Prognostic impact of genetic variants of CYP19A1 and UGT2B17 in a randomized trial for endocrine-responsive postmenopausal breast cancer.

Polymorphisms of genes involved in estrogen synthesis have been linked to breast cancer risk, prognosis, and treatment response. We investigated the prognostic impact of a deletion spanning the entire UGT2B17 gene (UGT2B17*2) and genetic variants of the aromatase CYP19A1 and estrogen receptor α (ESR1) in 125 postmenopausal women with ER-positive breast cancer enrolled in a randomized pre-surgical trial. The UGT2B17*2 was estimated by copy number variation assays and the CYP19A1 rs10046/rs4646 and ESR1 rs2077647/rs2234693/rs9340799 by TaqMan allelic discrimination assays. Serum exemestane/17-hydroxy exemestane were determined by MS and estrone (E1)/estradiol (E2)/ by GC-MS/MS. The association of genetic polymorphisms with "any event" was assessed by the Cox proportional hazards models adjusted for confounders. The UGT2B17*2 was associated with higher levels of 17-hydroxy exemestane (P = 0.04) and better prognosis (HR = 0.45; 95% CI: 0.20-1.01; P = 0.05) compared with homozygote UGT2B17 wt. The CYP19A1 rs10046 A and rs4646 C alleles were associated with higher estrogen levels: rs10046 AA vs. AG/GG genotypes had median E1 of 35.9 vs. 27.4 pg/mL (P = 0.05) and E2 of 7.57 vs. 3.9 pg/mL (P < 0.004). After a median follow-up of 7 years, women carrying the "low estrogen" alleles rs10046 G and rs4646 A had a better prognosis compared with homozygote wt for both polymorphisms (HR = 0.40; 95% CI: 0.17-0.93; P = 0.03). Our analysis points to an impact of UGT2B17 and CYP19A1 in postmenopausal endocrine responsive breast cancer. Carriers of UGT2B17*2 and CYP19A1 low estrogen variants may have better prognosis, supporting studies addressing the role of these polymorphisms in optimizing endocrine therapy. Trial registration: http://www.isrctn.com/ISRCTN86894592.

SLCO1B1 polymorphisms and plasma estrone conjugates in postmenopausal women with ER+ breast cancer: genome-wide association studies of the estrone pathway.

BACKGROUND: Estrone (E1), the major circulating estrogen in postmenopausal women, promotes estrogen-receptor positive (ER+) breast tumor growth and proliferation. Two major reactions contribute to E1 plasma concentrations, aromatase (CYP19A1) catalyzed E1 synthesis from androstenedione and steroid sulfatase (STS) catalyzed hydrolysis of estrone conjugates (E1Cs). E1Cs have been associated with breast cancer risk and may contribute to tumor progression since STS is expressed in breast cancer where its activity exceeds that of aromatase. METHODS: We performed genome-wide association studies (GWAS) to identify SNPs associated with variation in plasma concentrations of E1Cs, E1, and androstenedione in 774 postmenopausal women with resected early-stage ER+ breast cancer. Hormone concentrations were measured prior to aromatase inhibitor therapy. RESULTS: Multiple SNPs in SLCO1B1, a gene encoding a hepatic influx transporter, displayed genome-wide significant associations with E1C plasma concentrations and with the E1C/E1 ratio. The top SNP for E1C concentrations, rs4149056 (p = 3.74E-11), was a missense variant that results in reduced transporter activity. Patients homozygous for the variant allele had significantly higher average E1C plasma concentrations than did other patients. Furthermore, three other SLCO1B1 SNPs, not in LD with rs4149056, were associated with both E1C concentrations and the E1C/E1 ratio and were cis-eQTLs for SLCO1B3. GWAS signals of suggestive significance were also observed for E1, androstenedione, and the E1/androstenedione ratio. CONCLUSION: These results suggest a mechanism for genetic variation in E1C plasma concentrations as well as possible SNP biomarkers to identify ER+ breast cancer patients for whom STS inhibitors might be of clinical value.

Centre-level variation in dental treatment and oral health and individual- and area-level predictors of oral health in 5-year-old children with non-syndromic unilateral cleft lip and palate: the Cleft Care UK study. Part 3.

OBJECTIVES: To explore centre-level variation in fluoride treatment and oral health outcomes and to examine the association of individual- and area-level risk factors with dental decay in Cleft Care UK (CCUK). SETTING: Two hundred and sixty-eight 5-year-old British children with non-syndromic unilateral cleft lip and palate (UCLP). MATERIALS AND METHODS: Data on caries and developmental defects of enamel (DDE) were collected. The child's history of fluoride ingestion and postcode was used to assess exposure to fluoridated water. Centre-level variation in fluoride exposure and caries was examined using hierarchical regression. Poisson regression was used to estimate the association between individual- and area-level fluoride exposures and outcome. RESULTS: Children had high levels of caries, rampant caries and DDE. There was no evidence of variation between centres in the number of children with caries or rampant decay. There was evidence of variation in prescription of fluoride tablets and varnish and the type of toothpaste used. Area level of deprivation was associated with a higher risk of dental caries-risk ratio (RR) in the lowest quartile versus the rest was 1.43 (95% CI 1.13 to 1.81). Use of fluoride tablets and varnish was associated with higher risk of caries-RR 1.73 (95% CI 1.29 to 2.32) and RR 1.33 (95% CI 1.04 to 1.70), respectively, adjusted for age, sex and deprivation. CONCLUSION: The association with use of fluoride tablets and varnish probably reflects reverse causality but indicates the need for early preventative interventions in children with UCLP.

CpG islands of chicken are concentrated on microchromosomes.

The chicken karyotype comprises 39 chromosome pairs of which at least 29 are 'microchromosomes'. Microchromosomes account for about 25% of the genomic DNA, but they are cytologically indistinguishable from one another (1). Due to technical limitations there is a strong bias of mapped genes within the chicken genome database ChickGBASE (2) towards macrochromosomes 1-6 and Z, with specific assignments to only one microchromosome (3,4). Several genes have, however, been assigned to the microchromosome group as a whole (3,5-9), demonstrating that these tiny chromosomes do not represent genetically inert DNA. To determine the overall chromosomal distribution of genes, as well as to provide a mapping resource, we prepared a CpG island library from chicken using differential binding to a methyl-CpG chicken using differential binding to a methyl-CpG binding column before and after de novo methylation (10). Surprisingly, we found that chicken CpG islands are highly concentrated on the microchromosomes, whereas macrochromosomes 1-6 are comparatively gene-poor by this assay. Our results raise the possibility that gene density on chicken microchromosomes approaches the maximum value known for vertebrates.

Think globally, measure locally: The MIREN standardized protocol for monitoring plant species distributions along elevation gradients.

Climate change and other global change drivers threaten plant diversity in mountains worldwide. A widely documented response to such environmental modifications is for plant species to change their elevational ranges. Range shifts are often idiosyncratic and difficult to generalize, partly due to variation in sampling methods. There is thus a need for a standardized monitoring strategy that can be applied across mountain regions to assess distribution changes and community turnover of native and non-native plant species over space and time. Here, we present a conceptually intuitive and standardized protocol developed by the Mountain Invasion Research Network (MIREN) to systematically quantify global patterns of native and non-native species distributions along elevation gradients and shifts arising from interactive effects of climate change and human disturbance. Usually repeated every five years, surveys consist of 20 sample sites located at equal elevation increments along three replicate roads per sampling region. At each site, three plots extend from the side of a mountain road into surrounding natural vegetation. The protocol has been successfully used in 18 regions worldwide from 2007 to present. Analyses of one point in time already generated some salient results, and revealed region-specific elevational patterns of native plant species richness, but a globally consistent elevational decline in non-native species richness. Non-native plants were also more abundant directly adjacent to road edges, suggesting that disturbed roadsides serve as a vector for invasions into mountains. From the upcoming analyses of time series, even more exciting results can be expected, especially about range shifts. Implementing the protocol in more mountain regions globally would help to generate a more complete picture of how global change alters species distributions. This would inform conservation policy in mountain ecosystems, where some conservation policies remain poorly implemented.

Transcranial direct current stimulation's effect on novice versus experienced learning.

Transcranial direct current stimulation (TDCS) is a non-invasive form of brain stimulation applied via a weak electrical current passed between electrodes on the scalp. In recent studies, TDCS has been shown to improve learning when applied to the prefrontal cortex (e.g., Kincses et al. in Neuropsychologia 42:113-117, 2003; Clark et al. Neuroimage in 2010). The present study examined the effects of TDCS delivered at the beginning of training (novice) or after an hour of training (experienced) on participants' ability to detect cues indicative of covert threats. Participants completed two 1-h training sessions. During the first 30 min of each training session, either 0.1 mA or 2.0 mA of anodal TDCS was delivered to the participant. The anode was positioned near F8, and the cathode was placed on the upper left arm. Testing trials immediately followed training. Accuracy in classification of images containing and not-containing threat stimuli during the testing sessions indicated: (1) that mastery of threat detection significantly increased with training, (2) that anodal TDCS at 2 mA significantly enhanced learning, and (3) TDCS was significantly more effective in enhancing test performance when applied in novice learners than in experienced learners. The enhanced performance following training with TDCS persisted into the second session when TDCS was delivered early in training.

The neural networks underlying auditory sensory gating.

One of the most consistent electrophysiological deficits reported in the schizophrenia literature is the failure to inhibit, or properly gate, the neuronal response to the second stimulus of an identical pair (i.e., sensory gating). Although animal and invasive human studies have consistently implicated the auditory cortex, prefrontal cortex and hippocampus in mediating the sensory gating response, localized activation in these structures has not always been reported during non-invasive imaging modalities. In the current experiment, event-related FMRI and a variant of the traditional gating paradigm were utilized to examine how the gating network differentially responded to the processing of pairs of identical and non-identical tones. Two single-tone conditions were also presented so that they could be used to estimate the HRF for paired stimuli, reconstructed based on actual hemodynamic responses, to serve as a control non-gating condition. Results supported an emerging theory that the gating response for both paired-tone conditions was primarily mediated by auditory and prefrontal cortex, with potential contributions from the thalamus. Results also indicated that the left auditory cortex may play a preferential role in determining the stimuli that should be inhibited (gated) or receive further processing due to novelty of information. In contrast, there was no evidence of hippocampal involvement, suggesting that future work is needed to determine what role it may play in the gating response.

Contraceptives and dysplasia: higher rate for pill choosers.

Among women choosing the pill in preference to other contraceptive methods there is a higher rate of the cancer precursor, dysplasia of the cervix, before any possible effect of the pill.

Nonmethylated transposable elements and methylated genes in a chordate genome.

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.

The effect of face inversion on activity in human neural systems for face and object perception.

The differential effect of stimulus inversion on face and object recognition suggests that inverted faces are processed by mechanisms for the perception of other objects rather than by face perception mechanisms. We investigated the face inversion using functional magnetic resonance imaging (fMRI). The principal effect of face inversion on was an increased response in ventral extrastriate regions that respond preferentially to another class of objects (houses). In contrast, house inversion did not produce a similar change in face-selective regions. Moreover, stimulus inversion had equivalent, minimal effects for faces in in face-selective regions and for houses in house-selective regions. The results suggest that the failure of face perception systems with inverted faces leads to the recruitment of processing resources in object perception systems, but this failure is not reflected by altered activity in face perception systems.

Diversity cascades in alfalfa fields: from plant quality to agroecosystem diversity.

To examine top-down and bottom-up influences on managed terrestrial communities, we manipulated plant resources and arthropod abundance in alfalfa (Medicago sativa L.) fields. We modified arthropod communities using three nonfactorial manipulations: pitfall traps to remove selected arthropods, wooden crates to create habitat heterogeneity, and an arthropod removal treatment using a reversible leaf blower. These manipulations were crossed with fertilizer additions, which were applied to half of the plots. We found strong effects of fertilizer on plant quality and biomass, and these effects cascaded up to increase herbivore abundance and diversity. The predator community also exhibited a consistent positive effect on the maintenance of herbivore species richness and abundance. These top-down changes in arthropods did not cascade down to affect plant biomass; however, plant quality (saponin content) increased with higher herbivore densities. These results corroborate previous studies in alfalfa that show complex indirect effects, such as trophic cascades, can operate in agricultural systems, but the specifics of the interactions depend on the assemblages of arthropods involved.

The use of cell salvage during obstetric procedures: an audit of Scotland's maternity units.

BACKGROUND: Concerns about the safety and supply of donor blood mean that clinicians are increasingly looking for alternatives to allogenic blood transfusion. One such alternative is cell salvage. Theoretical concerns about the safety of giving salvaged blood to obstetric patients have so far limited its use in maternity patients, but its use in obstetrics is now growing. AIMS: To determine how many Scottish maternity units use cell salvage and what barriers anaesthetists see to its use in obstetrics. METHODS: A survey was posted to one consultant anaesthetist at each of Scotland's 18 consultant led maternity units. RESULTS: Two out of 18 maternity units in Scotland use cell salvage. Perceived barriers to use include lack of machine, insufficient cases and lack of familiarity with the technology. Only 4/15 anaesthetists saw safety concerns as a barrier to using the technology. CONCLUSION: It would appear that practical issues such as staff training and maintaining familiarity with the technology are greater barriers to the use of cell salvage during obstetric procedures than concerns over safety or financial costs. Although cell salvage would appear to be safe, its use in obstetrics must be accompanied by ongoing audit and detailed data should be collected for each case.

IMRT treatment planning for prostate cancer using prioritized prescription optimization and mean-tail-dose functions.

Treatment planning for intensity modulated radiation therapy (IMRT) is challenging due to both the size of the computational problems (thousands of variables and constraints) and the multi-objective, imprecise nature of the goals. We apply hierarchical programming to IMRT treatment planning. In this formulation, treatment planning goals/objectives are ordered in an absolute hierarchy, and the problem is solved from the top-down such that more important goals are optimized in turn. After each objective is optimized, that objective function is converted into a constraint when optimizing lower-priority objectives. We also demonstrate the usefulness of a linear/quadratic formulation, including the use of mean-tail-dose (mean dose to the hottest fraction of a given structure), to facilitate computational efficiency. In contrast to the conventional use of dose-volume constraints (no more than x% volume of a structure should receive more than y dose), the mean-tail-dose formulation ensures convex feasibility spaces and convex objective functions. To widen the search space without seriously degrading higher priority goals, we allowed higher priority constraints to relax or 'slip' a clinically negligible amount during lower priority iterations. This method was developed and tuned for external beam prostate planning and subsequently tested using a suite of 10 patient datasets. In all cases, good dose distributions were generated without individual plan parameter adjustments. It was found that allowance for a small amount of 'slip,' especially in target dose homogeneity, often resulted in improved normal tissue dose burdens. Compared to the conventional IMRT treatment planning objective function formulation using a weighted linear sum of terms representing very different dosimetric goals, this method: (1) is completely automatic, requiring no user intervention, (2) ensures high-priority planning goals are not seriously degraded by lower-priority goals, and (3) ensures that lower priority, yet still important, normal tissue goals are separately pushed as far as possible without seriously impacting higher priority goals.

Methylation of genomes and genes at the invertebrate-vertebrate boundary.

Patterns of DNA methylation in animal genomes are known to vary from an apparent absence of modified bases, via methylation of a minor fraction of the genome, to genome-wide methylation. Representative genomes from 10 invertebrate phyla comprise predominantly nonmethylated DNA and (usually but not always) a minor fraction of methylated DNA. In contrast, all 27 vertebrate genomes that have been examined display genome-wide methylation. Our studies of chordate genomes suggest that the transition from fractional to global methylation occurred close to the origin of vertebrates, as amphioxus has a typically invertebrate methylation pattern whereas primitive vertebrates (hagfish and lamprey) have patterns that are typical of vertebrates. Surprisingly, methylation of genes preceded this transition, as many invertebrate genes have turned out to be heavily methylated. Methylation does not preferentially affect genes whose expression is highly regulated, as several housekeeping genes are found in the heavily methylated fraction whereas several genes expressed in a tissue-specific manner are in the nonmethylated fraction.

Multimodal Neuroimaging in Schizophrenia: Description and Dissemination.

In this paper we describe an open-access collection of multimodal neuroimaging data in schizophrenia for release to the community. Data were acquired from approximately 100 patients with schizophrenia and 100 age-matched controls during rest as well as several task activation paradigms targeting a hierarchy of cognitive constructs. Neuroimaging data include structural MRI, functional MRI, diffusion MRI, MR spectroscopic imaging, and magnetoencephalography. For three of the hypothesis-driven projects, task activation paradigms were acquired on subsets of ~200 volunteers which examined a range of sensory and cognitive processes (e.g., auditory sensory gating, auditory/visual multisensory integration, visual transverse patterning). Neuropsychological data were also acquired and genetic material via saliva samples were collected from most of the participants and have been typed for both genome-wide polymorphism data as well as genome-wide methylation data. Some results are also presented from the individual studies as well as from our data-driven multimodal analyses (e.g., multimodal examinations of network structure and network dynamics and multitask fMRI data analysis across projects). All data will be released through the Mind Research Network's collaborative informatics and neuroimaging suite (COINS).

Trophic diversity in two grassland ecosystems.

The roles of consumers (top-down forces) versus resources (bottom-up forces) as determinants of alpha diversity in a community are not well studied. Numerous community ecology models and empirical studies have provided a framework for understanding how density at various trophic levels responds to variation in the relative strength of top-down and bottom-up forces. The resulting trophic theory can be applied to understanding variation in insect diversity at different trophic levels. The objective of this research was to elucidate the strengths of direct and indirect interactions between plants and entire arthropod communities to determine the effects of trophic interactions on arthropod diversity. Grassland plant and insect diversity was measured in July 2001 to document patterns of diversity at multiple trophic levels. The study site includes riparian grasslands in North-Central Colorado on the Carpenter Ranch, owned and managed by The Nature Conservancy. This pastureland consists of sites with different management regimes: unmanaged pasture intermixed along riparian forest, and cattle grazed pasture with flood irrigation. Plant abundance and richness were higher on the grazed-irrigated pasture versus the unmanaged field. Path analysis revealed strong effects of herbivore diversity on diversity of other trophic levels. For the managed fields, top-down forces were important, with increases in enemy diversity depressing herbivore diversity, which in turn depressed plant abundance. For the unmanaged fields, bottom-up forces dominated, with increases in plant diversity causing increased herbivore diversity, which in turn increased enemy diversity. These results support hypotheses from other empirical studies, demonstrating that changes in diversity of a single trophic level can cascade to effect diversity at other, nonadjacent trophic levels.

Cytokeratin characterization of human prostatic carcinoma and its derived cell lines.

Two murine monoclonal anti-cytokeratin antibodies with defined specificity were shown to distinguish between basal cells and luminal cells in human prostate tissue. Forty-one biopsies or transurethral resection specimens were characterized using these two antibodies. In cases of benign prostatic hyperplasia, focal loss of the basal cell layer was noted in areas of glandular proliferation. Ten cases of adenocarcinoma of the prostate, varying in Gleason's histological grade from 2 to 4, were also studied. In each case the carcinoma was shown to represent the luminal cell phenotype with no evidence of involvement of the basal cell phenotype. An analysis of three established metastatic prostatic carcinoma cell lines (DU-145, PC-3, and LNCaP) using two-dimensional electrophoresis showed that the cytokeratin complement of each cell line was slightly different but retained the phenotype of the luminal cell. It was concluded that during both hyperplasia and neoplastic transformation of the prostate, the luminal cell phenotype is primarily involved and that the basal cell phenotype does not appear to contribute to either intraluminal proliferation or invasive cell populations.

Bioanalytical method transfer considerations of chromatographic-based assays.

Bioanalysis is an important part of the modern drug development process. The business practice of outsourcing and transferring bioanalytical methods from laboratory to laboratory has increasingly become a crucial strategy for successful and efficient delivery of therapies to the market. This chapter discusses important considerations when transferring various types of chromatographic-based assays in today's pharmaceutical research and development environment.