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

Lack of Cul4b, an E3 Ubiquitin Ligase Component, Leads to Embryonic Lethality and Abnormal Placental Development

Cullin-RING ligases (CRLs) complexes participate in the regulation of diverse cellular processes, including cell cycle progression, transcription, signal transduction and development. Serving as the scaffold protein, cullins are crucial for the assembly of ligase complexes, which recognize and target various substrates for proteosomal degradation. Mutations in human CUL4B, one of the eight members in cullin family, are one of the major causes of X-linked mental retardation. We here report the generation and characterization of Cul4b knockout mice, in which exons 3 to 5 were deleted. In contrast to the survival to adulthood of human hemizygous males with CUL4B null mutation, Cul4b null mouse embryos show severe developmental arrest and usually die before embryonic day 9.5 (E9.5). Accumulation of cyclin E, a CRL (CUL4B) substrate, was observed in Cul4b null embryos. Cul4b heterozygotes were recovered at a reduced ratio and exhibited a severe developmental delay. The placentas in Cul4b heterozygotes were disorganized and were impaired in vascularization, which may contribute to the developmental delay. As in human CUL4B heterozygotes, Cul4b null cells were selected against in Cul4b heterozygotes, leading to various degrees of skewed X-inactivation in different tissues. Together, our results showed that CUL4B is indispensable for embryonic development in the mouse

Investigation of the Electroluminescence Mechanism of GaN-Based Blue and Green Light-Emitting Diodes with Junction Temperature Range of 120–373 K

Junction temperature (Tj) and current have important effects on light-emitting diode (LED) properties. Therefore, the electroluminescence (EL) spectra of blue and green LEDs were investigated in a Tj range of 120–373 K and in a current range of 80–240 mA based on accurate real-time measurements of Tj using an LED with a built-in sensor unit. Two maxima of the emission peak energy with changing Tj were observed for the green LED, while the blue LED showed one maximum. This was explained by the transition between the donor-bound excitons (DX) and free excitons A (FXA) in the green LED. At low temperatures, the emission peak energy, full width at half maximum (FWHM), and radiation power of the green LED increase rapidly with increasing current, while those of the blue LED increase slightly. This is because when the strong spatial potential fluctuation and low exciton mobility in the green LED is exhibited, with the current increasing, more bonded excitons are found in different potential valleys. With a shallower potential valley and higher exciton mobility, excitons are mostly bound around the potential minima. The higher threshold voltage of the LEDs at low temperatures may be due to the combined effects of the band gap, dynamic resistance, piezoelectric polarization, and electron-blocking layer (EBL)

Leaf Nitrogen Spectral Reflectance Model of Winter Wheat (Triticum Aestivum) based on PROSPECT: Simulation and Inversion

Through its association with proteins and plant pigments, leaf nitrogen (N) plays an important regulatory role in photosynthesis, leaf respiration, and net primary production. However, the traditional methods of measurement leaf N are rooted in sample-based spectroscopy in laboratory. There is a big challenge of deriving leaf N from the nondestructive field-measured leaf spectra. In this study, the original PROSPECT model was extended by replacing the absorption coefficient of chlorophyll in the original PROSPECT model with an equivalent N absorption coefficient to develop a nitrogen-based PROSPECT model (N-PROSPECT). N-PROSPECT was evaluated by comparing the model-simulated reflectance values with the measured leaf reflectance values. The validated results show that the correlation coefficient (R) was 0.98 for the wavelengths of 400 to 2500 nm. Finally, N-PROSPECT was used to simulate leaf reflectance using different combinations of input parameters, and partial least squares regression (PLSR) was used to establish the relationship between the N-PROSPECT simulated reflectance and the corresponding leaf nitrogen density (LND). The inverse of the PLSR-based N-PROSPECT model was used to retrieve LND from the measured reflectance with a relatively high accuracy (R2=0.77, RMSE=22.15  μg cm−2). This result demonstrates that the N-PROSPECT model established in this study can accurately simulate nitrogen spectral contributions and retrieve LND

Evaluation of ASTER-Like Daily Land Surface Temperature by Fusing ASTER and MODIS Data during the HiWATER-MUSOEXE

Land surface temperature (LST) is an important parameter that is highly responsive to surface energy fluxes and has become valuable to many disciplines. However, it is difficult to acquire satellite LSTs with both high spatial and temporal resolutions due to tradeoffs between them. Thus, various algorithms/models have been developed to enhance the spatial or the temporal resolution of thermal infrared (TIR) data or LST, but rarely both. The Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) is the widely-used data fusion algorithm for Landsat and MODIS imagery to produce Landsat-like surface reflectance. In order to extend the STARFM application over heterogeneous areas, an enhanced STARFM (ESTARFM) approach was proposed by introducing a conversion coefficient and the spectral unmixing theory. The aim of this study is to conduct a comprehensive evaluation of the ESTARFM algorithm for generating ASTER-like daily LST by three approaches: simulated data, ground measurements and remote sensing products, respectively. The datasets of LST ground measurements, MODIS, and ASTER images were collected in an arid region of Northwest China during the first thematic HiWATER-Multi-Scale Observation Experiment on Evapotranspiration (MUSOEXE) over heterogeneous land surfaces in 2012 from May to September. Firstly, the results of the simulation test indicated that ESTARFM could accurately predict background with temperature variations, even coordinating with small ground objects and linear ground objects. Secondly, four temporal ASTER and MODIS data fusion LSTs (i.e., predicted ASTER-like LST products) were highly consistent with ASTER LST products. Here, the four correlation coefficients were greater than 0.92, root mean square error (RMSE) reached about 2 K and mean absolute error (MAE) ranged from 1.32 K to 1.73 K. Finally, the results of the ground measurement validation indicated that the overall accuracy was high (R2 = 0.92, RMSE = 0.77 K), and the ESTARFM algorithm is a highly recommended method to assemble time series images at ASTER spatial resolution and MODIS temporal resolution due to LST estimation error less than 1 K. However, the ESTARFM method is also limited in predicting LST changes that have not been recorded in MODIS and/or ASTER pixels

Evaluation of ASTER-Like Daily Land Surface Temperature by Fusing ASTER and MODIS Data during the HiWATER-MUSOEXE

Land surface temperature (LST) is an important parameter that is highly responsive to surface energy fluxes and has become valuable to many disciplines. However, it is difficult to acquire satellite LSTs with both high spatial and temporal resolutions due to tradeoffs between them. Thus, various algorithms/models have been developed to enhance the spatial or the temporal resolution of thermal infrared (TIR) data or LST, but rarely both. The Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) is the widely-used data fusion algorithm for Landsat and MODIS imagery to produce Landsat-like surface reflectance. In order to extend the STARFM application over heterogeneous areas, an enhanced STARFM (ESTARFM) approach was proposed by introducing a conversion coefficient and the spectral unmixing theory. The aim of this study is to conduct a comprehensive evaluation of the ESTARFM algorithm for generating ASTER-like daily LST by three approaches: simulated data, ground measurements and remote sensing products, respectively. The datasets of LST ground measurements, MODIS, and ASTER images were collected in an arid region of Northwest China during the first thematic HiWATER-Multi-Scale Observation Experiment on Evapotranspiration (MUSOEXE) over heterogeneous land surfaces in 2012 from May to September. Firstly, the results of the simulation test indicated that ESTARFM could accurately predict background with temperature variations, even coordinating with small ground objects and linear ground objects. Secondly, four temporal ASTER and MODIS data fusion LSTs (i.e., predicted ASTER-like LST products) were highly consistent with ASTER LST products. Here, the four correlation coefficients were greater than 0.92, root mean square error (RMSE) reached about 2 K and mean absolute error (MAE) ranged from 1.32 K to 1.73 K. Finally, the results of the ground measurement validation indicated that the overall accuracy was high (R2 = 0.92, RMSE = 0.77 K), and the ESTARFM algorithm is a highly recommended method to assemble time series images at ASTER spatial resolution and MODIS temporal resolution due to LST estimation error less than 1 K. However, the ESTARFM method is also limited in predicting LST changes that have not been recorded in MODIS and/or ASTER pixels

Evaluation of cardiac index and right ventricular hypertrophy index in rats under a chronic hypoxic environment at high altitude

High-altitude areas are characterized by low pressure and hypoxia, which have a significant impact on various body systems. This study aimed to investigate the alterations in cardiac index and right ventricular hypertrophy index(RVHI) in rats at different altitudes.Twenty-one male Sprague-Dawley (SD) rats aged 4 weeks were randomly divided into three groups based on altitude. The rats were raised for 28 weeks and then transferred to Qinghai University Plateau Medicine Laboratory. Body weight was measured, heart organs were isolated and weighed, and cardiac index and right ventricular hypertrophy index were determined. Statistical analysis was performed on the data from the three groups. Compared with the plain group, the body weight of the middle-altitude group was significantly decreased (P < 0.05), and cardiac index, RVHI-1, RVHI-2 increased significantly ((P < 0.05). The body weight, whole heart mass, right ventricular mass were significantly decreased in high-altitude group (P < 0.05), RVHI-1 and RVHI-2 were significantly increased (P < 0.05). Compared with the middle-altitude group, the body weight, whole heart mass and right ventricular mass of the high-altitude group were significantly decreased (P < 0.05), and RVHI-1 and RVHI-2 were significantly increased (P < 0.05). Increasing altitude led to a decrease in body weight, whole heart mass, and right ventricular mass in rats, indicating structural changes in the right heart. Additionally, the proportion of right heart to body weight and whole heart increased with altitude

DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome

The DNA phosphorothioate (PT) modification existing in many prokaryotes, including bacterial pathogens and commensals, confers multiple characteristics, including restricting gene transfer, influencing the global transcriptional response, and reducing fitness during exposure to chemical mediators of inflammation. While PT-containing bacteria have been investigated in a variety of environments, they have not been studied in the human microbiome. Here, we investigated the distribution of PT-harboring strains and verified their existence in the human microbiome. We found over 2000 PT gene-containing strains distributed in different body sites, especially in the gastrointestinal tract. PT-modifying genes are preferentially distributed within several genera, including Pseudomonas, Clostridioides, and Escherichia, with phylogenic diversities. We also assessed the PT modification patterns and found six new PT-linked dinucleotides (CpsG, CpsT, ApsG, TpsG, GpsC, ApsT) in human fecal DNA. To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. These results confirmed that human microbiome is a rich reservoir for PT-containing microbes and contains a wide variety of PT modification patterns.National Natural Science Foundation of China (31630002, 31700029, 31770038 and 21661140002)National Key R & D Program of China (2018YFA0900400)National Science Foundation (CHE-1709364

A new marine epipsammic diatom species, Ambo dajingensis sp. nov. (Bacillariophyceae), from the coast of Southeast China

Ambo dajingensis HH Liu, Z Wang, YH Gao & CP Chen, sp. nov. is described as a new species in samples collected from sand grains at Dajing Beach, Ningde City, Fujian Province, China. Morphological details of the new species with respect to valve shape, size and valve ultrastructure are presented based on light microscopy (LM) and scanning electron microscopy (SEM). The main features of Ambo dajingensis under a light microscope are elongated elliptic valves with rounded apices, two internal costae on the valve and rectangular in girdle views. SEM observation showed that externally, the frustules are comprised of two valves with a relatively deep mantle and a transition between the valve faces. Small, flabelliform spines are present along the valve margin. Internally, the valves are divided into three sectors by robust costae, which penetrate the whole valve lumen and are thickest at the mantle interior and thinner toward the center. The sternum is narrow and linear, visible only in the valve apex, set off by costae. The striae are comprised of small, round areolae and they are parallel in the middle to slightly radiate at the apices. The new species is compared with other species in the genus Ambo