Crystal structure of E. coli arginyl-tRNA synthetase and ligand binding studies revealed key residues in arginine recognition

The arginyl-tRNA synthetase (ArgRS) catalyzes the esterification reaction between L-arginine and its cognate tRNA(Arg). Previously reported structures of ArgRS shed considerable light on the tRNA recognition mechanism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS (eArgRS) complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry (ITC). Combined with previously reported work on ArgRS, our results elucidated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13238-013-0012-1) contains supplementary material, which is available to authorized users

Exosomes serve as tumour markers for personalized diagnostics owing to their important role in cancer metastasis

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License CC BY-NC 4.0 ( http://creativecommons.org/licenses/by-nc/4.0/ ), permitting all non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Exosomes, membrane vesicles of 40-100 nm in diameter, are derived from endosomes in various cells. The bioactive molecules specifically packed into exosomes can be horizontally transferred into recipient cells changing their biological properties, by which tumour cells continuously modify their surrounding microenvironment and distant target cells favouring cancer metastasis. It has been suspected for a long time that exosomes participate in the whole process of tumour metastasis. Although there is much unknown and many controversies in the role of cancer exosome, the major contribution of tumour-associated exosomes to different steps of cancer metastasis are demonstrated in this review. Mainly because these exosomes are easily accessible and capable of representing their parental cells, exosomes draw much attention as a promising biomarker for tumour screening, diagnosis and prognosis. Currently, researchers have found numerous biomarkers in exosomes with great potential to be utilized in personalized medicine. In this article, we summarize the roles of biomarkers, which are validated by clinical samples. Even though many conundrums remain, such as exosome extraction, large multicentre validation of biomarkers and data interpretation, exosomes are certain to be used in clinical practice in the near future as the field rapidly expands.Peer reviewedFinal Published versio

KCAT: A Knowledge-Constraint Typing Annotation Tool

Fine-grained Entity Typing is a tough task which suffers from noise samples extracted from distant supervision. Thousands of manually annotated samples can achieve greater performance than millions of samples generated by the previous distant supervision method. Whereas, it's hard for human beings to differentiate and memorize thousands of types, thus making large-scale human labeling hardly possible. In this paper, we introduce a Knowledge-Constraint Typing Annotation Tool (KCAT), which is efficient for fine-grained entity typing annotation. KCAT reduces the size of candidate types to an acceptable range for human beings through entity linking and provides a Multi-step Typing scheme to revise the entity linking result. Moreover, KCAT provides an efficient Annotator Client to accelerate the annotation process and a comprehensive Manager Module to analyse crowdsourcing annotations. Experiment shows that KCAT can significantly improve annotation efficiency, the time consumption increases slowly as the size of type set expands.Comment: 6 pages, acl2019 demo pape

Space advanced technology demonstration satellite

The Space Advanced Technology demonstration satellite (SATech-01), a mission for low-cost space science and new technology experiments, organized by Chinese Academy of Sciences (CAS), was successfully launched into a Sun-synchronous orbit at an altitude of similar to 500 km on July 27, 2022, from the Jiuquan Satellite Launch Centre. Serving as an experimental platform for space science exploration and the demonstration of advanced common technologies in orbit, SATech-01 is equipped with 16 experimental payloads, including the solar upper transition region imager (SUTRI), the lobster eye imager for astronomy (LEIA), the high energy burst searcher (HEBS), and a High Precision Magnetic Field Measurement System based on a CPT Magnetometer (CPT). It also incorporates an imager with freeform optics, an integrated thermal imaging sensor, and a multi-functional integrated imager, etc. This paper provides an overview of SATech-01, including a technical description of the satellite and its scientific payloads, along with their on-orbit performance

The adenovirus major core protein VII is dispensable for virion assembly but is essential for lytic infection

The Adenovirus (Ad) genome within the capsid is tightly associated with a virus-encoded, histone-like core protein—protein VII. Two other Ad core proteins, V and X/μ, also are located within the virion and are loosely associated with viral DNA. Core protein VII remains associated with the Ad genome during the early phase of infection. It is not known if naked Ad DNA is packaged into the capsid, as with dsDNA bacteriophage and herpesviruses, followed by the encapsidation of viral core proteins, or if a unique packaging mechanism exists with Ad where a DNA-protein complex is simultaneously packaged into the virion. The latter model would require an entirely new molecular mechanism for packaging compared to known viral packaging motors. We characterized a virus with a conditional knockout of core protein VII. Remarkably, virus particles were assembled efficiently in the absence of protein VII. No changes in protein composition were evident with VII−virus particles, including the abundance of core protein V, but changes in the proteolytic processing of some capsid proteins were evident. Virus particles that lack protein VII enter the cell, but incoming virions did not escape efficiently from endosomes. This greatly diminished all subsequent aspects of the infectious cycle. These results reveal that the Ad major core protein VII is not required to condense viral DNA within the capsid, but rather plays an unexpected role during virus maturation and the early stages of infection. These results establish a new paradigm pertaining to the Ad assembly mechanism and reveal a new and important role of protein VII in early stages of infection

E2F/Rb Family Proteins Mediate Interferon Induced Repression of Adenovirus Immediate Early Transcription to Promote Persistent Viral Infection

<div><p>Interferons (IFNs) are cytokines that have pleiotropic effects and play important roles in innate and adaptive immunity. IFNs have broad antiviral properties and function by different mechanisms. IFNs fail to inhibit wild-type Adenovirus (Ad) replication in established cancer cell lines. In this study, we analyzed the effects of IFNs on Ad replication in normal human cells. Our data demonstrate that both IFNα and IFNγ blocked wild-type Ad5 replication in primary human bronchial epithelial cells (NHBEC) and TERT-immortalized normal human diploid fibroblasts (HDF-TERT). IFNs inhibited the replication of divergent adenoviruses. The inhibition of Ad5 replication by IFNα and IFNγ is the consequence of repression of transcription of the E1A immediate early gene product. Both IFNα and IFNγ impede the association of the transactivator GABP with the E1A enhancer region during the early phase of infection. The repression of E1A expression by IFNs requires a conserved E2F binding site in the E1A enhancer, and IFNs increased the enrichment of the E2F-associated pocket proteins, Rb and p107, at the E1A enhancer <i>in vivo</i>. PD0332991 (Pabociclib), a specific CDK4/6 inhibitor, dephosphoryles pocket proteins to promote their interaction with E2Fs and inhibited wild-type Ad5 replication dependent on the conserved E2F binding site. Consistent with this result, expression of the small E1A oncoprotein, which abrogates E2F/pocket protein interactions, rescued Ad replication in the presence of IFNα or IFNγ. Finally, we established a persistent Ad infection model <i>in vitro</i> and demonstrated that IFNγ suppresses productive Ad replication in a manner dependent on the E2F binding site in the E1A enhancer. This is the first study that probes the molecular basis of persistent adenovirus infection and reveals a novel mechanism by which adenoviruses utilize IFN signaling to suppress lytic virus replication and to promote persistent infection.</p></div

Crowd science and engineering: concept and research framework

Purpose – The synthetic application and interaction of/between the internet, Internet of Things, cloud computing, big data, Industry 4.0 and other new patterns and new technologies shall breed future Web-based industrial operation system and social operation management patterns, manifesting as a crowd cyber eco-system composed of multiple interconnected intelligent agents (enterprises, individuals and governmental agencies) and its dynamic behaviors. This paper aims to explore the basic principles and laws of such a system and its behavior. Design/methodology/approach – The authors propose the concepts of crowd science and engineering (CSE) and expound its main content, thus forming a research framework of theories and methodologies of crowd science. Findings – CSE is expected to substantially promote the formation and development of crowd science and thus lay a foundation for the advancement of Web-based industrial operation system and social operation management patterns. Originality/value – This paper is the first one to propose the concepts of CSE, which lights the beacon for the future research in this area

Detecting Melanocortin 1 Receptor Gene’s SNPs by CRISPR/enAsCas12a

Beyond its powerful genome-editing capabilities, the CRISPR/Cas system has opened up a new era of molecular diagnostics due to its highly specific base recognition and trans-cleavage activity. However, most CRISPR/Cas detection systems are mainly used to detect nucleic acids of bacteria or viruses, while the application of single nucleotide polymorphism (SNP) detection is limited. The MC1R SNPs were investigated by CRISPR/enAsCas12a and are not limited to the protospacer adjacent motif (PAM) sequence in vitro. Specifically, we optimized the reaction conditions, which proved that the enAsCas12a has a preference for divalent magnesium ion (Mg2+) and can effectively distinguish the genes with a single base difference in the presence of Mg2+, and the Melanocortin l receptor (MC1R) gene with three kinds of SNP sites (T305C, T363C, and G727A) was quantitatively detected. Since the enAsCas12a is not limited by PAM sequence in vitro, the method shown here can extend this extraordinary CRISPR/enAsCas12a detection system to other SNP targets, thus providing a general SNP detection toolbox

IFN inhibition of replication is conserved among different Ad serotypes.

<p>(A) Nucleotide sequence alignment of the E1A enhancer regions from different Ad subgroups (serotypes Ad5, Ad3, Ad4, Ad9 and Ad12 corresponding to Ad subgroups C, B, E, D and A, respectively). Homologies (≥75% identity) are shaded in blue. The GABP and E2F binding sites, as well packaging repeats (arrowhead A1-5), are indicated. (B) HDF-TERT cells were treated with IFNs or left untreated for 24 hr and then infected with 25 virus particles/cell Ad5, Ad3, Ad4, or Ad12 or 5 virus particles/cell Ad9. Nuclear DNA was isolated at 6 hr post-infection to determine virus input and at 72 hr post-infection with Ad3, Ad4, Ad9 and Ad12 or at 48 hr post-infection with Ad5 to measure replication. Viral DNA levels were quantified by qPCR using a primer that recognizes conserved sequence in E1A (AdE1A-Pan) in combination with a serotype-specific primer (S1 Table in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005415#ppat.1005415.s001" target="_blank">S1 Materials and Methods</a>). The values were normalized to 1.0 in untreated cells and are plotted as mean ± sd, n = 3.</p