A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational Taxonomic Units (OTUs) and therefore leading to the overestimation of microbial diversity. Sequencing errors will also result in OTUs that are not accurate reconstructions of the original biological sequences. Herein we present the Poisson binomial filtering algorithm (PBF), which minimizes both problems by calculating the error-probability distribution of a sequence from its quality scores. In order to validate our method, we quality-filtered 37 publicly available datasets obtained by sequencing mock and environmental microbial communities with the Roche 454, Illumina MiSeq and IonTorrent PGM platforms, and compared our results to those obtained with previous approaches such as the ones included in mothur, QIIME and USEARCH. Our algorithm retained substantially more reads than its predecessors, while resulting in fewer and more accurate OTUs. This improved sensitiveness produced more faithful representations, both quantitatively and qualitatively, of the true microbial diversity present in the studied samples. Furthermore, the method introduced in this work is computationally inexpensive and can be readily applied in conjunction with any existent analysis pipeline.     

A Lower Olfactory Capacity Is Related to Higher Circulating Concentrations of Endocannabinoid 2-Arachidonoylglycerol and Higher Body Mass Index in Women

The endocannabinoid (eCB) system can promote food intake by increasing odor detection in mice. The eCB system is over-active in human obesity. Our aim is to measure circulating eCB concentrations and olfactory capacity in a human sample that includes people with obesity and explore the possible interaction between olfaction, obesity and the eCB system. The study sample was made up of 161 females with five groups of body mass index sub-categories ranging from under-weight to morbidly obese. We assessed olfactory capacity with the “Sniffin´Sticks” test, which measures olfactory threshold-discrimination-identification (TDI) capacity. We measured plasma concentrations of the eCBs 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamine or anandamide (AEA), and several eCB-related compounds, 2-acylglycerols and N-acylethanolamines. 2-AG and other 2-acylglycerols fasting plasma circulating plasma concentrations were higher in obese and morbidly obese subjects. AEA and other N-acylethanolamine circulating concentrations were lower in under-weight subjects. Olfactory TDI scores were lower in obese and morbidly obese subjects. Lower TDI scores were independently associated with higher 2-AG fasting plasma circulating concentrations, higher %body fat, and higher body mass index, after controlling for age, smoking, menstruation, and use of contraceptives. Our results show that obese subjects have a lower olfactory capacity than non-obese ones and that elevated fasting plasma circulating 2-AG concentrations in obesity are linked to a lower olfactory capacity. In agreement with previous studies we show that eCBs AEA and 2-AG, and their respective congeners have a distinct profile in relation to body mass index. The present report is the first study in humans in which olfactory capacity and circulating eCB concentrations have been measured in the same subjects.     

Neuronal XBP-1 Activates Intestinal Lysosomes to Improve Proteostasis in C. elegans

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Lysophosphatidic acid inhibits ghrelin secretion in the human gastric adenocarcinoma AGS cell line: role of mitogenic activated protein kinase signaling pathway

Ghrelin, the endogenous ligand for the growth hormone secretagogue receptor type 1a (GHS-R1a), is a 28 amino acid residue with a post-translational octanoyl modification on Ser3. Despite the biomedical interest in this hormone, the fine details of its regulation and the mechanisms controlling its secretion are largely unknown. The present study analyzes the molecular steps involved in the full lysophosphatidic acid (LPA) receptor-mediated activation of the mitogenic extracellular signal-regulated kinase (ERK) pathway and its consequent role as an inhibitor of ghrelin secretion in the gastric adenocarcinoma cell line AGS. ERK1/2 phosphorylation mediated by LPA proceeds via activation of the type 2 LPA receptor, activation of the nonreceptor tyrosine kinase c-Src, and subsequent transactivation of the epidermal growth factor receptor. Furthermore, LPA-induced ERK activation was found to be independent of matrix metalloproteinases; thus, c-Src acted as the scaffold-transactivating epidermal growth factor receptor. Finally, a correlation was observed between the mitogenic effects of LPA and ghrelin secretion in the human gastric adenocarcinoma cell line AGS. These data suggest a possible physiological role of LPA in ghrelin secretion. The relationship found between LPA and ghrelin secretion might explain the low circulating levels of ghrelin observed in obese patients, as a bona fide reflex of the energetic stores.     

Regulation of Resistin by Gonadal,Thyroid Hormone,and Nutritional Status

Objective: Resistin was recently identified as a hormone secreted by adipocytes that is under hormonal and nutritional control. This hormone has been suggested to be the link between obesity and type 2 diabetes. The aim of this study was to assess the influence of gender, gonadal status, thyroid hormones, pregnancy, and food restriction on resistin mRNA levels in adipose tissue of rats. Research Methods and Procedures: We have determined resistin mRNA expression by Northern blot analysis in all experimental sets. Results: Resistin mRNA expression is influenced by age, with the highest hormone levels existing at 45 days after birth and decreasing thereafter. Resistin mRNA expression is higher in men than in women. Moreover, we studied the effect of orchidectomy and ovariectomy in rats of different ages and showed that gonadal hormones increase adipose tissue resistin mRNA expression in male rats. Resistin is also regulated by thyroid hormones; it is severely decreased in hyperthyroid rats. Our results clearly show that chronic food restriction (30% of ad libitum food intake) led to a decrease in adipose tissue mRNA levels in normal cycling female rats and pregnant rats. In pregnancy, resistin mRNA levels were enhanced particularly at midgestation. Discussion: Our observations indicate that resistin is influenced by gender, gonadal status, thyroid hormones, and pregnancy. These findings suggest that resistin could explain the decreased insulin sensitivity during puberty and could be the link between sex steroids and insulin sensitivity. Moreover, resistin could mediate the effect of thyroid hormones on insulin resistance and the state of insulin resistance present during pregnancy.     

Women with endometriosis improved their peripheral antioxidant markers after the application of a high antioxidant diet

Background  

Oxidative stress has been identified in the peritoneal fluid and peripheral blood of women with endometriosis. However, there is little information on the antioxidant intake for this group of women. The objectives of this work were 1) to compare the antioxidant intake among women with and without endometriosis and 2) to design and apply a high antioxidant diet to evaluate its capacity to reduce oxidative stress markers and improve antioxidant markers in the peripheral blood of women with endometriosis.     

Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein Levels

Background

As the first pathway-specific enzyme in carotenoid biosynthesis, phytoene synthase (PSY) is a prime regulatory target. This includes a number of biotechnological approaches that have successfully increased the carotenoid content in agronomically relevant non-green plant tissues through tissue-specific PSY overexpression. We investigated the differential effects of constitutive AtPSY overexpression in green and non-green cells of transgenic Arabidopsis lines. This revealed striking similarities to the situation found in orange carrot roots with respect to carotenoid amounts and sequestration mechanism.

Methology/Principal Findings

In Arabidopsis seedlings, carotenoid content remained unaffected by increased AtPSY levels although the protein was almost quantitatively imported into plastids, as shown by western blot analyses. In contrast, non-photosynthetic calli and roots overexpressing AtPSY accumulated carotenoids 10 and 100-fold above the corresponding wild-type tissues and contained 1800 and 500 µg carotenoids per g dry weight, respectively. This increase coincided with a change of the pattern of accumulated carotenoids, as xanthophylls decreased relative to β-carotene and carotene intermediates accumulated. As shown by polarization microscopy, carotenoids were found deposited in crystals, similar to crystalline-type chromoplasts of non-green tissues present in several other taxa. In fact, orange-colored carrots showed a similar situation with increased PSY protein as well as carotenoid levels and accumulation patterns whereas wild white-rooted carrots were similar to Arabidopsis wild type roots in this respect. Initiation of carotenoid crystal formation by increased PSY protein amounts was further confirmed by overexpressing crtB, a bacterial PSY gene, in white carrots, resulting in increased carotenoid amounts deposited in crystals.

Conclusions

The sequestration of carotenoids into crystals can be driven by the functional overexpression of one biosynthetic enzyme in non-green plastids not requiring a chromoplast developmental program as this does not exist in Arabidopsis. Thus, PSY expression plays a major, rate-limiting role in the transition from white to orange-colored carrots.     

Efficacy of different antifouling treatments for seawater cooling systems

In an industrial seawater cooling system, the effects of three different antifouling treatments, viz. sodium hypochlorite (NaClO), aliphatic amines (Mexel?432) and UV radiation, on the characteristics of the fouling formed were evaluated. For this study a portable pilot plant, as a side-stream monitoring system and seawater cooling system, was employed. The pilot plant simulated a power plant steam condenser, having four titanium tubes under different treatment patterns, where fouling progression could be monitored. The nature of the fouling obtained was chiefly inorganic, showing a clear dependence on the antifouling treatment employed. After 72 days the tubes under treatment showed a reduction in the heat transfer resistance (R) of around 70% for NaClO, 48% for aliphatic amines and 55% for UV, with respect to the untreated tube. The use of a logistic model was very useful for predicting the fouling progression and the maximum asymptotic value of the increment in the heat transfer resistance (ΔR(max)). The apparent thermal conductivity (λ) of the fouling layer showed a direct relationship with the percentage of organic matter in the collected fouling. The characteristics and mode of action of the different treatments used led to fouling with diverse physicochemical properties.