Thyroid hormone-regulated gene expression in juvenile mouse liver: identification of thyroid response elements using microarray profiling and in silico analyses

<p>Abstract</p> <p>Background</p> <p>Disruption of thyroid hormone signalling can alter growth, development and energy metabolism. Thyroid hormones exert their effects through interactions with thyroid receptors that directly bind thyroid response elements and can alter transcriptional activity of target genes. The effects of short-term thyroid hormone perturbation on hepatic mRNA transcription in juvenile mice were evaluated, with the goal of identifying genes containing active thyroid response elements. Thyroid hormone disruption was induced from postnatal day 12 to 15 by adding goitrogens to dams' drinking water (hypothyroid). A subgroup of thyroid hormone-disrupted pups received intraperitoneal injections of replacement thyroid hormones four hours prior to sacrifice (replacement). An additional group received only thyroid hormones four hours prior to sacrifice (hyperthyroid). Hepatic mRNA was extracted and hybridized to Agilent mouse microarrays.</p> <p>Results</p> <p>Transcriptional profiling enabled the identification of 28 genes that appeared to be under direct thyroid hormone-regulation. The regulatory regions of the genome adjacent to these genes were examined for half-site sequences that resemble known thyroid response elements. A bioinformatics search identified 33 thyroid response elements in the promoter regions of 13 different genes thought to be directly regulated by thyroid hormones. Thyroid response elements found in the promoter regions of Tor1a, 2310003H01Rik, Hect3d and Slc25a45 were further validated by confirming that the thyroid receptor is associated with these sequences <it>in vivo </it>and that it can bind directly to these sequences <it>in vitro</it>. Three different arrangements of thyroid response elements were identified. Some of these thyroid response elements were located far up-stream (> 7 kb) of the transcription start site of the regulated gene.</p> <p>Conclusions</p> <p>Transcriptional profiling of thyroid hormone disrupted animals coupled with a novel bioinformatics search revealed new thyroid response elements associated with genes previously unknown to be responsive to thyroid hormone. The work provides insight into thyroid response element sequence motif characteristics.</p

Front propagation into unstable and metastable states in Smectic C* liquid crystals: linear and nonlinear marginal stability analysis

We discuss the front propagation in ferroelectric chiral smectics (SmC*) subjected to electric and magnetic fields applied parallel to smectic layers. The reversal of the electric field induces the motion of domain walls or fronts that propagate into either an unstable or a metastable state. In both regimes, the front velocity is calculated exactly. Depending on the field, the speed of a front propagating into the unstable state is given either by the so-called linear marginal stability velocity or by the nonlinear marginal stability expression. The cross-over between these two regimes can be tuned by a magnetic field. The influence of initial conditions on the velocity selection problem can also be studied in such experiments. SmC$^*$ therefore offers a unique opportunity to study different aspects of front propagation in an experimental system

Circulation and water mass transformation in a model of the Chukchi Sea

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): C05025, doi:10.1029/2005JC003364.The circulation and water mass transformation in a regional ocean-ice model of the Chukchi Sea are discussed. The model has horizontal resolution of O(4 km), is forced by fluxes derived from daily NCEP reanalysis fields, and has seasonally varying transport, temperature, and salinity imposed at Bering Strait. Many of the observed characteristics of the mean circulation and seasonal cycle in the Chukchi Sea are reproduced. The discussion focuses on: the branching of the inflow transport into pathways following Herald Canyon, Central Channel, and the Alaskan coast; the pattern of ice melt; and the water mass transformation and formation of winter water and hypersaline water. The ice melt pattern and timing is strongly influenced by advection through Bering Strait. High frequency forcing results in a larger region of ice melt, particularly over the shoals and in the northern Chukchi Sea, compared to monthly mean forcing. In the model, the seasonal cycle of salinity in the southern and central Chukchi Sea is dominated by advection through Bering Strait, while local atmospheric forcing and brine rejection are more important north of Herald and Hanna Shoals and in Barrow Canyon. However, since the residence time in the Chukchi Sea is generally less than 1 year, interannual variability in the Bering Strait salinity will be reflected in the salinity across the Chukchi Sea and at Barrow Canyon.This material is based upon work supported by the National Science Foundation Office of Polar Programs under grant 0421904

The cool magnetic DAZ white dwarf NLTT 10480

We have identified a new, cool magnetic white dwarf in the New Luyten Two-Tenths (NLTT) catalogue. The high proper-motion star NLTT 10480 (mu=0.5"/year) shows weak Zeeman-split lines of calcium, as well as characteristic Halpha and beta Zeeman triplets. Using VLT X-shooter spectra we measured a surface-averaged magnetic field B_S ~ 0.5 MG. The relative intensity of the pi and sigma components of the calcium and hydrogen lines imply a high inclination (i > 60 deg). The optical-to-infrared V-J colour index and the CaI/CaII ionization balance indicate a temperature between 4900 and 5200 K, while the Balmer line profiles favour a higher temperature of 5400 K. The discrepancy is potentially resolved by increasing the metallicity to 0.03x solar, hence increasing the electron pressure. However, the measured calcium abundance and abundance upper limits for other elements (Na, Al, Si. and Fe) imply a low photospheric metallicity < 10^{-4} solar. Assuming diffusion steady-state, a calcium accretion rate of log(dM/dt)(g/s)=5.6+/-0.3 is required to sustain a calcium abundance of log(n(Ca)/n(H))=-10.30+/-0.30 in the white dwarf atmosphere. We examine the implications of this discovery for the incidence of planetary debris and weak magnetic fields in cool white dwarf stars.Comment: Accepted for publication in A&

Contributions of a global network of tree diversity experiments to sustainable forest plantations

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Methodological challenges in collecting social and behavioural data regarding the HIV epidemic among gay and other men who have sex with men in Australia

©2014 Zablotska et al. Background: Behavioural surveillance and research among gay and other men who have sex with men (GMSM) commonly relies on non-random recruitment approaches. Methodological challenges limit their ability to accurately represent the population of adult GMSM. We compared the social and behavioural profiles of GMSM recruited via venue-based, online, and respondent-driven sampling (RDS) and discussed their utility for behavioural surveillance. Methods: Data from four studies were selected to reflect each recruitment method. We compared demographic characteristics and the prevalence of key indicators including sexual and HIV testing practices obtained from samples recruited through different methods, and population estimates from respondent-driven sampling partition analysis. Results: Overall, the socio-demographic profile of GMSM was similar across samples, with some differences observed in age and sexual identification. Men recruited through time-location sampling appeared more connected to the gay community, reported a greater number of sexual partners, but engaged in less unprotected anal intercourse with regular (UAIR) or casual partners (UAIC). The RDS sample overestimated the proportion of HIV-positive men and appeared to recruit men with an overall higher number of sexual partners. A single-website survey recruited a sample with characteristics which differed considerably from the population estimates with regards to age, ethnically diversity and behaviour. Data acquired through time-location sampling underestimated the rates of UAIR and UAIC, while RDS and online sampling both generated samples that underestimated UAIR. Simulated composite samples combining recruits from time-location and multi-website online sampling may produce characteristics more consistent with the population estimates, particularly with regards to sexual practices. Conclusion: Respondent-driven sampling produced the sample that was most consistent to population estimates, but this methodology is complex and logistically demanding. Time-location and online recruitment are more cost-effective and easier to implement; using these approaches in combination may offer the potential to recruit a more representative sample of GMSM

Non-monotonic changes in clonogenic cell survival induced by disulphonated aluminum phthalocyanine photodynamic treatment in a human glioma cell line

<p>Abstract</p> <p>Background</p> <p>Photodynamic therapy (PDT) involves excitation of sensitizer molecules by visible light in the presence of molecular oxygen, thereby generating reactive oxygen species (ROS) through electron/energy transfer processes. The ROS, thus produced can cause damage to both the structure and the function of the cellular constituents resulting in cell death. Our preliminary investigations of dose-response relationships in a human glioma cell line (BMG-1) showed that disulphonated aluminum phthalocyanine (AlPcS₂) photodynamically induced loss of cell survival in a concentration dependent manner up to 1 μM, further increases in AlPcS₂concentration (>1 μM) were, however, observed to decrease the photodynamic toxicity. Considering the fact that for most photosensitizers only monotonic dose-response (survival) relationships have been reported, this result was unexpected. The present studies were, therefore, undertaken to further investigate the concentration dependent photodynamic effects of AlPcS₂.</p> <p>Methods</p> <p>Concentration-dependent cellular uptake, sub-cellular localization, proliferation and photodynamic effects of AlPcS₂were investigated in BMG-1 cells by absorbance and fluorescence measurements, image analysis, cell counting and colony forming assays, flow cytometry and micronuclei formation respectively.</p> <p>Results</p> <p>The cellular uptake as a function of extra-cellular AlPcS₂concentrations was observed to be biphasic. AlPcS₂was distributed throughout the cytoplasm with intense fluorescence in the perinuclear regions at a concentration of 1 μM, while a weak diffuse fluorescence was observed at higher concentrations. A concentration-dependent decrease in cell proliferation with accumulation of cells in G₂+M phase was observed after PDT. The response of clonogenic survival after AlPcS₂-PDT was non-monotonic with respect to AlPcS₂concentration.</p> <p>Conclusions</p> <p>Based on the results we conclude that concentration-dependent changes in physico-chemical properties of sensitizer such as aggregation may influence intracellular transport and localization of photosensitizer. Consequent modifications in the photodynamic induction of lesions and their repair leading to different modes of cell death may contribute to the observed non-linear effects.</p

Thyroid Hormone May Regulate mRNA Abundance in Liver by Acting on MicroRNAs

MicroRNAs (miRNAs) are extensively involved in diverse biological processes. However, very little is known about the role of miRNAs in mediating the action of thyroid hormones (TH). Appropriate TH levels are known to be critically important for development, differentiation and maintenance of metabolic balance in mammals. We induced transient hypothyroidism in juvenile mice by short-term exposure to methimazole and perchlorate from post natal day (PND) 12 to 15. The expression of miRNAs in the liver was analyzed using Taqman Low Density Arrays (containing up to 600 rodent miRNAs). We found the expression of 40 miRNAs was significantly altered in the livers of hypothyroid mice compared to euthyroid controls. Among the miRNAs, miRs-1, 206, 133a and 133b exhibited a massive increase in expression (50- to 500-fold). The regulation of TH on the expression of miRs-1, 206, 133a and 133b was confirmed in various mouse models including: chronic hypothyroid, short-term hyperthyroid and short-term hypothyroid followed by TH supplementation. TH regulation of these miRNAs was also confirmed in mouse hepatocyte AML 12 cells. The expression of precursors of miRs-1, 206, 133a and 133b were examined in AML 12 cells and shown to decrease after TH treatment, only pre-mir-206 and pre-mir-133b reached statistical significance. To identify the targets of these miRNAs, DNA microarrays were used to examine hepatic mRNA levels in the short-term hypothyroid mouse model relative to controls. We found transcripts from 92 known genes were significantly altered in these hypothyroid mice. Web-based target predication software (TargetScan and Microcosm) identified 14 of these transcripts as targets of miRs-1, 206, 133a and 133b. The vast majority of these mRNA targets were significantly down-regulated in hypothyroid mice, corresponding with the up-regulation of miRs-1, 206, 133a and 133b in hypothyroid mouse liver. To further investigate target genes, miR-206 was over-expressed in AML 12 cells. TH treatment of cells over-expressing miR-206 resulted in decreased miR-206 expression, and a significant increase in two predicted target genes, Mup1 and Gpd2. The results suggest that TH regulation of these genes may occur secondarily via miR-206. These studies provide new insight into the role of miRNAs in mediating TH regulation of gene expression

A multilevel study of the determinants of area-level inequalities in colorectal cancer survival

Background: In Australia, associations between geographic remoteness, socioeconomic disadvantage, and colorectal cancer (CRC) survival show that survival rates are lowest among residents of geographically remote regions and those living in disadvantaged areas. At present we know very little about the reasons for these inequalities, hence our capacity to intervene to reduce the inequalities is limited. Methods/Design: This study, the first of its type in Australia, examines the association between CRC survival and key area- and individual-level factors. Specifically, we will use a multilevel framework to investigate the possible determinants of area- and individual-level inequalities in CRC survival and quantify the relative contribution of geographic remoteness, socioeconomic and demographic factors, disease stage, and access to diagnostic and treatment services, to these inequalities. The multilevel analysis will be based on survival data relating to people diagnosed with CRC in Queensland between 1996 and 2005 (n = 22,723) from the Queensland Cancer Registry (QCR), area-level data from other data custodians such as the Australian Bureau of Statistics, and individual-level data from the QCR (including extracting stage from pathology records) and Queensland Hospitals. For a subset of this period (2003 and 2004) we will utilise more detailed, individual-level data (n = 1,966) covering a greater range of risk factors from a concurrent research study. Geo-coding and spatial technology will be used to calculate road travel distances from patients’ residence to treatment centres. The analyses will be conducted using a multilevel Cox proportional hazards model with Level 1 comprising individual-level factors (e.g. occupation) and level 2 area level indicators of remoteness and area socioeconomic disadvantage. Discussion: This study focuses on the health inequalities for rural and disadvantaged populations that have often been documented but poorly understood, hence limiting our capacity to intervene. This study utilises and develops emerging statistical and spatial technologies that can then be applied to other cancers and health outcomes. The findings of this study will have direct implications for the targeting and resourcing of cancer control programs designed to reduce the burden of colorectal cancer, and for the provision of diagnostic and treatment services

Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global consistency would imply that traits could serve as valuable proxies for the complex suite of factors that determine growth rate, and, therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively, growth rates may depend more strongly on the local environment or growth–trait relationships may vary along environmental gradients. 3. We tested these alternative hypotheses using data on 27 352 juvenile trees, representing 278 species from 27 sites on all forested continents, and extensive functional trait data, 38% of which were obtained at the same sites at which growth was assessed. Data on potential evapotranspiration (PET), which summarizes the joint ecological effects of temperature and precipitation, were obtained from a global data base. 4. We estimated size-standardized relative height growth rates (SGR) for all species, then related them to functional traits and PET using mixed-effect models for the fastest growing species and for all species together. 5. Both the mean and 95th percentile SGR were more strongly associated with functional traits than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing SLA and decreased with increasing wood density and seed mass, but these traits explained only 3.1% of the variation in SGR. SGR–trait relationships were consistently weak across families and biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional traits in plant ecology were poor predictors of tree growth over large scales. 6. Synthesis. We conclude that these functional traits alone may be unsuitable for predicting growth of trees over broad scales. Determining the functional traits that predict vital rates under specific environmental conditions may generate more insight than a monolithic global relationship can offer