Bayesian Phylogeography of Crimean-Congo Hemorrhagic Fever Virus in Europe

Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In order to reconstruct the origin and pathway of the worldwide dispersion of the virus at global and regional (eastern European) level, we investigated the phylogeography of the infection by analysing 121 publicly available CCHFV S gene sequences including two recently characterised Albanian isolates. The spatial and temporal phylogeny was reconstructed using a Bayesian Markov chain Monte Carlo approach, which estimated a mean evolutionary rate of 2.96 x 10^-4 (95%HPD=1.6 and 4.7 x 10^-4) substitutions/site/year for the analysed fragment. All of the isolates segregated into seven highly significant clades that correspond to the known geographical clades: in particular the two new isolates from northern Albania clustered significantly within the Europe 1 clade. Our phylogeographical reconstruction suggests that the global CCHFV clades originated about one thousand years ago from a common ancestor probably located in Africa. The virus then spread to Asia in the XV century and entered Europe on at least two occasions: the first in the early 1800s, when a still circulating but less or non-pathogenic virus emerged in Greece and Turkey, and the second in the early 1900s, when a pathogenic CCHFV strain began to spread in eastern Europe. The most probable location for the origin of this European clade 1 was Russia, but Turkey played a central role in spreading the virus throughout Europe. Given the close proximity of the infected areas, our data suggest that the movement of wild and domestic ungulates from endemic areas was probably the main cause of the dissemination of the virus in eastern Europe.     

Uremic Pruritus,Dialysis Adequacy,and Metabolic Profiles in Hemodialysis Patients: A Prospective 5-Year Cohort Study

Background

Uremic pruritus is a common and intractable symptom in patients on chronic hemodialysis, but factors associated with the severity of pruritus remain unclear. This study aimed to explore the associations of metabolic factors and dialysis adequacy with the aggravation of pruritus.

Methods

We conducted a 5-year prospective cohort study on patients with maintenance hemodialysis. A visual analogue scale (VAS) was used to assess the intensity of pruritus. Patient demographic and clinical characteristics, laboratory parameters, dialysis adequacy (assessed by Kt/V), and pruritus intensity were recorded at baseline and follow-up. Change score analysis of the difference score of VAS between baseline and follow-up was performed using multiple linear regression models. The optimal threshold of Kt/V, which is associated with the aggravation of uremic pruritus, was determined by generalized additive models and receiver operating characteristic analysis.

Results

A total of 111 patients completed the study. Linear regression analysis showed that lower Kt/V and use of low-flux dialyzer were significantly associated with the aggravation of pruritus after adjusting for the baseline pruritus intensity and a variety of confounding factors. The optimal threshold value of Kt/V for pruritus was 1.5 suggested by both generalized additive models and receiver operating characteristic analysis.

Conclusions

Hemodialysis with the target of Kt/V ≥1.5 and use of high-flux dialyzer may reduce the intensity of pruritus in patients on chronic hemodialysis. Further clinical trials are required to determine the optimal dialysis dose and regimen for uremic pruritus.     

A Whole-Cell Biosensor for the Detection of Gold

Geochemical exploration for gold (Au) is becoming increasingly important to the mining industry. Current processes for Au analyses require sampling materials to be taken from often remote localities. Samples are then transported to a laboratory equipped with suitable analytical facilities, such as Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) or Instrumental Neutron Activation Analysis (INAA). Determining the concentration of Au in samples may take several weeks, leading to long delays in exploration campaigns. Hence, a method for the on-site analysis of Au, such as a biosensor, will greatly benefit the exploration industry. The golTSB genes from Salmonella enterica serovar typhimurium are selectively induced by Au(I/III)-complexes. In the present study, the golTSB operon with a reporter gene, lacZ, was introduced into Escherichia coli. The induction of golTSB::lacZ with Au(I/III)-complexes was tested using a colorimetric β-galactosidase and an electrochemical assay. Measurements of the β-galactosidase activity for concentrations of both Au(I)- and Au(III)-complexes ranging from 0.1 to 5 µM (equivalent to 20 to 1000 ng g⁻¹ or parts-per-billion (ppb)) were accurately quantified. When testing the ability of the biosensor to detect Au(I/III)-complexes_(aq) in the presence of other metal ions (Ag(I), Cu(II), Fe(III), Ni(II), Co(II), Zn, As(III), Pb(II), Sb(III) or Bi(III)), cross-reactivity was observed, i.e. the amount of Au measured was either under- or over-estimated. To assess if the biosensor would work with natural samples, soils with different physiochemical properties were spiked with Au-complexes. Subsequently, a selective extraction using 1 M thiosulfate was applied to extract the Au. The results showed that Au could be measured in these extracts with the same accuracy as ICP-MS (P<0.05). This demonstrates that by combining selective extraction with the biosensor system the concentration of Au can be accurately measured, down to a quantification limit of 20 ppb (0.1 µM) and a detection limit of 2 ppb (0.01 µM).     

Computational comparison of the kinetic stabilities of diamino- and diamidocarbenes in the 1,2-H shift reaction

In this study, we performed several DFT, MP2, and BD(T) calculations on the 1,2-H shift reactions of two diaminocarbenes (1, 2) and a diamidocarbene (3) using the Gaussian 09 program. In Gaussian 09, the BD(T) method keyword requests a Brueckner doubles calculation including a perturbative triples contribution. Although N-heterocyclic carbenes (NHC) are typically known for their exceptional σ-donor abilities, recent studies have indicated that π-interactions also play a role in the bonding between NHCs and transition metals or BX₃ (X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br) (Nemcsok et al. Organomet 23:3640–3646, 2004, Esrafili. J Mol Model 18:2003–2011, 2012). In order to study the importance of π-interactions between carbenes and transition metals, Hobbs and co-workers (Hobbs et al. New J Chem 34:1295–1308, 2010) focused on the synthesis of NHCs with reduced-energy lowest unoccupied molecular orbitals. By introducing an oxalamide moiety into the heterocyclic backbone, they found the resulting carbene possessed higher electrophilicity than usual NHCs. According to our results, the N,N'-diamidocarbene should be more stable than the diaminocarbenes with respect to the 1,2-H shift reaction.

Proteomic analysis for Type I interferon antagonism of Japanese encephalitis virus NS5 protein

Japanese encephalitis virus (JEV) nonstructural protein 5 (NS5) exhibits a Type I interferon (IFN) antagonistic function. This study characterizes Type I IFN antagonism mechanism of NS5 protein, using proteomic approach. In human neuroblastoma cells, NS5 expression would suppress IFNβ‐induced responses, for example, expression of IFN‐stimulated genes PKR and OAS as well as STAT1 nuclear translocation and phosphorylation. Proteomic analysis showed JEV NS5 downregulating calreticulin, while upregulating cyclophilin A, HSP 60 and stress‐induced‐phosphoprotein 1. Gene silence of calreticulin raised intracellular Ca²⁺ levels while inhibiting nuclear translocalization of STAT1 and NFAT‐1 in response to IFNβ, thus, indicating calreticulin downregulation linked with Type I IFN antagonism of JEV NS5 via activation of Ca²⁺/calicineurin. Calcineurin inhibitor cyclosporin A attenuated NS5‐mediated inhibition of IFNβ‐induced responses, for example, IFN‐sensitive response element driven luciferase, STAT1‐dependent PKR mRNA expression, as well as phosphorylation and nuclear translocation of STAT1. Transfection with calcineurin (vs. control) siRNA enhanced nuclear translocalization of STAT1 and upregulated PKR expression in NS5‐expressing cells in response to IFNβ. Results prove Ca²⁺, calreticulin, and calcineurin involvement in STAT1‐mediated signaling as well as a key role of JEV NS5 in Type I IFN antagonism. This study offers insights into the molecular mechanism of Type I interferon antagonism by JEV NS5.     

Identification of miR-7 as an oncogene in renal cell carcinoma

MicroRNA-7 (miR-7) has been described as a tumor suppressor in several human cancers, but the results of a study to identify miRNAs associated with metastatic capability in breast cancer suggested that miR-7 may be characterized as an oncogene. The present study was to determine the expression and function of miR-7 in renal cell carcinoma. Quantitative real-time polymerase chain reaction was used to validate the expressions of miR-7 in 48 paired renal cell carcinomas (RCC) and normal tissues, based on the preliminary sequencing results of miRNAs. Furthermore, the impacts of miR-7 on cell migration, proliferation and apoptosis were analyzed using wound scratch assay, MTT and flow cytometry, respectively. The results demonstrated that miR-7 was up-regulated in RCC compared with normal tissues (p = 0.001). Down-regulation of miR-7 with synthesized inhibitor inhibited cell migration in vitro, suppressed cell proliferation and induced renal cancer cell apoptosis, prompting that miR-7 could be characterized as an oncogene in RCC. The present study was the first to reveal that miR-7 was up-regulated in RCC and it played an important role in RCC by affecting cellular migration, proliferation and apoptosis. Further researches should be conducted to explore the roles and target genes of miR-7 in RCC and other cancers.     

Eight new monoterpene acylglucosides from Sibiraea angustata

Chemical investigation of the aqueous extract of the aerial portion of Sibiraea angustata led to the isolation of eight new monoterpene acylglucosides named sibiraglucoside A–H (1–8) and two known monoterpenes, sibiraic acid (9) and sibiskoside (10). Their structures were elucidated through extensive spectroscopic data analysis (including 1D and 2D NMR and HRESIMS experiments) and compared to literature data. In the in vitro bioassay, all of the compounds showed moderate hypolipidemic effects.     

Effects of Added Organic Matter and Water on Soil Carbon Sequestration in an Arid Region

It is generally predicted that global warming will stimulate primary production and lead to more carbon (C) inputs to soil. However, many studies have found that soil C does not necessarily increase with increased plant litter input. Precipitation has increased in arid central Asia, and is predicted to increase more, so we tested the effects of adding fresh organic matter (FOM) and water on soil C sequestration in an arid region in northwest China. The results suggested that added FOM quickly decomposed and had minor effects on the soil organic carbon (SOC) pool to a depth of 30 cm. Both FOM and water addition had significant effects on the soil microbial biomass. The soil microbial biomass increased with added FOM, reached a maximum, and then declined as the FOM decomposed. The FOM had a more significant stimulating effect on microbial biomass with water addition. Under the soil moisture ranges used in this experiment (21.0%–29.7%), FOM input was more important than water addition in the soil C mineralization process. We concluded that short-term FOM input into the belowground soil and water addition do not affect the SOC pool in shrubland in an arid region.     

Improving but Inferior Survival in Patients with Chronic Lymphocytic Leukemia in Taiwan: A Population-Based Study, 1990–2004

Background

Chronic lymphocytic leukemia (CLL) is much less prevalent in Asian countries. Whether there are differences in survival outcomes between the East and West, however, remain unclear.

Methods

The survival data for CLL patients identified in the Taiwan Cancer Registry database between 1990 and 2004, together with corresponding data in the US Surveillance, Epidemiology, and End Results database, were retrieved. The relative survivals (RS, adjusted for the expected survival in the general population) were estimated in patients diagnosed in three 5-year periods of time.

Results

CLL drastically shortened patients’ life expectancy; more importantly, this negative impact in Taiwan was much larger than that in the US: the 5-year RS in Taiwan and US were 59% and 76%, and the 10-year RS, 45% and 56%, respectively. Nevertheless, survival in Taiwan was better in the periods after 1995 (5-year RS, from 53.0% to 60.6%), a time period corresponding to the introduction of the Taiwan National Health Insurance scheme. Such improvement was largely due to decreased mortality in patients younger than 65 (5-year RS, from 53.5% to 69.1%). Despite the improvement, patients’ RS in Taiwan in recent periods remain steadily 15∼20% inferior to that in the US in both younger and older patient groups.

Conclusions

The improved RS in Taiwan implies that therapeutic advances are changing the prognosis of CLL. The stable RS gap between Taiwanese and the US patients suggests the existence of an ethnic difference in CLL patients’ outcomes.     

Pyrosequencing to Identify Homogeneous Phenomenon When Using Recipients/Donors with Different CYP3A5*3 Genotypes in Living Donor Liver Transplantation

This study used pyrosequencing to determine the proportional distribution of CYP3A5*3 genotypes to further confirm the homogeneous phenomenon that is observed when recipients and donors in living donor liver transplantation (LDLT) have a different single nucleotide polymorphism (SNP) genotype. We enrolled 42 recipient/living donor pairs and the SNPs of CYP3A5*3 were identified by polymerase chain reaction-restriction fragment length polymorphism. We performed 120 liver graft biopsies as part of clinical investigations after LDLT. Pyrosequencing of the CYP3A5*3 SNPs revealed that among the 16 recipients with the G/G genotype, 94.68% had the G and 5.32% the A allele. Among the 14 recipients with the A/G genotype, 78.08% had the G and 21.92% the A allele, and among the 12 recipients with the A/A genotype, 18.45% had the G and 81.55% the A allele. Among the 12 donors with the G/G genotype, 93.85% had the G and 6.14% the A allele. Among the 26 donors with the A/G genotype, 75.73% had the G and 24.27% the A allele, and among the 4 donors with the A/A genotype, 11.09% had the G and 88.91% the A allele. There were a total of 120 liver graft biopsy samples; among the 37 recipients with the G/G genotype, 89.74% had the G and 10.26% the A allele, among the 70 recipients with the A/G genotype, 71.57% had the G and 28.43% the A allele, and among the 13 recipients with the A/A genotype, 48.25% had the G and 51.75% the A allele. The proportional distribution of G and A alleles of the CYP3A5*3 SNP between recipients/donors and liver grafts after LDLT was significantly different (p<0.001). Pyrosequencing was useful in identifying detailed proportional changes of the CYP3A5*3 SNP allele distribution, and to confirm the homogeneous phenomenon when recipients and donors in LDLT have a different genotype.