Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

Abstract Background RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. Results A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. Conclusion We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.

Nutritional strategies of physically active subjects with muscle dysmorphia

Abstract Background The aim of this study was to identify dietary strategies for physically active individuals with muscle dysmorphia based on a systematic literature review. Method References were included if the study population consisted of adults over 18 years old who were physically active in fitness centers. We identified reports through an electronic search ofScielo, Lilacs and Medline using the following keywords: muscle dysmorphia, vigorexia, distorted body image, and exercise. We found eight articles in Scielo, 17 in Medline and 12 in Lilacs. Among the total number of 37 articles, only 17 were eligible for inclusion in this review. Results The results indicated that the feeding strategies used by physically active individuals with muscle dysmorphia did not include planning or the supervision of a nutritionist. Diet included high protein and low fat foods and the ingestion of dietary and ergogenic supplements to reduce weight. Conclusion Physically active subjects with muscle dysmorphia could benefit from the help of nutritional professionals to evaluate energy estimation, guide the diet and its distribution in macronutrient and consider the principle of nutrition to functional recovery of the digestive process, promote liver detoxification, balance and guide to organic adequate intake of supplemental nutrients and other substances.

Effect of incorporation of amaranth on the physical properties and nutritional value of cheese bread

At the present celiac disease has no known cure, and its only treatment is a strict lifelong adherence to a gluten-free diet. Cheese bread is a traditional Brazilian product and a safe option for celiacs. However, like other gluten-free breads, it has inherent low levels of fibers and minerals. The objective of this study was to evaluate the effect of incorporation of whole amaranth flour on the physical properties and nutritional value of cheese bread. Amaranth flour was incorporated at 10, 15, and 20% proportions in different formulations. The increasing amaranth levels darkened the product, reduced specific volume, and increased compression force. Ten percent amaranth-content cheese breads exhibited slight differences in physical properties compared with the controls. These results demonstrated the possibility of incorporating 10% of whole amaranth flour in the formulation of cheese bread resulting in a product with higher dietary fiber and iron contents and the same level of acceptance as that of the conventional formulation. The aim of this approach is to increase the availability of gluten-free bakery products with added nutritional value contributing to increase the variety of the diet of celiac patients.

Papillary atrophy of the tongue and nutritional status of hospitalized alcoholics

BACKGROUND: Atrophy of the papillae, mucosa, and dorsum of the tongue are considered classical signs of nutritional deficiencies. OBJECTIVE: To assess the nutritional status of hospitalized alcoholics with or without papillary atrophy of the tongue. METHODS: This study was performed with 21 hospitalized alcoholics divided into Atrophic Glossitis Group (n=13) and Normal Tongue Group (n=8). Healthy, non-alcoholic volunteers composed the Control Group (n=8). Anthropometry and bioelectric impedance were performed, and serum vitamins A, E, and B12 were determined. RESULTS: There were no statistical differences in relation to age (46.7±8.7 vs. 46.8±15.8 years) or gender (92.3% vs. 87.5% male), respectively. Control Group volunteers were also paired in relation to age (47.5±3.1 years) and male predominance (62.5%). In relation to hospitalized alcoholics without atrophic lesions of the tongue and Control Group, patients with papillary atrophy showed lower BMI (18.6 ± 2,5 vs 23.8 ± 3.5 vs 26.7 ± 3,6 kg/m² ) and body fat content 7.6 ± 3.5 vs 13.3 ± 6.5 vs 19.5 ± 4,9 kg). When compared with the Control Group, alcoholic patients with or without papillary atrophy of the tongue showed lower values of red blood cells (10.8 ± 2.2 vs 11.8 ± 2.2 vs 14.5 ± 1,6g/dL) and albumin (3.6 ± 0.9 vs 3.6 ± 0.8 vs 4.4 ± 0.2g/dL). The seric levels of vitamins A, E, and B12 were similar amongst the groups. CONCLUSION: Hospitalized alcoholics with papillary atrophy of the tongue had lower BMI and fat body stores than controls, without associated hypovitaminosis.

Nutritional composition of rice bran submitted to different stabilization procedures

In order to inactivate enzymatic deterioration, whole rice bran samples were subjected to two stabilization methods. Changes in nutritional value in terms of, concerning chemical composition, minerals and fatty acid content, were evaluated to supplement existing data and promote the utilization of rice bran in the human diet. The following homemade heat treatments were applied: roasting on a conventional stove or heating in a microwave oven. Based on the results, the different heating methods affected sample composition, since the levels of some nutrients of treated samples showed significant changes (p<0.05) compared to corresponding raw samples. The rice bran treated on a conventional stove produced products with lower moisture (5.14±0.10 g/100 g) and nutrients such as sodium 11.8%; palmitic acid 9.9% and stearic acid 8.1%. The microwave oven procedure resulted in better nutrient preservation, with slightly higher moisture content (6.28±0.10 g/100 g), and appears to be a practical and rapid tool for home heat stabilization of rice bran.

Use of different commercial Artemia sp. Enrichements in Octopus Vulgaris, paralarval rearing at initial planctonic phase: effects on growth, survival and fatty acid composition of the paralarvae

[EN] Octopus "paralarvae", are planktonic, swim actively and have high metabolic rates, requiring large quantities of live prey of adequate motility and nutritional quality ( Iglesias et al., 2000; Navarro and Villanueva, 2000, 2003). During the planktonic phase, they undergo strong morphological changes, after which the octopuses start settling to the bottom. The potential of Octopus vulgaris as candiadate for diversification of marine aquacultures are mainly due to its high food conversion rate and fast growth.( Iglesias et al 2006). Despite the research effort taken until now, paralarval rearing of O. vulgaris still suffers high mortalities which limited the industrial culture of this species. The main problems in the paralarval rearing stages are the high mortality rates and poor growth. These are attributed to the lack of standardized culture techniques and nutritional deficiencies in the diet of paralarvae, especially in n-3 highly unsaturated fatty acids (n-3 HUFA). The objective if this experience was to test different commercial live prey enrichment to improve nutritional quality of the artemia.

Effect of different rotifers enrichment formula feed on growth and survival of sea bream larvae ("Sparus aurata")

Universidad de Las Palmas de Gran Canaria. Facultad de Ciencias del Mar. Final assignment for the Marine Science Degree ; 2013-2014

Nutritional strategies to control mycotoxin damages in swine

Mycotoxins are contaminants of agricultural products both in the field and during storage and can enter the food chain through contaminated cereals and foods (milk, meat, and eggs) obtained from animals fed mycotoxin contaminated feeds. Mycotoxins are genotoxic carcinogens that cause health and economic problems. Ochratoxin A and fumonisin B1 have been classified by the International Agency for Research on Cancer in 1993, as “possibly carcinogenic to humans” (class 2B). To control mycotoxins induced damages, different strategies have been developed to reduce the growth of mycotoxigenic fungi as well as to decontaminate and/or detoxify mycotoxin contaminated foods and animal feeds. Critical points, target for these strategies, are: prevention of mycotoxin contamination, detoxification of mycotoxins already present in food and feed, inhibition of mycotoxin absorption in the gastrointestinal tract, reduce mycotoxin induced damages when absorption occurs. Decontamination processes, as indicate by FAO, needs the following requisites to reduce toxic and economic impact of mycotoxins: it must destroy, inactivate, or remove mycotoxins; it must not produce or leave toxic and/or carcinogenic/mutagenic residues in the final products or in food products obtained from animals fed decontaminated feed; it must be capable of destroying fungal spores and mycelium in order to avoiding mycotoxin formation under favorable conditions; it should not adversely affect desirable physical and sensory properties of the feedstuff; it has to be technically and economically feasible. One important approach to the prevention of mycotoxicosis in livestock is the addition in the diets of the non-nutritionally adsorbents that bind mycotoxins preventing the absorption in the gastrointestinal tract. Activated carbons, hydrated sodium calcium aluminosilicate (HSCAS), zeolites, bentonites, and certain clays, are the most studied adsorbent and they possess a high affinity for mycotoxins. In recent years, there has been increasing interest on the hypothesis that the absorption in consumed food can be inhibited by microorganisms in the gastrointestinal tract. Numerous investigators showed that some dairy strains of LAB and bifidobacteria were able to bind aflatoxins effectively. There is a strong need for prevention of the mycotoxin-induced damages once the toxin is ingested. Nutritional approaches, such as supplementation of nutrients, food components, or additives with protective effects against mycotoxin toxicity are assuming increasing interest. Since mycotoxins have been known to produce damages by increasing oxidative stress, the protective properties of antioxidant substances have been extensively investigated. Purpose of the present study was to investigate in vitro and in vivo, strategies to counteract mycotoxin threat particularly in swine husbandry. The Ussing chambers technique was applied in the present study that for the first time to investigate in vitro the permeability of OTA and FB1 through rat intestinal mucosa. Results showed that OTA and FB1 were not absorbed from rat small intestine mucosa. Since in vivo absorption of both mycotoxins normally occurs, it is evident that in these experimental conditions Ussing diffusion chambers were not able to assess the intestinal permeability of OTA and FB1. A large number of LAB strains isolated from feces and different gastrointestinal tract regions of pigs and poultry were screened for their ability to remove OTA, FB1, and DON from bacterial medium. Results of this in vitro study showed low efficacy of isolated LAB strains to reduce OTA, FB1, and DON from bacterial medium. An in vivo trial in rats was performed to evaluate the effects of in-feed supplementation of a LAB strain, Pediococcus pentosaceus FBB61, to counteract the toxic effects induced by exposure to OTA contaminated diets. The study allows to conclude that feed supplementation with P. pentosaceus FBB61 ameliorates the oxidative status in liver, and lowers OTA induced oxidative damage in liver and kidney if diet was contaminated by OTA. This P. pentosaceus FBB61 feature joined to its bactericidal activity against Gram positive bacteria and its ability to modulate gut microflora balance in pigs, encourage additional in vivo experiments in order to better understand the potential role of P. pentosaceus FBB61 as probiotic for farm animals and humans. In the present study, in vivo trial on weaned piglets fed FB1 allow to conclude that feeding of 7.32 ppm of FB1 for 6 weeks did not impair growth performance. Deoxynivalenol contamination of feeds was evaluated in an in vivo trial on weaned piglets. The comparison between growth parameters of piglets fed DON contaminated diet and contaminated diet supplemented with the commercial product did not reach the significance level but piglet growth performances were numerically improved when the commercial product was added to DON contaminated diet. Further studies are needed to improve knowledge on mycotoxins intestinal absorption, mechanism for their detoxification in feeds and foods, and nutritional strategies to reduce mycotoxins induced damages in animals and humans. The multifactorial approach acting on each of the various steps could be a promising strategy to counteract mycotoxins damages.

Molecular characterization of the human gut microbiota: the effect of aging

Age-related physiological changes in the gastrointestinal tract, as well as modification in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota. The study presented here is focused on the application and comparison of two different microarray approaches for the characterization of the human gut microbiota, the HITChip and the HTF-Microb.Array, with particular attention to the effects of the aging process on the composition of this ecosystem. By using the Human Intestinal Tract Chip (HITChip), recently developed at the Wageningen University, The Netherland, we explored the age-related changes of gut microbiota during the whole adult lifespan, from young adults, through elderly to centenarians. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment of facultative anaerobes. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammation status, also known as inflamm-aging, as determined by a range of peripheral blood inflammatory markers. In parallel, we overtook the development of our own phylogenetic microarray with a lower number of targets, aiming the description of the human gut microbiota structure at high taxonomic level. The resulting chip was called High Taxonomic level Fingerprinting Microbiota Array (HTF-Microb.Array), and was based on the Ligase Detection Reaction (LDR) technology, which allowed us to develop a fast and sensitive tool for the fingerprint of the human gut microbiota in terms of presence/absence of the principal groups. The validation on artificial DNA mixes, as well as the pilot study involving eight healthy young adults, demonstrated that the HTF-Microb.Array can be used to successfully characterize the human gut microbiota, allowing us to obtain results which are in approximate accordance with the most recent characterizations. Conversely, the evaluation of the relative abundance of the target groups on the bases of the relative fluorescence intensity probes response still has some hindrances, as demonstrated by comparing the HTF.Microb.Array and HITChip high taxonomic level fingerprints of the same centenarians.

Modelling the effects of nitrogen deposition and carbon dioxide enrichment on forest carbon balance

Atmospheric CO2 concentration ([CO2]) has increased over the last 250 years, mainly due to human activities. Of total anthropogenic emissions, almost 31% has been sequestered by the terrestrial biosphere. A considerable contribution to this sink comes from temperate and boreal forest ecosystems of the northern hemisphere, which contain a large amount of carbon (C) stored as biomass and soil organic matter. Several potential drivers for this forest C sequestration have been proposed, including increasing atmospheric [CO2], temperature, nitrogen (N) deposition and changes in management practices. However, it is not known which of these drivers are most important. The overall aim of this thesis project was to develop a simple ecosystem model which explicitly incorporates our best understanding of the mechanisms by which these drivers affect forest C storage, and to use this model to investigate the sensitivity of the forest ecosystem to these drivers. I firstly developed a version of the Generic Decomposition and Yield (G’DAY) model to explicitly investigate the mechanisms leading to forest C sequestration following N deposition. Specifically, I modified the G’DAY model to include advances in understanding of C allocation, canopy N uptake, and leaf trait relationships. I also incorporated a simple forest management practice subroutine. Secondly, I investigated the effect of CO2 fertilization on forest productivity with relation to the soil N availability feedback. I modified the model to allow it to simulate short-term responses of deciduous forests to environmental drivers, and applied it to data from a large-scale forest Free-Air CO2 Enrichment (FACE) experiment. Finally, I used the model to investigate the combined effects of recent observed changes in atmospheric [CO2], N deposition, and climate on a European forest stand. The model developed in my thesis project was an effective tool for analysis of effects of environmental drivers on forest ecosystem C storage. Key results from model simulations include: (i) N availability has a major role in forest ecosystem C sequestration; (ii) atmospheric N deposition is an important driver of N availability on short and long time-scales; (iii) rising temperature increases C storage by enhancing soil N availability and (iv) increasing [CO2] significantly affects forest growth and C storage only when N availability is not limiting.