Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Perioperative nutrition is still a surgical orphan: results of a Swiss-Austrian survey.

Background/Objectives:There is strong evidence for the beneficial effects of perioperative nutrition in patients undergoing major surgery. We aimed to evaluate implementation of current guidelines in Switzerland and Austria.Subjects/Methods:A survey was conducted in 173 Swiss and Austrian surgical departments. We inquired about nutritional screening, perioperative nutrition and estimated clinical significance.Results:The overall response rate was 55%, having 69% (54/78) responders in Switzerland and 44% (42/95) in Austria. Most centres were aware of reduced complications (80%) and shorter hospital stay (59%). However, only 20% of them implemented routine nutritional screening. Non-compliance was because of financial (49%) and logistic restrictions (33%). Screening was mainly performed in the outpatient's clinic (52%) or during admission (54%). The nutritional risk score was applied by 14% only; instead, various clinical (78%) and laboratory parameters (56%) were used. Indication for perioperative nutrition was based on preoperative screening in 49%. Although 23% used preoperative nutrition, 68% applied nutritional support pre- and postoperatively. Preoperative nutritional treatment ranged from 3 days (33%), to 5 (31%) and even 7 days (20%).Conclusions:Although malnutrition is a well-recognised risk factor for poor post-operative outcome, surgeons remain reluctant to implement routine screening and nutritional support according to evidence-based guidelines.

Nutrition dans la bronchopneumopathie chronique obstructive [Nutrition in chronic obstructive bronchopneumopathy]

The respiratory system and nutrition are linked. Obesity is sometimes seen in chronic obstructive pulmonary disease (COPD), but its prevalence, the morbidity and mortality induced by it are not known. In addition, the prevalence of malnutrition is high in COPD and the more severe the COPD is, the higher percentage of malnutrition is present. Emphysematous patients are more frequently undernourished than those suffering from chronic bronchitis. Malnutrition is the consequence of the hypermetabolism induced by the higher cost of breathing in emphysema. The survival rate of these patients is negatively affected by malnutrition. A careful assessment of nutritional status must be performed in all COPD patients, especially during an episode of acute respiratory failure. When signs of malnutrition are present, a nutritional intervention should be initiated rapidly. An amount of calories sufficient to meet the energy expenditure increased by the disease must be given. Excessive intake may overstress the respiratory system whose functional reserve is limited in COPD. The diet must include a well balanced percentage of fat, carbohydrates and proteins. Preservation of the fat-free mass is the minimum goal to reach in acute respiratory failure. After the resolution of the acute phase, a gain of weight should be attempted within a rehabilitation program.

Un protocole de nutrition suffit-il à garantir des pratiques "evidence based" (EBM) - réalité clinique et propositions : P5

Le support nutritionnel en soins intensifs est désormais basé sur des études de niveau A et B. La participation du SMIA au «Nutrition Day 2008» avait mis en évidence des déviations par rapport aux recommandations. Cette étude a pour objectif de réaliser une analyse approfondie sur un mois. Méthodes: Analyse des patients sortis ayant séjourné plus de 3 jours en mars 2008 dans un service de 32 lits bénéficiant d'une diététicienne à 60% et du Protocole NUTSIA depuis 2006. Extraction de la database: variables démographiques, nutrition risk score (NRS), jours de démarrage et voie de nutrition, bilan calorique cumulé. Résultats: 69 patients âgés de 60 ± 17 ans ont séjourné 9 ± 10 jours. Le NRS est réalisé tardivement dans 29% des cas. A 48h, le support nutritionnel est défini chez 67% des patients avec 43% de nutrition artificielle, une prédominance de NE (73%) sur PN (27%). Seuls 3 patients ont un bilan cumulé < -10000 kcal. La couverture des séjours par la diététicienne est de 50%. Conclusion: Comparé à l'EBM, les pratiques nutritionnelles sont globalement satisfaisantes, mais l'évaluation systématique est insuffisante. L'introduction de la NE est tardive et sa progression trop lente comparé au protocole. Les remèdes proposés sont une administration de NE par défaut, une augmentation de la présence de la diététicienne et son «empowerment» sur la prescription.

The effects of nutrition, puberty and dancing on bone density in adolescent ballet dancers.

Ballet dancers have on average a low bone mineral content (BMC), with elevated fracture-risk, low body mass index (BMI) for age (body mass index, kg/m2), low energy intake, and delayed puberty. This study aims at a better understanding of the interactions of these factors, especially with regard to nutrition. During a competition for pre-professional dancers we examined 127 female participants (60 Asians, 67 Caucasians). They averaged 16.7 years of age, started dancing at 5.8 years, and danced 22 hours/week. Assessments were made for BMI, BMC (DXA), and bone mineral apparent density (BMAD) at the lumbar spine and femoral neck, pubertal stage (Tanner score), and nutritional status (EAT-40 questionnaire and a qualitative three-day dietary record). BMI for age was found to be normal in only 42.5% of the dancers, while 15.7% had a more or less severe degree of thinness (12.6% Grade2 and 3.1% Grade 3 thinness). Menarche was late (13.9 years, range 11 to 16.8 years). Food intake, evaluated by number of consumed food portions, was below the recommendations for a normally active population in all food groups except animal proteins, where the intake was more than twice the recommended amount. In this population, with low BMI and intense exercise, BMC was low and associated with nutritional factors; dairy products had a positive and non-dairy proteins a negative influence. A positive correlation between BMAD and years since menarche confirmed the importance of exposure to estrogens and the negative impact of delayed puberty. Because of this and the probable negative influence of a high intake of non-dairy proteins, such as meat, fish, and eggs, and the positive association with a high dairy intake, ballet schools should promote balanced diets and normal weight and should recognize and help dancers avoid eating disorders and delayed puberty caused by extensive dancing and inadequate nutrition.

The Ultrastructure of the Gastrodermis and the Nutrition of the Gill Parasitic Atriaster heterodus Lebedev and Paruchin, 1969 (Platyhelminthes: Monogenea)

The gastrodermis of Atriaster heterodus Lebedev & Paruchin, 1969 (Polyopisthocotylea), a gill parasite from Diplodus argenteus (Valenciennes, 1830), is composed of "U"-shape hematin cells and a connecting syncytium, both having cytoplasmic lamellae. These cells show outgrowths and bent folds which were seen to enclose lumen material. The trapped material was then subjected to endocytosis. The nature of ingested food material was comparatively analyzed by cytochemical and histochemical tests. Blood residues were detected in the gut but tests for mucins were negative. No intact erythrocytes were observed in the gut lumen.

Enteral nutrition in critically ill patients with severe hemodynamic failure after cardiopulmonary bypass.

BACKGROUND & AIMS: The study was designed to investigate and quantify nutritional support, and particularly enteral nutrition (EN), in critically ill patients with severe hemodynamic failure. METHODS: Prospective, descriptive study in a surgical intensive care unit (ICU) in a university teaching hospital: patients aged 67+/-13 yrs (mean+/-SD) admitted after cardiac surgery with extracorporeal circulation, staying 5 days in the ICU with acute cardiovascular failure. Severity of disease was assessed with SAPS II, and SOFA scores. Variables were energy delivery and balance, nutrition route, vasopressor doses, and infectious complications. Artificial feeding delivered according to ICU protocol. EN was considered from day 2-3. Energy target was set 25 kcal/kg/day to be reached stepwise over 5 days. RESULTS: Seventy out of 1114 consecutive patients were studied, aged 67+/-17 years, and staying 10+/-7 days in the ICU. Median SAPS II was 43. Nine patients died (13%). All patients had circulatory failure: 18 patients required intra-aortic balloon-pump support (IABP). Norepinephrine was required in 58 patients (83%). Forty patients required artificial nutrition. Energy delivery was very variable. There was no abdominal complication related to EN. As a mean, 1360+/-620 kcal/kg/day could be delivered enterally during the first 2 weeks, corresponding to 70+/-35% of energy target. Enteral nutrient delivery was negatively influenced by increasing dopamine and norepinephrine doses, but not by the use of IABP. CONCLUSION: EN is possible in the majority of patients with severe hemodynamic failure, but usually results in hypocaloric feeding. EN should be considered in patients with careful abdominal and energy monitoring.

Promoting Good Nutrition

Guidance and resources to support the use of 'MUST' across all care settings

Promoting Good Nutrition (PDF 2MB)

Guidance and resources to support the use of 'MUST' across all care settings

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of vif-defective HIV-1 infection and Alu retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and Alu transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function.

Mouse interleukin-2 receptor alpha gene expression. Delimitation of cis-acting regulatory elements in transgenic mice and by mapping of DNase-I hypersensitive sites.

The alpha chain of the interleukin-2 receptor (IL-2R alpha) is a key regulator of lymphocyte proliferation. To analyze the mechanisms controlling its expression in normal cells, we used the 5'-flanking region (base pairs -2539/+93) of the mouse gene to drive chloramphenicol acetyltransferase expression in four transgenic mouse lines. Constitutive transgene activity was restricted to lymphoid organs. In mature T lymphocytes, transgene and endogenous IL-2R alpha gene expression was stimulated by concanavalin A and up-regulated by IL-2 with very similar kinetics. In thymic T cell precursors, IL-1 and IL-2 cooperatively induced transgene and IL-2R alpha gene expression. These results show that regulation of the endogenous IL-2R alpha gene occurs mainly at the transcriptional level. They demonstrate that cis-acting elements in the 5'-flanking region present in the transgene confer correct tissue specificity and inducible expression in mature T cells and their precursors in response to antigen, IL-1, and IL-2. In a complementary approach, we screened the 5' end of the endogenous IL-2R alpha gene for DNase-I hypersensitive sites. We found three lymphocyte specific DNase-I hypersensitive sites. Two, at -0.05 and -5.3 kilobase pairs, are present in resting T cells. A third site appears at -1.35 kilobase pairs in activated T cells. It co-localizes with IL-2-responsive elements identified by transient transfection experiments.

Aspects of gastrointestinal immunology and nutrition in human immunodeficiency virus-1 infection in Brazil

Mucosal surfaces have a fundamental participation in many aspects of the human immunodeficiency virus (HIV) infection pathogenesis. In Brazilian HIV-1 infected subjects, loss of weight and appetite are among the most debilitating symptoms. In this review we describe a defined mucosal immunogen that has profound but transient effects on HIV viral load, and we suggest that gut associated lymphoid tissue under constant immunostimulation is likely to provide a major contribution to the total levels of HIV. We also show that hypermetabolism appears to play a role in the wasting process in Brazilian patients coinfected with HIV and tuberculosis.