Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system

Study of platforms of SDR for LTE-5G

RESUMEN: Según la encuesta realizada por el Instituto Nacional de Estadística (INE) en 2017, el83,4% de los hogares españoles tienen acceso al internet con un aumento de más de 1.5% en respeto con el año anterior. Esto refleja claramente que cada vez hay más dependencia con el internet debido a un incremento significante de la necesidad de información. A consecuencia de esto, el estándar 5Gestá pensado como una nueva tecnología que es capaz de cubrir la necesidad delos clientes, tales como el aumento de velocidad de transmisión de datos como la reducción del tiempo de latencia. Para ello, es fundamental el estudio de la red LTE, ya que servirá de base de5G.Por estos motivos, este proyecto se utiliza para entender profundamente la arquitectura de la tecnología LTE. Consta de dos partes: La primera se trata de la puesta en marcha de una red celular LTE de cuarta generación usando el software de código libre OAI (Open AIR Interface), tanto en máquinas virtuales como en escenas reales usando una tarjeta de desarrollo blade RFx40 como eNB, y por el lado, utilizar un dispositivo móvil como el equipo de usuario para conectarse a la estación base creada. A continuación, se sustituirá el equipo de usuario comercial anterior por uno virtualizado siguiendo las mismas ideas de implementaciones realizadas con el OAI. La segunda parte de este proyecto consiste en el análisis del resultado de las implementaciones de escenarios anteriores. De esta manera, se ha podido hacer una evaluación de esta plataforma y entender más fácilmente el funcionamiento de una red LTE.ABSTRACT: According to the survey conducted by the National Institute of Statistics (INE) in2017, 83.4% of Spanish households have access to the Internet with an increase of more than 1.5% in respect to the previous year. This reflects clearly that there is increasing dependence on the internet due to a significant increase in the need of information. As a result of this, the 5G standard is designed as a new technology that is able to meet the needs of customers, such as the increase in data transmission speed as the reduction of latency time. For this, the study of the LTE network is fundamental, since it will serve as the basis for 5G. For these reasons, this project is used to understand deeply the architecture of LTE technology. It consists of two parts: the first one talks about the implementation of the fourth generation LTE cellular network using the open source software OAI (Open AIR Interface), both in virtual machines and in real scenes using a development card called blade RFx40 as eNB (envolved Base Station), and by the side, use a mobile device as the user equipment to connect to the base station created. Later, the previous commercial user equipment will be replaced by a virtualized one following the same ideas of implementations made with the OAI. The second part of this project consists in the analysis of the results of the implementations of previous scenarios. In this way, it has been possible to evaluate this platform and understand more easily the operation of an LTE network.Grado en Ingeniería de Tecnologías de Telecomunicació

Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont

Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.</p

Developing a New Parameterization Scheme of Temperature Lapse Rate for the Hydrological Simulation in a Glacierized Basin Based on Remote Sensing

Temperature lapse rate (TLR) is an important parameter for simulations of snow/glacier melts in alpine watersheds. However, the traditional scheme estimates TLR mainly based on a limited number of stations and may not be suitable for alpine watersheds with scarce observations. To overcome this problem, this study developed a new basin-oriented TLR scheme based on Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature data which was applied in a typical glacierized watershed on the northern slope of the Himalayas. The new TLR scheme was evaluated by comparison with the station-based traditional TLR scheme in terms of performance in simulations of both snow cover area and runoff using the same hydrological model. The results showed that the monthly TLRs estimated by the new scheme presented a more reasonable seasonal pattern than those estimated by the traditional scheme. The model using the new TLR scheme showed better performance in discharge simulations of low-runoff months than that using the traditional TLR scheme. The R-squared value of multiyear mean monthly snow cover area of the former (0.82) was also higher than that of the latter (0.56). This study provides an efficient framework for estimating TLR based on remote sensing for alpine watersheds with scarce observations

Sleep-Related Factors and Work-Related Injuries among Farmers in Heilongjiang Province, People’s Republic of China

The association between sleep and work-related injuries among Chinese farmers has not been well studied. This study examined the impact of lack of sleep on agricultural work-related injuries among farmers in China. Data were from a cross-sectional survey of farm-workers in northeastern China. Information was obtained on injuries that occurred in 12 months prior to the survey, on eight sleep-related variables, and on socio-demographic variables. Logistic regression analyses were conducted to test the hypothesis that lack of sleep significantly increased the risk of work-related injuries after controlling for other injury-related risk- factors. Farmers who slept less than six hours per night were 59% more likely to be injured than those who slept more than eight hours per night (OR = 1.59; 95% CI = 1.04, 2.41). The odds of a work-related injury was 2.46 (1.56–3.89) for farmers who reported going to sleep after midnight at least once a week compared with farmers who reported going to sleep after midnight once a month. Farmers who reported having difficulty falling asleep or waking frequently during the night, who often having nightmares, or who experienced daytime sleepiness were at higher injury risk compared with the reference group after controlling for age, gender and alcohol consumption. Reduced sleep hours and poor sleep quality significantly increased the risk of work-related injuries in Chinese farmers. Sleep hours and sleep quality should be considered when assessing occupational safety among farmers

Protective Role of Sulodexide on Renal Injury Induced by Limb Ischemia-Reperfusion

Background. Though widely known as a potent antithrombin agent with protective effects on the kidney and other remote organs, it is currently ambiguous when it comes to sulodexide’s function on ischemia-reperfusion (I/R) injury. With this research, we pursued to further explore how sulodexide exerts its influence on limb I/R injury, in which deleterious effects on the kidney were what we primarily focused on. Methods. We randomized twenty-four C57BL/6 male rats into three groups, namely, sham operation group (control group), I/R group, and sulodexide pretreatment group. Hematoxylin and eosin staining was applied for discovery of renal histological changes. Serum creatinine (Cr) and serum urea nitrogen (BUN) were measured. Apoptotic parameters were detected by the TdT-mediated dUTP Nick-End Labeling method. To what extent and levels that antiapoptotic and proapoptotic proteins were expressed could be sensitively revealed by immunohistochemistry assay. Lipid peroxidation product propylene glycol and inflammatory factors were examined by enzyme-linked immunosorbent assay. Additionally, an extracorporeal hypoxia-reoxygenation (H/R) model of human renal proximal tubule epithelial HK2 cells was established. Our targets lay in cell proliferation and apoptosis, and we used western blotting to reflect apoptosis-related gene expression. Results. The levels of serum BUN, Cr, and inflammatory factors in sulodexide-intervened rats manifested significant reduction when compared with the I/R group. Also, sulodexide could protect the kidney from histological changes and could effectively inhibit intraparenchymal apoptosis. Furthermore, adding 2 μl/mL or 5 μl/mL of sulodexide to H/R model cells in vitro gave rise to significant restoration of the degenerative proliferation capacity of the HK2 cells following H/R injury and late cellular apoptosis experienced dramatic reduction versus the H/R group. When treated with 5 μl/mL of sulodexide at a dose of 10 mg/kg, the levels of the antiapoptotic proteins were increased, while the proapoptotic proteins showed opposite trends. Notable escalation on antiapoptotic protein expression level, in contrast with the opposite trends exhibited in proapoptotic proteins, was observed with 5 μl/mL sulodexide pretreatment with the dosage being 10 mg/kg. Conclusion. Sulodexide can protect against kidney damage caused by I/R injury of the lower limbs by enhancing cell proliferation, inhibiting apoptosis, reducing inflammatory reactions, and scavenging oxygen free radicals