Photomorphic analysis techniques: An interim spatial analysis using satellite remote sensor imagery and historical data

The use of machine scanning and/or computer-based techniques to provide greater objectivity in the photomorphic approach was investigated. Photomorphic analysis and its application in regional planning are discussed. Topics included: delineation of photomorphic regions; inadequacies of existing classification systems; tonal and textural characteristics and signature analysis techniques; pattern recognition and Fourier transform analysis; and optical experiments. A bibliography is included

High-sensitivity C-reactive protein is a predictive factor of adiposity in children : results of the Identification and prevention of Dietary- and lifestyle-induced health Effects in Children and InfantS (IDEFICS) study

Background-Whereas cross-sectional studies have shown that obesity is associated with increased C-reactive protein (CRP) levels in children, little is known about the impact of low-grade inflammation on body mass changes during growth. Methods and Results-We assessed cross-sectionally and longitudinally the association of high-sensitivity (hs)-CRP levels with overweight/obesity and related cardiometabolic risk factors in the Identification and prevention of Dietary-and lifestyle-induced health Effects in Children and InfantS (IDEFICS) cohort. 16 224 children from 8 European countries (2 to 9 years) were recruited during the baseline survey (T0). After the exclusion of 7187 children because of missing hs-CRP measurements and 2421 because of drug use during the previous week, the analysis was performed on 6616 children (Boys=3347; Girls=3269; age=6.3 +/- 1.7 years). Of them, 4110 were reexamined 2 years later (T1). Anthropometric variables, blood pressure, hs-CRP, blood lipids, glucose and insulin were measured. The population at T0 was divided into 3 categories, according to the baseline hs-CRP levels. Higher hs-CRP levels were associated with significantly higher prevalence of overweight/obesity, body mass index (BMI) z-score and central adiposity indices (P values all <0.0001), and with higher blood pressure and lower HDL-cholesterol levels. Over the 2-year follow-up, higher baseline hs-CRP levels were associated with a significant increase in BMI z-score (P<0.001) and significantly higher risk of incident overweight/obesity. Conclusions-Higher hs-CRP levels are associated to higher body mass and overweight/obesity risk in a large population of European children. Children with higher baseline levels of hs-CRP had a greater increase in BMI z-score and central adiposity over time and were at higher risk of developing overweight/obesity during growth

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

Background Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions. Results The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets. Conclusion JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage

DNA yield and quality of saliva samples and suitability for large scale epidemiological studies in children

Objective: To evaluate two saliva collection methods for DNA yield and quality as applied to a large, integrated, multicentre, European project involving the collection of biological material from children. Design: Cross-sectional multicentre comparative study in young children. Methods: Saliva samples were collected from 14 019 children aged 2-9 years from eight European countries participating in the IDEFICS (Identification and prevention of dietary-and lifestyle-induced health effects in children and infants) study. This involved either the collection of 2 ml of saliva from children who were able to spit, or using a sponge to collect whole saliva and buccal mucosal cells from the inside of the mouth of younger children unable to spit. Samples were assembled centrally in each participating centre and subsequently despatched for DNA extraction and biobanking to the University of Glasgow. A subgroup of 4678 samples (similar to 33% of sampled individuals) were chosen for DNA extraction before genotyping. Results: The whole-saliva collection method resulted in a higher DNA yield than the sponge collection method (mean +/- s.d.; saliva: 20.95 +/- 2.35 mu g, sponge: 9.13 +/- 2.25 mu g; P &lt; 0.001). DNA quality as measured by A(260)/A(280) was similar for the two collection methods. A minimum genotype calling success rate of 95% showed that both methods provide good-quality DNA for genotyping using TaqMan allelic discrimination assays. Conclusions: Our results showed higher DNA yield from the whole-saliva collection method compared with the assisted sponge collection. However, both collection methods provided DNA of sufficient quantity and quality for large-scale genetic epidemiological studies

Measuring satisfaction with health care in young persons with inflammatory bowel disease -an instrument development and validation study

Background: Patient satisfaction is a relevant prognostic factor in young persons with chronic disease and may be both age and disease specific. To assess health care quality from the patient's view in young persons with inflammatory bowel disease, an easy to use, valid, reliable and informative specific instrument was needed. Methods: All parts of the study were directed at persons with inflammatory bowel disease aged 15 to 24 (" youth"). A qualitative internet patient survey was used to generate items, complemented by a physician survey and literature search. A 2nd internet survey served to reduce items based on perceived importance and representativeness. Following pilot testing to assess ease of use and face validity, 150 respondents to a postal survey in patients from a paediatric clinical registry were included for validation analyses. Construct validity was assessed by relating summary scores to results from global questions on satisfaction with care using ANOVA. To assess test-retest reliability using intraclass correlation coefficients (ICC),a subset of patients were assessed twice within 3 months. Results: 302 persons with IBD and 55 physicians participated in the item generating internet survey, resulting in 3, 954 statements. After discarding redundancies 256 statements were presented in the 2nd internet survey. Of these, 32 items were retained. The resulting instrument assesses both the perceived relevance (importance) of an item as well as the performance of the care giver for each item for calculation of a summary satisfaction score (range 0 to 1). Sensibility testing showed good acceptance for most items. Construct validity was good, with mean scores of 0.63 (0.50 to 0.76),0.71 (0.69 to 0.74) and 0.81 (0.79 to 0.83) for no, some and good global satisfaction (ANOVA, p < 0.001). Test-retest reliability was satisfactory (ICC 0.6 to 0.7). Conclusions: We developed an easy to use, patient oriented, valid instrument to assess satisfaction with care in young persons with IBD for use in survey research

Blood cells as a source of transcriptional biomarkers of childhood obesity and its related metabolic alterations: results of the IDEFICS Study

Background: IDEFICS (Identification and Prevention of Dietary-and Lifestyle-Induced Health Effects in Children and Infants Project) is a European multicenter study on childhood obesity. One of its goals is to define early biomarkers of risk associated with obesity and its comorbid conditions. Objective: We considered blood cells as a new potential source of transcriptional biomarkers for these metabolic disorders and examined whether blood cell mRNA levels of some selected genes (LEPR, INSR, CPT1A, SLC27A2, UCP2, FASN, and PPAR alpha) were altered in overweight children and whether their expression levels could be defined as markers of the insulin-resistant or dyslipidemic state associated with overweight. Design: Blood samples were obtained from 306 normal-weight and overweight children, aged 2-9 yr, from eight different European countries. Whole-blood mRNA levels were assessed by quantitative RT-PCR. Results: LEPR, INSR, and CPT1A mRNA levels were higher in overweight compared with normal-weight children (the two latter only in males), whereas SLC27A2 mRNA levels were lower in overweight children. Significant associations were also found between expression levels of LEPR, INSR, CPT1A, SLC27A2, FASN, PPAR alpha, and different parameters, including body mass index, homeostasis model assessment index, and plasma triglycerides and cholesterol levels. These associations showed that high expression levels of CPT1A, SLC27A2, INSR, FASN, or PPAR alpha may be indicative of a lower risk for the insulin-resistant or dyslipidemic state associated with obesity, whereas low LEPR mRNA levels appear as a marker of high low-density lipoprotein cholesterol, independently of body mass index. Conclusions: These findings point toward the possibility of using the expression levels of these genes in blood cells as markers of metabolic status and can potentially provide an early warning of a future disorder

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs

Metrology best practice manuals

The outputs of workshops: genomic observatories (Ribocon and AWI), nutrients and oxygen sensor observations (Ifremer), carbonate chemistry sensors measurements (IO PAN) and trace elements measurements (UOP) will be turned into best practice manuals for free on-line dissemination

Early life course risk factors for childhood obesity : the IDEFICS case-control study

Background: The early life course is assumed to be a critical phase for childhood obesity; however the significance of single factors and their interplay is not well studied in childhood populations. Objectives: The investigation of pre-, peri- and postpartum risk factors on the risk of obesity at age 2 to 9. Methods: A case-control study with 1,024 1: 1-matched case-control pairs was nested in the baseline survey (09/2007-05/2008) of the IDEFICS study, a population-based intervention study on childhood obesity carried out in 8 European countries in pre- and primary school settings. Conditional logistic regression was used for identification of risk factors. Results: For many of the investigated risk factors, we found a raw effect in our study. In multivariate models, we could establish an effect for gestational weight gain (adjusted OR = 1.02; 95% CI 1.00-1.04), smoking during pregnancy (adjusted OR = 1.48; 95% CI 1.08-2.01), Caesarian section (adjusted OR = 1.38; 95% CI 1.10-1.74), and breastfeeding 4 to 11 months (adjusted OR = 0.77; 95% CI 0.62-0.96). Birth weight was related to lean mass rather than to fat mass, the effect of smoking was found only in boys, but not in girls. After additional adjustment for parental BMI and parental educational status, only gestational weight gain remained statistically significant. Both, maternal as well as paternal BMI were the strongest risk factors in our study, and they confounded several of the investigated associations. Conclusions: Key risk factors of childhood obesity in our study are parental BMI and gestational weight gain; consequently prevention approaches should target not only children but also adults. The monitoring of gestational weight seems to be of particular importance for early prevention of childhood obesity

Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered iberian lynx

Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples. Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of ‘presumptive’ aquaporin aqpZ genes and genes encoding ‘active’ lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding α-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of β-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of β-xylose containing plant N-glycans, although β-xylosidases sequences constituted only 1.5% of total glycosidases. These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80–100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed