The relationship between complaints of night-time heartburn and sleep-related gastroesophageal reflux.

This study investigated whether the complaint of night-time heartburn (NHB) as opposed to daytime heartburn (DHB) is a reliable reflection of actual sleep-related reflux events. Three groups of individuals were studied: individuals with complaints of NHB at least twice per week (n = 24), individuals with complaints of DHB (n = 23), and normal participants without any complaints of regular heartburn during the day or night (n = 25). All three groups were studied on one occasion with combined pH monitoring and polysomnography, and subjective questionnaires about sleep disturbance and sleep quality were given to all participants. The NHB group had significantly more sleep-related reflux events compared with both DHB and control groups (P < 0.01). DHB subjects had significantly (P < 0.05) more sleep-related reflux events than normal controls. Total acid contact time (ACT) was significantly (P < 0.05) elevated in the NHB group compared with both the DHB and control group. Sleep-related ACT was also significantly (P < 0.05) elevated in the NHB group compared with the other two groups, while upright (daytime) ACT was not significantly different. The NHB group was significantly (P < 0.05) worse regarding measures of both objective and subjective sleep quality. Subjects with exclusively DHB do have sleep-related reflux that is greater than normal controls. Subjects with NHB have significantly more sleep-related reflux, and both objective and subjective sleep abnormalities compared with normal controls. Complaints of NHB reflect sleep-related reflux events and may be indicative of a more clinically significant condition.

Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes.

BACKGROUND AND AIMS: Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. METHODS: To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. KEY RESULTS: The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. CONCLUSIONS: Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution.

Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with >5-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

Gene expression profiles associated with anaemia and ITPA genotypes in patients with chronic hepatitis C (CH-C).

Anaemia is a common side effect of ribavirin (RBV) which is used for the treatment of hepatitis C. Inosine triphosphatase gene polymorphism (C to A) protects against RBV-induced anaemia. The aim of our study was to genotype patients for inosine triphosphatase gene polymorphism rs1127354 SNP (CC or CA) and associate treatment-induced anaemia with gene expression profile and genotypes. We used 67 hepatitis C patients with available gene expression, clinical, laboratory data and whole-blood samples. Whole blood was used to determine inosine triphosphatase gene polymorphism rs1127354 genotypes (CC or CA). The cohort with inosine triphosphatase gene polymorphism CA genotype revealed a distinct pattern of protection against anaemia and a lower drop in haemoglobin. A variation in the propensity of CC carriers to develop anaemia prompted us to look for additional predictors of anaemia during pegylated interferon (PEG-IFN) and RBV. Pretreatment blood samples of patients receiving a full course of PEG-IFN and RBV were used to assess expression of 153 genes previously implicated in host response to viral infections. The gene expression data were analysed according to presence of anaemia and inosine triphosphatase gene polymorphism genotypes. Thirty-six genes were associated with treatment-related anaemia, six of which are involved in the response to hypoxia pathway (HIF1A, AIF1, RHOC, PTEN, LCK and PDGFB). There was a substantial overlap between sustained virological response (SVR)-predicting and anaemia-related genes; however, of the nine JAK-STAT pathway-related genes associated with SVR, none were implicated in anaemia. These observations exclude the direct involvement of antiviral response in the development of anaemia associated with PEG-IFN and RBV treatment, whereas another, distinct component within the SVR-associated gene expression response may predict anaemia. We have identified baseline gene expression signatures associated with RBV-induced anaemia and identified its functional pathways. In particular, we identified the hypoxia response pathway and the apoptosis/survival-related gene network, as differentially expressed in chronic hepatitis C patients with anaemia.

Differential expression of miRNAs in the visceral adipose tissue of patients with non-alcoholic fatty liver disease.

BACKGROUND: Progression of non-alcoholic fatty liver disease (NAFLD) can be facilitated by soluble molecules secreted by visceral adipose tissue (VAT). MicroRNAs (miRNAs) are likely to regulate some of these molecular pathways involved in pathogenesis of NAFLD. AIM: To profile miRNA expression in the visceral adipose tissue of patients with NAFLD. METHODS: Visceral adipose tissue samples were collected from NAFLD patients and frozen. Patients with biopsy-proven NAFLD were divided into non-alcoholic steatohepatitis (NASH) (n = 12) and non-NASH (n = 12) cohorts controlled for clinical and demographic characteristics. Extracted total RNA was profiled using TaqMan Human MicroRNA arrays. Univariate Mann-Whitney comparisons and multivariate regression analysis were performed to compare miRNA profiles. RESULTS: A total of 113 miRNA differentially expressed between NASH patients and non-NASH patients (P < 0.05). Of these, seven remained significant after multiple test correction (hsa-miR-132, hsa-miR-150, hsa-miR-433, hsa-miR-28-3p, hsa-miR-511, hsa-miR-517a, hsa-miR-671). Predicted target genes for these miRNAs include insulin receptor pathway components (IGF1, IGFR13), cytokines (CCL3, IL6), ghrelin/obestatin gene, and inflammation-related genes (NFKB1, RELB, FAS). In addition, two miRNA species, hsa-miR-197 and hsa-miR-99, were significantly associated with pericellular fibrosis in NASH patients (P < 0.05). Levels of IL-6 in the serum negatively correlated with the expression levels of all seven miRNAs capable of down regulating IL-6 encoding gene. CONCLUSIONS: miRNA expression from VAT may contribute to the pathogenesis of NAFLD - a finding which may distinguish relatively simple steatosis from NASH. This could help identify potential targets for pharmacological treatment regimens and candidate biomarkers for NASH.

Stable Hydrogen Isotope Fractionations during Autotrophic and Mixotrophic Growth of Microalgae.

Isotope effects, studied with precision isotope ratio mass spectrometry, have been used to locate critical steps in the H metabolism of plants. By manipulating the growth conditions of versatile microalgae, the discrimination of H isotopes between water in the growth medium and the organically bonded H in carbohydrates from these microalgae was -100 to -120 per thousand and was regulated by both the light and the dark reactions of photosynthesis. Photosynthetic electron transport discriminated against the heavy isotope of H and formed a pool of reductant available for biosynthesis that was enriched in the light isotope. Growth in red or white light activated phosphoglyceric acid reduction and H isotope discrimination, when H was fixed into organic matter. An additional fractionation of -30 to -60 per thousand occurred during the biosynthesis of proteins and lipids and was associated with glycolysis. This fractionation paralleled the isotope effect seen in carbohydrate metabolism, indicating that H metabolism in photosynthesis was coupled with that in dark biosynthetic reactions via the pool of reductant, probably NADPH.

Tracing food webs with stable hydrogen isotopes.

The hydrogen isotopic content of an animal's food, not water, determines that animal's hydrogen isotopic content. Liver and muscle tissue from mice reared on a diet such that the ratio of deuterium to hydrogen (DIH) of their food and water was kept constant, have the same average D/H ratio as the food source. In a simple, natural population of snails and their possible algal diets, Littorina obtusata (northern Atlantic intertidal snails that feed almost exclusively on the brown alga Fucus vesiculosus) has the same D/H ratio as Fucus vesiculosis and not that of the other algae available to the snails.

Carbon isotope fractionation by ribulose-1,5-bisophosphate carboxylase from various organisms.

Carbon isotope fractionation by structurally and catalytically distinct ribulose-1,5-bisphosphate carboxylases from one eucaryotic and four procaryotic organisms has been measured under nitrogen. The average fractionation for 40 experiments was -34.1 per thousand with respect to the delta(13)C of the dissolved CO(2) used, although average fractionations for each enzyme varied slightly: spinach carboxylase, -36.5 per thousand; Hydrogenomonas eutropha, -38.7 per thousand; Agmenellum quadruplicatum, -32.2 per thousand; Rhodospirillum rubrum, -32.1 per thousand; Rhodopseudomonas sphaeroides peak I carboxylase, -31.4 per thousand; and R. sphaeroides peak II carboxylase, -28.3 per thousand. The carbon isotope fractionation value was largely independent of method of enzyme preparation, purity, or reaction temperature, but in the case of spinach ribulose-1,5-bisphosphate carboxylase fractionation, changing the metal cofactor used for enzyme activation had a distinct effect on the fractionation value. The fractionation value of -36.5 per thousand with Mg(2+) as activator shifted to -29.9 per thousand with Ni(2+) as activator and to -41.7 per thousand with Mn(2+) as activator. These dramatic metal effects on carbon isotope fractionation may be useful in examining the catalytic site of the enzyme.

Evidence for the occurrence of specific iron (III)-binding compounds in near-shore marine ecosystems.

Aqueous extracts of samples from representtive types of near-shore marine ecosystems were examined for growth-promoting activity for the siderochrome auxotroph, Arthrobacter JG-9. Blue-green algal mat and sea grass samples gave strongly positive responses. Relative to Desferal (Ciba Pharmaceutical Co., Summit, N.J.), concentrations up to 110 ng/g (wet weight) of sample were found. In contrast, extracts of anaerobic muds or macroalgae gave no detectable activity. The hydroxamate type of iron chelator may be important in providing a form of iron in sea water readily utilized by the microalgae and marine higher plants.