Functional analysis of Chikungunya virus non-structural protein 3 alphavirus unique domain

Chikungunya virus (CHIKV) is a re-emerging alphavirus causing fever, joint pain, skin rash, arthralgia, and occasionally death. Antiviral therapies and/or effective vaccines are urgently required. CHIKV biology is poorly understood, in particular the functions of the non-structural protein 3 (nsP3). nsP3 consists of three domains, of these the macrodomain is reported to have ADP-ribose and RNA-binding activity, the hypervariable region is involved in various interaction with host proteins, however, the alphavirus unique domain (AUD), as a homologous sequence unique to alphaviruses, is essential for CHIKV replication with absolutely unknown functions. To investigate the function of AUD, a mutagenic analysis was performed. Informed by the structure of the Sindbis virus AUD and an alignment of amino acid sequences of multiple alphaviruses, a series of mutations in the AUD were generated in a CHIKV sub-genomic replicon. This analysis revealed an essential role for the AUD in CHIKV RNA replication, with mutants exhibiting species- and cell-type specific phenotypes. To test if the AUD played a role in other stages of the virus lifecycle, the mutant panel was also analysed in the context of infectious CHIKV. Results indicated that, in addition to a role in RNA replication, the AUD was also required for virus assembly. Further analysis revealed that one mutant (P247A/V248A) specifically blocked transcription of the subgenomic RNA leading to a dramatic reduction in synthesis of the structural proteins and concomitant reduction in virus production. This phenotype could be explained by both a reduction in the binding of the P247A/V248A mutant nsP3 to viral genomic RNA in vivo, and the reduced affinity of the mutant AUD for the subgenomic promoter RNA in vitro. A high-resolution confocal microscopy analysis on the track of nsP3, capsid protein and dsRNA confirmed the P247A/V248A replication defect. In parallel, this project also set out to investigate a variety of biochemical characters of nsP3/AUD, for example, RNAi suppression activity, self-multimerization and interactions with cellular proteins by the approach of quantitative proteomic analysis. In conclusion, this study reveals that the AUD is a pleiotropic protein domain, with multiple functions during CHIKV RNA synthesis

Conjunctival Flap Covering Combined with Antiviral and Steroid Therapy for Severe Herpes Simplex Virus Necrotizing Stromal Keratitis

Herpes simplex virus (HSV) necrotizing stromal keratitis is a common type of herpetic stromal keratitis (HSK). Antiviral medication alone cannot control the disease, and corticosteroid eye drops may aggravate the ulcer and result in corneal perforation. Amniotic membrane transplantation effectively treats superficial corneal ulcer resulting from necrotizing stromal HSK. However, the efficacy of this approach seems to be limited for more serious cases. This study presented the clinical treatment of severe HSV necrotizing stromal keratitis (ulcer depth greater than half of the corneal stroma) by conjunctival flap covering surgery in 25 patients (25 eyes) combined with antivirus and corticosteroid treatment at Shandong Eye Hospital from January 2007 to December 2013. Clinical results showed that the mean best spectacle-corrected visual acuity improved from preoperative 20/333 to postoperative 20/40 (P<0.05). All patients recovered ocular surface stabilization. There was recurrence in two eyes, which was cured with antiviral medication. Conjunctival flap covering combined with antivirus and corticosteroid treatment is effective in treating severe HSV necrotizing stromal keratitis

The Polarimetric Detection Optimization Filter and Its Statistical Test for Ship Detection

Ship detection via synthetic aperture radar (SAR) has been demonstrated to be very useful as polarimetric information helps discriminate between targets and sea clutter. Among the available polarimetric detectors, optimal polarimetric detection (OPD) theoretically provides the best detection performance under the assumption that the fully developed speckle hypothesis stands. This study proposes a polarimetric detection optimization filter (PDOF). The target clutter ratio (TCR) over the speckle variation was maximized using a matrix transform to derive the PDOF. The objective function based on a matrix transform instead of a vector transform is optimized to obtain synthetic effects by combining a polarimetric whitening filter (PWF) and a polarimetric matched filter (PMF). Subspace form of the PDOF (SPDOF) is also proposed, which gives performance comparable to the PDOF. Assuming a Wishart distribution, the exact and approximate expressions of the closed-form probability density function (PDF) of the PDOF are derived. The probability of false alarm (PFA) was derived in a closed-form expression, which allows obtaining the PDOF threshold analytically. Moreover, the gamma model is extended to a generalized gamma distribution (GΓD) to adapt complicated resolutions and sea states. Experiments with simulated and real data validate the correctness and effectiveness of the results. The PDOF detector achieves the best performance in most virtual and real-world environments, especially in cases where the target statistics and clutter are not Wishart-distributed

Role of Flavin-Containing Monooxygenase in Oxidative Metabolism of Voriconazole by Human Liver Microsomes

Voriconazole is a potent second generation triazole antifungal agent with broad-spectrum activity against clinically important fungi. It is cleared predominantly via metabolism in all species tested including humans. N-oxidation of the fluoropyrimidine ring, its hydroxylation, and hydroxylation of the adjacent methyl group are the known pathways of voriconazole oxidative metabolism, with the N-oxide being the major circulating metabolite in human. In vitro studies have shown that CYP2C19, CYP3A4, and to a lesser extent CYP2C9 contribute to the oxidative metabolism of voriconazole. When CYP-specific inhibitors and antibodies were used to evaluate the oxidative metabolism of voriconazole by human liver microsomes (HLM), the results suggested that CYP-mediated metabolism accounted for ~75% of the total oxidative metabolism. The studies presented here provide evidence that the remaining ~25% of the metabolic transformations are catalyzed by flavin-containing monooxygenase (FMO). This conclusion was based on the evidence that the NADPH-dependent metabolism of voriconazole was sensitive to heat (45 °C for 5 min), a condition known to selectively inactivate FMO without affecting CYP activity. The role of FMO in the metabolic formation of voriconazole N-oxide was confirmed by the use of recombinant FMO enzymes. Kinetic analysis of voriconazole metabolism by FMO1 and FMO3 yielded Km values of 3.0 mM and 3.4 mM and Vmax values of 0.025 pmol/min/pmol and 0.044 pmol/min/pmol, respectively. FMO5 did not metabolize voriconazole effectively. This is the first report of the role of FMO in the oxidative metabolism of voriconazole

Efficacy and mechanism of Baicao Fuyanqing suppository on mixed vaginitis based on 16S rRNA and metabolomics

BackgroundMixed vaginitis is the infection of the vagina by at least two different pathogens at the same time, both of which contribute to an abnormal vaginal environment leading to signs and symptoms. Baicao Fuyanqing suppository (BCFYQ) is a Miao ethnomedicine, used to treat various vaginitis. The aim of this study was to investigate the efficacy and possible mechanism of BCFYQ in the treatment of mixed vaginitis based on 16S rRNA high-throughput sequencing and metabonomics.MethodsEscherichia coli and Candida albicans were used to establish mixed vaginitis model in SD rats. Three groups of low, medium and high doses (0.18/0.36/0.64 g.kg-1) were established, and administered vaginally once a day for 6 consecutive days. After the last administration, vaginal pH and IL-1β, IL-2, IL-13 and IgA levels were measured, and the vaginal tissue was examined pathologically. In addition, the vaginal flora was characterised by 16S rRNA, and endogenous metabolites in the vaginal tissue were detected by UHPLC-Q-Exactive MS.ResultsCompared with the model group, BCFYQ can reduce the vaginal pH of rats, make it close to the normal group and improve the damaged vaginal epithelial tissue. The results of ELISA showed that BCFYQ decreased the levels of IL-1 β and IL-2 and increased the levels of IL-13 and IgA (P&lt;0.05). In addition, BCFYQ may increase the abundance of vaginal flora, especially Lactobacillus. The differential metabolite enrichment pathway suggests that the therapeutic mechanism of BCFYQ is mainly related to lipid metabolism and amino acid metabolism.ConclusionOur research shows that BCFYQ has a good therapeutic effect on mixed vaginitis. It repairs the damaged vaginal mucosa by regulating the vaginal flora and lipid metabolism disorders to improve the local immune function of the vagina and inhibit the growth and reproduction of pathogens

Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome

BACKGROUND: parent-of-origin effects (POE) play important roles in complex disease and thus understanding their regulation and associated molecular and phenotypic variation are warranted. Previous studies mainly focused on the detection of genomic regions or phenotypes regulated by POE. Understanding whether POE may be modified by environmental or genetic exposures is important for understanding of the source of POE-associated variation, but only a few case studies addressing modifiable POE exist. METHODS: in order to understand this high order of POE regulation, we screened 101 genetic and environmental factors such as ‘predicted mRNA expression levels’ of DNA methylation/imprinting machinery genes and environmental exposures. POE-mQTL-modifier interaction models were proposed to test the potential of these factors to modify POE at DNA methylation using data from Generation Scotland: The Scottish Family Health Study(N=2315). FINDINGS: a set of vulnerable/modifiable POE-CpGs were identified (modifiable-POE-regulated CpGs, N=3). Four factors, ‘lifetime smoking status’ and ‘predicted mRNA expression levels’ of TET2, SIRT1 and KDM1A, were found to significantly modify the POE on the three CpGs in both discovery and replication datasets. We further identified plasma protein and health-related phenotypes associated with the methylation level of one of the identified CpGs. INTERPRETATION: the modifiable POE identified here revealed an important yet indirect path through which genetic background and environmental exposures introduce their effect on DNA methylation, motivating future comprehensive evaluation of the role of these modifiers in complex diseases. FUNDING: NSFC (81971270),H2020-MSCA-ITN(721815), Wellcome (204979/Z/16/Z,104036/Z/14/Z), MRC (MC_UU_00007/10, MC_PC_U127592696), CSO (CZD/16/6,CZB/4/276, CZB/4/710), SFC (HR03006), EUROSPAN (LSHG-CT-2006-018947), BBSRC (BBS/E/D/30002276), SYSU, Arthritis Research UK, NHLBI, NIH

Bacteria-inducing legume nodules involved in the improvement of plant growth, health and nutrition

Bacteria-inducing legume nodules are known as rhizobia and belong to the class Alphaproteobacteria and Betaproteobacteria. They promote the growth and nutrition of their respective legume hosts through atmospheric nitrogen fixation which takes place in the nodules induced in their roots or stems. In addition, rhizobia have other plant growth-promoting mechanisms, mainly solubilization of phosphate and production of indoleacetic acid, ACC deaminase and siderophores. Some of these mechanisms have been reported for strains of rhizobia which are also able to promote the growth of several nonlegumes, such as cereals, oilseeds and vegetables. Less studied are the mechanisms that have the rhizobia to promote the plant health; however, these bacteria are able to exert biocontrol of some phytopathogens and to induce the plant resistance. In this chapter, we revised the available data about the ability of the legume nodule-inducing bacteria for improving the plant growth, health and nutrition of both legumes and nonlegumes. These data showed that rhizobia meet all the requirements of sustainable agriculture to be used as bio-inoculants allowing the total or partial replacement of chemicals used for fertilization or protection of crops