Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes.

Horizontal transfer of genetic materials between virus and host has been frequently identified. Three rice planthoppers, Laodelphax striatellus, Nilaparvata lugens, and Sogatella furcifera, are agriculturally important insects because they are destructive rice pests and also the vector of a number of phytopathogenic viruses. In this study, we discovered that a small region (∼300 nucleotides [nt]) of the genome of invertebrate iridescent virus 6 (IIV-6; genus Iridovirus, family Iridoviridae), a giant DNA virus that infects invertebrates but is not known to infect planthoppers, is highly homologous to the sequences present in high copy numbers in these three planthopper genomes. These sequences are related to the short interspersed nuclear elements (SINEs), a class of non-long terminal repeat (LTR) retrotransposons (retroposons), suggesting a horizontal transfer event of a transposable element from the rice planthopper genome to the IIV-6 genome. In addition, a number of planthopper transcripts mapped to these rice planthopper SINE-like sequences (RPSlSs) were identified and appear to be transcriptionally regulated along the different developmental stages of planthoppers. Small RNAs derived from these RPSlSs are predominantly 26 to 28 nt long, which is a typical characteristic of PIWI-interacting RNAs. Phylogenetic analysis suggests that IIV-6 acquires a SINE-like retrotransposon from S. furcifera after the evolutionary divergence of the three rice planthoppers. This study provides further examples of the horizontal transfer of an insect transposon to virus and suggests the association of rice planthoppers with iridoviruses in the past or present.IMPORTANCE This study provides an example of the horizontal transfer event from a rice planthopper genome to an IIV-6 genome. A small region of the IIV-6 genome (∼300 nt) is highly homologous to the sequences presented in high copy numbers of three rice planthopper genomes that are related to the SINEs, a class of retroposons. The expression of these planthopper SINE-like sequences was confirmed, and corresponding Piwi-interacting RNA-like small RNAs were identified and comprehensively characterized. Phylogenetic analysis suggests that the giant invertebrate iridovirus IIV-6 obtains this SINE-related sequence from Sogatella furcifera through a horizontal transfer event in the past. To the best of our knowledge, this is the first report of a horizontal transfer event between a planthopper and a giant DNA virus and also is the first evidence for the eukaryotic origin of genetic material in iridoviruses.

Na-H exchanger-1 (NHE-1) is expressed in the lung of rats. Accumulating evidence shows that Na-H exchangers are involved in inflammation. Amiloride, an inhibitor of NHE-1, inhibits the activation of macrophages and endothelial cells and reduces their production of cytokines. Since these processes have been implicated in acute lung injury (ALI) induced by lipopolysaccharide (LPS), we examined the protective effect of amiloride on ALI induced by LPS in rats.

Enhancer RNAs (eRNAs) are a group of lncRNAs transcribed from enhancers, whose regulatory effects on gene expression are an emerging area of interest. However, the role of eRNAs in regulating trophoblast cells and unexplained recurrent pregnancy loss (URPL) remains elusive.

Atherosclerosis is caused by chronic inflammation associated with the adhesion of neutrophils and endothelial cells (ECs) that is mediated by their respective cellular adhesive molecules to stiffened blood vessel walls. However, the stiffness dependence of calcium flux on neutrophils remains unclear yet. Here, the effect of substrate stiffness by ECs on neutrophils' calcium spike was quantified when the individual neutrophils that adhered to the human umbilical vascular endothelial cell (HUVEC) monolayer were pre-placed onto a stiffness-varied polyacrylamide substrate (5 or 34.88 kPa) or glass surface. Our data indicated that E-/P-selectins and intercellular adhesion molecule 1 (ICAM-1) on HUVECs and β2-integrins, P-selectin glycoprotein ligand 1 (PSGL-1), and CD44s on neutrophils were all involved in mediating neutrophil calcium spike in a stiffness-dependent manner, in which the increase in substrate stiffness enhanced the calcium intensity and the oscillation frequency (spike number). Such stiffness-dependent calcium response is associated with the induced selectin related to β2-integrin activation through the Syk/Src signaling pathway, and F-actin/myosin II are also involved in this. Moreover, tension-activated calcium ion channels displayed critical roles in initiating stiffness-dependent calcium spike. These results provide an insight into understanding how the stiffening of vascular walls could regulate the calcium flux of adhered neutrophils, and thus the immune responses in atherosclerosis.

An increased preoperative talar tilt (TT) angle was reported to be positively correlated with treatment failure after supramalleolar osteotomy (SMOT) for varus ankle osteoarthritis. Distraction arthroplasty was reported to have the ability to correct increased TT angles. The purpose of the current study was to compare the outcomes between SMOT with and without medial distraction arthroplasty (MDA) in the treatment of varus ankle osteoarthritis with increased TT angles.

Inflammasome activation and subsequent pyroptosis are critical defense mechanisms against microbes. However, overactivation of inflammasome leads to death of the host. Although recent studies have uncovered the mechanism of pyroptosis following inflammasome activation, how pyroptotic cell death drives pathogenesis, eventually leading to death of the host, is unknown. Here, we identified inflammasome activation as a trigger for blood clotting through pyroptosis. We have shown that canonical inflammasome activation by the conserved type III secretion system (T3SS) rod proteins from Gram-negative bacteria or noncanonical inflammasome activation by lipopolysaccharide (LPS) induced systemic blood clotting and massive thrombosis in tissues. Following inflammasome activation, pyroptotic macrophages released tissue factor (TF), an essential initiator of coagulation cascades. Genetic or pharmacological inhibition of TF abolishes inflammasome-mediated blood clotting and protects against death. Our data reveal that blood clotting is the major cause of host death following inflammasome activation and demonstrate that inflammasome bridges inflammation with thrombosis.

Results of previous studies on the association of the CpG island methylator phenotype (CIMP) with colorectal cancer (CRC) prognosis were inconsistent and mostly based on different CIMP definitions. The current study aimed to comprehensively investigate the associations between DNA methylation on genes previously used to define CIMP status with CRC survival.

Successful ST-segment elevation myocardial infarction (STEMI) management is time-sensitive and is based on prompt reperfusion mainly to reduce patient mortality. It has evolved from a single hospital care to an integrated regional network approach over the last decades. This prospective study, named the China STEMI Care Project (CSCAP), aims to show how implementation of different types of integrated regional STEMI care networks can improve the reperfusion treatment rate, shorten the total duration of myocardial ischaemia and lead to mortality reduction step by step.

Epstein-Barr virus (EBV), the first human tumor virus to have been discovered, sustains an asymptomatic lifelong infection in ∼95% of the world's population. Reportedly, EBV infection induces the expression of specific cellular microRNAs (miRNAs), such as miR-155, miR-146a, miR-21, which can contribute to the persistence of latently infected cells. In this study, we investigated whether C-X-C chemokine receptor type 4 (CXCR4) is a cellular target of human miR-146a. We also investigated the role of miR-146a and CXCR4 in EBV-associated cells. The results indicate that miR-146a is more abundantly expressed in EBV-positive than in EBV-negative cells. MiR-146a down-regulated CXCR4 expression in a dose- and time-dependent manner. Phenotypic experiments detected miR-146a mimics that could suppress cell proliferation and cell migration and promote cell apoptosis by targeting CXCR4. In addition, miR-146a mimics suppressed cell survival by decreasing the population of G0/G1 phase cells. Latent membrane protein (LMP)1, an importance oncoprotein, can stimulate miR-146a and inhibit the CXCR4 expression. Our findings indicate that LMP1-miR-146a-CXCR4 axis functions as a regulator in the EBV-associated cells.

Background: Primary carnitine deficiency (PCD) is attributed to a variation in the SLC22A5 (OCTN2) gene which encodes the key protein of the carnitine cycle, the OCTN2 carnitine transporter. PCD is typically identified in childhood by either hypoketotic hypoglycemia, or skeletal and cardiac myopathy. The aim of this study was to the clinical, biochemical, and molecular characteristics of PCD patients via newborn screening with tandem mass spectrometry (MS/MS). Methods: MS/MS was performed to screen newborns for inherited metabolic diseases. SLC22A5 gene mutations were detected in the individual and/or their family member by DNA mass array and next-generation sequencing (NGS). Results: Among the 236,368 newborns tested, ten exhibited PCD, and six others were diagnosed with low carnitine levels caused by their mothers, who had asymptomatic PCD. The incidence of PCD in the Xuzhou area is ~1:23,637. The mean initial free carnitine (C0) concentration of patients was 6.41 ± 2.01 μmol/L, and the follow-up screening concentration was 5.80 ± 1.29 μmol/L. After treatment, the concentration increased to 22.8 ± 4.13 μmol/L. Conclusion: This study demonstrates the important clinical value of combining MS/MS and NGS for the diagnosis of PCD and provides new insight into the diagnosis of PCD and maternal patients with PCD using C0 concentration and SLC22A5 mutations.

Titania nanotubes and mesopores with different diameter sizes were prepared by electrochemical oxidation of titanium. The responses of osteoblastic cells isolated from Sprague-Dawley rats to the nanotube and mesopore layers were investigated in sequential events of cell adhesion, morphology, actin cytoskeleton, proliferation, differentiation, and mineralization. Nano-structural features, especially diameters of the nanotubes and mesopores, obviously influenced on cell behaviors in the sequential events. The cells showed better proliferation and differentiation abilities on the specimens with the nanotubes and mesopores than on flat titanium disk. Higher levers of calcium mineralization were observed on the nanotube and mesopore layers. The cells adhered much faster onto the nanotubes with about 170 nm diameter and the mesopores with about 400 nm diameter than onto flat titanium disk and 50 nm nanotubes. There is an appropriate range of the tube/pore sizes, and in this present work, titania nantubes with 170 nm diameter is the best for enhancing functions of osteoblasts.

Maternal immune activation (MIA) during gestation can increase the later risk of schizophrenia in adult offspring. Neuroinflammation is believed to underlie this process. Postmortem brain studies have found changes in the neuroimmune systems of patients with schizophrenia. However, little is known about the dynamic changes in cerebral inflammation and behavior during the course of the disease.

There is increasing evidence indicating that inflammation represents a key pathological component of Alzheimer's disease (AD). A possible factor that may contribute to this process is netrin-1, a neuronal guidance molecule. This molecule has been shown to exert an unexpected immunomodulatory function. However, the potential changes and correlations of netrin-1 with T helper 17/regulatory T cells (Th17/Tregs) as related to inflammation in AD has yet to be examined. In this study, netrin-1 and Th17/Tregs balance were investigated, and the relationship among netrin-1, Th17/Tregs and cognitive function were analyzed in a rat model of AD. In this model, a bilateral intracerebroventricular administration of Amyloid β1-42 (Aβ1-42) was used to produce spatial learning and memory deficits, as well as increased neuronal apoptosis, which were detected 7 days after injection for AD7d group and 14 days for AD14d group. Netrin-1 concentrations were significantly down regulated in both serum and cerebrospinal fluid (CSF) of these AD rats, effects which were strongly correlated with cognitive deficits. Increased levels of interleukin (IL)-17 and deceased IL-10 were observed in both the circulation and CSF and were also correlated with the percent of time spent in the target quadrant of AD in these rats. These changes resulted in netrin-1 concentrations being negatively correlated with IL-17 but positively correlated with IL-10 concentrations in the serum and CSF. We also found that the Th17/Tregs balance was disrupted in these AD rats. Collectively, these findings reveal that the reduction in netrin-1 and the correlated disruption of Th17/Tregs balance in AD rats may diminish the immunosuppressive effect of netrin-1 on Th17/Tregs in AD pathogenesis.

Background: Aberrant expression of caveolin-1 (CAV-1) is involved in the pathogenesis of hepatocellular carcinoma (HCC); however, the results have been inconsistent due to the small size of sample in the individual study. Methods: We performed a meta-analysis and evaluated the association of CAV-1 protein overexpression and clinicopathological significance by using Review Manager 5.2. Pooled ORs and HR with corresponding CIs were calculated. Results: Nine studies were included in the meta-analysis with 810 HCC and 172 cirrhosis patients. CAV-1 protein overexpression was correlated with the risk of cirrhosis; OR was 3.25, p=0.01. Furthermore, the rate of CAV-1 protein overexpression was significantly higher in HCC with cirrhosis than HCC without cirrhosis, suggesting that the CAV-1 protein overexpression likely initiated carcinogenesis in liver with cirrhosis and subsequently contributed to the progression of HCC. In addition, CAV-1 protein overexpression was strongly associated with poor differentiated HCC and invasion; ORs were 2.61 and 2.71, respectively. CAV-1 protein overexpression was strongly correlated with poor overall survival in patients with HCC; HR was 0.4, p=0.03. Conclusions: In summary, CAV-1 protein overexpression is at risk for liver cirrhosis and HCC derived from cirrhosis, and CAV-1 is also a promising prognostic predictor in HCC.

Neurotensin receptor 1 (NTSR1) is a G-protein-coupled receptor (GPCR) that engages multiple subtypes of G protein, and is involved in the regulation of blood pressure, body temperature, weight and the response to pain. Here we present structures of human NTSR1 in complex with the agonist JMV449 and the heterotrimeric Gi1 protein, at a resolution of 3 Å. We identify two conformations: a canonical-state complex that is similar to recently reported GPCR-Gi/o complexes (in which the nucleotide-binding pocket adopts more flexible conformations that may facilitate nucleotide exchange), and a non-canonical state in which the G protein is rotated by about 45 degrees relative to the receptor and exhibits a more rigid nucleotide-binding pocket. In the non-canonical state, NTSR1 exhibits features of both active and inactive conformations, which suggests that the structure may represent an intermediate form along the activation pathway of G proteins. This structural information, complemented by molecular dynamics simulations and functional studies, provides insights into the complex process of G-protein activation.

It remains unclear why the clinically used anti-CTLA-4 antibodies, popularly called checkpoint inhibitors, have severe immunotherapy-related adverse effects (irAEs) and yet suboptimal cancer immunotherapeutic effects (CITE). Here we report that while irAE-prone Ipilimumab and TremeIgG1 rapidly direct cell surface CTLA-4 for lysosomal degradation, the non-irAE-prone antibodies we generated, HL12 or HL32, dissociate from CTLA-4 after endocytosis and allow CTLA-4 recycling to cell surface by the LRBA-dependent mechanism. Disrupting CTLA-4 recycling results in robust CTLA-4 downregulation by all anti-CTLA-4 antibodies and confers toxicity to a non-irAE-prone anti-CTLA-4 mAb. Conversely, increasing the pH sensitivity of TremeIgG1 by introducing designed tyrosine-to-histidine mutations prevents antibody-triggered lysosomal CTLA-4 downregulation and dramatically attenuates irAE. Surprisingly, by avoiding CTLA-4 downregulation and due to their increased bioavailability, pH-sensitive anti-CTLA-4 antibodies are more effective in intratumor regulatory T-cell depletion and rejection of large established tumors. Our data establish a new paradigm for cancer research that allows for abrogating irAE while increasing CITE of anti-CTLA-4 antibodies.

The present study aimed to investigate the characteristics of the ambulatory central artery stiffness index (AcASI) and its related factors. The association between AcASI and the left ventricular mass index (LVMI), and other factors related to atherosclerosis were explored.Patients with primary hypertension were enrolled into this study. Ambulatory central artery blood pressure (CABP) and ambulatory brachial artery blood pressure (BABP) were assessed using a Mobil-O-Graph NG hemomanometer, whereas AcASI and the ambulatory arterial stiffness index (AASI) were determined. LVMI was assessed by echocardiography.A total of 136 patients with primary hypertension were enrolled from May 2011 to January 2013 in Beijing Hospital. AcASI was significantly associated with AASI (r = 0.879, P < .001). AcASI was significantly lower than AASI (0.422 ± 0.302 vs 0.482 ± 0.270; P < .001). AcASI increased with age, ambulatory brachial mean blood pressure (MBP), and fasting glucose. AcASI was significantly associated with office pulse pressure (PP), ambulatory brachial PP, ambulatory central PP, and pulse wave velocity (PWV). AcASI, but not AASI, was significantly associated with LVMI. Receiver operator characteristic analysis indicated that AcASI and AASI could may be a predictor of left ventricular hypertrophy (LVH). Multiple regression analysis indicated that AcASI, chronic kidney disease, and hypertension course were associated with LVMI, but AASI was not.AcASI, which is obtained from ambulatory CABP monitoring, could be a new marker for the evaluation of atherosclerosis. AcASI may be stronger associated with LVH than AASI.

Long noncoding RNA (lncRNA) has played the important function in regulation of various biological processes and in diagnostic value has been widely appreciated. In the present study, we have found that LOC101928316 was significantly downregulated in gastric cancer (GC) tissues specimen, GC cell lines, and associated with the GC patients tumor, node, and metastasis (TNM) stage and degree of differentiation (P ＜ 0.05). LOC101928316 overexpression can significantly inhibit SGC-7901 cell migration, invasion, and proliferation (P＜0.05). LOC101928316 molecular mechanism investigates suggested that LOC101928316 can regulate PI3K-Akt-mTOR signaling pathway and change the GC development progression in vivo and in vitro. In vivo experiment also revealed that LOC101928316-Overexpression can inhibit the tumorigenicity of GC cells in tumor-burdened experimental nude mice (P ＜ 0.05). LOC101928316 may function as anti-oncogene and also plays an important role in GC tumorigenesis. Collectively, our data provided the key role of LOC101928316 in the tumorigenesis of GC. In addition, the present study elucidates LOC101928316 potential regulatory network, which may help us to lead a better knowing of the pathogenesis of GC and probe the lncRNA as a novel biomarker to diagnosis and therapy for this malignant tumor.

The blacklegged tick, Ixodes scapularis, is the primary vector of the Lyme disease spirochete Borrelia burgdorferi in North America. Though the tick is found across the eastern United States, Lyme disease is endemic to the northeast and upper midwest and rare or absent in the southern portion of the vector's range. In an effort to better understand the tick microbiome from diverse geographic and climatic regions, we analysed the bacterial community of 115 I. scapularis adults collected from vegetation in Texas and Massachusetts, representing extreme ends of the vector's range, by massively parallel sequencing of the 16S V4 rRNA gene. In addition, 7 female I. scapularis collected from dogs in Texas were included in the study.