Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex.

High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic methods using these data are sparse. Here we use multiple phylogenetic and population genetic methods for genotyping-by-sequencing data to assess species relationships in a group of forest insect pests, the spruce budworm (Choristoneura fumiferana) species complex. With few exceptions, all methods agree on the same relationships, most notably placing C. pinus as basal to the remainder of the group, rather than C. fumiferana as previously suggested. We found strong support for the monophyly of C. pinus, C. fumiferana, and C. retiniana, but more ambiguous relationships and signatures of introgression in a clade of western lineages, including C. carnana, C. lambertiana, C. occidentalis occidentalis, C. occidentalis biennis, and C. orae. This represents the most taxonomically comprehensive genomic treatment of the spruce budworm species group, which is further supported by the broad agreement among multiple methodologies.

A plant growth form dataset for the New World.

This dataset provides growth form classifications for 67,413 vascular plant species from North, Central, and South America. The data used to determine growth form were compiled from five major integrated sources and two original publications: the Botanical Information and Ecology Network (BIEN), the Plant Trait Database (TRY), the SALVIAS database, the USDA PLANTS database, Missouri Botanical Garden's Tropicos database, Wright (2010), and Boyle (1996). We defined nine plant growth forms based on woodiness (woody or non-woody), shoot structure (self-supporting or not self-supporting), and root traits (rooted in soil, not rooted in soil, parasitic or aquatic): Epiphyte, Liana, Vine, Herb, Shrub, Tree, Parasite, or Aquatic. Species with multiple growth form classifications were assigned the growth form classification agreed upon by the majority (>2/3) of sources. Species with ambiguous or otherwise not interpretable growth form assignments were excluded from the final dataset but are made available with the original data. Comparisons with independent estimates of species richness for the Western hemisphere suggest that our final dataset includes the majority of New World vascular plant species. Coverage is likely more complete for temperate than for tropical species. In addition, aquatic species are likely under-represented. Nonetheless, this dataset represents the largest compilation of plant growth forms published to date, and should contribute to new insights across a broad range of research in systematics, ecology, biogeography, conservation, and global change science.

Epidemiology and molecular typing of VRE bloodstream isolates in an Irish tertiary care hospital.

OBJECTIVES: Ireland has the highest rate of vancomycin-resistant Enterococcus faecium (VREfm) isolated from blood of nosocomial patients in Europe, which rose from 33% (110/330) in 2007 to 45% (178/392) in 2012. No other European country had a VREfm rate from blood cultures of >25%. Our aim was to elucidate the reasons for this significantly higher rate in Ireland. METHODS: The epidemiology and molecular typing of VRE from bloodstream infections (BSIs) was examined in a tertiary care referral hospital and isolates were compared with those from other tertiary care referral centres in the region. RESULTS: The most common source of VRE BSIs was intra-abdominal sepsis, followed by line-related infection and febrile neutropenia. Most of the isolates were positive for vanA; 52% (43/83) possessed the esp gene and 12% (10/83) possessed the hyl gene. Genotyping by SmaI macrorestriction analysis (PFGE) of isolates revealed clonal relatedness between bloodstream isolates and environmental isolates. VRE BSI isolates from two other tertiary care hospitals in the Dublin region showed relatedness by PFGE analysis. MLST revealed four STs (ST17, ST18, ST78 and ST203), all belonging to the clonal complex of hospital-associated strains. CONCLUSIONS: Irish VRE BSI isolates have virulence factor profiles as previously reported from Europe. Typing analysis shows the spread of individual clones within the hospital and between regional tertiary care hospitals. Apart from transmission of VRE within the hospital and transfer of colonized patients between Irish hospitals, no other explanation for the persistently high VREfm BSI rate in Ireland has been found.

The application of FAIMS gas analysis in medical diagnostics.

There is an ever increasing need to develop new tools to aid in the diagnosis and monitoring of human diseases. Such tools will ultimately reduce the cost of healthcare by identifying disease states more quickly and cheaply than current practices. One method showing promise is the analysis of gas-phase biomarkers from human breath, urine, sweat and stool that reflect bodily metabolism. Analysis of these volatiles by GC MS requires specialised infra-structure and staff, making it unsuitable for a clinical setting. Point of care sensor based technologies such as eNoses often suffer from stability and sensitivity issues. Field-Asymmetric Ion Mobility Spectrometry (FAIMS) has potential to fulfil this clinical need. In this paper we review the medical need, the technology, sampling methods and medical evidence thus far. We conclude with reflecting on future developmental steps necessary to bring the device into medical practice.

Prevalence and risk of Down syndrome in monozygotic and dizygotic multiple pregnancies in Europe: implications for prenatal screening.

OBJECTIVE: To determine risk of Down syndrome (DS) in multiple relative to singleton pregnancies, and compare prenatal diagnosis rates and pregnancy outcome. DESIGN: Population-based prevalence study based on EUROCAT congenital anomaly registries. SETTING: Eight European countries. POPULATION: 14.8 million births 1990-2009; 2.89% multiple births. METHODS: DS cases included livebirths, fetal deaths from 20 weeks, and terminations of pregnancy for fetal anomaly (TOPFA). Zygosity is inferred from like/unlike sex for birth denominators, and from concordance for DS cases. MAIN OUTCOME MEASURES: Relative risk (RR) of DS per fetus/baby from multiple versus singleton pregnancies and per pregnancy in monozygotic/dizygotic versus singleton pregnancies. Proportion of prenatally diagnosed and pregnancy outcome. STATISTICAL ANALYSIS: Poisson and logistic regression stratified for maternal age, country and time. RESULTS: Overall, the adjusted (adj) RR of DS for fetus/babies from multiple versus singleton pregnancies was 0.58 (95% CI 0.53-0.62), similar for all maternal ages except for mothers over 44, for whom it was considerably lower. In 8.7% of twin pairs affected by DS, both co-twins were diagnosed with the condition. The adjRR of DS for monozygotic versus singleton pregnancies was 0.34 (95% CI 0.25-0.44) and for dizygotic versus singleton pregnancies 1.34 (95% CI 1.23-1.46). DS fetuses from multiple births were less likely to be prenatally diagnosed than singletons (adjOR 0.62 [95% CI 0.50-0.78]) and following diagnosis less likely to be TOPFA (adjOR 0.40 [95% CI 0.27-0.59]). CONCLUSIONS: The risk of DS per fetus/baby is lower in multiple than singleton pregnancies. These estimates can be used for genetic counselling and prenatal screening.

Trends in the prevalence, risk and pregnancy outcome of multiple births with congenital anomaly: a registry-based study in 14 European countries 1984-2007.

OBJECTIVE: To assess the public health consequences of the rise in multiple births with respect to congenital anomalies. DESIGN: Descriptive epidemiological analysis of data from population-based congenital anomaly registries. SETTING: Fourteen European countries. POPULATION: A total of 5.4 million births 1984-2007, of which 3% were multiple births. METHODS: Cases of congenital anomaly included live births, fetal deaths from 20 weeks of gestation and terminations of pregnancy for fetal anomaly. MAIN OUTCOME MEASURES: Prevalence rates per 10,000 births and relative risk of congenital anomaly in multiple versus singleton births (1984-2007); proportion prenatally diagnosed, proportion by pregnancy outcome (2000-07). Proportion of pairs where both co-twins were cases. RESULTS: Prevalence of congenital anomalies from multiple births increased from 5.9 (1984-87) to 10.7 per 10,000 births (2004-07). Relative risk of nonchromosomal anomaly in multiple births was 1.35 (95% CI 1.31-1.39), increasing over time, and of chromosomal anomalies was 0.72 (95% CI 0.65-0.80), decreasing over time. In 11.4% of affected twin pairs both babies had congenital anomalies (2000-07). The prenatal diagnosis rate was similar for multiple and singleton pregnancies. Cases from multiple pregnancies were less likely to be terminations of pregnancy for fetal anomaly, odds ratio 0.41 (95% CI 0.35-0.48) and more likely to be stillbirths and neonatal deaths. CONCLUSIONS: The increase in babies who are both from a multiple pregnancy and affected by a congenital anomaly has implications for prenatal and postnatal service provision. The contribution of assisted reproductive technologies to the increase in risk needs further research. The deficit of chromosomal anomalies among multiple births has relevance for prenatal risk counselling.

Long-term adherence to first-line highly active antiretroviral therapy in a hospital-based cohort: predictors and impact on virologic response and relapse.

A high level of adherence to highly active antiretroviral therapy (HAART) is essential to minimize the risk of treatment failure and HIV disease progression. This cohort study evaluated the prevalence and predictors of long-term adherence with first-line HAART in a hospital-based unselected sample of HIV patients from central Italy, and examined the association between adherence and virological response or relapse. Between July 1996 and June 2004, 171 patients (67.3% males; mean age, 41.2 years) were followed for at least 24 weeks and up to 8 years. Adherence was measured by patient self-reports and confirmed using pharmacy records. The prevalence of high-level adherence (>or=90%) at 6 months was 88.3%; slightly less than 80% at 12 months. The incidence of adherence failure in the sample remained fairly stable until 24 months of follow-up, then it declined about 5% every 6 months. Cox analysis showed that compared to single/separated patients, homeless and married persons were, respectively, 1.95 times more likely and two times less likely to experience adherence failure (p < 0.05). The adjusted risk of adherence failure among patients who did not suffer drug-related toxicity was 0.57 (p < 0.05). Medication adherence was significantly associated with shorter time to virological response and longer time to relapse. Adherents were 1.69 times more likely to achieve viral suppression and nine times less likely to experience relapse than nonadherents (p < 0.01). Efforts at improving adherence should be prolonged for at least 24 months. A protective role of marriage for adherence failure is promising but requires confirmation in further research, that should also clarify the exact mechanisms determining the association.

Effect of tamoxifen on the multidrug-resistant phenotype in human breast cancer cells: isobologram, drug accumulation, and M(r) 170,000 glycoprotein (gp170) binding studies.

We have performed isobologram analyses of the ability of tamoxifen (TAM) to alter the response to Adriamycin (ADR) and vinblastine (VBL) in human breast cancer cells. MCF-7 cells express functional receptors for estrogen and progesterone but do not express detectable levels of M(r) 170,000 glycoprotein (gp170). CL 10.3 and MCF-7ADR cells are MCF-7 variants which express gp170. CL 10.3 but not MCF-7ADR cells express functional steroid hormone receptors. Tamoxifen (1-2.5 microM) interacts synergistically with ADR and VBL in CL 10.3 and MCF-7ADR cells. TAM increases the cytotoxicity of VBL and ADR and the intracellular levels of [3H]VBL by approximately 2-3-fold. TAM also prevents the binding of [3H]azidopine to gp170. The ability of TAM to concurrently increase the cytotoxic effects of ADR and VBL, increase VBL accumulation, and inhibit the binding of azidopine to gp170 strongly implies that the synergistic effects of TAM are mediated through its effects on gp170. TAM produces an antagonistic to additive interaction with ADR and VBL in MCF-7 cells, and at high concentrations (5 microM) the synergy apparent in CL 10.3 and MCF-7ADR cells is lost. While TAM clearly has a significant potential for use as a chemosensitizing agent, the design of clinical trials may require careful consideration.

Whole-genome sequencing improves discrimination of relapse from reinfection and identifies transmission events among patients with recurrent Clostridium difficile infections.

BACKGROUND: Recurrent Clostridium difficile infection (CDI) represents a significant healthcare challenge. Patients may suffer multiple episodes of CDI with the index strain (relapse) or become infected by another strain acquired nosocomially (reinfection). AIM: We aimed to characterize C. difficile isolates causing recurrent CDI at a tertiary referral hospital by whole-genome sequencing (WGS) to assess strain similarities at the highest level of genetic resolution and accurately detect relapse, reinfection, and putative strain transmission events. METHODS: An 18-month prospective study of recurrent CDI was undertaken. Clostridium difficile was cultured from stool samples collected longitudinally from any patients suffering ≥2 clinically defined CDI episodes. Patient demographics and clinical data were recorded, and strain relatedness investigated by both polymerase chain reaction (PCR)-based ribotyping and WGS. FINDINGS: Nineteen patients were identified with ≥2 clinically defined CDI episodes who cumulatively suffered 39 recurring CDI episodes (58 total episodes). Patients had a median length of stay (LOS) of 144 days and experienced between two and seven CDI episodes. Ribotyping indicated 27 apparent same-strain relapses, five reinfections and the predominance of ribotypes 078 (ST-11) and 020 (ST-2). WGS allowed characterization of relapse with increased certainty and identified emergent within-strain single nucleotide variants (SNVs) with potential functional impact on diverse genes. Shared ribotypes among 14 patients with recurrent CDI suggested 10 possible patient-to-patient transmission events. However, WGS revealed greater diversity at the sub-ribotype level, excluding all but four transmission events. CONCLUSION: WGS exhibits several advantages over PCR-based ribotyping in terms of its ability to distinguish relapse from reinfection, to identify patient-to-patient transmission events, and to exact fine structure characterization of recurrent CDI epidemiology. This offers the potential for more focused infection prevention strategies to eliminate strain transmission among patients with recurrent CDI.

Flow cytometric analysis of DNA ploidy, percent S-phase fraction, and total proliferative fraction as prognostic indicators of local control and survival following radiation therapy for prostate carcinoma.

PURPOSE: Treatment recommendations for localized prostate cancer may be improved by the identification of tumor factors prognostic for local control and survival. In this retrospective study, flow cytometric deoxyribonucleic acid (DNA) ploidy analysis and cell cycle analysis were performed on paraffin-embedded biopsy material to determine if additional prognostic factors could be identified in patients treated with radiation therapy. METHODS AND MATERIALS: Seventy patients with T1-4NxM0 tumors were identified in whom the primary treatment had been radical radiation therapy with no prior or concurrent endocrine therapy and in whom sufficient prostatic tissue was available for flow cytometric analysis. There were 40 diploid, 26 aneuploid, and 4 multiploid cases. Aneuploid and multiploid cases were combined for analysis. Cell cycle data were obtained on all diploid and 10 aneuploid cases. RESULTS: The histologic differentiation of the tumor (well or moderate vs. poor) was an independent predictor of overall survival and disease-free survival (p = 0.05 and 0.01, respectively). Local control was worse in the poorly differentiated patients, although this was not statistically significant in a multivariate analysis (p = 0.08). Neither T-stage, deoxyribonucleic acid ploidy (diploid vs. nondiploid), percent S-phase fraction, nor total proliferative fraction (S-phase fraction + G2M) significantly predicted for any of these endpoints. Within the diploid and well or moderately differentiated subgroup (n = 25), S-phase (< 4.2 vs. > or = 4.2) was a significant predictor of local control (100% vs. 51%, p = 0.03). A comparable distinction could be made using total proliferative fraction (< 10% vs. > or = 10%) with local control rates of 100% vs. 56% (p = 0.05). Among the poorly differentiated tumors, no similarly favorable subgroup was identified. CONCLUSIONS: This retrospective and multivariate analysis identifies both histology and percent S-phase or total proliferative fraction as predictors of local control following irradiation, and confirms that histology, but not DNA ploidy, is significant for overall survival. If these previously unreported findings are confirmed by prospective studies, S-phase should be added to histology as a parameter in the evaluation of clinical trials.

Thalidomide stimulates T cell responses and interleukin 12 production in HIV-infected patients.

We performed a placebo-controlled study to evaluate the effects of immunomodulatory treatment with thalidomide on HIV levels, TNF-alpha levels, and immune status of 31 HIV-infected individuals, after temporary suppression of viral replication with antiretroviral drugs. Treatment with a combination of zidovudine and lamivudine (ZDV/LMV) for 14 days resulted in a median decline in plasma viremia of 1.94 log10 RNA equivalents/ml. After discontinuation of ZDV/LMV, thalidomide therapy (200 mg/day for 4 weeks) did not retard the prompt return of HIV titers to the pretreatment levels, and had no effect on plasma levels of TNF-alpha. In contrast, thalidomide treatment resulted in significant immune stimulation. We observed increased levels of plasma soluble IL-2 receptor, soluble CD8 antigen, and IL-12 (p < 0.01 for all parameters), as well as increased cutaneous delayed-type hypersensitivity reactions to recall antigens (p < 0.01) in thalidomide-treated patients. These changes were associated with a median increase in HIV titer of 0.2 log10 RNA equivalents/ml in the thalidomide-treated group (p < 0.05), which resolved after stopping the drug. Further studies were performed in vitro to elucidate the mechanism of thalidomide-induced immune stimulation. When purified T cells from HIV-infected individuals were stimulated by immobilized anti-CD3 in the presence of thalidomide, a costimulatory effect of the drug was observed, resulting in increased production of IL-2 and IFN-gamma, and increased T cell-proliferative responses. Further experiments showed that thalidomide increased IL-12 production by antigen-presenting cells in a T cell-dependent manner. Our findings suggest a potential application for thalidomide as a novel immune adjuvant in HIV disease.

Differential regulation of a fibroblast growth factor-binding protein by receptor-selective analogs of retinoic acid.

We have demonstrated earlier that a secreted fibroblast growth factor-binding protein (FGF-BP) can enhance angiogenesis and promote tumor growth in vivo. Furthermore, we found that FGF-BP expression in squamous cell carcinoma (SCC) is reduced by concentrations of retinoids that are effective in the treatment of SCC and that this repression can occur at the transcriptional and post-transcriptional level. To further examine the mechanism of regulation of FGF-BP by retinoids and the role played by retinoid receptor subtypes, we utilized retinoic acid receptor (RAR)-selective (TTNPB) and retinoid X receptor (RXR)-selective (LG100268) ligands. In ME-180 SCC cells, FGF-BP mRNA was down-regulated by TTNPB with an IC(50) value of 1 nM, whereas transcription was only repressed at 10,000-fold higher concentrations (IC(50) > 10 microM). This suggests that the major effects of retinoids on FGF-BP occur at the post-transcriptional level. In four additional SCC cell lines, FGF-BP was also down-regulated by TTNPB with IC(50) values of

Sperm motility enhancement by nitric oxide produced by the oocytes of fathead minnows, Pimephelas promelas.

The effects of nitric oxide (NO) on sperm motility were examined in the fathead minnow, Pimephelas promelas, using computer-assisted sperm analysis (CASA). The observed effects underscore the dual nature of NO as both a low-concentration regulatory agent and, at higher doses, a cytotoxic agent. At 1 x 10(-6) M concentration, NO donor sodium nitroprusside (SNP) enhanced sperm motility percentages and increased CASA velocity parameters curvilinear velocity, straight-line velocity, and average path velocity, whereas 1 x 10(-2) M concentration inhibited percent motility and decreased velocities. Fathead minnow ova-produced NO was subsequently trapped as a paramagnetic ferrous iron complex and detected by electron spin resonance spectroscopy. The distinctive triplet spectrum, with a(N) = 12.5G and g(iso) = 2.04, was recorded during a critical 5-minute period following laying. Nitric oxide synthase (NOS) was histochemically localized at the micropyle of mature unfertilized fathead eggs, and an inhibitor of NOS blocked histochemical staining. CASA analysis of sperm motility in the presence of ovaproduced NO over an 8-minute time course reveals an optimum motility enhancement at 4 minutes that is similar to the effect of 1 x 10(-6) M SNP. This transient NO production by freshly laid ova and the localization of NOS near the site of sperm entry, together with the motility-enhancing effect of 1 x 10(-6) M SNP on sperm, indicates an active role for low-concentration NO in fertilization.

Q fever endocarditis revisited.

A diagnosis of Q fever endocarditis was made in 7 patients, 6 with predisposing factors and 3 with occupational risk factors. Prompt recognition of Coxiella burnettii endocarditis is required when clinical signs of endocarditis such as fever, anaemia, elevated liver transaminases, congestive cardiac failure are accompanied by negative blood cultures. Serological evidence of elevated antibody titres to Phase I and Phase II antigens of Coxiella burnettii are diagnostic. Prolonged antimicrobial therapy combined with surgery has resulted in the marked reduction of mortality from 50 per cent of 17 per cent when Q fever endocarditis is revisited almost 20 yr later.

The imaging center option: where the buck stops.

In another examination of the freestanding imaging option, Ms. O'Boyle discusses the highly concentrated management demands placed on the center administrator, who functions as the place where personnel, marketing, purchasing and accounting responsibilities all stop.

BAC library construction, screening and clone sequencing of lake whitefish (Coregonus clupeaformis, Salmonidae) towards the elucidation of adaptive species divergence.

Genomic DNA sequences and other genomic resources are essential towards the elucidation of the genomic bases of adaptive divergence and reproductive isolation. Here, we describe the construction, characterization and screening of a nonarrayed BAC library for lake whitefish (Coregonus clupeaformis). We then show how the combined use of BAC library screening and next-generation sequencing can lead to efficient full-length assembly of candidate genes. The lake whitefish BAC library consists of 181,050 clones derived from a single heterozygous fish. The mean insert size is 92 Kb, representing 5.2 haploid genome equivalents. Ten BAC clones were isolated following a quantitative real-time PCR screening approach that targeted five previously identified candidate genes. Sequencing of these clones on a 454 GS FLX system yielded 178,000 reads with a mean length of 358 bp, for a total of 63.8 Mb. De novo assembly and annotation then allowed retrieval of contigs corresponding to each candidate gene, which also contained up- and/or downstream noncoding sequences. These results suggest that the lake whitefish BAC library combined with next-generation sequencing technologies will be key resources to achieve a better understanding of both adaptive divergence and reproductive isolation in lake whitefish species pairs as well as salmonid evolution in general.

Serum cardiac troponin I concentrations transiently increase in rats given rosiglitazone.

Rosiglitazone, a peroxisome proliferator-activated receptor γ (PPARγ) agonist of the thiazolidinedione class, is a major insulin-sensitizing drug widely used to treat type-2 diabetes. Rosiglitazone causes myocardial hypertrophy in rodents and increases the risk of cardiac events in man. To better characterize its cardiac effects, male Wistar rats were orally administered 0, 10 or 80 mg/kg/day rosiglitazone. Myocardial gene expression profiling, hematology, histopathology and clinical chemistry, including measurement of serum cardiac troponin (cTn) I concentration with the ultrasensitive assay, were evaluated after 6 and 24h and 7 and 14 days of dosing. Heart weight was increased 10% after 7 days and 16% after 14 days of dosing at 80 mg/kg/day in the absence of microscopic changes. At the transcriptomic level, the number of differentially expressed probes was small: it was most at 24h in rats given 80 mg/kg rosiglitazone with 356 differentially regulated probes (fold change >1.3 fold, p<0.05). Also, gene categories typically associated with myocardial damage were not over-represented. Most importantly, serum cTnI concentrations in 5/9 rats after 7 days of dosing at 80 mg/kg/day were above the upper limit of serum cTnI concentration. cTnI concentrations after 14 days of dosing were similar between rats given the vehicle and rosiglitazone at 80 mg/kg. This is the first study to detect increases of serum cTnI concentrations in rats administered rosiglitazone. In light of reported cardiac events in patients chronically dosed with PPARγ agonists, our results support serum cTnI concentrations as an early biomarker of cardiac liability.