Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genomescale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de ChinaFil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; ChinaFil: Baldwin, Carole C.. National Museum of Natural History; Estados UnidosFil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto RicoFil: Li, Chenhong. Shanghai Ocean University; ChinaFil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Wang, Min. Beijing Genomics Institute; ChinaFil: Fang, Chao. Chinese Academy of Sciences; República de ChinaFil: Xie, Bing. Bgi-shenzhen; ChinaFil: Zhoui, Zhuocheng. China Fisheries Association; ChinaFil: Huang, Hai. Hainan Tropical Ocean University; ChinaFil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; ChinaFil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;Fil: Shi, Qiong. Chinese Academy of Sciences; República de Chin

Light-Responsive Micelles Loaded With Doxorubicin for Osteosarcoma Suppression

The enhancement of tumor targeting and cellular uptake of drugs are significant factors in maximizing anticancer therapy and minimizing the side effects of chemotherapeutic drugs. A key challenge remains to explore stimulus-responsive polymeric nanoparticles to achieve efficient drug delivery. In this study, doxorubicin conjugated polymer (Poly-Dox) with light-responsiveness was synthesized, which can self-assemble to form polymeric micelles (Poly-Dox-M) in water. As an inert structure, the polyethylene glycol (PEG) can shield the adsorption of protein and avoid becoming a protein crown in the blood circulation, improving the tumor targeting of drugs and reducing the cardiotoxicity of doxorubicin (Dox). Besides, after ultraviolet irradiation, the amide bond connecting Dox with PEG can be broken, which induced the responsive detachment of PEG and enhanced cellular uptake of Dox. Notably, the results of immunohistochemistry in vivo showed that Poly-Dox-M had no significant damage to normal organs. Meanwhile, they showed efficient tumor-suppressive effects. This nano-delivery system with the light-responsive feature might hold great promises for the targeted therapy for osteosarcoma

Analysis of heat and mass transfer characteristics of supercritical CO

The heat and mass exchange of CO2 in a vertical U-tube under supercritical pressure was simulated. The effects of the geometry of the bend area, The center arc radius of the bend area and the different bend orientations on the flow heat transfer of supercritical CO2 in the U-tube were analyzed. The results show that in the bend area, the flow is affected by the combined action of centrifugal force and gravity, as well as the pipe structure, so the flow mixing is intense, and the heat transfer capacity is significantly enhanced. When the direction of the bend changes, the interaction between centrifugal force and gravity will affect the heat transfer at pipe bending. When the central arc radius r of the bend area increases from 0.5D to 3D, the heat transfer at the bend can be strengthened, but will weaken the heat transfer at the bend outlet area

Genetic and morphological differences between yellowtail kingfish (Seriola lalandi) from the Bohai Sea, China and the Southern Ocean, Australia

The aquaculture of yellowtail kingfish (Seriola lalandi) has expanded around the globe, including China. Genetic resource of Chinese S. lalandi urgently needs to be assessed for improving production. Here, we collected wild S. lalandi samples from the Bohai Sea, China and evaluated its genetic diversity based on 17,690 nuclear loci. A population from the Southern Ocean, Australia was used for comparison. The analyses showed that the Chinese and Australian S. lalandi formed two completely distinct clusters and there was no genetic introgression from the Australian S. lalandi into the Chinese S. lalandi population. The genetic diversity is slightly lower, but comparable in Chinese versus Australian yellowtail kingfish (Chinese population, expected heterozygosity: 0.19, observed heterozygosity: 0.19, nucleotide diversity: 0.19 ± 0.09; Australian population, expected heterozygosity: 0.23, observed heterozygosity: 0.22, nucleotide diversity: 0.22 ± 0.11). Overall, our results indicated that Chinese S. lalandi could be a potential subject for genetic breeding programs. We also investigated morphological characters and developed molecular markers for population identification. Comparison of meristic characters between the Chinese population and the Australian population revealed that main shape difference were in the number of dorsal spines, dorsal fin rays and the number of upper gill rakers. Geometric morphology based on eight landmarks also revealed significant difference between the two populations including the distance between the tip of snout to origin of pelvic fin and the distance between the tip of snout to origin of pectoral fin. These morphological characters can be used for easy identification of the Chinese S. lalandi

Hyperspectral Unmixing with Gaussian Mixture Model and Spatial Group Sparsity

In recent years, endmember variability has received much attention in the field of hyperspectral unmixing. To solve the problem caused by the inaccuracy of the endmember signature, the endmembers are usually modeled to assume followed by a statistical distribution. However, those distribution-based methods only use the spectral information alone and do not fully exploit the possible local spatial correlation. When the pixels lie on the inhomogeneous region, the abundances of the neighboring pixels will not share the same prior constraints. Thus, in this paper, to achieve better abundance estimation performance, a method based on the Gaussian mixture model (GMM) and spatial group sparsity constraint is proposed. To fully exploit the group structure, we take the superpixel segmentation (SS) as preprocessing to generate the spatial groups. Then, we use GMM to model the endmember distribution, incorporating the spatial group sparsity as a mixed-norm regularization into the objective function. Finally, under the Bayesian framework, the conditional density function leads to a standard maximum a posteriori (MAP) problem, which can be solved using generalized expectation-maximization (GEM). Experiments on simulated and real hyperspectral data demonstrate that the proposed algorithm has higher unmixing precision compared with other state-of-the-art methods

Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma

Abstract Background Fungal and bacterial microbiota play an important role in development of asthma. We aim to characterize airway microbiome (mycobiome, bacteriome) and functional genes in asthmatics and controls. Methods Sputum microbiome of controls, untreated asthma patients and inhaled corticosteroid (ICS) receiving patients was detected using high throughput sequencing. Metagenomic sequencing was used to examine the functional genes of microbiome. Results 1. Mycobiome: α diversity was lower in untreated asthma group than that in controls. Mycobiome compositions differed among the three groups. Compared with controls, untreated asthma group has higher abundance of Wallemia, Mortierella and Fusarium. Compared with untreated asthma patients, ICS receiving patients has higher abundance of Fusarium and Mortierella, lower frequency of Wallemia, Alternaria and Aspergillus. 2. Bacteriome: α diversity was lower in untreated asthma group than that in controls. There are some overlaps of bacteriome compositions between controls and untreated asthma patients which were distinct from ICS receiving patients. Untreated asthma group has higher Streptococcus than controls. 3. Potential fungal and bacterial biomarkers of asthma: Trametes, Aspergillus, Streptococcus, Gemella, Neisseria, etc. 4. Correlation network: There are dense and homogenous correlations in controls but a dramatically unbalanced network in untreated asthma and ICS receiving patients, which suggested the existence of disease-specific inter-kingdom and intra-kingdom alterations. 5. Metagenomic analysis: functional pathways were associated with the status of asthma, microbiome and functional genes showed different correlations in different environment. Conclusion We showed mycobiome and bacteriome dysbiosis in asthma featured by alterations in biodiversity, community composition, inter-kingdom and intra-kingdom network. We also observed several functional genes associated with asthma

Mechanisms Affecting Physical Aging and Swelling by Blending an Amphiphilic Component

Polymer blending is a promising method to overcome stability obstacles induced by physical aging and swelling of implant scaffolds prepared from amorphous polymers in biomedical application, since it will not bring potential toxicity compared with chemical modification. However, the mechanism of polymer blending still remains unclearly explained in existing studies that fail to provide theoretical references in material R&D processes for stability improvement of the scaffold during ethylene oxide (EtO) sterilization, long-term storage, and clinical application. In this study, amphiphilic poly(ethylene glycol)-co-poly(lactic acid) (PELA) was blended with amorphous poly(lactic-co-glycolic acid) (PLGA) because of its good miscibility so as to adjust the glass transition temperature (Tg) and hydrophilicity of electrospun PLGA membranes. By characterizing the morphological stability and mechanical performance, the chain movement and the glass transition behavior of the polymer during the physical aging and swelling process were studied. This study revealed the modification mechanism of polymer blending at the molecular chain level, which will contribute to stability improvement and performance adjustment of implant scaffolds in biomedical application