Nutrigenomics of hepatic steatosis in a feline model: effect of monosodium glutamate, fructose, and Trans-fat feeding

Nonalcoholic fatty liver disease begins with a relatively benign hepatic steatosis, often associated with increased adiposity, but may progress to a more severe nonalcoholic steatohepatitis with inflammation. A subset of these patients develops progressive fibrosis and ultimately cirrhosis. Various dietary components have been shown to contribute to the development of liver disease, including fat, sugars, and neonatal treatment with high doses of monosodium glutamate (MSG). However, rodent models of progressive disease have been disappointing, and alternative animal models of diet-induced liver disease would be desirable, particularly if they contribute to our knowledge of changes in gene expression as a result of dietary manipulation. The domestic cat has previously been shown to be an appropriate model for examining metabolic changes–associated human diseases such as diabetes. Our aim was therefore to compare changes in hepatic gene expression induced by dietary MSG, with that of a diet containing Trans-fat and high fructose corn syrup (HFCS), using a feline model. MSG treatment increased adiposity and promoted hepatic steatosis compared to control (P < 0.05). Exposure to Trans-fat and HFCS promoted hepatic fibrosis and markers of liver dysfunction. Affymetrix microarray analysis of hepatic gene expression showed that dietary MSG promoted the expression of genes involved in cholesterol and steroid metabolism. Conversely, Trans-fat and HFCS feeding promoted the expression of genes involved in lipolysis, glycolysis, liver damage/regeneration, and fibrosis. Our feline model examining gene–diet interactions (nutrigenomics) demonstrates how dietary MSG, Trans-fat, and HFCS may contribute to the development of hepatic steatosis.     

Pathway databases and tools for their exploitation: benefits,current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue.     

Commercial harvest and export of snapping turtles (Chelydra serpentina) in the United States: trends and the efficacy of size limits at reducing harvest

As Asian turtle populations have crashed, China has increasingly turned to international import to meet domestic demand, which has increased pressure on global turtle populations. Snapping turtles (Chelydra serpentina) are being harvested in unprecedented numbers in the United States (US) to meet the needs of this international market. Here we report US snapping turtle live export from 1999 to 2013, and for the first time test the effectiveness of size limits in reducing commercial harvest numbers. Over three million live snapping turtles from farm and wild caught stock were exported from the US to Asia in 2012–14 alone. Increases in the export of wild caught snapping turtles to over 200,000 individuals in 2012 and 2014, compared to under 50,000 in other years, may indicate that farms are becoming unable to keep up with increasing demand. Annual harvest pressure at the state level increased linearly from 1998 to 2013, mirroring trends in federal export over the same time period. Our model estimates that size-limits were effective at reducing harvest by 30–87% in years with high harvest pressure. However, the majority of size limit regulations result in the removal of larger breeding adults, which has been shown to be detrimental to long term population viability. Regulatory approaches dedicated to the long term management of this iconic species will need to balance the short term gains, in the form of reduced harvest rates, with long term population viability.     

Triglyceride reference database: large scale storage of 3D triglyceride conformers and web-based analysis tools

The Triglyceride Reference Database (TRDB) contains conformer libraries of two triglycerides (tributyrin and triacetin) optimized at various levels of theory. The purpose of the TRDB project and its accompanying interface is to generate, store, process and retrieve triglyceride conformers; hence, it addresses problems and questions concerning geometrical properties, or relative conformer energies, that are of importance (among other uses) to force field evaluations.     

Approaching Drosophila development through proteomic tools and databases: At the hub of the post-genomic era

The past decade has witnessed an explosion in the growth of proteomics. The completion of numerous genome sequences, the development of powerful protein analytical technologies, as well as the design of innovative bioinformatics tools have marked the beginning of a new post-genomic era. Proteomics, the large-scale analysis of proteins in an organism, organ or organelle encompasses different aspects: (1) the identification, analysis of post-translational modifications and quantification of proteins; (2) the study of protein-protein interactions; and (3) the functional analysis of interactome networks. Here, we briefly summarize the emerging analytical tools and databases that are paving the way for studying Drosophila development by proteomic approaches.     

斑马鱼资源的开发保藏与国家斑马鱼资源中心

斑马鱼是一种新兴的脊椎模式动物。在过去的30年中,斑马鱼已被广泛应用于生命科学、健康科学、环境农业等诸多科研领域。为了满足不同的科研需要,研究人员开发和利用各种技术创建了大量的斑马鱼基因突变和转基因品系,这些品系已成为开展相关科学研究的宝贵资源。为了更好地保藏和利用这些资源,在全球范围内建设有多个规模不一的斑马鱼资源库。2012年,我国的国家斑马鱼资源中心（http：//zfish.cn）在中国科学院水生生物研究所正式成立。本文将重点介绍全球斑马鱼资源的开发和保藏情况,以及我国国家斑马鱼资源中心的最新建设进展。     

Development of the AGREE II,part 2: assessment of validity of items and tools to support application

Background

We established a program of research to improve the development, reporting and evaluation of practice guidelines. We assessed the construct validity of the items and user’s manual in the β version of the AGREE II.

Methods

We designed guideline excerpts reflecting high-and low-quality guideline content for 21 of the 23 items in the tool. We designed two study packages so that one low-quality and one high-quality version of each item were randomly assigned to each package. We randomly assigned 30 participants to one of the two packages. Participants reviewed and rated the guideline content according to the instructions of the user’s manual and completed a survey assessing the manual.

Results

In all cases, content designed to be of high quality was rated higher than low-quality content; in 18 of 21 cases, the differences were significant (p < 0.05). The manual was rated by participants as appropriate, easy to use, and helpful in differentiating guidelines of varying quality, with all scores above the mid-point of the seven-point scale. Considerable feedback was offered on how the items and manual of the β-AGREE II could be improved.

Interpretation

The validity of the items was established and the user’s manual was rated as highly useful by users. We used these results and those of our study presented in part 1 to modify the items and user’s manual. We recommend AGREE II (available at www.agreetrust.org) as the revised standard for guideline development, reporting and evaluation.For clinical practice guidelines to achieve their full potential as tools to assist in clinical, policy-related and system-level decisions,^1–3 they need to be of high quality and developed using rigorous methods.⁴ Thus, strategies are required to facilitate the development and reporting of guidelines and tools able to distinguish guidelines of varying quality. The AGREE Collaboration (Appraisal of Guidelines, Research and Evaluation) was the first to create a generic tool to assess the process of guideline development and reporting,^5,6 and it quickly became the standard for guideline evaluation.⁷As with any new assessment tool, ongoing development of the instrument was required to improve its measurement properties and advance the guideline enterprise. The AGREE Next Steps Consortium undertook a program of research to achieve these goals and create the next version of the tool, the AGREE II.⁸ The consortium completed two studies (parts 1 and 2). In part 1, also reported in this issue,⁹ we conducted an analysis of the performance of the new seven-point response scale, explored the usefulness of the AGREE items, and systematically identified ways in which the items and supporting document could be improved.In part 2, reported here, we aimed to test the construct validity of the items and evaluate the new supporting documentation, which was intended to facilitate efficient and accurate application of the tool.The validity of the original AGREE instrument was explored in three ways.⁵ Appraisers’ attitudes about the instrument’s usefulness and the helpfulness of the supporting documents (i.e., a user guide and training manual) were used as measures of face validity. The construct validity of the instrument was tested using three core hypotheses for each of the six domains; 3 of the possible 18 tests were supported. In retrospect, whether the hypotheses were generalizable across contexts was somewhat questionable. Finally, to establish criterion validity, correlations between users’ overall global endorsement and quality ratings of individual items were calculated. Whether global endorsements were a reasonable proxy gold standard was somewhat questionable. Further, for both the construct validity and the criterion validity, guidelines chosen in these studies were nominated by members of the research team as representing a range of quality, creating significant risks of bias.Together, these findings and methodological limitations illustrated the need for additional work to test and establish the instrument’s validity. The most fundamental concept of construct validity, in particular, had not been yet addressed —are guidelines known to be of higher quality rated more favourably using the AGREE instrument than guidelines known to be of lower quality? In addition, no study to date has tested specifically whether the instructions for applying the tool are perceived to be appropriate, implementable, and helpful in differentiating among guidelines of varying quality. These perceptions are important components that contribute to the face validity of the tool.We tested two specific research questions in this study. First, do the items in β-AGREE II differentiate between guideline content of known, varying quality? Second, is the new user’s manual perceived by users as appropriate, easy to apply and helpful in differentiating good quality guidelines from poor quality guidelines?     

Autotaxin inhibition: Development and application of computational tools to identify site-selective lead compounds

Autotaxin (ATX) catalyzes the conversion of lysophosphatidyl choline (LPC) to lysophosphatidic acid (LPA). Both ATX and LPA have been linked to pathophysiologies ranging from cancer to neuropathic pain. Inhibition of LPA production by ATX is therefore of therapeutic interest. Here we report the application of previously-developed, subsite-targeted pharmacophore models in a screening workflow that involves either docking or binary QSAR as secondary filters to identify ATX inhibitors from previously unreported structural types, four of which have sub-micromolar inhibition constants. Cell-based assays demonstrate that ATX inhibition and cytotoxicity structure–activity-relationships (SAR) exhibit selectivity cliffs, characterized by structurally similar compounds exhibiting similar biological activities with respect to ATX inhibition but very different biological activities with respect to cytotoxicity. Thus, general cytotoxicity should not be used as an early filter to eliminate candidate ATX inhibitor scaffolds from further SAR studies. Assays using two substrates of vastly different sizes demonstrate that the tools developed to identify compounds binding outside the central core of the active site did identify compounds acting at an allosteric site. In contrast, tools developed to identify active-site directed compounds did not identify active-site directed compounds. The stronger volume overlap imposed when selecting screening candidates expected to bind outside the active site is likely responsible for the stronger match between intended and actual target site.     

国家斑马鱼资源中心的资源、技术和服务建设

随着我国斑马鱼研究群体的日益壮大,对各类斑马鱼研究资源和技术的需求日益增加,国家斑马鱼资源中心(China Zebrafish Resource Center, CZRC, 网址:http://zfish.cn)于2012年在中国科学院水生生物研究所成立。目前,CZRC已发展成为国内规模最大的单体斑马鱼养殖系统,建成包含1200多个斑马鱼品系和10 000余份冻存精子的斑马鱼资源保藏库,其中有超过200个突变和转基因品系是由CZRC自主创制。在此基础上,CZRC建立了安全规范的斑马鱼养殖和健康平台、高效的基因操作平台和稳定高效的精子冻存平台。CZRC致力于为国内外从事斑马鱼研究的科研人员提供各类服务,包括提供斑马鱼品系等资源服务、转基因和基因敲除等技术服务、养殖和健康等咨询服务,以及技术培训和学术会议服务等。经过5年的建设,CZRC已成为国际学术界公认的全球三大斑马鱼资源库之一。     

Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome

Major progress has been made in catfish genomics including construction of high-density genetic linkage maps, BAC-based physical maps, and integration of genetic linkage and physical maps. Large numbers of ESTs have been generated from both channel catfish and blue catfish. Microarray platforms have been developed for the analysis of genome expression. Genome repeat structures are studied, laying grounds for whole genome sequencing. USDA recently approved funding of the whole genome sequencing project of catfish using the next generation sequencing technologies. Generation of the whole genome sequence is a historical landmark of catfish research as it opens the real first step of the long march toward genetic enhancement. The research community needs to be focused on aquaculture performance and production traits, take advantage of the unprecedented genome information and technology, and make real progress toward genetic improvements of aquaculture brood stocks.     

Cross-contamination in the kitchen: estimation of transfer rates for cutting boards, hands and knives

Aims: To quantify cross-contamination in the home from chicken to ready-to-eat salad. Methods and Results: Based on laboratory scenarios performed by de Jong et al. (2008) , transfer rates were estimated for Campylobacter jejuni and Lactobacillus casei as a tracer organism. This study showed that transfer characteristics for both micro-organisms were comparable when washing regimes and transfer via items (cutting board, hands and knives) were compared. Furthermore, the study showed that the use of separate transfer rates for transfer from chicken to items and from items to salad will lead to an overestimation of campylobacteriosis risk. Applying good hygienic practices resulted in final levels of bacteria in the salad below the detection limit. Our study showed that it is important to include these data points in model fitting. Conclusions: Results obtained in observational studies with Lact. casei can be translated to Camp. jejuni using the transfer rates obtained in this study. Cross-contamination by hands, cutting boards and knives was equally important. Significance and Impact of the Study: Cross-contamination should be incorporated in microbiological risk assessments. The present study contributes to this by quantifying transfer of Camp. jejuni and Lact. casei from raw chicken via various contact surfaces into the ready-to-eat product.     

Genetic governance: The risks,oversight and regulation of genetic databases in the UK

Increasing scientific and commercial interest is being paid to the creation of large population-based genetic databases to study the relationship between genes and disease. This paper will use ideas from the sociology of technology to look at the network of actors involved in the production, use and commercial exploitation of human genetic data, the social and ethical issues posed by genetic databases and the development of new governance arrangements in this domain. It will be argued that we are witnessing the creation of a new type of research system in the field of human genetics, which also forms the centre of an emerging market for personal and population-based genetic information. Some proposals for improving the governance of human genetic data in the UK will be offered in conclusion.     

Introduction to the Special Issue,Commitment to Alterity and Its Disavowal: The Politics of Display of Belonging

ABSTRACT

As multiple ethnic/race affiliation is highlighted more and more, we lack analytical frameworks to examine diverse ways individuals navigate through them as they balance aspirations, fears, desires, pride, responsibility, and pragmatic necessities. Existing studies of identification practices offer little examination of practices of those who disavow identifying with certain ethnic/race categories except for the ones focused on a narrow field of social relations, such as the academic achievement and career success in ‘acting White.’ This introductory piece introduces the main theoretical ideas in the special issue, commitment to alterity and its disavowal, which expands the scope of analysis to a wider range of identification practices and fields of social relations. This piece also briefly describes each contributing article, which further develops these notions to analyse various contours and degrees of belonging and links to wider cultural politics and power relations.     

Filling in the GAPS: evaluating completeness and coverage of open‐access biodiversity databases in the United States

Primary biodiversity data constitute observations of particular species at given points in time and space. Open‐access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open‐access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records from the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). We aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well‐surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well‐surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well‐surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. This comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.     

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.