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

Phytase-producing Bacillus sp. inoculation increases phosphorus availability in cattle manure

Organic wastes rich in phosphorus (P) are considered an alternative to decrease the dependence on chemical P fertilization in crops and pastures. Microbial inoculants are being studied as a tool to increase plant P availability in organic wastes. In this study, we explore the effect of inoculation with Bacillus sp. MQH-19 (a native phytase-producing bacterium) on the release of inorganic phosphorus (Pi) in cattle manure with low available P but a high total P content. Bacteria inoculation resulted in a higher release of Pi (8% in NaHCÜ3 and 13% in NaOH-EDTA extracts) compared with that of uninoculated manure (0.7% in NaHCÜ3 and 0.1% in NaOH-EDTA extracts). However, a greater amount of Pi was released in inoculated manure supplemented with phytate (47% in NaHCÜ3 and 117% in NaOH-EDTA extracts) compared with that of uninoculated manure supplemented with phytate (30% in NaHCÜ3 and 15% in NaOH-EDTA extracts). In addition, the use of denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) revealed that the bacterial community structure in manure was affected by inoculation and that the prevalence of Bacillus sp. MQH-19 decreased during incubation (6 days). This study demonstrates that Pi availability in cattle manure can be increased by phytase-producing bacteria inoculation. Phytase-producing bacteria inoculation might represent an attractive strategy to increase P availability in agricultural wastes, which are used as organic fertilizers in crops and pastures

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

The Solar Spectrum in the Atacama Desert

The Atacama Desert has been pointed out as one of the places on earth where the highest surface irradiance may occur. This area is characterized by its high altitude, prevalent cloudless conditions and relatively low columns of ozone and water vapor. Aimed at the characterization of the solar spectrum in the Atacama Desert, we carried out in February-March 2015 ground-based measurements of the spectral irradiance (from the ultraviolet to the near infrared) at seven locations that ranged from the city of Antofagasta (on the southern pacific coastline) to the Chajnantor Plateau (5,100 m altitude). Our spectral measurements allowed us to retrieve the total ozone column, the precipitable water, and the aerosol properties at each location. We found that changes in these parameters, as well as the shorter optical path length at high-altitude locations, lead to significant increases in the surface irradiance with the altitude. Our measurements show that, in the range 0?5100 m altitude, surface irradiance increases with the altitude by about 27% in the infrared range, 6% in the visible range, and 20% in the ultraviolet range. Spectral measurements carried out at the Iza?a Observatory (Tenerife, Spain), in Hannover (Germany) and in Santiago (Chile), were used for further comparisons

The Challenge of Machine Learning in Space Weather Nowcasting and Forecasting

The numerous recent breakthroughs in machine learning (ML) make imperative to carefully ponder how the scientific community can benefit from a technology that, although not necessarily new, is today living its golden age. This Grand Challenge review paper is focused on the present and future role of machine learning in space weather. The purpose is twofold. On one hand, we will discuss previous works that use ML for space weather forecasting, focusing in particular on the few areas that have seen most activity: the forecasting of geomagnetic indices, of relativistic electrons at geosynchronous orbits, of solar flares occurrence, of coronal mass ejection propagation time, and of solar wind speed. On the other hand, this paper serves as a gentle introduction to the field of machine learning tailored to the space weather community and as a pointer to a number of open challenges that we believe the community should undertake in the next decade. The recurring themes throughout the review are the need to shift our forecasting paradigm to a probabilistic approach focused on the reliable assessment of uncertainties, and the combination of physics-based and machine learning approaches, known as gray-box.Comment: under revie

Surface Solar Extremes in the Most Irradiated Region on Earth, Altiplano

Satellites have consistently pointed to the Altiplano of the Atacama Desert as the place on Earth where the world’s highest surface irradiance occurs. This region, near the Tropic of Capricorn, is characterized by its high elevation, prevalent cloudless conditions, and relatively low concentrations of ozone, aerosols, and precipitable water. Aimed at studying the variability of the surface solar irradiance and detecting atmospheric composition changes in the Altiplano, an atmospheric observatory was set up in 2016 at the northwestern border of the Chajnantor Plateau (5,148 m MSL, 22.95°S, 67.78°W, Chile). Here, we report on the first 5 years of measurements at this observatory that establish the Altiplano as the region that receives the highest-known irradiation on Earth and illuminate the unique features of surface solar extremes at high-altitude locations. We found that the global horizontal shortwave (SW) irradiance on the plateau is on average 308 W m−2 (equivalent to an annual irradiation of 2.7 MWh m−2 yr−1, the highest worldwide). We also found that forward scattering by broken clouds often leads to intense bursts of SW irradiance; a record of 2,177 W m−2 was measured, equivalent to the extraterrestrial SW irradiance expected at approximately 0.79 astronomical units (AU) from the Sun. These cloud-driven surface solar extremes occur on the Chajnantor Plateau at a frequency, intensity, and duration not previously seen anywhere in the world, making the site an ideal location for studying the response of photovoltaic (PV) power plants to periods of enhanced SW variability.</p

How does a generalist seabird species use its marine habitat? The case of the kelp gull in a coastal upwelling area of the Humboldt Current

Indexación:Scopus.The distribution of kelp gulls (Larus dominicanus) was studied by ship-based transect counts in the SE Pacific Ocean off Chile, South America. Some 96-98% of the kelp gulls were in a band less than 20 km from the coast, mainly near the breeding colony on Pájaros Island and the City of Coquimbo. Abundance did not change significantly among years, but was influenced significantly by distance to land. Principal component analysis yielded two components that jointly explain 53% of the standardized variance. The first (explaining 36% of the variance) includes distance to the nearest coast and water depth, the second (17%) associates with the presence of fishing vessels. The results suggest that the stability of the summer distribution of kelp gulls is generated by the large and semi-permanent offer of food at fish markets and city sewage works, as well as the location of the breeding colonies. Further analysis on other temporal scales (seasonal, decadal) associated with reproductive or non-reproductive changes within the population and/or ENSO cycles will be necessary to confirm the multiscale stability of the pattern described. © 2007 International Council for the Exploration of the Sea. Published by Oxford Journals. All rights reserved.https://academic-oup-com.recursosbiblioteca.unab.cl/icesjms/article/64/7/1348/72823

Persistent extreme ultraviolet irradiance in Antarctica despite the ozone recovery onset

Attributable to the Montreal Protocol, the most successful environmental treaty ever, human-made ozone-depleting substances are declining and the stratospheric Antarctic ozone layer is recovering. However, the Antarctic ozone hole continues to occur every year, with the severity of ozone loss strongly modulated by meteorological conditions. In late November and early December 2020, we measured at the northern tip of the Antarctic Peninsula the highest ultraviolet (UV) irradiances recorded in the Antarctic continent in more than two decades.The support of INACH (RT_69-20 & RT_70-18), ANID (ANILLO ACT210046, FONDECYT 1191932 & 1221122, DFG190004 and REDES180158), CORFO (19BP-117358 & 18BPE-93920) is gratefully acknowledged

Evaluation of MODIS-derived estimates of the albedo over the Atacama Desert using ground-based spectral measurements

Surface albedo is an important forcing parameter that drives the radiative energy budget as it determines the fraction of the downwelling solar irradiance that the surface reflects. Here we report on ground-based measurements of the spectral albedo (350–2200 nm) carried out at 20 sites across a North–South transect of approximately 1300 km in the Atacama Desert, from latitude 18° S to latitude 30° S. These spectral measurements were used to evaluate remote sensing estimates of the albedo derived from the Moderate Resolution Imaging Spectroradiometer (MODIS). We found that the relative mean bias error (RMBE) of MODIS-derived estimates was within ± 5% of ground-based measurements in most of the Atacama Desert (18–27° S). Although the correlation between MODIS-derived estimates and ground-based measurements remained relatively high (R= 0.94), RMBE values were slightly larger in the southernmost part of the desert (27–30° S). Both MODIS-derived data and ground-based measurements show that the albedo at some bright spots in the Atacama Desert may be high enough (up to 0.25 in visible range) for considerably boosting the performance of bifacial photovoltaic technologies (6–12%)

Alphavirus replicon-based enhancement of mucosal and systemic immunity is linked to the innate response generated by primary immunization

Venezuelan equine encephalitis virus replicon particles (VRP) function as an effective systemic, cellular and mucosal adjuvant when codelivered with antigen, and show promise for use as a component in new and existing human vaccine formulations. We show here that VRP are effective at low dose and by intramuscular delivery, two useful features for implementation of VRP as a vaccine adjuvant. In mice receiving a prime and boost with antigen, we found that VRP are required in prime only to produce a full adjuvant effect. This outcome indicates that the events triggered during prime with VRP are sufficient to establish the nature and magnitude of the immune response to a second exposure to antigen. Events induced by VRP in the draining lymph node after prime include robust secretion of many inflammatory cytokines, upregulation of CD69 on leukocytes, and increased cellularity, with a disproportionate increase of a cell population expressing CD11c, CD11b, and F4/80. We show that antigen delivered 24 hours after administration of VRP does not benefit from an adjuvant effect, indicating that the events which are critical to VRP-mediated adjuvant activity occur within the first 24 hours. Further studies of the events induced by VRP will help elucidate the mechanism of VRP adjuvant activity and will advance the safe implementation of this adjuvant in human vaccines