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Accumulation of plastics in the marine environment has widespread detrimental consequences for ecosystems and wildlife. Marine plastics are rapidly colonised by a wide diversity of bacteria, including human pathogens, posing potential risks to human health. Here, we investigate the effect of polymer type, residence time and estuarine location on bacterial colonisation of common household plastics, including pathogenic bacteria. To do so, we submerged five main household plastic types: low-density PE (LDPE), high-density PE (HDPE), polypropylene (PP), polyvinyl chloride (PVC) and polyethylene terephthalate (PET) at an estuarine site in Cornwall (U.K.) and tracked bacterial colonisation dynamics. Using both culture-dependent and culture-independent approaches, we found that bacteria rapidly colonised plastics irrespective of polymer type. While biofilm community composition changed with colonisation time, no difference was observed between polymer types. Likewise, the presence of pathogenic bacteria, quantified using the insect model Galleria mellonella, increased over a five-week period, with no consistent differences observed between polymer types. Pathogens isolated from plastic biofilms using Galleria enrichment included Serratia and Enterococcus species and harboured a wide range of antimicrobial resistance genes. Our findings show that plastics in coastal waters are rapidly colonised by a wide diversity of bacteria, including known human pathogens, independent of polymer type.

Limpets and barnacles are important components of intertidal assemblages worldwide. This study examines the effects of barnacles on the foraging behaviour of the limpetPatella vulgata, which is the main algal grazer in the North-west Atlantic. The behaviour of limpets on a vertical seawall on the Isle of Man (UK) was investigated using autonomous radio-telemetry, comparing their activity patterns on plots characterized by dense barnacle cover and plots from which the barnacles had been removed. Limpet behaviour was investigated at mid-shore level, but two different elevations were considered. This experiment revealed a significant effect of barnacle cover on the activity ofP. vulgata. Limpets on smooth surfaces spent a greater proportion of total time active than did limpets on barnacles. Movement activity was also greater in areas that were lower down in the tidal range. In general, limpets were either predominantly active during diurnal high or nocturnal low tides and always avoided nocturnal high tides. Individuals on barnacles at the higher elevation concentrated their activity during nocturnal low water. All the other groups of limpets (smooth surfaces on the upper level and all individuals on the lower shore) had more excursions centred around daylight hours with an equal distribution of activity between periods of low and high water. Inter-individual variability was, however, pronounced.

Parasites impose strong selection on their hosts, but the level of any evolved resistance may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource-mediated selection are rare, particularly in nonmodel organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and any associated trade-offs in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole-genome resequencing, we identify genetic markers of resistance that vary between the nutritional environments during selection. We do not find consistent evolution of resistance in the presence of virus but rather see substantial variation among replicate populations. Resistance in a low-nutrition environment is negatively correlated with growth rate, consistent with an established trade-off between immunity and development, but this relationship is highly context dependent. Whole-genome resequencing of the host shows that resistance mechanisms are likely to be highly polygenic and although the underlying genetic architecture may differ between high and low-nutrition environments, similar mechanisms are commonly used. As a whole, our results emphasize the importance of the resource environment on influencing the evolution of resistance.

Parasites impose strong selection on their hosts, but the level of resistance evolved may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource mediated selection are rare, particularly in non-model organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and associated trade-offs, in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole genome sequencing we identify putative mechanisms of resistance that depend on the nutritional environment during selection. We find that the evolution of resistance is specific to diet, with adaptation to a low nutrition diet constraining resistance when challenged with the pathogen on a high nutrition diet. Resistance in a low nutrition environment is negatively correlated with growth rate, consistent with an established trade-off between immunity and development. Whole genome resequencing of the host shows that resistance mechanisms are highly polygenic and suggests evidence for trade-offs at the genetic level. Critically when populations evolve in high resource conditions, resistance is linked to metabolic and immune pathways, however it is more closely associated with cytoskeleton organisation when selected under low nutrition. Our results emphasise the importance of resources on the evolution of resistance.

In turbocharged gasoline engines, the violation of the compressor surge constraint can be prevented by exploiting predictive control techniques based on the reference governor (RG). In this paper, two RG designs are considered: an inner-and an outer-loop RG. The inner-loop design governs the throttle command, and the outer-loop governs the requested air charge command. Numerical simulations and the experimental vehicle results are presented, showing that both designs enforce the surge constraint without the use of a compressor bypass valve, but that the inner-loop design requires scheduling in order to do so.

We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific-filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.

Microsatellite DNA loci, when used in population genetic studies, are usually assumed to be neutral (unaffected by natural selection, either directly or as a result of tight linkage), but this assumption is rarely tested. Here, the assumption of neutrality is examined using established methods, principally that based on the expected relationship between F ST and heterozygosity, at 12 putative neutral microsatellite loci utilised in a study of Atlantic herring Clupea harengus in the north east Atlantic (west of Great Britain and around Ireland) and in the Baltic Sea. All but two of these loci demonstrate relationships that suggest that they may be regarded as neutral genetic markers. Of the other two loci, however, one shows a relationship suggestive of the action of directional selection and the other of balancing natural selection, though other locus-specific effects may operate. Thus, the latter two loci may provide inaccurate inference if used in phylogeographic studies and also demonstrate the danger of assuming neutrality at all microsatellite loci without explicit testing. However, such loci, particularly those affected by directional as opposed to balancing selection, may be of great use in stock discrimination studies, and selected loci in general, have considerably potential in studies of adaptation.

We investigate control strategies for traditional throttle-in-bore as well as low-cost cartridge-style throttle bodies for the air-intake system (AIS) throttle used in low-pressure exhaust-gas recirculation (LPEGR) on a turbocharged gasoline engine. Pressure sensors placed upstream and downstream of the AIS throttle are available as signals from the vehicle’s engine control unit, however, we do not use high-bandwidth feedback control of the AIS throttle in order to maintain frequency separation from the higher-rate EGR loop, which uses the downstream pressure sensor for feedback control. A design-of-experiments conducted using a feed-forward lookup table-based AIS throttle control strategy exposes controller sensitivity to part-to-part variations. For accurate tracking in the presence of these variations, we explore the use of adaptive feedback control. In particular, we use an algebraic model representing the throttle plate effective opening area to develop a recursive least-squares (RLS)-based estimation routine. A low-pass filtered version of the estimated model parameters is subsequently used in the forward-path AIS throttle controller. Results are presented comparing the RLS-based feedback algorithm with the feed-forward lookup table-based control strategy. RLS is able to adapt for part-to-part and change-over-time variabilities and exhibits an improved steady-state tracking response compared to the feed-forward control strategy.Copyright © 2015 by ASME

Status involves group members evaluating themselves relative to fellow group members according to some shared standard of value. Status has been described in economics, sociology and evolutionary anthropology. Based on this work, we treat status and the associated recognition by others as an intrinsic preference of all group members. There is disagreement about whether status competition enhances group performance by pushing group members to work harder, or whether it retards performance by causing unproductive behavior. We build a dynamic simulation model of a work group, where members are paid a bonus based on group performance. In addition to compensation, group members value a high status relative to their peers. Status is influenced both by contribution to group output and by non-productive, social activities of status enhancement. Group members allocate their total time between working and non-productive status enhancement, trying to maximize the combined utility from compensation and status rank. We show that status competition can serve to push group members to work hard and perform, provided that it is mainly based on merit. However, if status is also based on political maneuvering, status competition can lead to low group performance, especially in larger groups. Moreover, group performance may fluctuate and be unstable over time if the result of effort is noisy or if the group does not allow the sharing of ranks. The susceptibility to fluctuation depends on how status is awarded and updated over time. Thus, although a firm may not be able to avoid status competition, it may succeed in influencing its effects indirectly. We demonstrate these results analytically and via simulation.

Cyclic feeding schedules are now commonly used in conjunction with closed enteral feeding systems. Some manufacturers and clinicians have speculated that closed system cyclic feeding may promote formula contamination via retrograde movement of bacteria during the "no-flow" periods. Using both laboratory and clinical settings, our study evaluated whether retrograde bacterial movement under "no-flow" conditions results in contamination of closed system feeding containers. The clinical phase was conducted with 57 closed system feeding containers used to feed nursing home residents. In both laboratory and clinical testing there was no evidence of container contamination at 36-48 h, nor was there evidence of retrograde movement of bacteria beyond the drip chamber. Formula waste and costs were also analyzed using several 24- or 36-h hang time scenarios. Provided the appropriate container size is used, potential cost savings between $67 to $135 per patient per month may be achieved with the 36-h hang time scenarios. Retrograde movement of bacteria does not appear to be a source of closed system feeding container contamination in systems that incorporate a drip chamber. Using the appropriate size feeding container and systems with at least a 36-h hang time will result in significant cost savings.

Human African trypanosomiasis is caused by two subspecies of Trypanosoma brucei. Trypanosoma brucei rhodesiense is found in East Africa and frequently causes acute disease, while Trypanosoma brucei gambiense is found in West Africa and is associated with chronic disease. Samples taken from a single focus of a Ugandan outbreak of T. b. rhodesiense in the 1980s were associated with either chronic or acute disease. We sequenced the whole genomes of two of these isolates, which showed that they are genetically distinct from each other. Analysis of single nucleotide polymorphism markers in a panel of 31 Ugandan isolates plus 32 controls revealed a mixture of East African and West African haplotypes, and some of these haplotypes were associated with the different virulence phenotypes. It has been shown recently that T. b. brucei and T. b. rhodesiense populations undergo genetic exchange in natural populations. Our analysis showed that these strains from the Ugandan epidemic were intermediate between the reference genome sequences of T. b. gambiense and T. b. brucei and contained haplotypes that were present in both subspecies. This suggests that the human-infective subspecies of T. brucei are not genetically isolated, and our data are consistent with genomic introgression between East African and West African T. b. brucei subspecies. This has implications for the control of the parasite, the spread of drug resistance, and understanding the variation in virulence and the emergence of human infectivity., IMPORTANCE We present a genetic study of the acute form of “sleeping sickness” caused by the protozoan parasite Trypanosoma brucei rhodesiense from a single outbreak in Uganda. This represents an advance in our understanding of the relationship between the T. b. rhodesiense and Trypanosoma brucei gambiense subspecies that have previously been considered geographically distinct. Our data suggest that introgression of West African-derived T. brucei haplotypes may be associated with differences in disease presentation in the East African disease. These findings are not only of scientific interest but also important for parasite control, as they suggest that the human-infective T. brucei subspecies are not genetically isolated.

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

The α-proteobacterium Wolbachia is probably the most prevalent, vertically transmitted symbiont on Earth. In contrast with its wide distribution in arthropods, Wolbachia is restricted to one family of animal-parasitic nematodes, the Onchocercidae. This includes filarial pathogens such as Onchocerca volvulus, the cause of human onchocerciasis, or river blindness. The symbiosis between filariae and Wolbachia is obligate, although the basis of this dependency is not fully understood. Previous studies suggested that Wolbachia may provision metabolites (e.g., haem, riboflavin, and nucleotides) and/or contribute to immune defense. Importantly, Wolbachia is restricted to somatic tissues in adult male worms, whereas females also harbor bacteria in the germline. We sought to characterize the nature of the symbiosis between Wolbachia and O. ochengi, a bovine parasite representing the closest relative of O. volvulus. First, we sequenced the complete genome of Wolbachia strain wOo, which revealed an inability to synthesize riboflavin de novo. Using RNA-seq, we also generated endobacterial transcriptomes from male soma and female germline. In the soma, transcripts for membrane transport and respiration were up-regulated, while the gonad exhibited enrichment for DNA replication and translation. The most abundant Wolbachia proteins, as determined by geLC-MS, included ligands for mammalian Toll-like receptors. Enzymes involved in nucleotide synthesis were dominant among metabolism-related proteins, whereas the haem biosynthetic pathway was poorly represented. We conclude that Wolbachia may have a mitochondrion-like function in the soma, generating ATP for its host. Moreover, the abundance of immunogenic proteins in wOo suggests a role in diverting the immune system toward an ineffective antibacterial response.

The developments of novel electrochemical sensors to detect phenol (phenol derivatives) and heavy metals in solution have been a focus of our inquiry-based laboratory experiences. Our students are engaged into the applications of Controlled Potential Electrolysis (CPE) to create a modified working electrode to detect the common contaminants such as phenols and heavy metals in solutions by electroanalytical techniques such as cyclic voltammetry (CV), differential pulse voltammetry (DPV), and square wave anodic stripping voltammetry (SWASV). Additional analytical instrumentation skills were required through out these inquiry-based learning experiences to confirm the modified working electrodes (TiO2/ZrO2, Polymers and Carbon Nanotube, CNT) were electrochemically created by such instrumentation such as Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), Raman Spectroscopy and X-Ray Fluorescence. The students content gains were assessed through out these lab modules according to the R.R. Hake’ method. These content gains assessed will be discussed as well to exemplify the inquiry-based learning experiences of our undergraduate students experiences to meet the needs of todays workforce.

Our research group has developed a novel carbon paste composite electrode, in which titanium dioxide/zirconium dioxide was incorporated into graphite carbon paste, to detect cadmium and lead in aqueous solution by utilizing electrochemistry. In the current work, the newly developed titanium dioxide/zirconium dioxide carbon paste composite electrode was used to quantify lead and cadmium, individually and simultaneously, utilizing square wave anodic stripping voltammetry. Detection limits in the low ppb were achieved and the mechanism and the morphology of the electrode sensor designed were studied. The sensor was also tested in river water and well water samples to illustrate its potential for real world application will be illustrated. Scanning electron microscopy and X-ray Photoelectron Spectroscopy (XPS) were employed to investigate and characterize the electrode surface morphology and the mechanism will be discussed.

The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43-54% of the Bowtie SNPs and 57-58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.

Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of sequencing a backcrossed line in limiting the number of SNPs considered. We identify a SNP in the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype.

This thesis examines the various methods the Navy has used to develop and foster competition. It also discusses the economic analysis of using more than one source of supply. Rising costs and budgetary pressures have forced the Navy to reexamine its acquisition process. With the impending force draw down, the Program Manager is faced with reduced quantity requirements. Since the enactment of the Competition in Contracting Act in 1984, the Navy has required the use of dual sources in major weapons systems. However, this method of acquisition may no longer be economically feasible. Faced with reduced requirements and limited resources, the Program Manager must reevaluate the costs and benefits of his acquisition method. http://archive.org/details/annalysisofvaria1094527676 Lieutenant Commander, United States Navy Approved for public release; distribution is unlimited.

The film of microalgae and macroalgal propagules which coats intertidal rocks is the main food resource of limpets, the dominant grazers on exposed shores of north-west Europe. Spatial and temporal variability in feeding activity of limpets and abundance of microalgae were examined at mid-tide level across a European gradient from the Isle of Man in the British Isles to south-west Portu- gal. Feeding activity was assessed as the frequency of radula scrapes on wax surfaces placed on the shore. This was undertaken monthly at 2 shores at each of 4 locations, the Isle of Man, south-west Eng- land, northern Spain and south-west Portugal, over 1 yr. The abundance of the microalgal film was de- termined simultaneously at 3 of the 4 locations by measuring the concentration of chlorophyll a on the rock surface. The density and species diversity of limpets increased with decreasing latitude. This was mirrored by a trend of increased levels of limpet grazing, although 1 location (northern Spain) did not fit this trend. Seasonal changes in limpet grazing intensity were found at 3 of the 4 locations, charac- terised by elevated grazing during the summer and autumn. The seasonal variations resulted from changes in the level of foraging of individual limpets and were positively correlated with mean sea temperature in the Isle of Man and south-west England. The pattern of grazing activity was not solely a function of sea temperature. In the Isle of Man, grazing by Patella vulgata declined during the later stages of gonad development and increased following spawning. Seasonal variation in the standing stock of microalgae, measured as the concentration of chlorophyll a, was found at all 3 locations ex- amined, the Isle of Man, south-west England and northern Spain, with greater abundance in the win- ter compared to summer. This pattern was consistent over both large (among locations: 100s of kilo- metres) and medium (between shores: 1000s of metres) scales. There were no correlations between microalgal abundance and limpet grazing activity at any location. There were significant negative cor- relations between chlorophyll a and maximum monthly air temperature and monthly sunshine hours. Comparison of microalgal abundance among locations showed a general decline in standing stock with decreasing latitude, but differences between specific locations varied with season. South-west England showed similar levels of microalgal abundance to the most northerly location (Isle of Man) in winter, and to the most southerly location (northern Spain) in the summer.

BACKGROUND: Entamoeba histolytica is a significant cause of disease worldwide. However, little is known about the genetic diversity of the parasite. We re-sequenced the genomes of ten laboratory cultured lines of the eukaryotic pathogen Entamoeba histolytica in order to develop a picture of genetic diversity across the genome. RESULTS: The extreme nucleotide composition bias and repetitiveness of the E. histolytica genome provide a challenge for short-read mapping, yet we were able to define putative single nucleotide polymorphisms in a large portion of the genome. The results suggest a rather low level of single nucleotide diversity, although genes and gene families with putative roles in virulence are among the more polymorphic genes. We did observe large differences in coverage depth among genes, indicating differences in gene copy number between genomes. We found evidence indicating that recombination has occurred in the history of the sequenced genomes, suggesting that E. histolytica may reproduce sexually. CONCLUSIONS: E. histolytica displays a relatively low level of nucleotide diversity across its genome. However, large differences in gene family content and gene copy number are seen among the sequenced genomes. The pattern of polymorphism indicates that E. histolytica reproduces sexually, or has done so in the past, which has previously been suggested but not proven.

International audience; After ten years of continuous development and innovation, the cryptomarket and the Blockchain technology are still very much challenged and far from the mainstream adoption. We thus propose a risk assessment, as well as a market analysis of the Blockchain technology and the cryptomarket. This study is conceived as a two-level analysis. We first start with the micro-level analysis by performing a detailed risk assessment. Here, we take into consideration technological issues, such as such as consensus, network, cryptographic primitives, quantum and smart contract attacks, together with financial concerns such as market, information, liquidity, supply, reputation and environmental risks. Moreover, we propose ways to determine the probability that technological vulnerabilities can trigger financial risk. Here, we tackle concepts such as financial behavior, responsible investment and Blockchain literacy, as possible tools for assessing risk. Then, we complete this study with a macro-level analysis, which consists of the crypto-market appraisal performed with the Porter's five forces model. This market analysis is performed with respect to its stakeholders, such as the business process managers, investors, regulators, firms, developers, miners, hackers, exchange and trading platforms, etc. The results are relative to: 1. an identified continuity between the technological risks and financial ones; 2. a way to determine the likelihood of triggering financial risks through technical vulnerabilities; 3. a long-term profitability of the stakeholders’ strategy / position within the market.