Isolation, identification, and complete genome sequence of a bovine adenovirus type 3 from cattle in China

<p>Abstract</p> <p>Background</p> <p>Bovine adenovirus type 3 (BAV-3) belongs to the <it>Mastadenovirus </it>genus of the family <it>Adenoviridae </it>and is involved in respiratory and enteric infections of calves. The isolation of BAV-3 has not been reported prior to this study in China. In 2009, there were many cases in cattle showing similar clinical signs to BAV-3 infection and a virus strain, showing cytopathic effect in Madin-Darby bovine kidney cells, was isolated from a bovine nasal swab collected from feedlot cattle in Heilongjiang Province, China. The isolate was confirmed as a bovine adenovirus type 3 by PCR and immunofluorescence assay, and named as HLJ0955. So far only the complete genome sequence of prototype of BAV-3 WBR-1 strain has been reported. In order to further characterize the Chinese isolate HLJ0955, the complete genome sequence of HLJ0955 was determined.</p> <p>Results</p> <p>The size of the genome of the Chinese isolate HLJ0955 is 34,132 nucleotides in length with a G+C content of 53.6%. The coding sequences for gene regions of HLJ0955 isolate were similar to the prototype of BAV-3 WBR-1 strain, with 80.0-98.6% nucleotide and 87.5-98.8% amino acid identities. The genome of HLJ0955 strain contains 16 regions and four deletions in inverted terminal repeats, E1B region and E4 region, respectively. The complete genome and DNA binding protein gene based phylogenetic analysis with other adenoviruses were performed and the results showed that HLJ0955 isolate belonged to BAV-3 and clustered within the <it>Mastadenovirus </it>genus of the family <it>Adenoviridae</it>.</p> <p>Conclusions</p> <p>This is the first study to report the isolation and molecular characterization of BAV-3 from cattle in China. The phylogenetic analysis performed in this study supported the use of the DNA binding protein gene of adenovirus as an appropriate subgenomic target for the classification of different genuses of the family <it>Adenoviridae </it>on the molecular basis. Meanwhile, a large-scale pathogen and serological epidemiological investigations for BVA-3 infection might be carried out in cattle in China. This report will be a good beginning for further studies on BAV-3 in China.</p

The Mesozoic magmatic, metamorphic, and tectonic evolution of the eastern Gangdese magmatic arc, southern Tibet

Magmatic arcs are natural laboratories for studying the growth of continental crusts. The Gangdese arc, southern Tibet, is an archetypal continental magmatic arc that formed due to Mesozoic subduction of the Neo-Tethyan oceanic lithosphere; however, its formation and evolution remain controversial. In this contribution, we combine newly reported and previously published geochemical and geochronological data for Mesozoic magmatic rocks in the eastern Gangdese arc to reveal its magmatic and metamorphic histories and review its growth, thickening, and fractionation and mineralization processes. Our results show that: (1) the Gangdese arc consists of multiple Mesozoic arc-type magmatic rocks and records voluminous juvenile crustal growth. (2) The Mesozoic magmatic rocks experienced Late Cretaceous granulite-facies metamorphism and partial melting, thus producing hydrous and metallogenic element-rich migmatites that form a major component of the lower arc crust and are a potential source for the Miocene ore-hosting porphyries. (3) The Gangdese arc witnessed crustal thickening and reworking during the Middle to Late Jurassic and Late Cretaceous. (4) Crystallization-fractionation of mantle-derived magmas and partial melting of thickened juvenile lower crust induced intracrustal chemical differentiation during subduction. We suggest that the Gangdese arc underwent the following main tectonic, magmatic, and metamorphic evolution processes: normal subduction and associated mantle-derived magmatism during the Late Triassic to Jurassic; shallow subduction during the Early Cretaceous and an associated magmatic lull; and mid-oceanic ridge subduction, high-temperature metamorphism and an associated magmatic flare-up during the early Late Cretaceous, and flat subduction, high-temperature and high-pressure metamorphism, partial melting, and associated crust-derived magmatism during the late Late Cretaceous. Key issues for further research include the temporal and spatial distributions of Mesozoic magmatic rocks, the evolution of the components and compositions of arc crust over time, and the metallogenic processes that occur in such environments during subduction

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans

Histones are the major proteinaceous component of chromatin in eukaryotic cells and an important part of the epigenome, affecting most DNA-related events, including transcription, DNA replication, and chromosome segregation. The properties of histones are greatly influenced by their post-translational modifications (PTMs), over 200 of which are known today. Given this large number, researchers need sophisticated methods to study histone PTMs comprehensively. In particular, mass spectrometry (MS)-based approaches have gained popularity, allowing for the quantification of dozens of histone PTMs at once. Using these approaches, even the study of co-occurring PTMs and the discovery of novel PTMs become feasible. The success of MS-based approaches relies substantially on obtaining pure and well-preserved histones for analysis, which can be difficult depending on the source material. Caenorhabditis elegans has been a popular model organism to study the epigenome, but isolation of pure histones from these animals has been challenging. Here, we address this issue, presenting a method for efficient isolation of pure histone proteins from C. elegans at good yield. Further, we describe an MS pipeline optimized for accurate relative quantification of histone PTMs from C. elegans. We alkylate and tryptically digest the histones, analyze them by bottom-up MS, and then evaluate the resulting data by a C. elegans-adapted version of the software EpiProfile 2.0. Finally, we show the utility of this pipeline by determining differences in histone PTMs between C. elegans strains that age at different rates and thereby achieve very different lifespans. © 2020 The Authors. Basic Protocol 1: Large-scale growth and harvesting of synchronized C. elegans Basic Protocol 2: Nuclear preparation, histone extraction, and histone purification Basic Protocol 3: Bottom-up mass spectrometry analysis of histone PTMs and histone variants

Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells

In mammalian cells, when tandem affinity purification (TAP) approach is employed, the existence of untagged endogenous target protein and repetitive washing steps together result in overall low yield of purified/stable complexes and the loss of weakly and transiently interacting partners of biological significance. To avoid the trade-offs involving in methodological sensitivity, precision, and throughput here we introduce an integrated method, biotin tagging coupled with amino acid-coded mass tagging (BioCAT) for highly sensitive and accurate screening of mammalian protein-protein interactions (PPIs). Without the need of establishing a stable cell line, using a short peptide tag which could be specifically biotinylated in vivo, the biotin-tagged target/bait protein was then isolated along with its associates efficiently by streptavidin magnetic microbeads in a single step. In a pulled-down complex amino acid-coded mass tagging (AACT) serves as ‘in-spectra’ quantitative markers to distinguish those bait-specific interactors from non-specific background proteins under stringent criteria. Applying this BioCAT approach, we first biotin-tagged in vivo a multi-functional protein family member, 14-3-3ε, which was expressed at close to endogenous level. Starting with approximately 20 millions of 293T cells which were significantly less than what needed for a TAP run, 266 specific interactors of 14-3-3ε were identified in high confidence

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

Motivation: Identification of post-translationally modified proteins has become one of the central issues of current proteomics. Spectral library search is a new and promising computational approach to mass spectrometry-based protein identification. However, its potential in identification of unanticipated post-translational modifications has rarely been explored. The existing spectral library search tools are designed to match the query spectrum to the reference library spectra with the same peptide mass. Thus, spectra of peptides with unanticipated modifications cannot be identified

Hollow Sodium Tungsten Bronze (Na0.15WO3) Nanospheres: Preparation, Characterization, and Their Adsorption Properties

We report herein a facile method for the preparation of sodium tungsten bronzes hollow nanospheres using hydrogen gas bubbles as reactant for chemical reduction of tungstate to tungsten and as template for the formation of hollow nanospheres at the same time. The chemical composition and the crystalline state of the as-prepared hollow Na0.15WO3nanospheres were characterized complementarily, and the hollow structure formation mechanism was proposed. The hollow Na0.15WO3nanospheres showed large Brunauer–Emment–Teller specific area (33.8 m2 g−1), strong resistance to acids, and excellent ability to remove organic molecules such as dye and proteins from aqueous solutions. These illustrate that the hollow nanospheres of Na0.15WO3should be a useful adsorbent

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead