Entire genome sequences of two new HCV subtypes, 6r and 6s, and characterization of unique HVR1 variation patterns within genotype 6

Hepatitis C virus genotype 6 currently contains 21 recognized subtypes, 6a-6u, for which 6r and 6s lack complete genome sequences. In this study, we entirely sequenced variants QC245 and QC66 from Cambodian immigrants in Canada representing subtypes 6r and 6s, respectively. The two genomes shared 75.3% nucleotide similarities to each other and 72.0-82.9% to 21 reference sequences representing subtypes 6a-6q, 6t-6u and variants km41 and gz52557. QC66 and QC245 displayed genome lengths of 9473 and 9450 nt and each contained a single open reading frame of 9051 nt. In 10 protein encoding regions QC245 and QC66 shared common sizes with TV249/6t and 537796/6l isolates, respectively. Phylogenetic analyses demonstrated that QC245 was more closely related to subtype 6f, but both QC66 and QC245 were subtypically different from all other genotype 6 subtypes. Our full-length sequence data confirmed the status of subtype 6r and 6s within genotype 6. Analysis of partial sequences revealed seven 6t and two 6s isolates that were all isolated from Cambodian immigrants. Analysis of the hypervariable region 1 sequences of 81 genotype 6 variants revealed two unique patterns of variation. First, most variants showed an amino acid deletion at the 4th position and second, many contained a basic residue at the 7th position. Possible roles of these two variation patterns are further discussed.

Impact of a simple intervention that improves colon cancer lymph node yield and assessement

e15058

Background: The National Quality Forum has endorsed the 12 lymph node (LN) benchmark as a quality metric. Currently, less than 40% of institutions meet this requirement. The purpose of this study was to determine whether implementation of a simple pathology template with dedicated fields for LN reporting led to an increase in the number of colon cancer resections where >12 LNs were reported. Methods: A simple pathology template, derived from the College of American Pathology, using standardized terminology and dedicated fields for LN reporting was implemented in August 2007. Using a pre and post- test design, all consecutive pathology cases were retrospectively reviewed. Inclusion criteria consisted of all stage 0-IV colon cancer patients who underwent surgical resection at a single Veterans Affairs Medical Center. The primary outcome was the percentage of cases in which >12 LNs were assessed between the pre and post-template group. Age, gender, anatomic location, and stage were also collected. Statistical comparisons were made using chi-square and Fisher's exact t-test. Results: 111 pre-template and 71 post-template cases were analyzed. The majority of patients were Caucasian (74%) males (97%). There were no significant differences between the two groups (see Table 1 ), however there was a trend towards more right-sided colon cancers in the pre-template group. 51% of all pre-template pathology reports evaluated >12 LNs compared to 68% of post-template reports (33% improvement in LN yield; p=0.03). Conclusions: Examination of >12 LNs has important therapeutic and prognostic implications in colon cancer patients. Use of a standardized pathology template with dedicated fields for LN reporting is a simple intervention that can increase yield of LN reporting. This can have a significant impact for institutions striving to reach the 12 LN quality metric.

[Table: see text]

No significant financial relationships to disclose.

Phase I trial of anti-PSMA designer T-cell autografting in prostate cancer

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Background: We created chimeric immunoglobulin-T cell receptors (IgTCR) specific for prostate specific membrane antigen (PSMA). When expressed in patient T cells, these “designer T cells” specifically kill prostate cancer cells in vitro and in vivo in animal models, with 5/9 (55%) of xenografted mice experiencing complete remissions (Ma et al. Prostate 2004:61:12–25). A Phase I clinical trial was approved by the FDA in metastatic prostate cancers. Methods: Patient T cells are retrovirally transduced and expanded ex vivo to span dose levels of 10^9 to 10^11 T cells. Adapting methods of Dudley, Rosenberg and colleagues, patients undergo prior non-myeloablative (NMA) conditioning to create a “hematologic space” into which the infused designer T cells will stably engraft for prolonged in vivo efficacy. Patients are co-administered continuous infusion IL2. Outcomes will include Phase Ia goals of safety and toxicity and Phase Ib goals of establishing an optimal biologic dose in terms of designer T cell engraftment and tumor response. Results: For the first two patients, excellent T cell modifications of 50–60% were obtained. After NMA conditioning, T cells were infused and stable engraftments of 1–5% were observed post recovery, even at this lowest 10^9 T cell dose level, thus affirming one of the study end-points. The patients had PSA reductions of 50 and 70% in the two months following treatment. Patients experienced neutropenia and lymphopenia after conditioning, but no designer T cell-related toxicities. Results with additional patients will be described in terms of safety, engraftment efficiency and tumor responses. Conclusions: A new approach to adoptive immune therapy in metastatic prostate cancer has been devised. This clinical trial is funded by the US Army/DOD.

No significant financial relationships to disclose.

Inhibition by lenalidomide of growth factor and hypoxia-induced signaling in endothelial and epithelial tumor cells, and effects within the tumor cell microenvironment

e14620

Background: Lenalidomide, an immunomodulatory and anti-angiogenic agent, has activity in many hematological malignancies. It has direct anti-proliferative activity in hematological cells but there is no evidence of direct activity in solid tumor cells. In solid tumors, lenalidomide is being advanced in combination with other agents to take advantage of its immune-enhancing properties in combination with direct anti-tumor agents. Lenalidomide studies in CLL and MM suggest that it may also attenuate pro-survival signals generated by interaction of stroma with the malignant cell itself. Lysophosphatidic acid (LPA) is a key pro-survival factor present at high levels within the ascites of ovarian cancer patients which confers increased tumor invasiveness and reduced survival. Hypoxia-induced factor (HIF)-1α is the key initiator of angiogenesis and tumor invasiveness. Methods: The effect of lenalidomide on growth factor-induced Akt phosphorylation was investigated in endothelial cells, NHL cells, and ovarian cancer cells in vitro. Ovarian cancer cell lines SKOV-3 and OVCAR-3 were treated with LPA and the effect of lenalidomide on invasiveness via enhanced p-Akt was investigated. The effect of lenalidomide on HIF-1α expression by endothelial cells and epithelial cells was also investigated. Results: Lenalidomide inhibited growth factor-induced Akt phosphorylation. Treatment of ovarian tumor cells with LPA increased tumor cell invasiveness via enhanced p-Akt. Lenalidomide strongly inhibited invasion and p-Akt (at S308 but not T473) in a dose-dependent manner. Hypoxic endothelial cells and epithelial tumor cells showed enhanced HIF-1α expression. Lenalidomide inhibited hypoxia-induced HIF-1α expression by endothelial cells and by epithelial tumor cells, including prostate, breast, pancreatic, renal and ovarian tumor cells. Conclusions: Lenalidomide may act within the tumor microenvironment to inhibit key signals of tumor cells survival, growth, and invasiveness. These studies support the potential utility of lenalidomide in combination with other agents in the treatment of patients with solid tumors.

[Table: see text]

Association of GCKR rs780094, alone or in combination with GCK rs1799884, with type 2 diabetes and related traits in a Han Chinese population

AIMS/HYPOTHESIS

The GCKR rs780094 and GCK rs1799884 polymorphisms have been reported to be associated with dyslipidaemia and type 2 diabetes in white Europeans. The aim of this study was to replicate these associations in Han Chinese individuals and to identify the potential mechanisms underlying these associations.

METHODS

The single nucleotide polymorphisms rs780094 and rs1799884 were genotyped in a population-based sample of Han Chinese individuals (n = 3,210) and tested for association with risk of type 2 diabetes and related phenotypes.

RESULTS

The GCKR rs780094 A allele was marginally associated with reduced risk of type 2 diabetes (OR 0.85, 95% CI 0.73-1.00, p value under an additive model [p((add))] = 0.05) and significantly associated with reduced risk of impaired fasting glucose (IFG) or type 2 diabetes (OR 0.86, 95% CI 0.77-0.96, p([add]) = 0.0032). It was also significantly associated with decreased fasting glucose and increased HOMA of beta cell function (HOMA-B) and fasting triacylglycerol levels (p([add]) = 0.0169-5.3 x 10(-6)), but not with HOMA of insulin sensitivity (HOMA-S). The associations with type 2 diabetes and IFG remained significant after adjustment for BMI, while adjustment for HOMA-B abolished the associations. The GCKR rs780094 was also associated with obesity and BMI, independently of its association with type 2 diabetes. The GCK rs1799884 A allele was significantly associated with decreased HOMA-B (p([add]) = 0.0005), but not with type 2 diabetes or IFG. Individuals with increasing numbers of risk alleles for both variants had significantly lower HOMA-B (p([add]) = 5.8 x 10(-5)) in the combined analysis.

CONCLUSIONS/INTERPRETATION

Consistent with observations in white Europeans, the GCKR rs780094 polymorphism contributes to the risk of type 2 diabetes and dyslipidaemia in Han Chinese individuals. In addition, we showed that the effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity.

The H19 gene imprinting in normal pregnancy and pre-eclampsia

OBJECTIVES

To characterize the H19 gene imprinting in the placental tissues of normal pregnancy and pre-eclampsia.

METHODS

A total of 188 subjects at 5-9 weeks, 54 at 10-12 weeks, 50 at the second trimester, 65 at term of gestation, and 30 with pre-eclampsia at the third trimester were recruited. Their DNA and RNA were extracted from the placental tissues. The H19 genotypes for individuals were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and the H19 gene imprinting was identified by reverse transcription-PCR (RT-PCR) and the RsaI-based RFLP. The levels of H19 RNA transcripts in the pre-eclampsia patients with the H19 heterozygote were measured by quantitative RT-PCR. The frequency of the H19 heterozygote, the H19 imprinting status among different trimesters of pregnancy and the clinical symptoms in the pre-eclampsia patients were analyzed.

RESULTS

(1) About 40-46% of subjects at varying stages of normal pregnancy showed the H19 heterozygote, and 24 out of 87 (27.59%) heterozygous cases were at 5-9 weeks of gestation, but no single one in other stages displayed biallelic expression of the H19 gene. (2) Thirteen out of 30 pre-eclampsia patients were H19 heterozygous and six of these showed the biallelic expression of the H19 gene (loss of imprinting). (3) The pre-eclampsia patients with the biallelic expression of H19 tended to have severer hypertension although their H19 RNA transcription level was similar to that in those with monoallelic expression.

CONCLUSIONS

(1) The biallelic expression of the H19 gene exists in some cases at the early stage of normal pregnancy and changes into monoallelic expression near 10 weeks of gestation. The dynamic alternations in the patterns of the H19 gene imprinting may regulate the maintenance of normal pregnancy. (2) The loss of the H19 gene imprinting in the placental tissues of pre-eclampsia patients may be associated with severe hypertension, contributing to the pathogenic process of pre-eclampsia.

Bilateral nocardial endophthalmitis in a prothonotary warbler (Protonotaria citrea)

A 7-year-old captive female prothonotary warbler (Protonotaria citrea) died following chronic feather and weight loss. At necropsy, the right eye had a 2 x 2 x 1 mm corneal plaque of inspissated yellow-tan material and edema of the lower eyelid. Microscopically, both eyes exhibited diffuse, severe pyogranulomatous endophthalmitis with retinal necrosis and detachment. Numerous intralesional branching, gram-positive, beaded, filamentous bacteria formed a thick mat attached to the retinal pigmented epithelium and extending into the pecten. Bacteria were strongly acid-fast positive by Fite's stain but only occasionally acid-fast positive by Ziehl-Neelsen staining, a characteristic consistent with a Nocardia spp. Infected regions demonstrated positive in situ hybridization reactivity with a probe complementary to the 16S rRNA gene of Nocardia spp. There was no evidence of primary bacterial infection in the other organs examined.

Production and synthetic dyes decolourization capacity of a recombinant laccase from Pichia pastoris

AIMS

To produce and purify a recombinant laccase from Pichia pastoris and to test its ability in decolourization of synthetic dyes.

METHODS AND RESULTS

A cDNA encoding for a laccase was isolated from Pycnoporus sanguineus and was expressed in P. pastoris strain SMD1168H under the control of the alcohol oxidase (AOX1) promoter. The laccase native signal peptide efficiently directed the secretion of the recombinant laccase in an active form. Factors influencing laccase expression, such as cultivation temperature, pH, copper concentration and methanol concentration, were investigated. The recombinant enzyme was purified to electrophoretic homogeneity, and was estimated to have a molecular mass of about 62.8 kDa. The purified enzyme showed a similar behaviour to the native laccase produced by P. sanguineus. Four different synthetic dyes including azo, anthraquinone, triphenylmethane and indigo dyes could be efficiently decolourized by the purified recombinant laccase without the addition of redox mediators.

CONCLUSIONS

Heterologous production of P. sanguineus laccase in P. pastoris was successfully achieved. The purified recombinant laccase could efficiently decolourize synthetic dyes in the absence of mediators.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first report on the synthetic dye decolourization by the recombinant P. sanguineus laccase. The decolourization capacity of this recombinant enzyme suggested that it could be a useful biocatalyst for the treatment of dye-containing effluents.

Revealing the maximum strength in nanotwinned copper

The strength of polycrystalline materials increases with decreasing grain size. Below a critical size, smaller grains might lead to softening, as suggested by atomistic simulations. The strongest size should arise at a transition in deformation mechanism from lattice dislocation activities to grain boundary-related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced strain hardening and tensile ductility. The strongest twin thickness originates from a transition in the yielding mechanism from the slip transfer across twin boundaries to the activity of preexisting easy dislocation sources.

Hexakis(2-amino-pyridinium) di-μ(6)-oxido-tetra-μ(3)-oxido-tetra-deca-μ(2)-oxido-octa-oxidodeca-vanadium(V) dihydrate

In the title compound, (C(5)H(7)N(2))(6)[V(10)O(28)]·2H(2)O, the [V(10)O(28)](6-) anion is generated by crystallographic inversion symmetry and each of the five vanadium centres adopts a distorted VO(6) octa-hedral geometry. In the crystal structure, a network of N-H⋯O, N-H⋯(O,O) and O-H⋯O hydrogen bonds helps to establish the packing.

Kinetics of manganese absorption in ligated small intestinal segments of broilers

Two experiments were conducted with 28-day-old male commercial broilers to study mechanisms of Mn absorption and the effect of Mn treatment on divalent metal transporter 1 (DMT1) mRNA levels in ligated segments from different intestinal regions of broilers. The results from experiment 1 showed that the amount of Mn absorption was asymptotic with respect to time within 40 min after perfusion of the duodenal, jejunal, and ileal segments of broilers with 2.18 mmol/L of Mn as MnSO(4). In experiment 2, a kinetic study of Mn absorption was performed with duodenal, jejunal, and ileal loops perfused with solutions containing 0, 0.13, 0.27, 0.54, 1.09, 2.18, 4.37, or 8.74 mmol/L of Mn as MnSO(4). Manganese concentrations in perfusates were determined at 5 min after perfusion. In the control group and in the group treated with 2.18 mmol/L Mn as MnSO(4), DMT1 mRNA levels of ligated intestinal regions at 30 min after perfusion were analyzed by real-time reverse transcription PCR. The kinetic curves of Mn absorption showed that Mn absorption was a carrier-mediated process in the duodenum and jejunum. The maximum absorption rate (J(max)) in duodenal segments was greater (P < 0.05) than that in the jejunum (94.08 vs. 81.17 nmol/cm per min). There was no significant difference (P = 0.85) in the Michaelis-Menten constant (K(m)) values between the duodenum and jejunum (3.41 vs. 3.60 mmol/L). In the ileum of Mn-deficient broilers, the most probable mechanism of Mn absorption was a nonsaturable diffusion process, and the diffusive constant (P; means +/- SE) was 2.42 x 10(-2) +/- 5.22 x 10(-4) cm(2)/min. The DMT1 mRNA levels in the duodenum and jejunum of broilers were greater (P < 0.001) than the level in the ileum. The DMT1 mRNA level in the small intestine of broilers in the Mn treatment group decreased significantly (P < 0.001) compared with that of the control. The different mechanisms of Mn absorption found in different intestinal segments suggest that the ileum is the main site of Mn absorption in the small intestine of broilers.

Effect of village income and household income on sanitation facilities, hygiene behaviours and child undernutrition during rapid economic growth in a rural cross-border area, Yunnan, China

BACKGROUND

The study aimed to examine the effects of village income and household income on child nutrition status through basic sanitation and hygiene behaviours.

METHODS

A survey was conducted in a rural cross-border area of Yunnan, China. Data on village income in 2002-2006 and household income in 2002-2007 were obtained from an official report and a household survey respectively. Anthropometric measurement of the children aged 6 months to 5 years (n = 1801) was used to determine their nutrition status. Child caretakers were interviewed about household sanitation facilities and their hygiene behaviours using a structured questionnaire.

RESULTS

Households with incomes below the national poverty line decreased from 22% in 2002 to less than 8% in 2007. The coverage of safe drinking water and water-sealed latrines gradually increased, but was still inadequate. The prevalence of stunting and underweight in children was 37% and 17.5% respectively. Village income had a greater positive effect than household income on exclusive breastfeeding, drinking boiled water, handwashing with soap, as well as reducing the prevalence of stunting. Village income at one lag year had the greatest effect on the availability of basic sanitation compared with other lag years, while household income had a small but significant effect through all lag years.

CONCLUSIONS

Rapid economic growth is not always followed by improved child nutrition status. Village income has a greater effect than household income on sanitation facilities, hygiene behaviours of caretakers and child nutrition status.

Intracellular levels of hepatitis B virus DNA and pregenomic RNA in peripheral blood mononuclear cells of chronically infected patients

It remains uncertain whether hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) and pregenomic RNA (pgRNA) can be detected in the serum or peripheral blood mononuclear cells (PBMC) of patients with chronic hepatitis B (CHB) infection. We examined HBV cccDNA and pgRNA in the serum and PBMC, and investigated the effect of lamivudine therapy on the viral loads in the PBMC of CHB patients. Paired serum and PBMC samples from 50 treatment-naïve CHB patients [25 hepatitis B e antigen (HBeAg) positive and 25 HBeAg negative] were quantified for total HBV DNA, cccDNA and pgRNA by real time polymerase chain reaction. HBV cccDNA and pgRNA were below the lower detection limit in all serum samples, and in 84% of PBMC. HBV DNA (r = 0.889, P < 0.001) and pgRNA (r = 0.696, P < 0.001) in PBMC correlated with the HBV DNA in serum. In the longitudinal study, 30 patients treated with lamivudine therapy for a median duration of 34 weeks (range 12-48 weeks) were examined. The median HBV DNA reduction in PBMC before and after treatment was 1.318 (range -0.471 to 3.846) log units, which was significantly lower than serum HBV DNA reduction [3.371 (range -0.883 to 9.454) log units, P < 0.05]. HBV cccDNA and pgRNA were undetectable in the serum of CHB patients. HBV viral loads in PBMC correlated with serum HBV DNA. Lamivudine therapy had less effect on the HBV viral loads in PBMC compared with the serum viral loads.

Application of cumulative odds logistic model on risk factors analysis for sexually transmitted infections among female sex workers in Kaiyuan city, Yunnan province, China

OBJECTIVES

To investigate the epidemiology of sexually transmitted infections (STI) among female sex workers (FSW) in Kaiyuan city, Yunnan province, China, and to identify risk factors associated with STI.

METHODS

A cross-sectional study of 737 FSW was carried out from March to May 2006, with confidential interviews and laboratory tests for STI. A cumulative logit model was used to evaluate the risk factors for STI.

RESULTS

The overall prevalence of HIV is 10.3%. The prevalence of syphilis, herpes simplex virus type 2, gonorrhoea, chlamydia and trichomonas was 7.5%, 68.1%, 8.3%, 25.9% and 10.6%, respectively. In multivariate cumulative odds logistic analysis, the factors associated with STI were education level, living in the entertainment location, injection drug use, non-injection drug use, over five clients in the previous week and inconsistent use of condoms with clients.

CONCLUSION

The findings highlight the gravity of the STI epidemic among FSW in China, where sexual transmission has now overtaken unsafe injection practices as the dominant mode of HIV transmission. Targeted intervention programmes for FSW should focus on increasing condom use, strengthening knowledge and awareness of STI/HIV and encouraging routine screening and treatment-seeking behaviours. Reducing the spread of STI also has profound implications for the prevention of HIV.

Genetic modulation of striatal volume by loci on Chrs 6 and 17 in BXD recombinant inbred mice

Natural variation in the absolute and relative size of different parts of the human brain is substantial, with a range that often exceeds a factor of 2. Much of this variation is generated by the cumulative effects of sets of unknown gene variants that modulate the proliferation, growth and death of neurons and glial cells. Discovering and testing the functions of these genes should contribute significantly to our understanding of differences in brain development, behavior and disease susceptibility. We have exploited a large population of genetically well-characterized strains of mice (BXD recombinant inbred strains) to map gene variants that influence the volume of the dorsal striatum (caudate-putamen without nucleus accumbens). We used unbiased methods to estimate volumes bilaterally in a sex-balanced sample taken from the Mouse Brain Library (www.mbl.org). We generated a matched microarray data set to efficiently evaluate candidate genes (www.genenetwork.org). As in humans, volume of the striatum is highly heritable, with greater than twofold differences among strains. We mapped a locus that modulates striatal volume on chromosome (Chr) 6 at 88 +/- 5 Mb. We also uncovered an epistatic interaction between loci on Chr 6 and Chr 17 that modulates striatal volume. Using bioinformatic tools and the corresponding expression database, we have identified positional candidates in these quantitative trait locus intervals.

A non-synonymous single nucleotide polymorphism in IFNAR1 affects susceptibility to chronic hepatitis B virus infection

The type I interferon (IFN-alpha/beta) receptor 1 (IFNAR1) mediates the potent antiviral and immuno-regulatory effects of IFN-alpha/beta that are believed to be pivotal to eradicate hepatitis B virus (HBV) infection. IFNAR1 promoter polymorphisms (at -568/-77) have been shown to be associated with susceptibility to chronic HBV infection; however, whether these markers are genetic determinants of HBV infection remains unknown. The functional significance of promoter -568/-77 polymorphisms was assessed by mutagenesis and luciferase assays. Sequencing and restriction fragment length polymorphisms in 328 chronic HBV patients, 130 spontaneous resolvers and 148 healthy blood donors identified other polymorphism at IFNAR1 open reading frame. IFNAR1 expression levels in peripheral blood cells were detected by flow cytometry. We found that the -568/-77 promoter variants were unlikely to affect transcription levels. A C/G single nucleotide polymorphism, in strong linkage disequilibrium with the promoter polymorphisms, was found in the coding sequence of IFNAR1 (nt19158). This resulted in a nonsynonymous substitution in the extracellular region of IFNAR1 protein and correlated with susceptibility to chronic HBV infection. Bioinformatic analysis suggested decreased stability of the IFNAR1 protein. Chronic HBV patients with the 19158C/C genotype (Leu141) exhibited higher IFNAR1 protein expression levels in peripheral blood monocytes than those with the 19158G/G genotype (Val141). In conclusion, IFNAR1 19158C/G polymorphism is primarily associated with susceptibility to chronic HBV infection.