SinEx DB: a database for single exon coding sequences in mammalian genomes

Indexación: Web of Science.Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.https://academic.oup.com/database/article-lookup/doi/10.1093/database/baw09

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

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

Intestinal microbiota transplantation to germ-free mice in a in vivo model of nafld associated with a quercetin treatment

15 p.To select mice donors for intestinal microbiota transplantation based on its metabolic phenotype in response to a high fat diet (HFD) and quercetin treatment (Q). Intestinal microbiota. Resumen de un trabajo resultado del proyecto de investigación financiado por la Consejería de Educación de la Junta de Castilla y León (referencia LE063U16)S

Metabolic Phenotype Transfer Through Gut Microbiota Transplantation from HFD-Fed and Quercetin Treated Donors Modulates Obesity-Related NAFLD in Germ-Free Mice

1 p.Gut microbiota is involved in obesity, metabolic syndrome and nonalcoholic fatty liver disease (NAFLD). Strategies to modulate it, including faecal transplantation and administration of prebiotics as quercetin, are actively being examined. The present study aims to investigate benefits of experimental gut microbiota transfer from donors to germ-free mice (GFm) in a high-fat diet (HFD)-based NAFLD model. Resumen de un trabajo resultado del proyecto de investigación financiado por la Consejería de Educación de la Junta de Castilla y León (referencia LE063U16)S

Intestinal Microbiota Transplantation From HFD-fed and Quercetin Treated Donors Results in a Complex Metabolic Phenotype Transfer that Modulates Obesity-Related NAFLD in Germ Free Mice

2 p.Intestinal microbiota imbalance and related gut-liver axis activation have been identified as key mechanisms in nonalcoholic fatty liver disease (NAFLD) development. Modulation of intestinal microbiota, through administration of prebiotics or faecal microbiota transplantation, is a promising therapeutic approach for obesity associated diseases including NAFLD. The aim of the present study is to evaluate the benefits of gut microbiota transplantation from donors to germ free mice (GFm) following an experimental treatment with the flavonoid quercetin in a high fat diet (HFD)-based NAFLD model. Resumen de un trabajo resultado del proyecto de investigación financiado por la Consejería de Educación de la Junta de Castilla y León (referencia LE063U16)S

Akkermansia spp. mediates protection from obesity-associated NAFLD development in germ free mice following intestinal microbiota transplantation from high fat diet and quercetin treated donors

1 p.Dysbiosis and gut-liver axis alteration have been pointed as important contributors to obesity and non-alcoholic fatty liver disease (NAFLD) development. Modulation of intestinal microbiota (IM) emerge as a promising therapeutic strategy for obesity-associated NAFLD. This study aims to determine the effect of IM transplantation and quercetin supplementation in a high fat diet (HFD)-based NAFLD model in germ free mice (GFm). Resumen de un trabajo resultado del proyecto de investigación financiado por la Consejería de Educación de la Junta de Castilla y León (referencia LE063U16)S

Zinc-phthalocyanine-loaded extracellular vesicles increase efficacy and selectivity of photodynamic therapy in co-culture and preclinical models of colon cancer

Photodynamic therapy (PDT) is a promising and clinically approved method for the treatment of cancer. However, the efficacy of PDT is often limited by the poor selectivity and distribution of the photosensitizers (PS) toward the malignant tumors, resulting in prolonged periods of skin photosensitivity. In this work, we present a simple and straightforward strategy to increase the tumor distribution, selectivity, and efficacy of lipophilic PS zinc phthalocyanine (ZnPc) in colon cancer by their stabilization in purified, naturally secreted extracellular vesicles (EVs). The PS ZnPc was incorporated in EVs (EV-ZnPc) by a direct incubation strategy that did not affect size distribution or surface charge. By using co-culture models simulating a tumor microenvironment, we determined the preferential uptake of EV-ZnPc toward colon cancer cells when compared with macrophages and dendritic cells. We observed that PDT promoted total tumor cell death in normal and immune cells, but showed selectivity against cancer cells in co-culture models. In vivo assays showed that after a single intravenous or intratumoral injection, EV-ZnPc were able to target the tumor cells and strongly reduce tumor growth over 15 days. These data expose opportunities to enhance the potential and efficacy of PDT using simple non-synthetic strategies that might facilitate translation into clinical practice.Imaging- and therapeutic targets in neoplastic and musculoskeletal inflammatory diseas

In search for the sources of plastic marine litter that contaminates the Easter Island Ecoregion

Subtropical gyres are the oceanic regions where plastic litter accumulates over long timescales, exposing surrounding oceanic islands to plastic contamination, with potentially severe consequences on marine life. Islands’ exposure to such contaminants, littered over long distances in marine or terrestrial habitats, is due to the ocean currents that can transport plastic over long ranges. Here, this issue is addressed for the Easter Island ecoregion (EIE). High-resolution ocean circulation models are used with a Lagrangian particle-tracking tool to identify the connectivity patterns of the EIE with industrial fishing areas and coastline regions of the Pacific basin. Connectivity patterns for “virtual” particles either floating (such as buoyant macroplastics) or neutrally-buoyant (smaller microplastics) are investigated. We find that the South American shoreline between 20°S and 40°S, and the fishing zone within international waters off Peru (20°S, 80°W) are associated with the highest probability for debris to reach the EIE, with transit times under 2 years. These regions coincide with the most-densely populated coastal region of Chile and the most-intensely fished region in the South Pacific. The findings offer potential for mitigating plastic contamination reaching the EIE through better upstream waste management. Results also highlight the need for international action plans on this important issue

Protective effect of quercetin treatment on HFD-induced intestinal dysbiosis and barrier dysfunction in an in vivo model of non-alcoholic fatty liver disease

1 p.Gut microbiota is involved in obesity, metabolic syndrome and nonalcoholic fatty liver disease (NAFLD). Quercetin may have the ability to modulate the intestinal microbiota composition, suggesting therapeutic potential in NAFLD. The present study aims to investigate the beneficial effect of quercetin treatment on dysbiosis, intestinal barrier dysfunction and gut-liver axis alteration in high-fat diet (HFD)-fed mice. Resumen de un trabajo resultado del proyecto de investigación financiado por la Consejería de Educación de la Junta de Castilla y León (referencia LE063U16)S