The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-Containing DNA Virus

Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-Å resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel β-barrel, “jelly-roll” domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-Å diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus

On the thermal and mechanical properties of Mg0.2_{0.2}Co0.2_{0.2}Ni0.2_{0.2}Cu0.2_{0.2}Zn0.2_{0.2}O across the high-entropy to entropy-stabilized transition

As various property studies continue to emerge on high entropy and entropy-stabilized ceramics, we seek further understanding of property changes across the phase boundary between \enquote{high-entropy} and \enquote{entropy-stabilized}. The thermal and mechanical properties of bulk ceramic entropy stabilized oxide composition Mg$_{0.2}$Co$_{0.2}$Ni$_{0.2}$Cu$_{0.2}$Zn$_{0.2}$O are investigated across this critical transition temperature via the transient plane-source method, temperature-dependent X-ray diffraction, and nano-indentation. Thermal conductivity remains constant within uncertainty across the multi-to-single phase transition at a value of ~2.5 W/mK, while the linear coefficient of thermal expansion increases nearly 24 % from 10.8 to 14.1 x 10$^{-6}$ K$^{-1}$. Mechanical softening is also observed across the transition.Comment: 14 pages, 4 figures, to be published in APL Material

Preliminary Results on Light Conditions Manipulation in Octopus vulgaris (Cuvier, 1797) Paralarval Rearing

High paralarvae mortality is a major bottleneck currently hindering the control over the lifecycle of common octopus (Octopus vulgaris Cuvier, 1797). It is believed that this problem might be related to either zoo-technical and/or nutritional aspects. The present paper is focused on the study of different zoo-technical aspects related to light conditions on the rearing of paralarvae, including the effects of polarization in prey ingestion, the use of a blue filter to simulate natural conditions, and the use of focused light to avoid reflections of the rearing tank’s walls. In the first experiment, O. vulgaris paralarvae ingestion of Artemia sp. and copepods (Tisbe sp.) was assessed under either normal or polarized light. In the second experiment, the effect of a blue filter with natural light or focused artificial light on growth and mortality was assessed over 15 days of rearing. Ingestion rate was not influenced by light polarization. Nonetheless, a significantly higher ingestion of Artemia sp. with respect to copepods was observed. The blue filter promoted the use of natural light conditions in Octopus paralarval culture, while focused light reduced the collision of the paralarvae against the walls. However, no significant differences were found in paralarval growth nor survivalEn prens

Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior

Purpose We describe a novel neurobehavioral phenotype of autism spectrum disorder (ASD), intellectual disability, and/or attention-deficit/hyperactivity disorder (ADHD) associated with de novo or inherited deleterious variants in members of the RFX family of genes. RFX genes are evolutionarily conserved transcription factors that act as master regulators of central nervous system development and ciliogenesis. Methods We assembled a cohort of 38 individuals (from 33 unrelated families) with de novo variants in RFX3, RFX4, and RFX7. We describe their common clinical phenotypes and present bioinformatic analyses of expression patterns and downstream targets of these genes as they relate to other neurodevelopmental risk genes. Results These individuals share neurobehavioral features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. Conclusion These results establish a likely role of deleterious variation in RFX3, RFX4, and RFX7 in cases of monogenic intellectual disability, ADHD and ASD, and position these genes as potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis

Genome Expression Profile Analysis of the Immature Maize Embryo during Dedifferentiation

Maize is one of the most important cereal crops worldwide and one of the primary targets of genetic manipulation, which provides an excellent way to promote its production. However, the obvious difference of the dedifferentiation frequency of immature maize embryo among various genotypes indicates that its genetic transformation is dependence on genotype and immature embryo-derived undifferentiated cells. To identify important genes and metabolic pathways involved in forming of embryo-derived embryonic calli, in this study, DGE (differential gene expression) analysis was performed on stages I, II, and III of maize inbred line 18-599R and corresponding control during the process of immature embryo dedifferentiation. A total of ∼21 million cDNA tags were sequenced, and 4,849,453, 5,076,030, 4,931,339, and 5,130,573 clean tags were obtained in the libraries of the samples and the control, respectively. In comparison with the control, 251, 324 and 313 differentially expressed genes (DEGs) were identified in the three stages with more than five folds, respectively. Interestingly, it is revealed that all the DEGs are related to metabolism, cellular process, and signaling and information storage and processing functions. Particularly, the genes involved in amino acid and carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis and signal transduction mechanism have been significantly changed during the dedifferentiation. To our best knowledge, this study is the first genome-wide effort to investigate the transcriptional changes in dedifferentiation immature maize embryos and the identified DEGs can serve as a basis for further functional characterization

Computational studies and optimization of wakefield accelerators

Laser- and particle beam-driven plasma wakefield accelerators produce accelerating fields thousands of times higher than radio-frequency accelerators, offering compactness and ultrafast bunches to extend the frontiers of high energy physics and to enable laboratory-scale radiation sources. Large-scale kinetic simulations provide essential understanding of accelerator physics to advance beam performance and stability and show and predict the physics behind recent demonstration of narrow energy spread bunches. Benchmarking between codes is establishing validity of the models used and, by testing new reduced models, is extending the reach of simulations to cover upcoming meter-scale multi-GeV experiments. This includes new models that exploit Lorentz boosted simulation frames to speed calculations. Simulations of experiments showed that recently demonstrated plasma gradient injection of electrons can be used as an injector to increase beam quality by orders of magnitude. Simulations are now also modeling accelerator stages of tens of GeV, staging of modules, and new positron sources to design next-generation experiments and to use in applications in high energy physics and light sources

Effect of Magnesium and Zinc Ions on the Hydration Kinetics of C3S

Impure tricalcium silicate (C3S) in portland cement may contain various foreign ions. These ions can stabilize different polymorphs of C3S at room temperature and may affect its reactivity. In this paper, the effects of magnesium and zinc on the polymorph type, hydration kinetics, and the hydrate morphology of C3S were investigated. The pure C3S has the T1 structure while magnesium and zinc stabilize polymorphs M3 and T2/T3, respectively. The two elements have distinct effects on the hydration kinetics. Zinc increases the maximum heat released. Magnesium increases the hydration peak width. The C-S-H morphology is modified, leading to longer needles in the presence of zinc and thicker needles in the presence of magnesium. Zinc is incorporated into C-S-H, while magnesium is only incorporated slightly, if at all, but rather seems to inhibit nucleation. Implementing experimentally measured parameters for C-S-H nucleation and growth in the ic hydration model captured well the observed changes in hydration kinetics. This supports C-S-H nucleation and growth to be rate controlling in the hydration of C3S

On the thermal and mechanical properties of Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O across the high-entropy to entropy-stabilized transition

As various property studies continue to emerge on high entropy and entropy-stabilized ceramics, we seek a further understanding of the property changes across the phase boundary between “high-entropy” and “entropy-stabilized” phases. The thermal and mechanical properties of bulk ceramic entropy stabilized oxide composition Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O are investigated across this critical transition temperature via the transient plane-source method, temperature-dependent x-ray diffraction, and nano-indentation. The thermal conductivity remains constant within uncertainty across the multi-to-single phase transition at a value of ≈2.5 W/mK, while the linear coefficient of thermal expansion increases nearly 24% from 10.8 to 14.1 × 10−6 K−1. Mechanical softening is also observed across the transition

Drafting the Kensington Pride Mango Genome

The mango industry in Australia is worth in excess of $150 million annually with the Kensington Pride (KP) cultivar capturing 60% of the domestic market. Valued by consumers for desirable taste and colour characteristics, KP has been used extensively as a parent in the Department of Agriculture and Fisheries’ (Queensland, Australia) mango breeding program with over 400 hybrid trees sharing KP as the male parent. In order to gain a better understanding of Australia’s most significant mango variety, Horticulture Innovation Australia had led an international collaboration between the Queensland Department of Agriculture and Fisheries (Australia), the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, India) and the Beijing Genomics Institute (China) to sequence the KP genome. Preliminary de novo assembly of illumina short read sequence data suggests that the KP genome is highly heterozygous and has an estimated genome size of 407 Mb. As refinements and additional sequence data are added to the assembly, a more complete picture of the mango genome will be elucidated