University of Guelph

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.

Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.

Abstract When the atmospheric turbulent flux of a minor constituent such as CO2 (or of water vapour as a special case) is measured by either the eddy covariance or the mean gradient technique, account may need to be taken of variations of the constituent's density due to the presence of a flux of heat and/or water vapour. In this paper the basic relationships are discussed in the context of vertical transfer in the lower atmosphere, and the required corrections to the measured flux are derived. If the measurement involves sensing of the fluctuations or mean gradient of the constituent's mixing ratio relative to the dry air component, then no correction is required; while with sensing of the constituent's specific mass content relative to the total moist air, a correction arising from the water vapour flux only is required. Correspondingly, if in mean gradient measurements the constituent's density is measured in air from different heights which has been pre‐dried and brought to a common temperature, then again no correction is required; while if the original (moist) air itself is brought to a common temperature, then only a correction arising from the water vapour flux is required. If the constituent's density fluctuations or mean gradients are measured directly in the air in situ , then corrections arising from both heat and water vapour fluxes are required. These corrections will often be very important. That due to the heat flux is about five times as great as that due to an equal latent heat (water vapour) flux. In CO2 flux measurements the magnitude of the correction will commonly exceed that of the flux itself. The correction to measurements of water vapour flux will often be only a few per cent but will sometimes exceed 10 per cent.

All terrestrial ecosystems consist of aboveground and belowground components that interact to influence community- and ecosystem-level processes and properties. Here we show how these components are closely interlinked at the community level, reinforced by a greater degree of specificity between plants and soil organisms than has been previously supposed. As such, aboveground and belowground communities can be powerful mutual drivers, with both positive and negative feedbacks. A combined aboveground-belowground approach to community and ecosystem ecology is enhancing our understanding of the regulation and functional significance of biodiversity and of the environmental impacts of human-induced global change phenomena.

With millions of species and their life-stage transformations, the animal kingdom provides a challenging target for taxonomy. Recent work has suggested that a DNA-based identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), can aid the resolution of this diversity. While past work has validated the ability of COI sequences to diagnose species in certain taxonomic groups, the present study extends these analyses across the animal kingdom. The results indicate that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria. This success in species diagnosis reflects both the high rates of sequence change at COI in most animal groups and constraints on intraspecific mitochondrial DNA divergence arising, at least in part, through selective sweeps mediated via interactions with the nuclear genome.

Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain known as lipid A (or endotoxin), a nonrepeating "core" oligosaccharide, and a distal polysaccharide (or O-antigen). Recent genomic data have facilitated study of LPS assembly in diverse Gram-negative bacteria, many of which are human or plant pathogens, and have established the importance of lateral gene transfer in generating structural diversity of O-antigens. Many enzymes of lipid A biosynthesis like LpxC have been validated as targets for development of new antibiotics. Key genes for lipid A biosynthesis have unexpectedly also been found in higher plants, indicating that eukaryotic lipid A-like molecules may exist. Most significant has been the identification of the plasma membrane protein TLR4 as the lipid A signaling receptor of animal cells. TLR4 belongs to a family of innate immunity receptors that possess a large extracellular domain of leucine-rich repeats, a single trans-membrane segment, and a smaller cytoplasmic signaling region that engages the adaptor protein MyD88. The expanding knowledge of TLR4 specificity and its downstream signaling pathways should provide new opportunities for blocking inflammation associated with infection.

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.

Previously described methods to quantify the proportion of root length colonized by vesicular-arbuscular (VA) mycorrhizal fungi are reviewed. It is argued that these methods give observer-dependent measures of colonization which cannot be used to compare, quantitatively, roots examined by different researchers. A modified method is described here to estimate VA mycorrhizal colonization on an objective scale of measurement, involving inspection of intersections between the microscope eyepiece crosshair and roots at magnification × 200; it is referred to as the magnified intersections method. Whether the vertical eyepiece crosshair crosses one or more arbuscules is noted at each intersection. The estimate of colonization is the proportion of root length containing arbuscules, called the arbuscular colonization (AC). The magnified intersections method also determines the proportion of root length containing vesicles, the vesicular colonization (VC), and the proportion of root length containing hyphae, the hyphal colonization (HC). However, VC and HC should be interpreted with caution because vesicles and hyphae, unlike arbuscules, can be produced in roots by non-mycorrhizal fungi.

Astraptes fulgerator, first described in 1775, is a common and widely distributed neotropical skipper butterfly (Lepidoptera: Hesperiidae). We combine 25 years of natural history observations in northwestern Costa Rica with morphological study and DNA barcoding of museum specimens to show that A. fulgerator is a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic divergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.

This article offers a new approach to celebrity endorsement. Previous explanations, especially the source credibility and source attractiveness models are criticized, and an alternative meaning transfer model is proposed. According to this model, celebrities' effectiveness as endorsers stems from the cultural meanings with which they are endowed. The model shows how meanings pass from celebrity to product and from product to consumer. The implications of this model for our understanding of the consumer society are considered. Research avenues suggested by the model are also discussed. Copyright 1989 by the University of Chicago.

BACKGROUND: The scoping review has become an increasingly popular approach for synthesizing research evidence. It is a relatively new approach for which a universal study definition or definitive procedure has not been established. The purpose of this scoping review was to provide an overview of scoping reviews in the literature. METHODS: A scoping review was conducted using the Arksey and O'Malley framework. A search was conducted in four bibliographic databases and the gray literature to identify scoping review studies. Review selection and characterization were performed by two independent reviewers using pretested forms. RESULTS: The search identified 344 scoping reviews published from 1999 to October 2012. The reviews varied in terms of purpose, methodology, and detail of reporting. Nearly three-quarter of reviews (74.1%) addressed a health topic. Study completion times varied from 2 weeks to 20 months, and 51% utilized a published methodological framework. Quality assessment of included studies was infrequently performed (22.38%). CONCLUSIONS: Scoping reviews are a relatively new but increasingly common approach for mapping broad topics. Because of variability in their conduct, there is a need for their methodological standardization to ensure the utility and strength of evidence.

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Observations of neutral-current $\ensuremath{\nu}$ interactions on deuterium in the Sudbury Neutrino Observatory are reported. Using the neutral current (NC), elastic scattering, and charged current reactions and assuming the standard ${}^{8}\mathrm{B}$ shape, the ${\ensuremath{\nu}}_{e}$ component of the ${}^{8}\mathrm{B}$ solar flux is ${\ensuremath{\varphi}}_{e}{\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1.76}_{\ensuremath{-}0.05}^{+0.05}(\mathrm{stat}{)}_{\ensuremath{-}0.09}^{+0.09}(\mathrm{syst})\ifmmode\times\else\texttimes\fi{}{10}^{6}\phantom{\rule{0ex}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}{\mathrm{s}}^{\ensuremath{-}1}$ for a kinetic energy threshold of 5 MeV. The non- ${\ensuremath{\nu}}_{e}$ component is ${\ensuremath{\varphi}}_{\ensuremath{\mu}\ensuremath{\tau}}{\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}3.41}_{\ensuremath{-}0.45}^{+0.45}(\mathrm{stat}{)}_{\ensuremath{-}0.45}^{+0.48}(\mathrm{syst})\ifmmode\times\else\texttimes\fi{}{10}^{6}\phantom{\rule{0ex}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}{\mathrm{s}}^{\ensuremath{-}1}$, $5.3\ensuremath{\sigma}$ greater than zero, providing strong evidence for solar ${\ensuremath{\nu}}_{e}$ flavor transformation. The total flux measured with the NC reaction is ${\ensuremath{\varphi}}_{\mathrm{NC}}{\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}5.09}_{\ensuremath{-}0.43}^{+0.44}(\mathrm{stat}{)}_{\ensuremath{-}0.43}^{+0.46}(\mathrm{syst})\ifmmode\times\else\texttimes\fi{}{10}^{6}\phantom{\rule{0ex}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}{\mathrm{s}}^{\ensuremath{-}1}$, consistent with solar models.

BACKGROUND: People who are prescribed self administered medications typically take only about half their prescribed doses. Efforts to assist patients with adherence to medications might improve the benefits of prescribed medications. OBJECTIVES: The primary objective of this review is to assess the effects of interventions intended to enhance patient adherence to prescribed medications for medical conditions, on both medication adherence and clinical outcomes. SEARCH METHODS: We updated searches of The Cochrane Library, including CENTRAL (via http://onlinelibrary.wiley.com/cochranelibrary/search/), MEDLINE, EMBASE, PsycINFO (all via Ovid), CINAHL (via EBSCO), and Sociological Abstracts (via ProQuest) on 11 January 2013 with no language restriction. We also reviewed bibliographies in articles on patient adherence, and contacted authors of relevant original and review articles. SELECTION CRITERIA: We included unconfounded RCTs of interventions to improve adherence with prescribed medications, measuring both medication adherence and clinical outcome, with at least 80% follow-up of each group studied and, for long-term treatments, at least six months follow-up for studies with positive findings at earlier time points. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted all data and a third author resolved disagreements. The studies differed widely according to medical condition, patient population, intervention, measures of adherence, and clinical outcomes. Pooling results according to one of these characteristics still leaves highly heterogeneous groups, and we could not justify meta-analysis. Instead, we conducted a qualitative analysis with a focus on the RCTs with the lowest risk of bias for study design and the primary clinical outcome. MAIN RESULTS: The present update included 109 new RCTs published since the previous update in January 2007, bringing the total number of RCTs to 182; we found five RCTs from the previous update to be ineligible and excluded them. Studies were heterogeneous for patients, medical problems, treatment regimens, adherence interventions, and adherence and clinical outcome measurements, and most had high risk of bias. The main changes in comparison with the previous update include that we now: 1) report a lack of convincing evidence also specifically among the studies with the lowest risk of bias; 2) do not try to classify studies according to intervention type any more, due to the large heterogeneity; 3) make our database available for collaboration on sub-analyses, in acknowledgement of the need to make collective advancement in this difficult field of research. Of all 182 RCTs, 17 had the lowest risk of bias for study design features and their primary clinical outcome, 11 from the present update and six from the previous update. The RCTs at lowest risk of bias generally involved complex interventions with multiple components, trying to overcome barriers to adherence by means of tailored ongoing support from allied health professionals such as pharmacists, who often delivered intense education, counseling (including motivational interviewing or cognitive behavioral therapy by professionals) or daily treatment support (or both), and sometimes additional support from family or peers. Only five of these RCTs reported improvements in both adherence and clinical outcomes, and no common intervention characteristics were apparent. Even the most effective interventions did not lead to large improvements in adherence or clinical outcomes. AUTHORS' CONCLUSIONS: Across the body of evidence, effects were inconsistent from study to study, and only a minority of lowest risk of bias RCTs improved both adherence and clinical outcomes. Current methods of improving medication adherence for chronic health problems are mostly complex and not very effective, so that the full benefits of treatment cannot be realized. The research in this field needs advances, including improved design of feasible long-term interventions, objective adherence measures, and sufficient study power to detect improvements in patient-important clinical outcomes. By making our comprehensive database available for sharing we hope to contribute to achieving these advances.

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

Abstract Cultural meaning in a consumer society moves ceaselessly from one location to another. In the usual trajectory, cultural meaning moves first from the culturally constituted world to consumer goods and then from these goods to the individual consumer. Several instruments are responsible for this movement: advertising, the fashion system, and four consumption rituals. This article analyzes the movement of cultural meaning theoretically, showing both where cultural meaning is resident in the contemporary North American consumer system and the means by which this meaning is transferred from one location in this system to another.

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies. The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources. The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

Active oxygen species (AOS) are believed to have important roles in plants in general and in plant—pathogen interactions in particular. They are believed to be involved in signal transduction, cell wall reinforcement, hypersensitive response (HR) and phytoalexin production, and to have direct antimicrobial effects. Since current methods are inadequate for localizing AOS in intact plant tissue, most studies have been conducted using cell suspension culture/elicitors systems. 3,3‐diaminobenzidine (DAB) polymerizes instantly and locally as soon as it comes into contact with H 2 O 2 in the presence of peroxidase, and it was found that, by allowing the leaf to take up this substrate, in‐vivo and in‐situ detection of H 2 O 2 can be made at subcellular levels. This method was successfully used to detect H 2 O 2 in developing papillae and surrounding haloes (cell wall appositions) and whole cells of barley leaves interacting with the powdery mildew fungus. Thus, H 2 O 2 can be detected in the epidermal cell wall subjacent to the primary germ tube from 6 h after inoculation, and subjacent to the appressorium from 15 h. The earliest time point for observation of H 2 O 2 in relation to epidermal cells undergoing HR is 15 h after inoculation, first appearing in the zones of attachment to the mesophyll cells underneath, and eventually in the entire epidermal cell. Furthermore, it was observed that proteins in papillae and HR cells are cross‐linked, a process believed to be fuelled by H 2 O 2 . This cross‐linking reinforces the apposition, presumably assisting the arrest of the pathogen.