On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the “functional similarity” between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the “ortholog conjecture” (or, more properly, the “ortholog functional conservation hypothesis”). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis

Energy and macronutrient intake and dietary pattern among school children in Bahrain: a cross-sectional study

Abstract Background Obesity is increasing in Bahrain and there is lack of information on the energy and macronutrient intake of children. The objective of this research was to study the energy and macronutrient intake as well as food frequency pattern of Bahraini school children. Methods This is a cross-sectional descriptive study conducted on Bahraini school boys and girls aged 6-18 years from all the 11 populated regions of the country. Data on food intake consisted of a 24-hour dietary recall and was obtained by interviewing a sub-sample of the study population. Information was also obtained through a self-administered questionnaire for the entire sample on the weekly frequency of food items that were grouped into 7 categories based on similarity of nutrient profiles. Dietary analysis was performed using the Nutritionist 5 (First Data Bank Version 1.6 1998). Results While the average energy intake of students was close to the Estimated Average Requirements of the UK Reference standards, protein intake substantially exceeded the Reference Nutrient Intake values as did daily sugar consumption. Dietary fiber fell short of the Dietary Recommended Values (UK) and 36%-50% students exceeded the Energy % limits for total fat, saturated fat and cholesterol. The Polyunsaturated: Saturated fat ratio remained at an unacceptable level of 0.6 for girls and boys. While sweets, snacks and regular soda drinks were popular, milk, fruits and vegetables were not commonly consumed. Conclusions High sugar consumption, low intake of dietary fiber and high energy % of saturated fat and dietary cholesterol by many Bahraini children, is likely to increase their risk of obesity and cardiovascular diseases in later life. Nutrition education programs in schools should emphasize the importance of healthy balanced diets for growth and health maintenance of children as well as dietary prevention of diseases.</p

Ethnic Differences in Body Composition and Obesity Related Risk Factors: Study in Chinese and White Males Living in China

The purpose of this cross-sectional observational study was to identify ethnic differences in body composition and obesity-related risk factors between Chinese and white males living in China. 115 Chinese and 114 white male pilots aged 28–63 years were recruited. Fasting body weight, height and blood pressure were measured following standard procedures. Whole-body and segmental body composition were measured using an 8-contact electrode bioimpedance analysis (BIA) system. Fasting serum glucose, fasting plasma total cholesterol (TC), high-density lipoprotein (HDL) cholesterol, and triglycerides (TG) were assessed using automatic biochemistry analyzer. After adjusting for age and body mass index (BMI), Chinese males had significantly higher percentage of body fat (PBF) both with respect to whole body (Chinese: 23.7%±0.2% vs. Whites: 22.4%±0.2%) and the trunk area (Chinese: 25.0%±0.3% vs. Whites: 23.2%±0.3%) compared to their white counterparts. At all BMIs, Chinese males had significantly higher fasting glucose levels (Chinese: 5.7±1.0 mmol/L vs. Whites: 5.2±1.0 mmol/L) but lower high-density lipoprotein levels (Chinese: 0.8±1.0 mmol/L vs. Whites: 1.0±1.0 mmol/L) than white males. In addition, a marginally significantly higher diastolic blood pressure was found among Chinese men than that among white men (Chinese: 80±1.0 mmHg vs. Whites: 77±1.0 mmHg). Chinese males had more body fat and a greater degree of central fat deposition pattern than that seen in white males in the present study. Furthermore, data on blood pressure, fasting glucose and blood lipids suggest that Chinese men may be more prone to obesity-related risk factors than white men

Differences in dietary pattern between obese and eutrophic children

<p>Abstract</p> <p>Background</p> <p>Excessive consumption of energy is a decisive factor of obesity, but a simple quantitative assessment of consumption between obese and eutrophic individuals not always explains the problem, raising questions about the importance of the qualitative aspects of food. Therefore, the purpose of this study was to evaluate the differences in nutrient composition and meal patterns between eutrophic and obese schoolchildren.</p> <p>Methods</p> <p>The diet of 83 children (42 obese and 41 eutrophic), aged between 7 and 11 years of age, was assessed by two non-consecutive dietary recalls. After the software analysis of macro and micronutrients composition, the different types and amount of legumes, fruits and vegetables were analyzed to verify the dietary patterns.</p> <p>Results</p> <p>No differences were verified in energy consumption between the groups (eutrophic = 1934.2 ± 672.7 kcal, obese = 1835.8 ± 621.2 kcal). In general, children showed consumption within the recommended ranges of carbohydrates, lipids and proteins. The average consumption of fiber was higher in the eutrophic group (20.7 g) when compared to the obese group (14.8 g). The dietary fiber was strongly correlated with the number of servings of beans (r = 0.77), when compared to fruits (r = 0.44) and leafy vegetables (r = 0.13). It was also observed that the higher the consumption of fiber and beans, the lower the proportion of dietary fat (r = -0.22) in the diet. Generally, there was a low consumption of fiber (20.7 g = eutrophic group/14.8 g = obese group), beans (1.1 portions in the eutrophic and obese groups), fruits (0.7 portions eutrophic group and 0.6 obese group) and vegetables (1.3 eutrophic group and 1.1 obese group).</p> <p>Conclusions</p> <p>It is concluded that the obesity was more related to a dietary pattern of low intake of dietary fiber than excessive energy consumption and macronutrients imbalance.</p

Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection

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Expression Profiling Reveals Novel Hypoxic Biomarkers in Peripheral Blood of Adult Mice Exposed to Chronic Hypoxia

Hypoxia induces a myriad of changes including an increase in hematocrit due to erythropoietin (EPO) mediated erythropoiesis. While hypoxia is of importance physiologically and clinically, lacunae exist in our knowledge of the systemic and temporal changes in gene expression occurring in blood during the exposure and recovery from hypoxia. To identify these changes expression profiling was conducted on blood obtained from cohorts of C57Bl-10 wild type mice that were maintained at normoxia (NX), exposed for two weeks to normobaric chronic hypoxia (CH) or two weeks of CH followed by two weeks of normoxic recovery (REC). Using stringent bioinformatic cut-offs (0% FDR, 2 fold change cut-off), 230 genes were identified and separated into four distinct temporal categories. Class I) contained 1 transcript up-regulated in both CH and REC; Class II) contained 202 transcripts up-regulated in CH but down-regulated after REC; Class III) contained 9 transcripts down-regulated both in CH and REC; Class IV) contained 18 transcripts down-regulated after CH exposure but up-regulated after REC. Profiling was independently validated and extended by analyzing expression levels of selected genes as novel biomarkers from our profile (e.g. spectrin alpha-1, ubiquitin domain family-1 and pyrroline-5-carboxylate reductase-1) by performing qPCR at 7 different time points during CH and REC. Our identification and characterization of these genes define transcriptome level changes occurring during chronic hypoxia and normoxic recovery as well as novel blood biomarkers that may be useful in monitoring a variety of physiological and pathological conditions associated with hypoxia

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe