Improved ontology for eukaryotic single-exon coding sequences in biological databases

Indexación: Scopus.Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases. © The Author(s) 2018. Published by Oxford University Press.https://academic.oup.com/database/article/doi/10.1093/database/bay089/509943

Milk consumption after exercise decreases electrolyte excretion.

La rehidratación es fundamental para la correcta recuperación posterior al ejercicio físico y el deporte. Las bebidas lácteas parecen ser una buena opción como bebidas rehidratantes después del ejercicio, pero aún los mecanismos no están completamente dilucidados. El presente estudio tiene por objetivo medir los efectos en la excreción de electrolitos en la orina al rehidratar con una bebida láctea baja en grasa o una bebida isotónica tras la realización de una sesión de ejercicio intermitente. 14 sujetos físicamente activos (23 ± 4 años), se dividieron en dos grupos: 1) rehidratación con bebida isotónica (ISO) y 2) rehidratación con bebida láctea baja en grasa (LBG). Se evaluó la gravedad específica de la orina (GEO), electrolitos (Na+ y K+) en orina y retención de fluidos, después del ejercicio y 4 horas posterior a la rehidratación. Se encontraron diferencias significativas en la GEO y en la excreción de K+ en el grupo LBG (p<0.005), ambos grupos muestran diferencias significativas en la excreción de Na+. Los resultados muestran que la rehidratación con bebida láctea mejora la GEO y disminuyen la excreción de K+ de forma más eficiente que la bebida isotónica posterior al ejercicioRehydration is essential for post-exercise and sport recovery. Milk seems to be a good option like sport drinks after exercise, yet the rehydration mechanisms are still not fully understood. The aim of this study was to measure the effect of drinking low-fat milk and an isotonic beverage after intermittent exercise on urine electrolytes. 14 physically active men (23 ± 4 y) were split into two groups: 1) rehydration with isotonic drink (ISO), and 2) rehydration with low-fat milk (LBG). Specific gravity (GEO) and electrolytes (Na+ and K+) were measured in urine before and after exercise with rehydration. Significant differences were found for the GEO and in K+ excretion in the LBG group (p <0.05). Both groups showed significant differences for Na+ excretion concentrations. We conclude that drinking low fat milk after exercise when compared to an isotonic drink, improves GEO and K excretio

Presencia de cetáceos frente a la Segunda Región de Chile = The presence of cetaceans off northern Chilean coast

Although some 35 species of cetaceans have been reported for chilean waters, the amount of published data remains very limited. Historical information on the cetofauna of northern Chile is next to inexistent. Presented here is a preliminary compilation of cetaceans recorded from sightings. strandings and by-catches, off the coast of the Second Region of Chile (210 27' S to 260 07' SI between 1980 and 1986. Evidence for the following species is available; Eubalaena australis, Balaenoptera acutorostrata, B, edeni and/or B. borealis. Phocoena spinipinnis, Delphinus delphis, Lagenorhynchus obscurus, Tursiops truncatus, Ussodelphis peronii, Globicephala melaena, G. macrorhynchus, Orcinus orca, Grampus griseus, Physeter macrocephalus. Twenty nine cetaceen specimens conserved at the Instituto de Investigaciones Oceanol6gicas (Universidad de Antofagasta) are listed. The urgent need for future systematical collection of specimens and sighting data in the study area is expressed

Accounting for food availability reveals contaminant-induced breeding impairment, food-modulated contaminant effects, and endpoint-specificity of exposure indicators in free ranging avian populations

It remains unclear how sub-lethal effects of contaminants play out in relation to other stressors encountered by free-ranging populations. Effects may be masked or influenced by interactions with field stressors such as food availability. We predicted that (1) including food availability, and particularly its interaction with Hg, would reveal or enhance associations between Hg and breeding endpoints. We further predicted that (2) breeding impairment associated with Hg would be higher under food stress conditions. We monitored Hg and nest success of great egrets (Ardea alba) in eight breeding colonies in the Florida Everglades over 11 years. We characterized variation in local food availability among colonies and years using fish biomass and recession range -a proxy to fish vulnerability. We used two Hg exposure indicators (egg albumen Hg and nestling feather Hg) and six breeding endpoints (clutch-size, brood-size, fledged-size, hatching success, post-hatching success and fledglings per egg) to assess whether variation in food availability influenced associations between Hg and these endpoints. Accounting for interactions between Hg and food availability, we identified statistically significant associations in all 12 indicator-endpoint combinations, while only three were detectable without food. Further, 10 combinations showed interactions between Hg and components of food availability. Our results also indicated an endpoint-specific affinity, with albumen [Hg] explaining more variation in hatching success while nestling feather [Hg] explained more variation in post-hatching survival. Both Hg indicators accounted for relevant (6-10%) amounts of variation in fledglings produced per egg laid, an integrative endpoint. Increased Hg exposure resulted in overall reduced reproductive success when food availability was low, but our models predicted low or no effects of increasing Hg exposure when food availability was high. Our results indicate that Hg induced impairment is strongly driven by food availability, providing a framework that accommodates previously contradictory results in the literature.This work was supported by the U.S. Army Corps of Engineers (Cooperative Agreement W912HZ-12-02-0007) and by grants of equipment from the University of Florida Institute of Food and Agricultural Sciences. Egret monitoring was performed under University of Florida IACUC permit 201708650. Fish samplingwas supported by Cooperative Agreements W912HZ-11-2-0048 and W912HZ-16-2-0008 between Florida International University (FIU) and the U.S. Army Corps of Engineers and Contract 4600001083 between FIU and the South Florida Water Management District. Fish monitoring was performed under FIU IACUC permits including IACUC-08-004, -09-029, -10-026, 12-020, -13-060, and -16-033

Effect of source/sink ratio on leaf and fruit traits of blueberry fruiting canes in the field

The source/sink relationship affects plant production and fruit quality in the field. This study aims to evaluate leaf and fruit traits of two field-grown blueberry cultivars as affected by variability of source/sink ratio (expressed as cm(2) leaf area-to-fruit number ratio) at fruiting cane level. We found that range of source/sink ratio was larger in cv. 'Legacy' than cv. 'Bluegold' with no effect of season on this variable. There was a curvilinear increase of leaf dry mass-to-leaf area ratio (LMA) with source/sink ratio, which suggests that leaves acted as alternative carbon sinks to fruits. The relation between theses variable was no affected by cultivar. Mass-based nitrogen linearly decreased with source/sink ratio, while area-based nitrogen increased in curvilinear form by the effect of LMA. For leaf nitrogen values, a notable difference between cultivars was observed. Stomatal conductance (g(s)) dropped with increasing source/sink ratios with 'Bluegold' achieving higher g(s) than 'Legacy' for any given source/sink ratio. Dry (DWf) and fresh mass, diameter and total soluble solids (SS) of the fruit were related to source/sink ratio through curvilinear fit in both cultivars. The observed relations were similar between cultivars for DWf and SS, which suggest that the rate of the response of fruit carbon gain to changing source/sink ratios was conservative between the studied cultivars. Our results showed that fruit-bearing blueberry canes are semiautonomous regulating their resource allocation as function of source/sink rati

NOTAS MICOLOGICAS: Hortaea werneckii EN AMBIENTES SALINOS DEL NORTE CHILENO

Mediante determinaciones morfológicas y fsiológicas, se describe el primer  aislamienlo del hongo dematiáceo le vaduriforme  Hortaea werneckii en aguade mar y moluscos del norte chileno (Antofagasta, IIRegión).Se comenta al mismo tiempo junto a los aportes de la literatura, algunos datos ecológicos, epidemiológicos y taxonómicos de esta levadura negra

Holographic surface measurement system for the Fred Young Submillimeter Telescope

We describe a system being developed for measuring the shapes of the mirrors of the Fred Young Submillimeter Telescope (FYST), now under construction for the CCAT Observatory. "Holographic" antenna-measuring techniques are an efficient and accurate way of measuring the surfaces of large millimeter-wave telescopes and they have the advantage of measuring the wave-front errors of the whole system under operational conditions, e.g. at night on an exposed site. Applying this to FYST, however, presents significant challenges because of the high accuracy needed, the fact that the telescope consists of two large off-axis mirrors, and a requirement that measurements can be made without personnel present. We use a high-frequency (~300GHz) source which is relatively close to the telescope aperture (<1/100th of the Fresnel distance) to minimize atmospheric effects. The main receiver is in the receiver cabin and can be moved under remote control to different positions, so that the wave-front errors in different parts of the focal plane can be measured. A second receiver placed on the yoke provides a phase reference. The signals are combined in a digital cross-correlation spectrometer. Scanning the telescope provides a map of the complex beam pattern. The surface errors are found by inference, i.e. we make models of the reflectors with errors and calculate the patterns expected, and then iterate to find the best match to the data. To do this we have developed a fast and accurate method for calculating the patterns using the Kirchhoff-Fresnel formulation. This paper presents details of the design and outlines the results from simulations of the measurement and inference process. These indicate that a measurement accuracy of ~3 microns rms is achievable.Comment: Proceedings Volume 11445, Ground-based and Airborne Telescopes VIII SPIE Astronomical Telescopes + Instrumentation, 2020, Online Only Conferenc

Application of lca methodology to the production of strawberry on substrates with peat and sediments from ports

The Life Cycle Assessment (LCA) methodology was applied to identify the potential environmental impact of dredged sediments used as growing media for food crops. The dredged sediments used came from Livorno port and were previously phytoremediated. For the assay, strawberry plants (Fragaria x ananassa Duch vr. ‘San Andreas’) were used. The plants were cultivated on three different substrates (100% peat, 100% dredged sediment and 50% mix peat/sediment) to identify the real impact of the culture media on the growing process. LCA was calculated and analyzed according to ISO 14040:2006 by SimaPro software. ReCipe Midpoint (E) V1.13/Europe Recipe E method was applied. One kilogram of produced strawberry, for each crop media tested, was defined as the functional unit. Eighteen impact categories were selected where Marine Eutrophication (ME), Human Toxicity (HT) and Freshwater Ecotoxicity (FET) were identified as relevant impact categories. The LCA results showed an increase in the environmental impact of strawberry cultivation using 100% sediment against 100% peat, due to the decrease in fruit production caused by the sediment. Nevertheless, the decrease in the environmental impact and the fruit production increase identified when the sediment is used mixed (<50%) with other substrates. The appropriate use of these substrates would be justified within the context of the circular economy

Ceramide and palmitic acid inhibit macrophage-mediated epithelial-mesenchymal transition in colorectal cancer

Accumulating evidence indicates that ceramide (Cer) and palmitic acid (PA) possess the ability to modulate switching of macrophage phenotypes and possess anti-tumorigenic effects; however, the underlying molecular mechanisms are largely unknown. The aim of the present study was to investigate whether Cer and PA could induce switching of macrophage polarization from the tumorigenic M2- towards the pro-inflammatory M1-phenotype, and whether this consequently altered the potential of colorectal cancer cells to undergo epithelial-mesenchymal transition (EMT), a hallmark of tumor progression. Our study showed that Cer- and PA-treated macrophages increased expression of the macrophage 1 (M1)-marker CD68 and secretion of IL-12 and attenuated expression of the macrophage 2 (M2)-marker CD163 and IL-10 secretion. Moreover, Cer and PA abolished M2 macrophage-induced EMT and migration of colorectal cancer cells. At the molecular level, this coincided with inhibition of SNAI1 and vimentin expression and upregulation of E-cadherin. Furthermore, Cer and PA attenuated expression levels of IL-10 in colorectal cancer cells co-cultured with M2 macrophages and downregulated STAT3 and NF-kappa B expression. For the first time, our findings suggest the presence of an IL-10-STAT3-NF-kappa B signaling axis in colorectal cancer cells co-cultured with M2 macrophages, mimicking the tumor microenvironment. Importantly, PA and Cer were powerful inhibitors of this signaling axis and, consequently, EMT of colorectal cancer cells. These results contribute to our understanding of the immunological mechanisms that underlie the anti-tumorigenic effects of lipids for future combination with drugs in the therapy of colorectal carcinoma.Imaging- and therapeutic targets in neoplastic and musculoskeletal inflammatory diseas