Search

Systemic lupus erythematosus (SLE) is a complex autoimmune disease involving multiple immune cells. To elucidate SLE pathogenesis, it is essential to understand the dysregulated gene expression pattern linked to various clinical statuses with a high cellular resolution. Here, we conducted a large-scale transcriptome study with 6,386 RNA sequencing data covering 27 immune cell types from 136 SLE and 89 healthy donors. We profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively. We then identified candidate biological processes unique to each signature. This study suggested the clinical value of disease-activity signatures, which were associated with organ involvement and therapeutic responses. However, disease-activity signatures were less enriched around SLE risk variants than disease-state signatures, suggesting that current genetic studies may not well capture clinically vital biology. Together, we identified comprehensive gene signatures of SLE, which will provide essential foundations for future genomic and genetic studies.

Early rehabilitation for acute stroke patients is widely recommended. We tested the hypothesis that daily intervention by speech therapists promotes safe oral intake of patients with acute stroke.We analyzed hospitalized patients who experienced cerebral infarction and cerebral hemorrhage and who underwent rehabilitation between October 2010 and September 2014 at our hospital. In total, 936 patients were analyzed, and 452 patients underwent daily speech therapy. We examined the association of training frequency and eating status.Multiple linear regression analysis indicated that daily speech therapy was correlated significantly and positively with a reduction in the number of days of hospitalization until oral intake commenced (coefficient, -.998; 95% confidence interval, -1.793 to -.202; P .05), and was not correlated with the cessation of oral intake due to aspiration pneumonia after resuming oral intake.Our retrospective cohort study demonstrated that daily intervention by speech therapists in patients with acute stroke shortens the number of days until oral intake without increasing the incidence of aspiration pneumonia.

Summary Genetic studies have revealed many variant loci that are associated with immune-mediated diseases. To elucidate the disease pathogenesis, it is essential to understand the function of these variants, especially under disease-associated conditions. Here, we performed a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis. Our dataset consists of 28 distinct immune cell subsets from 337 patients diagnosed with 10 categories of immune-mediated diseases and 79 healthy volunteers. Our dataset captured distinctive gene-expression profiles across immune cell types and diseases. Expression quantitative trait loci (eQTL) analysis revealed dynamic variations of eQTL effects in the context of immunological conditions, as well as cell types. These cell-type-specific and context-dependent eQTLs showed significant enrichment in immune disease-associated genetic variants, and they implicated the disease-relevant cell types, genes, and environment. This atlas deepens our understanding of the immunogenetic functions of disease-associated variants under in vivo disease conditions.

The flavonoids quercetin, and its natural glycosides isoquercetin and rutin, are phytochemicals commonly consumed in plant-derived foods. Semi-synthetic water-soluble isoquercetin and rutin glycosides, maltooligosyl isoquercetin, monoglucosyl rutin and maltooligosyl rutin were developed by synthetic glycosylation to overcome solubility challenges for improved incorporation in food and medicinal applications. Quercetin and its natural glycosides are known to induce genetic instability and decrease cell proliferation. Using a system of Chinese hamster ovary (CHO) cells, this study examined the differences in cytotoxic and genotoxic responses induced by natural and synthetic flavonoids. Bioactivity evaluations using poly(ADP-ribose) polymerase (PARP) ELISA showed that the synthetic flavonoids were less effective in inhibiting PARP than the natural flavonoids, where PARP inhibitory effects decreased with glycosylation of flavonoids. In the genotoxic studies, treatments with flavonoids at a concentration range of 0.2 μM-1 mM induced significant frequencies of sister chromatid exchange (SCE) and micronuclei in CHO cells compared to spontaneous occurrences. The synthetic flavonoids monoglucosyl rutin and maltooligosyl rutin induced less genotoxic effects than the natural flavonoids. However, maltooligosyl isoquercetin induced similar responses as isoquercetin and rutin. The growth inhibition studies showed glycosylation dependent cytotoxicity in natural flavonoids. The quercetin aglycone exhibited the highest toxicity out of all the flavonoids studied. Differences in growth inhibition were not observed between the synthetic flavonoids, maltooligosyl isoquercetin and monoglucosyl rutin, and natural isoquercetin and rutin, respectively. Maltooligosyl rutin induced less cytotoxicity than rutin and monoglucosyl rutin. Our in vitro studies demonstrated that the synthetic flavonoids generally induced less genotoxic responses than their natural counterparts.

Flavivirus infections (including Japanese encephalitis, West Nile encephalitis and dengue fever/severe dengue) present a worldwide public health problem. Recent climate change may affect the geographical distribution of the arthropod vectors for these viruses and so the risk of flavivirus epidemics may increase. Many methods have been developed for the serological diagnosis of flavivirus infections, such as haemagglutination inhibition assay, enzyme-linked immunosorbent assay, and immunofluorescence in staining. However, the specificity of these assays varies. The plaque reduction neutralizing test (PRNT) using live viruses is currently the 'gold standard' for the differential serodiagnosis of flaviviruses. The specificity of results obtained with PRNT is better than that for other protocols and many laboratories apply the PRNT protocol to the differential serodiagnosis of flaviviruses. Here, recent refinements to the PRNT protocols with genetically modified recombinant viruses or reporter-harbouring virus-like particles are reviewed. Further, the problems associated with the differential serodiagnosis of flaviviruses using PRNT are discussed.

Viral reverse genetics, particularly infectious cloning, is a valuable tool with applications to many areas of viral research including the generation of vaccine candidates. However, this technology is sometimes insufficient for the construction cDNA clones as the genome sequences and/or encoding proteins of some viral agents may be toxic to the host cells used for cloning. To circumvent this problem, we developed a polymerase chain reaction (PCR)-based protocol for generating a complete West Nile virus (WNV) cDNA. The fragmented cDNAs were synthesized from WNV RNA by reverse transcription-PCR, and subsequently cloned into plasmids for use as templates for WNV cDNA synthesis. The fragmented cDNAs were amplified and assembled by PCR to generate a full-length WNV cDNA. Using this cDNA as a template, WNV RNA was synthesized in vitro and transfected into mammalian cells. We also examined the generation of a mutant recombinant WNV containing a site-directed mutation within the viral genome sequence. Here, we discuss the possibility of developing a method for the generation of recombinant WNVs.

A new protocol for the generation of West Nile virus (WNV) replicons was developed. Fragmented cDNAs that covered the entire WNV RNA sequence, except the sequence corresponding to nucleotides 190-2379, were amplified separately by polymerase chain reactions (PCRs) using primer set franking with overlapping sequences of 40-50 bp at the 5'- and the 3'-ends of each fragment. All amplified fragments were mixed together and annealed to each other at the overlapping sequences. The annealed-DNA fragments were elongated by DNA polymerase and amplified by short-cycle PCRs to generate full-sized WNV replicon cDNAs. The WNV replicons were transcribed in vitro using the replicon cDNAs as templates. When the in vitro-transcribed replicon was introduced into mammalian cells, the viral envelope protein and viral positive- and negative-strand RNAs were detected in the replicon-transfected cells. It is noteworthy that the synthesis of the replicon cDNAs and the replicons took just 1 week, and that the use of a high-fidelity DNA polymerase afforded stability to the sequence of the synthetic replicon.

In the first step of flavivirus replication, the 5′-end of viral genomic RNA is thought to interact with the 3′-end of the genomic RNA at the complimentary sequences (CSs) located at both ends of the genomic RNA. However, there is little evidence of direct interaction between the two ends of the viral genomic RNA in virus-replicating cells. Herein, we show that viral small negative-strand RNA species, composed of two ends corresponding to the upstream of the 5′-end CS and the downstream of the 3′-end CS of viral genomic RNA, were synthesized during viral replication. We hypothesized that the viral small negative-sense RNAs were synthesized during viral negative-sense RNA synthesis through the template-jumping of viral RNA-dependent RNA polymerase from the 3′-end to the 5′-end of viral genomic RNA used as a template. Our present results strongly indicate that the two ends of viral genomic RNA associate with each other during viral replication.

Coronavirus small envelope protein E has two known biological functions: it plays a pivotal role in virus envelope formation, and the murine coronavirus E protein induces apoptosis in E protein-expressing cultured cells. The E protein is an integral membrane protein. Its C-terminal region extends cytoplasmically in the infected cell and in the virion toward the interior. The N-terminal two-thirds of the E protein is hydrophobic and lies buried within the membrane, but its orientation in the lipid membrane is not known. Immunofluorescent analyses of cells expressing biologically active murine coronavirus E protein with a hydrophilic short epitope tag at the N-terminus showed that the epitope tag was exposed cytoplasmically. Immunoprecipitation analyses of the purified microsomal membrane vesicles that contain the same tagged E protein revealed the N-terminal epitope tag outside the microsomal membrane vesicles. These analyses demonstrated that the epitope tag at the N-terminus of the E protein was exposed cytoplasmically. Our data were consistent with an E protein topology model, in which the N-terminal two-thirds of the transmembrane domain spans the lipid bilayer twice, exposing the C-terminal region to the cytoplasm or virion interior.

Coronavirus E protein is a small viral envelope protein that plays an essential role in coronavirus assembly; coexpression of coronavirus M and E proteins results in the production of virus-like particles. The present study demonstrated that mouse hepatitis virus (MHV) E protein was released as an integral membrane protein in lipid vesicles from E-protein-expressing mammalian cells, in the absence of other MHV proteins. Furthermore, our data indicated that the E-protein-containing vesicles, which had a slightly lighter buoyant density than that of MHV, were released from MHV-infected cells. These data implied that E protein alone can drive the production and release of coronavirus envelope in the absence of M protein.

Bone morphogenetic proteins (BMPs) are peptide growth factors belonging to the TGF-β superfamily. A large number of these ligands, including BMP-2, -4 and -7 is expressed during early embryogenesis in the vertebrate embryo. In this study, we demonstrate that BMP-7 has ventralizing activity both in ectodermal explants as well as in whole embryos. As it was the case for BMP-2 and BMP-4, BMP-7 is a very poor inducer when provided as a homodimer protein. Because of this weak mesoderm inducing activity, it has been suggested that mesoderm induction by BMPs might represent an artifact of overexpression. We provide evidence demonstrating that unlike the homodimers of BMP-4 or BMP-7, the purified recombinant heterodimer of Xenopus BMP-4 and BMP-7 (BMP-4/7) has a potent mesoderm inducing activity at physiological concentrations. These results provide the first evidence for an embryonic function of BMP-4/7 heterodimers in the vertebrate embryo.