The representation of protein complexes in the Protein Ontology

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/

Comparison of explicit vs. implicit measurements in predicting food purchases

In this study, we aimed to investigate the relation between consumer purchases of three branded blueberry flavored quarks and respective responses of the same consumers to these products using 1) traditional explicit consumer surveys measuring verbalized impressions, 2) novel explicit pictorial emoji scores and 3) implicit behavioral responses produced during an approach-avoidance task (AAT). Explicit measures (n=134) were collected before product tasting (expectation condition) during an online survey, and after product tasting (perception condition) during a Central Location Test (CLT). Implicit measures were collected with a subset of 56 randomly selected subjects during the CLT. These included electroencephalographic (EEG) measures, joystick response speed and pupil size responses. During one month following the CLT, respondents registered their purchases via an online diary. Bivariate correlations indicated that explicit scores correlate better with product purchase amounts in the perception condition than in the expectation condition. Furthermore, verbalized ratings correlated better with product purchase amounts than pictorial emoji scores. Of the implicit responses, EEG responses produced the strongest correlations with purchase behavior, similar to those observed for verbalized explicit ratings in the expectation condition. Multiple linear regression modelling indicated that the best-fitting model consisted of an emoji score, purchase intention score, pleasantness score, brand relationship score, and implicit joystick response speed. Overall, purchase behavior was associated stronger with explicit responses than with implicit responses. Yet, the prominent role of implicit joystick response speed in the multivariate regression model suggests its unique contribution to the understanding of purchase behavior.Peer reviewe

Protein Ontology: A controlled structured network of protein entities

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments

The representation of protein complexes in the Protein Ontology (PRO)

BACKGROUND: Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. DESCRIPTION: We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. CONCLUSION: PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species

Effects of Visual Priming on Taste-Odor Interaction

Little is known about the influence of visual characteristics other than colour on flavor perception, and the complex interactions between more than two sensory modalities. This study focused on the effects of recognizability of visual (texture) information on flavor perception of odorized sweet beverages

Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer's Disease

Background 1Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset. Principal Findings We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD. Significance Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches

Correction: genetic evidence implicates the immune system and cholesterol metabolism in the aetiology of Alzheimer's disease.

[This corrects the article on p. e13950 in vol. 5.]. Background: Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology: We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset. Principal Findings: We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD. Significance: Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches

The Gene Ontology in 2010: extensions and refinements

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Oxford University Press. The published article can be found at: http://nar.oxfordjournals.org/

Role of saliva and oral processing in sensory perception of maltodextrin solutions

In human, food oral processing plays a role in our perception of taste, aroma and texture. This study aimed at investigating the role played by individual salivary flow rate and composition and oral mechanisms in the sensory perception of sweetened and thickened solutions. Thirty one subjects were selected with high differences in salivary flow rates and composition (protein concentration and amylase activity). They consumed twelve thickened solutions (varying independently in maltodextrin type (2), viscosity level (2) and sucrose level (3)) and rated the perceived thickness and sweetness intensities. After rating, boluses were collected in order to evaluate moistening by saliva. Residual oral coating was determined from oral rinsing water collected after bolus collection.Overall perceived thickness intensity increased with solution viscosity and sucrose concentration but did not depend on maltodextrin type; which was in line with rheological measurements of the solutions. Sweetness intensity was modified by sucrose concentration but also by changes in viscosity and maltodextrin. Bolus moistening by saliva varied between 43 and 89 % and the amount of solution coating the oral cavity varied between 0 to 3% (dry matter), depending on the solution. Regressions analyses were performed in order to evaluate the role of saliva and oral processing on sensory perception, while considering individual differences. Perceived thickness increased with oral coating, stimulated salivary flow rate and low amylase activity. This supposes an impact of temporal stimulation and oral enzymatic breakdown in texture perception. Perceived sweetness was similarly affected by these parameters but also increased with salivary flow rate at rest and bolus moistening, suggesting a higher clearance and thus a better dilution/ transport of sweet compounds to the taste buds. All together this study demonstrated that characterizing oral physiology and food oral processing can provide relevant information to explain inter-individual differences in sensory perception

Immediate sweetening effect of Image presentation.

<p>Re-referenced sweetness ratings for odor-taste stimuli during image trials, compared to the sustained sweetening effect of an image context (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023857#pone-0023857-g003" target="_blank">Figure 3</a>). The vertical axe represents the <i>additional</i> sweetening effects of Image trials compared to no-image trials within an image context. Note that ratings were not compared to baseline Odor-Taste ratings which included no exposure to Images at all. Image×Figurativeness: Compared to the no-image trials within an image context, there is an increase in sweetness rating when a Non-Figurative image is present. The trials with a figurative image, however, do not show an additional increase in sweetness ratings. We cannot exclude the possibility that this is due to a ceiling effect of the figurative context (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023857#pone-0023857-g003" target="_blank">Figure 3</a>). The negative effect of Figurative Images was not significant.</p