The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

Recent advances in sequencing technology have created unprecedented opportunities for biological research. However, the increasing throughput of these technologies has created many challenges for data management and analysis. As the demand for sophisticated analyses increases, the development time of software and algorithms is outpacing the speed of traditional publication. As technologies continue to be developed, methods change rapidly, making publications less relevant for users. The SEQanswers wiki (SEQwiki) is a wiki database that is actively edited and updated by the members of the SEQanswers community (http://SEQanswers.com/). The wiki provides an extensive catalogue of tools, technologies and tutorials for high-throughput sequencing (HTS), including information about HTS service providers. It has been implemented in MediaWiki with the Semantic MediaWiki and Semantic Forms extensions to collect structured data, providing powerful navigation and reporting features. Within 2 years, the community has created pages for over 500 tools, with approximately 400 literature references and 600 web links. This collaborative effort has made SEQwiki the most comprehensive database of HTS tools anywhere on the web. The wiki includes task-focused mini-reviews of commonly used tools, and a growing collection of more than 100 HTS service providers. SEQwiki is available at: http://wiki.SEQanswers.com/

Expression analysis of mammaglobin A (SCGB2A2) and lipophilin B (SCGB1D2) in more than 300 human tumors and matching normal tissues reveals their co-expression in gynecologic malignancies

BACKGROUND: Mammaglobin A (SCGB2A2) and lipophilin B (SCGB1D2), two members of the secretoglobin superfamily, are known to be co-expressed in breast cancer, where their proteins form a covalent complex. Based on the relatively high tissue-specific expression pattern, it has been proposed that the mammaglobin A protein and/or its complex with lipophilin B could be used in breast cancer diagnosis and treatment. In view of these clinical implications, the aim of the present study was to analyze the expression of both genes in a large panel of human solid tumors (n = 309), corresponding normal tissues (n = 309) and cell lines (n = 11), in order to evaluate their tissue specific expression and co-expression pattern. METHODS: For gene and protein expression analyses, northern blot, dot blot hybridization of matched tumor/normal arrays (cancer profiling arrays), quantitative RT-PCR, non-radioisotopic RNA in situ hybridization and immunohistochemistry were used. RESULTS: Cancer profiling array data demonstrated that mammaglobin A and lipophilin B expression is not restricted to normal and malignant breast tissue. Both genes were abundantly expressed in tumors of the female genital tract, i.e. endometrial, ovarian and cervical cancer. In these four tissues the expression pattern of mammaglobin A and lipophilin B was highly concordant, with both genes being down-, up- or not regulated in the same tissue samples. In breast tissue, mammaglobin A expression was down-regulated in 49% and up-regulated in 12% of breast tumor specimens compared with matching normal tissues, while lipophilin B was down-regulated in 59% and up-regulated in 3% of cases. In endometrial tissue, expression of mammaglobin A and lipophilin B was clearly up-regulated in tumors (47% and 49% respectively). Both genes exhibited down-regulation in 22% of endometrial tumors. The only exceptions to this concordance of mammaglobin A/lipophilin B expression were normal and malignant tissues of prostate and kidney, where only lipophilin B was abundantly expressed and mammaglobin A was entirely absent. RNA in situ hybridization and immunohistochemistry confirmed expression of mammaglobin A on a cellular level in endometrial and cervical cancer and their corresponding normal tissues. CONCLUSION: Altogether, these data suggest that expression of mammaglobin A and lipophilin B might be controlled in different tissues by the same regulatory transcriptional mechanisms. Diagnostic assays based on mammaglobin A expression and/or the mammaglobin A/lipophilin B complex appear to be less specific for breast cancer, but with a broader spectrum of potential applications, which includes gynecologic malignancies

General scientific guidance for stakeholders on health claim applications

The European Food Safety Authority (EFSA) asked the Panel on Dietetic Products Nutrition and Allergies (NDA) to update the General guidance for stakeholders on the evaluation of Article 13.1, 13.5 and 14 health claims published in March 2011. Since then, the NDA Panel has completed the evaluation of Article 13.1 claims except for claims put on hold by the European Commission, and has evaluated additional health claim applications submitted pursuant to Articles 13.5, 14 and also 19. In addition, comments received from stakeholders indicate that general issues that are common to all health claims need to be further clarified and addressed. This guidance document aims to explain the general scientific principles applied by the NDA Panel for the evaluation of all health claims and outlines a series of steps for the compilation of applications. The general guidance document represents the views of the NDA Panel based on the experience gained to date with the evaluation of health claims, and it may be further updated, as appropriate, when additional issues are addressed

A fixed carbohydrate: protein ratio <= 1.8 on an energy basis consumed in the context of an energy-restricted diet and reduction of body weight: evaluation of a health claim pursuant to Article 13(5) of Regulation (EC) No 1924/2006.

Following an application from Marks and Spencer PLC, submitted for authorisation of a health claim pursuant to Article 13(5) of Regulation (EC) No 1924/2006 via the Competent Authority of the United Kingdom, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on the scientific substantiation of a health claim related to a CHO:P ratio &lt;= 1.8 on an energy basis in the context of an energy-restricted diet and body weight. The Panel considers that the food/constituent that is the subject of the health claim is sufficiently characterised. The Panel also considers that reduction of body weight in the context of an energy-restricted diet is a beneficial physiological effect. The target population proposed by the applicant is 'adults between the ages of 18 and 70 years with excess body weight'. No conclusions could be drawn from two unpublished studies investigating the effect of ready-to-eat meals with a CHO: P ratio &lt;= 1.8 on body weight. The remaining 14 human intervention studies investigated the effect of diets targeting a CHO: P ratio &lt;= 1.8 as compared to diets targeting a CHO: P ratio &gt;= 3.0 on overweight and obese adults in the context of energy restriction. Four out of seven studies lasting &lt; 12 weeks reported an effect of a CHO: P ratio &lt;= 1.8 on body weight in overweight/obese subjects, whereas no significant effect was observed in six out of the seven studies lasting 12 weeks or more. The Panel considers that these studies do not provide evidence for a sustained effect of the food/constituent on body weight. The Panel concludes that a cause and effect relationship has not been established between the consumption of a fixed CHO: P ratio &lt;= 1.8 on an energy basis consumed in the context of an energy-restricted diet and reduction of body weight. (C) 2017 European Food Safety Authority

Dietary reference values for vitamin D

Following a request from the European Commission, the EFSA Panel&nbsp;on Dietetic Products, Nutrition and Allergies (NDA) derived dietary reference values (DRVs) for vitamin D. The Panel&nbsp;considers that serum 25(OH)D concentration, which reflects the amount of vitamin D attained from both cutaneous synthesis and dietary sources, can be used as a biomarker of vitamin D status in adult and children populations. The Panel&nbsp;notes that the evidence on the relationship between serum 25(OH)D concentration and musculoskeletal health outcomes in adults, infants and children, and adverse pregnancy-related health outcomes, is widely variable. The Panel&nbsp;considers that Average Requirements and Population Reference Intakes for vitamin D cannot be derived, and therefore defines adequate intakes (AIs), for all population groups. Taking into account the overall evidence and uncertainties, the Panel&nbsp;considers that a serum 25(OH)D concentration of 50&nbsp;nmol/L is a suitable target value for all population groups, in view of setting the AIs. For adults, an AI for vitamin D is set at 15&nbsp;\u3bcg/day, based on a meta-regression analysis and considering that, at this intake, the majority of the population will achieve a serum 25(OH)D concentration near or above the target of 50&nbsp;nmol/L. For children aged 1\u201317&nbsp;years, an AI for vitamin D is set at 15&nbsp;\u3bcg/day, based on the meta-regression analysis. For infants aged 7\u201311&nbsp;months, an AI for vitamin D is set at 10&nbsp;\u3bcg/day, based on trials in infants. For pregnant and lactating women, the Panel&nbsp;sets the same AI as for non-pregnant non-lactating women, i.e. 15&nbsp;\u3bcg/day. The Panel&nbsp;underlines that the meta-regression was done on data collected under conditions of assumed minimal cutaneous vitamin D synthesis. In the presence of cutaneous vitamin D synthesis, the requirement for dietary vitamin D is lower or may even be zero

Vitamin C and contribution to the normal function of the immune system: evaluation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006

Following an application from Specialised Nutrition Europe (formerly IDACE), submitted for authorisation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 via the Competent Authority of France, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on the scientific substantiation of a health claim related to vitamin C and ‘helps to support a healthy immune system’. The Panel considers that vitamin C is sufficiently characterised, and that contribution to the normal function of the immune system is a beneficial physiological effect. The Panel has previously assessed a claim on vitamin C and its contribution to the normal function of the immune system with a favourable outcome. The target population was the general population. The Panel considers that the role of vitamin C in the functioning of the immune system applies to all ages, including infants and young children (from birth to three years of age). The Panel concludes that a cause and effect relationship has been established between the dietary intake of vitamin C and contribution to the normal function of the immune system. The following wording reflects the scientific evidence: ‘Vitamin C contributes to the normal function of the immune system.’ The target population is infants and young children up to three years of age

Gender differences in the physiological responses and kinematic behaviour of elite sprint cross-country skiers

Gender differences in performance by elite endurance athletes, including runners, track cyclists and speed skaters, have been shown to be approximately 12%. The present study was designed to examine gender differences in physiological responses and kinematics associated with sprint cross-country skiing. Eight male and eight female elite sprint cross-country skiers, matched for performance, carried out a submaximal test, a test of maximal aerobic capacity (VO2max) and a shorter test of maximal treadmill speed (Vmax) during treadmill roller skiing utilizing the G3 skating technique. The men attained 17% higher speeds during both the VO2max and the Vmax tests (P < 0.05 in both cases), differences that were reduced to 9% upon normalization for fat-free body mass. Furthermore, the men exhibited 14 and 7% higher VO2max relative to total and fat-free body mass, respectively (P < 0.05 in both cases). The gross efficiency was similar for both gender groups. At the same absolute speed, men employed 11% longer cycles at lower rates, and at peak speed, 21% longer cycle lengths (P < 0.05 in all cases). The current study documents approximately 5% larger gender differences in performance and VO2max than those reported for comparable endurance sports. These differences reflect primarily the higher VO2max and lower percentage of body fat in men, since no gender differences in the ability to convert metabolic rate into work rate and speed were observed. With regards to kinematics, the gender difference in performance was explained by cycle length, not by cycle rate

Safety of betaine as a novel food pursuant to Regulation (EC) No 258/97

Following a request from the European Commission, the EFSA Panelon Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on betaine as a novel food (NF) pursuant to Regulation (EC) No 258/97. The information provided on the composition, the specifications, the batch-to-batch variability, stability and production process of the NF is sufficient and does not raise concerns about the safety of the NF. The NF is proposed to be used in foods intended to meet additional requirements for intense muscular effort with a maximum intake of 2.5 g/day of betaine for sports people above 10 years of age. Based on the lowest BMDL05, which was derived from a chronic toxicity study in rats in which a dose-related increase in platelet counts was observed, and the anticipated daily intake of the NF in the target population, the Margins of Exposure are 3.6 and 5, which are generally regarded as not sufficient. However, the total exposure to betaine from the diet (about 830 mg/day) is not known to be associated with adverse effects. Moreover, no adverse effects on platelet counts were noted in human intervention studies with exposure levels of 4 g/day of betaine for up to 6 months. A significant increase in total and low-density lipoprotein (LDL)-cholesterol concentrations was noted at intakes of 4 g/day of betaine in overweight subjects with metabolic syndrome but not in healthy subjects, nor at intakes of 3 g/day. Thus, considering 4 g/day of betaine as a reference point and applying an uncertainty factor of 10 to account for interindividual variability, an amount of 400 mg/day of betaine in addition to the background exposure is considered as safe. The Panelconsiders that the NF is safe to be used at maximum intake of 400 mg/day in the target population