Structure of the NS1 Protein N-Terminal Origin Recognition/Nickase Domain from the Emerging Human Bocavirus

This is the publisher's version, also available electronically from http://www.asm.org/Human bocavirus is a newly identified, globally prevalent, parvovirus that is associated with respiratory infection in infants and young children. Parvoviruses encode a large nonstructural protein 1 (NS1) that is essential for replication of the viral single-stranded DNA genome and DNA packaging and may play versatile roles in virus-host interactions. Here, we report the structure of the human bocavirus NS1 N-terminal domain, the first for any autonomous parvovirus. The structure shows an overall fold that is canonical to the histidine-hydrophobic-histidine superfamily of nucleases, which integrates two distinct DNA-binding sites: (i) a positively charged region mediated by a surface hairpin (residues 190 to 198) that is responsible for recognition of the viral origin of replication of the double-stranded DNA nature and (ii) the nickase active site that binds to the single-stranded DNA substrate for site-specific cleavage. The structure reveals an acidic-residue-rich subdomain that is present in bocavirus NS1 proteins but not in the NS1 orthologs in erythrovirus or dependovirus, which may mediate bocavirus-specific interaction with DNA or potential host factors. These results provide insights into recognition of the origin of replication and nicking of DNA during bocavirus genome replication. Mapping of variable amino acid residues of NS1s from four human bocavirus species onto the structure shows a scattered pattern, but the origin recognition site and the nuclease active site are invariable, suggesting potential targets for antivirals against this clade of highly diverse human viruses

The human parvovirus B19 non-structural protein 1 N-terminal domain specifically binds to the origin of replication in the viral DNA

The non-structural protein 1 (NS1) of human parvovirus B19 plays a critical role in viral DNA replication. Previous studies identified the origin of replication in the viral DNA, which contains four DNA elements, namely NSBE1 to NSBE4, that are required for optimal viral replication (Guan et al, 2009, J. Virology, 83, 9541-9553). Here we have demonstrated in vitro that the NS1 N-terminal domain (NS1N) binds to the origin of replication in a sequence-specific, length-dependent manner that requires NSBE1 and NSBE2, while NSBE3 and NSBE4 are dispensable. Mutagenesis analysis has identified nucleotides in NSBE1 and NSBE2 that are critical for NS1N binding. These results suggest that NS1 binds to the NSBE1-NSBE2 region in the origin of replication, while NSBE3 and NSBE4 may provide binding sites for potential cellular factors. Such a specialized nucleoprotein complex may enable NS1 to nick the terminal resolution site and separate DNA strands during replication

The human parvovirus B19 non-structural protein 1 N-terminal domain specifically binds to the origin of replication in the viral DNA

The non-structural protein 1 (NS1) of human parvovirus B19 plays a critical role in viral DNA replication. Previous studies identified the origin of replication in the viral DNA, which contains four DNA elements, namely NSBE1 to NSBE4, that are required for optimal viral replication (Guan et al, 2009, J. Virology, 83, 9541-9553). Here we have demonstrated in vitro that the NS1 N-terminal domain (NS1N) binds to the origin of replication in a sequence-specific, length-dependent manner that requires NSBE1 and NSBE2, while NSBE3 and NSBE4 are dispensable. Mutagenesis analysis has identified nucleotides in NSBE1 and NSBE2 that are critical for NS1N binding. These results suggest that NS1 binds to the NSBE1-NSBE2 region in the origin of replication, while NSBE3 and NSBE4 may provide binding sites for potential cellular factors. Such a specialized nucleoprotein complex may enable NS1 to nick the terminal resolution site and separate DNA strands during replication

Transcriptome-wide identification and characterization of miRNAs from Pinus densata

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) play key roles in diverse developmental processes, nutrient homeostasis and responses to biotic and abiotic stresses. The biogenesis and regulatory functions of miRNAs have been intensively studied in model angiosperms, such as <it>Arabidopsis thaliana</it>, <it>Oryza sativa </it>and <it>Populus trichocarpa</it>. However, global identification of <it>Pinus densata </it>miRNAs has not been reported in previous research.</p> <p>Results</p> <p>Here, we report the identification of 34 conserved miRNAs belonging to 25 miRNA families from a <it>P. densata </it>mRNA transcriptome database using local BLAST and MIREAP programs. The primary and/or precursor sequences of 29 miRNAs were further confirmed by RT-PCR amplification and subsequent sequencing. The average value of the minimal folding free energy indexes of the 34 miRNA precursors was 0.92. Nineteen (58%) mature miRNAs began with a 5' terminal uridine residue. Analysis of miRNA precursors showed that 19 mature miRNAs were novel members of 14 conserved miRNA families, of which 17 miRNAs were further validated by subcloning and sequencing. Using real-time quantitative RT-PCR, we found that the expression levels of 7 miRNAs were more than 2-fold higher in needles than in stems. In addition, 72 <it>P. densata </it>mRNAs were predicted to be targets of 25 miRNA families. Four target genes, including a nodal modulator 1-like protein gene, two GRAS family transcription factor protein genes and one histone deacetylase gene, were experimentally verified to be the targets of 3 <it>P. densata </it>miRNAs, pde-miR162a, pde-miR171a and pde-miR482a, respectively.</p> <p>Conclusions</p> <p>This study led to the discovery of 34 conserved miRNAs comprising 25 miRNA families from <it>Pinus densata</it>. These results lay a solid foundation for further studying the regulative roles of miRNAs in the development, growth and responses to environmental stresses in <it>P. densata</it>.</p

Comparisons of short-term and long-term results between laparoscopic between open pancreaticoduodenectomy for pancreatic tumors: A systematic review and meta-analysis

Objective: The efficacy of pancreaticoduodenectomy and open pancreaticoduodenectomy for pancreatic tumors is controversial. The study aims to compare the efficacy of laparoscopic pancreaticoduodenectomy (LPD) and open pancreaticoduodenectomy (OPD) in the treatment of pancreatic tumors through systematic evaluation and meta-analysis.Methods: PubMed, Embase, Cochrane Library and Web of science databases were searched for clinical studies on the treatment of pancreatic tumors with LPD and OPD. The end time for the searches was 20 July 2022. Rigorous inclusion and exclusion criteria were used to screen the articles, the Cochrane manual was used to evaluate the quality of the included articles, and the stata15.0 software was used for statistical analysis of the indicators.Results: In total, 16 articles were included, including two randomized controlled trials and 14 retrospective studies. Involving a total of 4416 patients, 1275 patients were included in the LPD group and 3141 patients in the OPD group. The results of the meta-analysis showed that: the operation time of LPD was longer than that of OPD [WMD = 56.14,95% CI (38.39,73.89), p = 0.001]; the amount of intraoperative blood loss of LPD was less than that of OPD [WMD = −120.82,95% CI (−169.33, −72.30), p = 0.001]. No significant difference was observed between LPD and OPD regarding hospitalization time [WMD = −0.5,95% CI (−1.35, 0.35), p = 0.250]. No significant difference was observed regarding postoperative complications [RR = 0.96,95% CI (0.86,1.07, p = 0.463]. And there was no significant difference regarding 1-year OS and 3-year OS: 1-year OS [RR = 1.02,95% CI (0.97,1.08), p = 0.417], 3-year OS [RR = 1.10 95% CI (0.75, 1.62), p = 0.614%].Conclusion: In comparison with OPD, LPD leads to less blood loss but longer operation time, therefore the bleeding rate per unit time of LPD is less than that of OPD. LPD has obvious advantages. With the increase of clinical application of LPD, the usage of LPD in patients with pancreatic cancer has very good prospect. Due to the limitations of this paper, in future studies, more attention should be paid to high-quality, multi-center, randomized controlled studies

Nomogram based on computed tomography images and clinical data for distinguishing between primary intestinal lymphoma and Crohn’s disease: a retrospective multicenter study

BackgroundDifferential diagnosis of primary intestinal lymphoma (PIL) and Crohn’s disease (CD) is a challenge in clinical diagnosis.AimsTo investigate the validity of the nomogram based on clinical and computed tomography (CT) features to identify PIL and CD.MethodsThis study retrospectively analyzed laboratory parameters, demographic characteristics, clinical manifestations, and CT imaging features of PIL and CD patients from two centers. Univariate logistic analysis was performed for each variable, and laboratory parameter model, clinical model and imaging features model were developed separately. Finally, a nomogram was established. All models were evaluated using the area under the curve (AUC), accuracy, sensitivity, specificity, and decision curve analysis (DCA).ResultsThis study collected data from 121 patients (PIL = 69, CD = 52) from Center 1. Data from 43 patients (PIL = 24, CD = 19) were collected at Center 2 as an external validation cohort to validate the robustness of the model. Three models and a nomogram were developed to distinguish PIL from CD. Most models performed well from the external validation cohort. The nomogram showed the best performance with an AUC of 0.921 (95% CI: 0.838–1.000) and sensitivities, specificities, and accuracies of 0.945, 0.792, and 0.860, respectively.ConclusionA nomogram combining clinical data and imaging features was constructed, which can effectively distinguish PIL from CD

Interleukin-22 Inhibits Bleomycin-Induced Pulmonary Fibrosis

Pulmonary fibrosis is a progressive and fatal fibrotic disease of the lungs with unclear etiology. Recent insight has suggested that early injury/inflammation of alveolar epithelial cells could lead to dysregulation of tissue repair driven by multiple cytokines. Although dysregulation of interleukin- (IL-) 22 is involved in various pulmonary pathophysiological processes, the role of IL-22 in fibrotic lung diseases is still unclear and needs to be further addressed. Here we investigated the effect of IL-22 on alveolar epithelial cells in the bleomycin- (BLM-) induced pulmonary fibrosis. BLM-treated mice showed significantly decreased level of IL-22 in the lung. IL-22 produced γδT cells were also decreased significantly both in the tissues of lungs and spleens. Administration of recombinant human IL-22 to alveolar epithelial cell line A549 cells ameliorated epithelial to mesenchymal transition (EMT) and partially reversed the impaired cell viability induced by BLM. Furthermore, blockage of IL-22 deteriorated pulmonary fibrosis, with elevated EMT marker (α-smooth muscle actin (α-SMA)) and overactivated Smad2. Our results indicate that IL-22 may play a protective role in the development of BLM-induced pulmonary fibrosis and may suggest IL-22 as a novel immunotherapy tool in treating pulmonary fibrosis