and the metal-to-nonmetal transition in fluid lithium- and sodium-ammonia solutions.
J Phys Chem B
PUBLISHED: 09-13-2013
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(1)H, (7)Li, (14)N, and (23)Na high resolution nuclear magnetic resonance (NMR) measurements are reported for fluid solutions of lithium and sodium in anhydrous liquid ammonia across the metal-to-nonmetal transition (MNM transition), paying particular attention to the phenomenon of liquid-liquid phase separation which occurs in the composition/temperature region close to the MNM transition. Our results are discussed in terms of the electronic structure of fluid metal-ammonia solutions at low temperatures (ca. 240 K). We find that the electronic phase transition to the metallic state in these solutions, especially at temperatures close to the liquid-liquid critical consolute temperature, occurs from a nonmetallic, electrolytic solution containing a predominance of electron spin-paired, (diamagnetic) charged bosonic states. The possible implications of these observations to the nature of the liquid-liquid phase separation are discussed, both from the views of N. F. Mott, regarding the MNM transition in sodium-ammonia solutions, and those of R. A. Ogg, regarding the possibility of high-temperature superconductivity in these solutions. Similarities between the electronic structure of metal-ammonia solutions and the high-temperature cuprate superconductors are also briefly emphasized.
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Badger--an accessible genome exploration environment.
Bioinformatics
PUBLISHED: 08-11-2013
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High-quality draft genomes are now easy to generate, as sequencing and assembly costs have dropped dramatically. However, building a user-friendly searchable Web site and database for a newly annotated genome is not straightforward. Here we present Badger, a lightweight and easy-to-install genome exploration environment designed for next generation non-model organism genomes.
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Volumetric determination of apolipoprotein stoichiometry of circulating HDL subspecies.
J. Lipid Res.
PUBLISHED: 07-23-2013
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Although HDL is inversely correlated with coronary heart disease, elevated HDL-cholesterol is not always protective. Additionally, HDL has biological functions that transcend any antiatherogenic role: shotgun proteomics show that HDL particles contain 84 proteins (latest count), many correlating with antioxidant and anti-inflammatory properties of HDL. ApoA-I has been suggested to serve as a platform for the assembly of these protein components on HDL with specific functions - the HDL proteome. However, the stoichiometry of apoA-I in HDL subspecies is poorly understood. Here we use a combination of immunoaffinity chromatography data and volumetric analysis to evaluate the size and stoichiometry of LpA-I and LpA-I,A-II particles. We conclude that there are three major LpA-I subspecies: two major particles, HDL[4] in the HDL3 size range (d = 85.0 ± 1.2 Å) and HDL[7] in the HDL2 size range (d = 108.5 ± 3.8 Å) with apoA-I stoichiometries of 3 and 4, respectively, and a small minor particle, HDL[1] (d = 73.8 ± 2.1Å) with an apoA-I stoichiometry of 2. Additionally, we conclude that the molar ratio of apolipoprotein to surface lipid is significantly higher in circulating HDL subspecies than in reconstituted spherical HDL particles, presumably reflecting a lack of phospholipid transfer protein in reconstitution protocols.
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MD simulations suggest important surface differences between reconstituted and circulating spherical HDL.
J. Lipid Res.
PUBLISHED: 07-15-2013
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Since spheroidal HDL particles (sHDL) are highly dynamic, molecular dynamics (MD) simulations are useful for obtaining structural models. Here we use MD to simulate sHDL with stoichiometries of reconstituted and circulating particles. The hydrophobic effect during simulations rapidly remodels discoidal HDL containing mixed lipids to sHDL containing a cholesteryl ester/triglyceride (CE/TG) core. We compare the results of simulations of previously characterized reconstituted sHDL particles containing two or three apoA-I created in the absence of phospholipid transfer protein (PLTP) with simulations of circulating human HDL containing two or three apoA-I without apoA-II. We find that circulating sHDL compared with reconstituted sHDL with the same number of apoA-I per particle contain approximately equal volumes of core lipid but significantly less surface lipid monolayers. We conclude that in vitro reconstituted sHDL particles contain kinetically trapped excess phospholipid and are less than ideal models for circulating sHDL particles. In the circulation, phospholipid transfer via PLTP decreases the ratio of phospholipid to apolipoprotein for all sHDL particles. Further, sHDL containing two or three apoA-I adapt to changes in surface area by condensation of common conformational motifs. These results represent an important step toward resolving the complicated issue of the protein and lipid stoichiometry of circulating HDL.
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Biodegradation of crude oil saturated fraction supported on clays.
Biodegradation
PUBLISHED: 05-02-2013
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The role of clay minerals in crude oil saturated hydrocarbon removal during biodegradation was investigated in aqueous clay/saturated hydrocarbon microcosm experiments with a hydrocarbon degrading microorganism community. The clay minerals used for this study were montmorillonite, palygorskite, saponite and kaolinite. The clay mineral samples were treated with hydrochloric acid and didecyldimethylammonium bromide to produce acid activated- and organoclays respectively which were used in this study. The production of organoclay was restricted to only montmorillonite and saponite because of their relative high CEC. The study indicated that acid activated clays, organoclays and unmodified kaolinite, were inhibitory to biodegradation of the hydrocarbon saturates. Unmodified saponite was neutral to biodegradation of the hydrocarbon saturates. However, unmodified palygorskite and montmorillonite were stimulatory to biodegradation of the hydrocarbon saturated fraction and appears to do so as a result of the clays ability to provide high surface area for the accumulation of microbes and nutrients such that the nutrients were within the vicinity of the microbes. Adsorption of the saturated hydrocarbons was not significant during biodegradation.
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Ground Anthrax Bacillus Refined Isolation (GABRI) method for analyzing environmental samples with low levels of Bacillus anthracis contamination.
BMC Microbiol.
PUBLISHED: 04-04-2013
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In this work are reported the results of a qualitative analytical method capable of detecting Bacillus anthracis spores when they are present in very low concentration in the soil. The Ground Anthrax Bacillus Refined Isolation (GABRI) method, assessed in our laboratory, was compared with the classic method. The comparison involved artificially anthrax-contaminated soil samples (500 spores/7.5 grams soil) and naturally contaminated soil samples collected in Bangladesh during a field investigation.
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Compositional changes of crude oil SARA fractions due to biodegradation and adsorption on colloidal support such as clays using Iatroscan.
Environ Sci Pollut Res Int
PUBLISHED: 03-12-2013
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The compositional changes of saturates, aromatics, resins and asphaltenes (SARA) fractions in aqueous clay/oil microcosm experiments with a hydrocarbon-degrading microorganism community were analysed using Iatroscan. The clay mineral samples used in this study were organomontmorillonite, acid-activated montmorillonite and K, Ca, Zn and Cr montmorillonites produced by modifying the original montmorillonite sample. The evaluation and quantification of biodegradation and adsorption were carried out using a combination of the Iatroscan and gravimetric analysis. The SARA compositions in the presence of organomontmorillonite and acid-activated montmorillonite after incubation follow the same pattern in which the aromatic fraction is higher than the other fractions unlike in the presence of unmodified, K, Ca and Zn montmorillonites, where the saturates fraction is higher than the other fractions. Changes in SARA fractions due to biodegradation seemed to occur most in the presence of unmodified and calcium montmorillonites; hence, the removal of SARA fractions due to biodegradation was significant and enhanced in the presence of these two clay samples. However, biodegradation in the presence of organomontmorillonite and acid-activated and Cr montmorillonites was hindered. The study indicated that Cr montmorillonite adsorbed resins most, whereas Zn and K montmorillonites adsorbed aromatics most after incubation.
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Predicting the future: towards symbiotic computational and experimental angiogenesis research.
Exp. Cell Res.
PUBLISHED: 02-01-2013
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Understanding the fundamental organisational principles underlying the complex and multilayered process of angiogenesis is the mutual aim of both the experimental and theoretical angiogenesis communities. Surprisingly, these two fields have in the past developed in near total segregation, with neither fully benefiting from the other. However, times are changing and here we report on the new direction that angiogenesis research is taking, where from well-integrated collaborations spring new surprises, experimental predictions and research avenues. We show that several successful ongoing collaborations exist in the angiogenesis field and analyse what aspects of their approaches led them to achieve novel and impactful biological insight. We conclude that there are common elements we can learn from for the future, and provide a list of guidelines to building a successful collaborative venture. Specifically, we find that a near symbiosis of computation with experimentation reaps the most impactful results by close cyclical feedback and communication between the two disciplines resulting in continual refinement of models, experimental directions and our understanding. We discuss high impact examples of predictive modelling from the wider, more established integrated scientific domains and conclude that the angiogenesis community can do nothing but benefit from joining this brave new, integrated world.
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The ortholog of the human proto-oncogene ROS1 is required for epithelial development in C. elegans.
Genesis
PUBLISHED: 01-30-2013
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The orphan receptor ROS1 is a human proto-oncogene, mutations of which are found in an increasing number of cancers. Little is known about the role of ROS1, however in vertebrates it has been implicated in promoting differentiation programs in specialized epithelial tissues. In this study we show that the C. elegans ortholog of ROS1, the receptor tyrosine kinase ROL-3, has an essential role in orchestrating the morphogenesis and development of specialized epidermal tissues, highlighting a potentially conserved function in coordinating crosstalk between developing epithelial cells. We also provide evidence of a direct relationship between ROL-3, the mucin SRAP-1, and BCC-1, the homolog of mRNA regulating protein Bicaudal-C. This study answers a longstanding question as to the developmental function of ROL-3, identifies three new genes that are expressed and function in the developing epithelium of C. elegans, and introduces the nematode as a potentially powerful model system for investigating the increasingly important, yet poorly understood, human oncogene ROS1.
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Pre-culturing islets with mesenchymal stromal cells using a direct contact configuration is beneficial for transplantation outcome in diabetic mice.
Cytotherapy
PUBLISHED: 01-12-2013
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We recently showed that co-transplantation of mesenchymal stromal cells (MSCs) improves islet function and revascularization in vivo. Pre-transplant islet culture is associated with the loss of islet cells. MSCs may enhance islet cell survival or function by direct cell contact mechanisms and soluble mediators. We investigated the capacity of MSCs to improve islet cell survival or ?-cell function in vitro using direct and indirect contact islet-MSC configurations. We also investigated whether pre-culturing islets with MSCs improves islet transplantation outcome.
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Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.
Front Genet
PUBLISHED: 01-01-2013
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Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment - whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.
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Ecological niche modeling of Bacillus anthracis on three continents: evidence for genetic-ecological divergence?
PLoS ONE
PUBLISHED: 01-01-2013
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We modeled the ecological niche of a globally successful Bacillus anthracis sublineage in the United States, Italy and Kazakhstan to better understand the geographic distribution of anthrax and potential associations between regional populations and ecology. Country-specific ecological-niche models were developed and reciprocally transferred to the other countries to determine if pathogen presence could be accurately predicted on novel landscapes. Native models accurately predicted endemic areas within each country, but transferred models failed to predict known occurrences in the outside countries. While the effects of variable selection and limitations of the genetic data should be considered, results suggest differing ecological associations for the B. anthracis populations within each country and may reflect niche specialization within the sublineage. Our findings provide guidance for developing accurate ecological niche models for this pathogen; models should be developed regionally, on the native landscape, and with consideration to population genetics. Further genomic analysis will improve our understanding of the genetic-ecological dynamics of B. anthracis across these countries and may lead to more refined predictive models for surveillance and proactive vaccination programs. Further studies should evaluate the impact of variable selection of native and transferred models.
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Specialized chromosomes and their uses in Caenorhabditis elegans.
Methods Cell Biol.
PUBLISHED: 11-29-2011
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Research on Caenorhabditis elegans involves the use of a wide range of genetic and molecular tools consisting of chromosomal material captured and modified for specific purposes. These "specialized chromosomes" come in many forms ranging from relatively simple gene deletions to complex rearrangements involving endogenous chromosomes as well as transgenic constructs. In this chapter, we describe the specialized chromosomes that are available in C. elegans, their origins, practical considerations, and methods for generation and evaluation. We will summarize their uses for biological studies, and their contribution to our knowledge about chromosome biology.
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Ancient lipids reveal continuity in culinary practices across the transition to agriculture in Northern Europe.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-24-2011
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Farming transformed societies globally. Yet, despite more than a century of research, there is little consensus on the speed or completeness of this fundamental change and, consequently, on its principal drivers. For Northern Europe, the debate has often centered on the rich archaeological record of the Western Baltic, but even here it is unclear how quickly or completely people abandoned wild terrestrial and marine resources after the introduction of domesticated plants and animals at ?4000 calibrated years B.C. Ceramic containers are found ubiquitously on these sites and contain remarkably well-preserved lipids derived from the original use of the vessel. Reconstructing culinary practices from this ceramic record can contribute to longstanding debates concerning the origins of farming. Here we present data on the molecular and isotopic characteristics of lipids extracted from 133 ceramic vessels and 100 carbonized surface residues dating to immediately before and after the first evidence of domesticated animals and plants in the Western Baltic. The presence of specific lipid biomarkers, notably ?-(o-alkylphenyl)alkanoic acids, and the isotopic composition of individual n-alkanoic acids clearly show that a significant proportion (?20%) of ceramic vessels with lipids preserved continued to be used for processing marine and freshwater resources across the transition to agriculture in this region. Although changes in pottery use are immediately evident, our data challenge the popular notions that economies were completely transformed with the arrival of farming and that Neolithic pottery was exclusively associated with produce from domesticated animals and plants.
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Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia.
Mol. Ecol.
PUBLISHED: 10-18-2011
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Broomcorn millet (Panicum miliaceum L.) is one of the worlds oldest cultivated cereals, with several lines of recent evidence indicating that it was grown in northern China from at least 10,000 cal bp. Additionally, a cluster of archaeobotanical records of P. miliaceum dated to at least 7000 cal bp exists in eastern Europe. These two centres of early records could either represent independent domestications or cross-continental movement of this cereal that would predate that of any other crop by some 2 millennia. Here, we analysed genetic diversity among 98 landrace accessions from across Eurasia using 16 microsatellite loci, to explore phylogeographic structure in the Old World range of this historically important crop. The major genetic split in the data divided the accessions into an eastern and a western grouping with an approximate boundary in northwestern China. A substantial number of accessions belonging to the western genetic group were also found in northeastern China. Further resolution subdivided the western and eastern genepools into 2 and 4 clusters respectively, each showing clear geographic patterning. The genetic data are consistent with both the single and multiple domestication centre hypotheses and add specific detail to what these hypotheses would entail regarding the spread of broomcorn millet. Discrepancies exist between the predictions from the genetic data and the current archaeobotanical record, highlighting priorities for investigation into early farming in Central Asia.
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Nature of the band gap and origin of the conductivity of PbO2 revealed by theory and experiment.
Phys. Rev. Lett.
PUBLISHED: 10-06-2011
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Lead dioxide has been used for over a century in the lead-acid battery. Many fundamental questions concerning PbO2 remain unanswered, principally: (i) is the bulk material a metal or a semiconductor, and (ii) what is the source of the high levels of conductivity? We calculate the electronic structure and defect physics of PbO2, using a hybrid density functional, and show that it is an n-type semiconductor with a small indirect band gap of ?0.2??eV. The origin of electron carriers in the undoped material is found to be oxygen vacancies, which forms a donor state resonant in the conduction band. A dipole-forbidden band gap combined with a large carrier induced Moss-Burstein shift results in a large effective optical band gap. The model is supported by neutron diffraction, which reveals that the oxygen sublattice is only 98.4% occupied, thus confirming oxygen substoichiometry as the electron source.
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A multisite assessment of the quantitative capabilities of the Xpert MTB/RIF assay.
Am. J. Respir. Crit. Care Med.
PUBLISHED: 08-13-2011
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The Xpert MTB/RIF is an automated molecular test for Mycobacterium tuberculosis that estimates bacterial burden by measuring the threshold-cycle (Ct) of its M. tuberculosis-specific real-time polymerase chain reaction. Bacterial burden is an important biomarker for disease severity, infection control risk, and response to therapy.
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Prevalence of Batrachochytrium dendrobatidis in Agalychnis moreletii (Hylidae) of El Salvador and association with larval jaw sheath depigmentation.
J. Wildl. Dis.
PUBLISHED: 07-02-2011
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Amphibian populations around the world have been declining at an alarming rate due to factors such as habitat destruction, pollution, and infectious diseases. Between May and July 2008, we investigated a fungal pathogen in the critically endangered Morelets treefrog (Agalychnis moreletii) at sites in El Salvador. Larvae were screened with a hand lens for indications of infection with Batrachochytrium dendrobatidis (Bd), a fungus that can cause lethal chytridiomycosis in amphibians. Subsets of inspected tadpoles were preserved for analysis by polymerase chain reaction to determine the effectiveness of hand lens screening for presence of Bd and to estimate infection prevalence at various sites. Because individuals with signs of infection were preferentially included, we used a novel method to generate unbiased estimates of infection prevalence from these biased samples. External mouthpart deformities, identified with a hand lens, successfully predicted Bd infection across a large spatial scale. Two of 13 sites sampled had high (? 89%) estimated prevalence, whereas little or no Bd was detected at the remaining sites. Although it appears that A. moreletii populations in this region are not suffering rapid declines due to Bd, further monitoring is required to determine the extent to which these populations are stably coexisting with the pathogen.
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Diagnosing and treating HIV infection.
Nurs Times
PUBLISHED: 06-21-2011
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In the past, HIV infection was regarded as synonymous with AIDS, but it is increasingly viewed as a long-term, treatable condition. This article identifies the main changes in diagnosing and treating HIV infection since testing was introduced in the UK 25 years ago.
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A combined experimental inelastic neutron scattering, Raman and ab initio lattice dynamics study of ?-lithium amidoborane.
Phys Chem Chem Phys
PUBLISHED: 06-02-2011
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A combination of inelastic neutron scattering (INS) spectroscopy and Raman spectroscopy with periodic density functional theory calculations is used to provide a complete assignment of the vibrational spectra of ?-lithium amidoborane (?-LiNH(2)BH(3)). The Born charge density and the atomic motion up to the decomposition temperature have been modelled. These models not only explain the nature of bonding in ?-LiNH(2)BH(3) but also provide an insight into the atomic mechanisms of its decomposition. The (INS) measurements were performed in the range of 0-4000 cm(-1) on the high-resolution time-of-flight TOSCA INS spectrometer at the ISIS Spallation Neutron Source at the Rutherford Appleton Laboratory.
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Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation.
Biochim. Biophys. Acta
PUBLISHED: 04-27-2011
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To develop a detailed double belt model for discoidal HDL, we previously scored inter-helical salt bridges between all possible registries of two stacked antiparallel amphipathic helical rings of apolipoprotein (apo) A-I. The top score was the antiparallel apposition of helix 5 with 5 followed closely by appositions of helix 5 with 4 and helix 5 with 6. The rationale for the current study is that, for each of the optimal scores, a pair of identical residues can be identified in juxtaposition directly on the contact edge between the two antiparallel helical belts of apoA-I. Further, these residues are always in the 9th position in one of the eighteen 11-mer repeats that make up the lipid-associating domain of apoA-I. To illustrate our terminology, 129j (LL5/5) refers to the juxtaposition of the C? atoms of G129 (in a 9th position) in the pairwise helix 5 domains. We reasoned that if identical residues in the double belt juxtapositions were mutated to a cysteine and kept under reducing conditions during disc formation, we would have a precise method for determining registration in discoidal HDL by formation of a disulfide-linked apoA-I homodimer. Using this approach, we conclude that 129j (LL5/5) is the major rotamer orientation for double belt HDL and propose that the small ubiquitous gap between the pairwise helix 5 portions of the double belt in larger HDL discoidal particles is significantly dynamic to hinge off the disc edge under certain conditions, e.g., in smaller particles or perhaps following binding of the enzyme LCAT. This article is part of a Special Issue entitled Advances in High Density Lipoprotein Formation and Metabolism: A Tribute to John F. Oram (1945-2010).
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Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces.
BMC Evol. Biol.
PUBLISHED: 04-18-2011
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Understanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm.
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Exceptional visible-light-driven photocatalytic activity over BiOBr-ZnFe2O4 heterojunctions.
Chem. Commun. (Camb.)
PUBLISHED: 04-04-2011
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An ultrasound-assisted, precipitation-deposition method has been developed to synthesise visible-light-responsive BiOBr-ZnFe(2)O(4) heterojunction photocatalysts. The heterojunctions with suitable BiOBr/ZnFe(2)O(4) ratios have a fascinating micro-spherical morphology and exhibit exceptional photocatalytic activity in visible-light degradation of Rhodamine B.
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jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units.
PLoS ONE
PUBLISHED: 03-31-2011
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DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies.
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The serious mental illness health improvement profile [HIP]: study protocol for a cluster randomised controlled trial.
Trials
PUBLISHED: 03-07-2011
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The serious mental illness Health Improvement Profile [HIP] is a brief pragmatic tool, which enables mental health nurses to work together with patients to screen physical health and take evidence-based action when variables are identified to be at risk. Piloting has demonstrated clinical utility and acceptability.
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"Sticky" and "promiscuous", the yin and yang of apolipoprotein A-I termini in discoidal high-density lipoproteins: a combined computational-experimental approach.
Biochemistry
PUBLISHED: 03-04-2011
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Apolipoprotein (apo) A-I-containing lipoproteins in the form of high-density lipoproteins (HDL) are inversely correlated with atherosclerosis. Because HDL is a soft form of condensed matter easily deformable by thermal fluctuations, the molecular mechanisms for HDL remodeling are not well understood. A promising approach to understanding HDL structure and dynamics is molecular dynamics (MD). In the present study, two computational strategies, MD simulated annealing (MDSA) and MD temperature jump, were combined with experimental particle reconstitution to explore molecular mechanisms for phospholipid- (PL-) rich HDL particle remodeling. The N-terminal domains of full-length apoA-I were shown to be "sticky", acting as a molecular latch largely driven by salt bridges, until, at a critical threshold of particle size, the associated domains released to expose extensive hydrocarbon regions of the PL to solvent. The "sticky" N-termini also associate with other apoA-I domains, perhaps being involved in N-terminal loops suggested by other laboratories. Alternatively, the overlapping helix 10 C-terminal domains of apoA-I were observed to be extremely mobile or "promiscuous", transiently exposing limited hydrocarbon regions of PL. Based upon these models and reconstitution studies, we propose that separation of the N-terminal domains, as particles exceed a critical size, triggers fusion between particles or between particles and membranes, while the C-terminal domains of apoA-I drive the exchange of polar lipids down concentration gradients between particles. This hypothesis has significant biological relevance since lipid exchange and particle remodeling are critically important processes during metabolism of HDL particles at every step in the antiatherogenic process of reverse cholesterol transport.
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Metachronous melanoma in breast reconstruction patients.
J Plast Reconstr Aesthet Surg
PUBLISHED: 01-29-2011
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The incidence and mortality due to malignant melanoma has increased three- to four-fold across males and females in England and Wales over the past thirty years. Ninety percent of patients with primary melanoma have no clinical evidence of lymphadenopathy at presentation. In this paper we describe our management of impalpable axillary melanoma deposits in a patient with a pedicled latissimus dorsi (LD) flap reconstruction to the ipsilateral breast. No such case has been previously described in the literature.
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iPhy: an integrated phylogenetic workbench for supermatrix analyses.
BMC Bioinformatics
PUBLISHED: 01-24-2011
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The increasing availability of molecular sequence data means that the accuracy of future phylogenetic studies is likely to by limited by systematic bias and taxon choice rather than by data. In order to take advantage of increasing datasets, user-friendly tools are required to facilitate phylogenetic analyses and to reduce duplication of dataset assembly efforts. Current phylogenetic pipelines are dependency-heavy and have significant technical barriers to use.
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Time-budgets and activity patterns of captive Sunda pangolins (Manis javanica).
Zoo Biol.
PUBLISHED: 01-16-2011
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This is the first assessment of Manis javanica behavior in captivity. The aim of the investigation was to assess behavior in order to suggest ways of improving captive care and management of the species. This was undertaken by constructing time-budgets and activity patterns and identifying any abnormal repetitive behavior (ARB) exhibited. Scan and focal animal sampling were implemented in observations of seven subjects. Analyses detailed idiosyncrasies in how subjects partitioned their active time. Peak activity occurred between 18:00 and 21:00 hr. Two ARBs, clawing and pacing, were identified and the cessation of clawing in one subject was possible by modifying its enclosure. Stress-related behavior, understood to be related to several factors, means maintaining this species in captivity remains problematic. Recommendations are made pertaining to husbandry, captive management, and future research.
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Sequence conservation of apolipoprotein A-I affords novel insights into HDL structure-function.
J. Lipid Res.
PUBLISHED: 12-14-2010
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We performed alignment of apolipoprotein A-I (apoA-I) sequences from 31 species of animals. We found there is specific conservation of salt bridge-forming residues in the first 30 residues of apoA-I and general conservation of a variety of residue types in the central domain, helix 2/3 to helix 7/8. In the lipid-associating domain, helix 7 and helix 10 are the most and least conserved helixes, respectively. Furthermore, eight residues are completely conserved: P66, R83, P121, E191, and P220, and three of seven Tyr residues in human apoA-I, Y18, Y115, and Y192, are conserved. Residue Y18 appears to be important for assembly of HDL. E191-Y192 represents the only completely conserved pair of adjacent residues in apoA-I; Y192 is a preferred target for site-specific oxidative modification within atheroma, and molecular dynamic simulations suggest that the conserved pair E191-Y192 is in a solvent-exposed loop-helix-loop. Molecular dynamics testing of human apoA-I showed that M112 and M148 interact with Y115, a microenvironment unique to human apoA-I. Finally, conservation of Arg residues in the ?11/3 helical wheel position 7 supports several possibilities: interactions with adjacent phospholipid molecules and/or oxidized lipids and/or binding of antioxidant enzymes through cation-? orbital interactions. We conclude that sequence alignment of apoA-I provides unique insights into apoA-I structure-function relationship.
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Assessment of the validity of the double superhelix model for reconstituted high density lipoproteins: a combined computational-experimental approach.
J. Biol. Chem.
PUBLISHED: 10-25-2010
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For several decades, the standard model for high density lipoprotein (HDL) particles reconstituted from apolipoprotein A-I (apoA-I) and phospholipid (apoA-I/HDL) has been a discoidal particle ?100 ? in diameter and the thickness of a phospholipid bilayer. Recently, Wu et al. (Wu, Z., Gogonea, V., Lee, X., Wagner, M. A., Li, X. M., Huang, Y., Undurti, A., May, R. P., Haertlein, M., Moulin, M., Gutsche, I., Zaccai, G., Didonato, J. A., and Hazen, S. L. (2009) J. Biol. Chem. 284, 36605-36619) used small angle neutron scattering to develop a new model they termed double superhelix (DSH) apoA-I that is dramatically different from the standard model. Their model possesses an open helical shape that wraps around a prolate ellipsoidal type I hexagonal lyotropic liquid crystalline phase. Here, we used three independent approaches, molecular dynamics, EM tomography, and fluorescence resonance energy transfer spectroscopy (FRET) to assess the validity of the DSH model. (i) By using molecular dynamics, two different approaches, all-atom simulated annealing and coarse-grained simulation, show that initial ellipsoidal DSH particles rapidly collapse to discoidal bilayer structures. These results suggest that, compatible with current knowledge of lipid phase diagrams, apoA-I cannot stabilize hexagonal I phase particles of phospholipid. (ii) By using EM, two different approaches, negative stain and cryo-EM tomography, show that reconstituted apoA-I/HDL particles are discoidal in shape. (iii) By using FRET, reconstituted apoA-I/HDL particles show a 28-34-? intermolecular separation between terminal domain residues 40 and 240, a distance that is incompatible with the dimensions of the DSH model. Therefore, we suggest that, although novel, the DSH model is energetically unfavorable and not likely to be correct. Rather, we conclude that all evidence supports the likelihood that reconstituted apoA-I/HDL particles, in general, are discoidal in shape.
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Rapid molecular detection of tuberculosis and rifampin resistance.
N. Engl. J. Med.
PUBLISHED: 09-10-2010
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Global control of tuberculosis is hampered by slow, insensitive diagnostic methods, particularly for the detection of drug-resistant forms and in patients with human immunodeficiency virus infection. Early detection is essential to reduce the death rate and interrupt transmission, but the complexity and infrastructure needs of sensitive methods limit their accessibility and effect.
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Confirmation of Bacillus anthracis from flesh-eating flies collected during a West Texas anthrax season.
J. Wildl. Dis.
PUBLISHED: 08-07-2010
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This case study confirms the interaction between necrophilic flies and white-tailed deer, Odocoileus virginianus, during an anthrax outbreak in West Texas (summer 2005). Bacillus anthracis was identified by culture and PCR from one of eight pooled fly collections from deer carcasses on a deer ranch with a well-documented history of anthrax. These results provide the first known isolation of B. anthracis from flesh-eating flies associated with a wildlife anthrax outbreak in North America and are discussed in the context of wildlife ecology and anthrax epizootics.
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Potassium(I) amidotrihydroborate: structure and hydrogen release.
J. Am. Chem. Soc.
PUBLISHED: 08-07-2010
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Potassium(I) amidotrihydroborate (KNH(2)BH(3)) is a newly developed potential hydrogen storage material representing a completely different structural motif within the alkali metal amidotrihydroborate group. Evolution of 6.5 wt % hydrogen starting at temperatures as low as 80 degrees C is observed and shows a significant change in the hydrogen release profile, as compared to the corresponding lithium and sodium compounds. Here we describe the synthesis, structure, and hydrogen release characteristics of KNH(2)BH(3).
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Changes in polycyclic aromatic hydrocarbon availability in River Tyne sediment following bioremediation treatments or activated carbon amendment.
Water Res.
PUBLISHED: 06-03-2010
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Bioremediation and activated carbon (AC) amendment were compared as remediation strategies for sediment from the River Tyne containing 16.4 +/- 7.3 microg/g polycyclic aromatic hydrocarbons (PAHs) and approximately 5% coal particles by total dry sediment weight. Unamended, nutrient amended (biostimulated) and nutrient and Pseudomonas putida amended (bioaugmented) sediment microcosms failed to show a significant decrease in total sediment PAH concentrations over a one month period. Polyethylene passive (PE) samplers were embedded for 21 days in these sediment microcosms in order to measure the available portion of PAHs and accumulated 4.70 +/- 0.25, 12.43 +/- 1.78, and 23.49 +/- 2.73 microg PAHs/g PE from the unamended, biostimulated, and bioaugmented microcosms, respectively. Higher PAH uptake by PE samplers in biostimulated and bioaugmented microcosms coincided with slower degradation of spiked phenanthrene in sediment-free filtrate from these microcosms compared to filtrate from the unamended microcosms. Microbial community analysis revealed changes in the bacterial community directly following the addition of nutrients, but the added P. putida community failed to establish itself. Addition of 2% by dry sediment weight activated carbon reduced PAH uptake by PE samplers to 0.28 +/- 0.01 microg PAHs/g PE, a greater than 90% reduction compared to the unamended microcosms.
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Evaluation of the analytical performance of the Xpert MTB/RIF assay.
J. Clin. Microbiol.
PUBLISHED: 05-26-2010
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We performed the first studies of analytic sensitivity, analytic specificity, and dynamic range for the new Xpert MTB/RIF assay, a nucleic acid amplification-based diagnostic system that detects Mycobacterium tuberculosis and rifampin (RIF) resistance in under 2 h. The sensitivity of the assay was tested with 79 phylogenetically and geographically diverse M. tuberculosis isolates, including 42 drug-susceptible isolates and 37 RIF-resistant isolates containing 13 different rpoB mutations or mutation combinations. The specificity of the assay was tested with 89 nontuberculosis bacteria, fungi, and viruses. The Xpert MTB/RIF assay correctly identified all 79 M. tuberculosis isolates and correctly excluded all 89 nontuberculosis isolates. RIF resistance was correctly identified in all 37 resistant isolates and in none of the 42 susceptible isolates. Dynamic range was assessed by adding 10(2) to 10(7) CFU of M. tuberculosis into M. tuberculosis-negative sputum samples. The assay showed a log-linear relationship between cycle threshold and input CFU over the entire concentration range. Resistance detection in the presence of different mixtures of RIF-resistant and RIF-susceptible DNA was assessed. Resistance detection was dependent on the particular mutation and required between 65% and 100% mutant DNA to be present in the sample for 95% certainty of resistance detection. Finally, we studied whether assay specificity could be affected by cross-contaminating amplicons generated by the GenoType MTBDRplus assay. M. tuberculosis was not detected until at least 10(8) copies of an MTBDRplus amplicon were spiked into 1 ml of sputum, suggesting that false-positive results would be unlikely to occur.
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Historical distribution and molecular diversity of Bacillus anthracis, Kazakhstan.
Emerging Infect. Dis.
PUBLISHED: 04-23-2010
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To map the distribution of anthrax outbreaks and strain subtypes in Kazakhstan during 1937-2005, we combined geographic information system technology and genetic analysis by using archived cultures and data. Biochemical and genetic tests confirmed the identity of 93 archived cultures in the Kazakhstan National Culture Collection as Bacillus anthracis. Multilocus variable number tandem repeat analysis genotyping identified 12 genotypes. Cluster analysis comparing these genotypes with previously published genotypes indicated that most (n = 78) isolates belonged to the previously described A1.a genetic cluster, 6 isolates belonged to the A3.b cluster, and 2 belonged to the A4 cluster. Two genotypes in the collection appeared to represent novel genetic sublineages; 1 of these isolates was from Krygystan. Our data provide a description of the historical, geographic, and genetic diversity of B. anthracis in this Central Asian region.
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Severe anthrax outbreaks in Italy in 2004: considerations on factors involved in the spread of infection.
New Microbiol.
PUBLISHED: 04-21-2010
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Anthrax is a disease of humans and animals caused by the encapsulated, spore-forming Bacillus anthracis. In Italy, anthrax is normally a sporadic disease. During the summer 2004, anthrax broke out in the Basilicata, in southern Italy, a region with a low prevalence of anthrax in which vaccination had been suspended since 1998. The disease involved several animals in few weeks and in a large area. Over 41 days, 81 cattle died, as well as 15 sheep, 9 goats, 11 horses and 8 deer. The Multiple-locus Variable-Number Tandem Repeats Analysis (MLVA) showed that all the 53 isolates belonged to the Cluster Ala, genotype 1. The results of the Single Nucleotide Repeats (SNRs) Analysis showed that 48/53 B. anthacis strains belonged to a single clonal lineage, the sub-genotype sgt - eB. Two sporadic mutants, sgt - eB,m1 and sgt - eB,m2, were isolated, only one managing to infect other herds. Factors that could have contributed to the spread of infection, such as the transmission of spores by insect vectors and the favourable weather conditions were evaluated.
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Stepwise phase transition in the formation of lithium amidoborane.
Inorg Chem
PUBLISHED: 04-01-2010
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A stepwise phase transition in the formation of lithium amidoborane via the solid-state reaction of lithium hydride and ammonia borane has been identified and investigated. Structural analyses reveal that a lithium amidoborane-ammonia borane complex (LiNH(2)BH(3).NH(3)BH(3)) and two allotropes of lithium amidoborane (denoted as alpha- and beta-LiNH(2)BH(3), both of which adopt orthorhombic symmetry) were formed in the process of synthesis. LiNH(2)BH(3).NH(3)BH(3) is the intermediate of the synthesis and adopts a monoclinic structure that features layered LiNH(2)BH(3) and NH(3)BH(3) molecules and contains both ionic and dihydrogen bonds. Unlike alpha-LiNH(2)BH(3), the units of the beta phase have two distinct Li(+) and [NH(2)BH(3)](-) environments. beta-LiNH(2)BH(3) can only be observed in energetic ball milling and transforms to alpha-LiNH(2)BH(3) upon extended milling. Both allotropes of LiNH(2)BH(3) exhibit similar thermal decomposition behavior, with 10.8 wt % H(2) released when heated to 180 degrees C; in contrast, LiNH(2)BH(3).NH(3)BH(3) releases approximately 14.3 wt % H(2) under the same conditions.
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Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern.
BMC Genomics
PUBLISHED: 02-23-2010
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The original sequencing and annotation of the Caenorhabditis elegans genome along with recent advances in sequencing technology provide an exceptional opportunity for the genomic analysis of wild-type and mutant strains. Using the Illumina Genome Analyzer, we sequenced the entire genome of Rec-1, a strain that alters the distribution of meiotic crossovers without changing the overall frequency. Rec-1 was derived from ethylmethane sulfonate (EMS)-treated strains, one of which had a high level of transposable element mobility. Sequencing of this strain provides an opportunity to examine the consequences on the genome of altering the distribution of meiotic recombination events.
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Modeling the potential distribution of Bacillus anthracis under multiple climate change scenarios for Kazakhstan.
PLoS ONE
PUBLISHED: 02-18-2010
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Anthrax, caused by the bacterium Bacillus anthracis, is a zoonotic disease that persists throughout much of the world in livestock, wildlife, and secondarily infects humans. This is true across much of Central Asia, and particularly the Steppe region, including Kazakhstan. This study employed the Genetic Algorithm for Rule-set Prediction (GARP) to model the current and future geographic distribution of Bacillus anthracis in Kazakhstan based on the A2 and B2 IPCC SRES climate change scenarios using a 5-variable data set at 55 km(2) and 8 km(2) and a 6-variable BioClim data set at 8 km(2). Future models suggest large areas predicted under current conditions may be reduced by 2050 with the A2 model predicting approximately 14-16% loss across the three spatial resolutions. There was greater variability in the B2 models across scenarios predicting approximately 15% loss at 55 km(2), approximately 34% loss at 8 km(2), and approximately 30% loss with the BioClim variables. Only very small areas of habitat expansion into new areas were predicted by either A2 or B2 in any models. Greater areas of habitat loss are predicted in the southern regions of Kazakhstan by A2 and B2 models, while moderate habitat loss is also predicted in the northern regions by either B2 model at 8 km(2). Anthrax disease control relies mainly on livestock vaccination and proper carcass disposal, both of which require adequate surveillance. In many situations, including that of Kazakhstan, vaccine resources are limited, and understanding the geographic distribution of the organism, in tandem with current data on livestock population dynamics, can aid in properly allocating doses. While speculative, contemplating future changes in livestock distributions and B. anthracis spore promoting environments can be useful for establishing future surveillance priorities. This study may also have broader applications to global public health surveillance relating to other diseases in addition to B. anthracis.
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Molecular basis of the waxy endosperm starch phenotype in broomcorn millet (Panicum miliaceum L.).
Mol. Biol. Evol.
PUBLISHED: 02-05-2010
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Waxy varieties of the tetraploid cereal broomcorn millet (Panicum miliaceum L.) have endosperm starch granules lacking detectable amylose. This study investigated the basis of this phenotype using molecular and biochemical methods. Iodine staining of starch granules in 72 plants from 38 landrace accessions found 58 nonwaxy and 14 waxy phenotype plants. All waxy types were in plants from Chinese and Korean accessions, a distribution similar to that of the waxy phenotype in other cereals. Granule-bound starch synthase I (GBSSI) protein was present in the endosperm of both nonwaxy and waxy individuals, but waxy types had little or no granule-bound starch synthase activity compared with the wild types. Sequencing of the GBSSI (Waxy) gene showed that this gene is present in two different forms (L and S) in P. miliaceum, which probably represent homeologues derived from two distinct diploid ancestors. Protein products of both these forms are present in starch granules. We identified three polymorphisms in the exon sequence coding for mature GBSSI peptides. A 15-bp deletion has occurred in the S type GBSSI, resulting in the loss of five amino acids from glucosyl transferase domain 1 (GTD1). The second GBSSI type (L) shows two sequence polymorphisms. One is the insertion of an adenine residue that causes a reading frameshift, and the second causes a cysteine-tyrosine amino acid polymorphism. These mutations appear to have occurred in parallel from the ancestral allele, resulting in three GBSSI-L alleles in total. Five of the six possible genotype combinations of the S and L alleles were observed. The deletion in the GBSSI-S gene causes loss of protein activity, and there was 100% correspondence between this deletion and the waxy phenotype. The frameshift mutation in the L gene results in the loss of L-type protein from starch granules. The L isoform with the tyrosine residue is present in starch granules but is nonfunctional. This loss of function may result from the substitution of tyrosine for cysteine, although it could not be determined whether the cysteine isoform of L represents the functional type. This is the first characterization of mutations that occur in combination in a functionally polyploid species to give a fully waxy phenotype.
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Structures of discoidal high density lipoproteins: a combined computational-experimental approach.
J. Biol. Chem.
PUBLISHED: 11-30-2009
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Conversion of discoidal phospholipid (PL)-rich high density lipoprotein (HDL) to spheroidal cholesteryl ester-rich HDL is a central step in reverse cholesterol transport. A detailed understanding of this process and the atheroprotective role of apolipoprotein A-I (apoA-I) requires knowledge of the structure and dynamics of these various particles. This study, combining computation with experimentation, illuminates structural features of apoA-I allowing it to incorporate varying amounts of PL. Molecular dynamics simulated annealing of PL-rich HDL models containing unesterified cholesterol results in double belt structures with the same general saddle-shaped conformation of both our previous molecular dynamics simulations at 310 K and the x-ray structure of lipid-free apoA-I. Conversion from a discoidal to a saddle-shaped particle involves loss of helicity and formation of loops in opposing antiparallel parts of the double belt. During surface expansion caused by the temperature-jump step, the curved palmitoyloleoylphosphatidylcholine bilayer surfaces approach planarity. Relaxation back into saddle-shaped structures after cool down and equilibration further supports the saddle-shaped particle model. Our kinetic analyses of reconstituted particles demonstrate that PL-rich particles exist in discrete sizes corresponding to local energetic minima. Agreement of experimental and computational determinations of particle size/shape and apoA-I helicity provide additional support for the saddle-shaped particle model. Truncation experiments combined with simulations suggest that the N-terminal proline-rich domain of apoA-I influences the stability of PL-rich HDL particles. We propose that apoA-I incorporates increasing PL in the form of minimal surface bilayers through the incremental unwinding of an initially twisted saddle-shaped apoA-I double belt structure.
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Dynamics of activation of lecithin:cholesterol acyltransferase by apolipoprotein A-I.
Biochemistry
PUBLISHED: 10-29-2009
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The product of transesterification of phospholipid acyl chains and unesterified cholesterol (UC) by the enzyme lecithin:cholesterol acyltransferase (LCAT) is cholesteryl ester (CE). Activation of LCAT by apolipoprotein (apo) A-I on nascent (discoidal) high-density lipoproteins (HDL) is essential for formation of mature (spheroidal) HDL during the antiatherogenic process of reverse cholesterol transport. Here we report all-atom and coarse-grained (CG) molecular dynamics (MD) simulations of HDL particles that have major implications for mechanisms of LCAT activation. Both the all-atom and CG simulations provide support for a model in which the helix 5/5 domains of apoA-I create an amphipathic "presentation tunnel" that exposes methyl ends of acyl chains at the bilayer center to solvent. Further, CG simulations show that UC also becomes inserted with high efficiency into the amphipathic presentation tunnel with its hydroxyl moiety (UC-OH) exposed to solvent; these results are consistent with trajectory analyses of the all-atom simulations showing that UC is being concentrated in the vicinity of the presentation tunnel. Finally, consistent with known product inhibition of CE-rich HDL by CE, CG simulations of CE-rich spheroidal HDL indicate partial blockage of the amphipathic presentation tunnel by CE. These results lead us to propose the following working hypothesis. After attachment of LCAT to discoidal HDL, the helix 5/5 domains in apoA-I form amphipathic presentation tunnels for migration of hydrophobic acyl chains and amphipathic UC from the bilayer to the phospholipase A2-like and esterification active sites of LCAT, respectively. This hypothesis is currently being tested by site-directed mutagenesis.
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Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology.
J. Clin. Microbiol.
PUBLISHED: 10-28-2009
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Current nucleic acid amplification methods to detect Mycobacterium tuberculosis are complex, labor-intensive, and technically challenging. We developed and performed the first analysis of the Cepheid Gene Xpert Systems MTB/RIF assay, an integrated hands-free sputum-processing and real-time PCR system with rapid on-demand, near-patient technology, to simultaneously detect M. tuberculosis and rifampin resistance. Analytic tests of M. tuberculosis DNA demonstrated a limit of detection (LOD) of 4.5 genomes per reaction. Studies using sputum spiked with known numbers of M. tuberculosis CFU predicted a clinical LOD of 131 CFU/ml. Killing studies showed that the assays buffer decreased M. tuberculosis viability by at least 8 logs, substantially reducing biohazards. Tests of 23 different commonly occurring rifampin resistance mutations demonstrated that all 23 (100%) would be identified as rifampin resistant. An analysis of 20 nontuberculosis mycobacteria species confirmed high assay specificity. A small clinical validation study of 107 clinical sputum samples from suspected tuberculosis cases in Vietnam detected 29/29 (100%) smear-positive culture-positive cases and 33/39 (84.6%) or 38/53 (71.7%) smear-negative culture-positive cases, as determined by growth on solid medium or on both solid and liquid media, respectively. M. tuberculosis was not detected in 25/25 (100%) of the culture-negative samples. A study of 64 smear-positive culture-positive sputa from retreatment tuberculosis cases in Uganda detected 63/64 (98.4%) culture-positive cases and 9/9 (100%) cases of rifampin resistance. Rifampin resistance was excluded in 54/55 (98.2%) susceptible cases. Specificity rose to 100% after correcting for a conventional susceptibility test error. In conclusion, this highly sensitive and simple-to-use system can detect M. tuberculosis directly from sputum in less than 2 h.
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Impacts of fertilization on water quality of a drained pine plantation: a worst case scenario.
J. Environ. Qual.
PUBLISHED: 09-14-2009
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Intensive plantation forestry will be increasingly important in the next 50 yr to meet the high demand for domestic wood in the United States. However, forest management practices can substantially influence downstream water quality and ecology. This study analyses, the effect of fertilization on effluent water quality of a low gradient drained coastal pine plantation in Carteret County, North Carolina using a paired watershed approach. The plantation consists of three watersheds, two mature (31-yr) and one young (8-yr) (age at treatment). One of the mature watersheds was commercially thinned in 2002. The mature unthinned watershed was designated as the control. The young and mature-thinned watersheds were fertilized at different rates with Arborite (Encee Chemical Sales, Inc., Bridgeton, NC), and boron. The outflow rates and nutrient concentrations in water drained from each of the watersheds were measured. Nutrient concentrations and loadings were analyzed using general linear models (GLM). Three large storm events occurred within 47 d of fertilization, which provided a worst case scenario for nutrient export from these watersheds to the receiving surface waters. Results showed that average nutrient concentrations soon after fertilization were significantly (alpha = 0.05) higher on both treatment watersheds than during any other period during the study. This increase in nutrient export was short lived and nutrient concentrations and loadings were back to prefertilization levels as soon as 3 mo after fertilization. Additionally, the mature-thinned watershed presented higher average nutrient concentrations and loadings when compared to the young watershed, which received a reduced fertilizer rate than the mature-thinned watershed.
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The ecology of Bacillus anthracis.
Mol. Aspects Med.
PUBLISHED: 08-24-2009
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The global distribution of anthrax is largely determined by soils with high calcium levels and a pH above 6.1, which foster spore survival. It is speculated that the spore exosporium probably plays a key part by restricting dispersal and thereby increasing the probability of a grazing animal acquiring a lethal dose. Anthrax Seasons are characterized by hot-dry weather which stresses animals and reduces their innate resistance to infection allowing low doses of spores to be infective. Necrophagic flies act as case-multipliers and haemophagic flies as space-multipliers; the latter are aided by climatic factors which play a key part in whether epidemics occur. Host death is a function of species sensitivity to the toxins. The major function of scavengers is to open the carcass, spill fluids, and thereby aid bacilli dispersal and initiate sporulation. In the context of landscape ecology viable spore distribution is a function of mean annual temperature, annual precipitation, elevation, mean NDVI, annual NDVI amplitude, soil moisture content, and soil pH.
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Using the serious mental illness health improvement profile [HIP] to identify physical problems in a cohort of community patients: a pragmatic case series evaluation.
Int J Nurs Stud
PUBLISHED: 06-03-2009
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The physical health of people with serious mental illness is a cause of growing concern to clinicians. Life expectancy in this population may be reduced by up to 25 years and patients often live with considerable physical morbidity that can dramatically reduce quality of life and contribute to social exclusion. This study sought to determine whether the serious mental illness health improvement profile [HIP], facilitated by mental health nurses [MHNs], has the clinical potential to identify physical morbidity and inform future evidence-based care.
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The monoammoniate of lithium borohydride, Li(NH3)BH4: an effective ammonia storage compound.
Chem Asian J
PUBLISHED: 05-02-2009
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Lithium borohydride absorbs anhydrous ammonia to form four stable ammoniates; Li(NH(3))(n)BH(4), mono-, di-, tri-, and tertraammoniate. This paper focuses on the monoammoniate, Li(NH(3))BH(4), which is readily formed on exposure of LiBH(4) to ammonia at room temperature and pressure. Ammonia loss from Li(NH(3))BH(4) commences around 40 degrees C and the compound transforms directly to LiBH(4). The crystal structure of Li(NH(3))BH(4) is reported here for the first time. Its close structural relationship with LiBH(4) provides a clear insight into the facile nature and mechanism of ammonia uptake and loss. These materials not only represent an excellent high weight-percent ammonia system but are also potentially important hydrogen stores.
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The complex origins of domesticated crops in the Fertile Crescent.
Trends Ecol. Evol. (Amst.)
PUBLISHED: 04-10-2009
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A combination of genetics and archaeology is revealing the complexity of the relationships between crop plants and their wild ancestors. Archaeobotanical studies are showing that acquisition of the full set of traits observed in domesticated cereals was a protracted process, intermediate stages being seen at early farming sites throughout the Fertile Crescent. New genetic data are confirming the multiregional nature of cereal domestication, correcting a previous view that each crop was domesticated by a rapid, unique and geographically localised process. Here we review the evidence that has prompted this reevaluation of the origins of domesticated crops in the Fertile Crescent and highlight the impact that this new multiregional model is having on modern breeding programmes.
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Anthrax undervalued zoonosis.
Vet. Microbiol.
PUBLISHED: 03-26-2009
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Anthrax is a non-contagious disease, known since ancient times. However, it became a matter of global public interest after the bioterrorist attacks in the U.S.A. during the autumn of 2001. The concern of politicians and civil authorities everywhere towards this emergency necessitated a significant research effort and the prevention of new bioterrorist acts. Anthrax is primarily a disease that affects livestock and wildlife; its distribution is worldwide; and it can represent a danger to humans but especially more so when it occurs in areas considered to be free and in atypical seasons and climatic conditions. The atypicality of the phenomenon may lead health workers to misdiagnose and, consequently, an inappropriately manage of affected carcasses with a consequent and inevitable increase in the risk of human infection. This article emphasises the importance of paying increasing attention to this zoonosis. The biggest risk is its underestimation.
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IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels.
Nucleic Acids Res.
PUBLISHED: 03-04-2009
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The IUPHAR database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 nonsensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated-like ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of approximately one-third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry. IUPHAR-DB provides a comprehensive description of the genes and their functions, with information on protein structure and interactions, ligands, expression patterns, signaling mechanisms, functional assays and biologically important receptor variants (e.g. single nucleotide polymorphisms and splice variants). In addition, the phenotypes resulting from altered gene expression (e.g. in genetically altered animals or in human genetic disorders) are described. The content of the database is peer reviewed by members of the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR); the data are provided through manual curation of the primary literature by a network of over 60 subcommittees of NC-IUPHAR. Links to other bioinformatics resources, such as NCBI, Uniprot, HGNC and the rat and mouse genome databases are provided. IUPHAR-DB is freely available at http://www.iuphar-db.org.
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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.