A comparative analysis of DNA barcode microarray feature size

<p>Abstract</p> <p>Background</p> <p>Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity.</p> <p>Results</p> <p>We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO) collection used for screens of pooled yeast (<it>Saccharomyces cerevisiae</it>) deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be <it>ALG7</it>.</p> <p>Conclusion</p> <p>We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.</p

The BeppoSAX X-ray view of reflection-dominated Seyfert Galaxies

We present new results from BeppoSAX observations of reflection-dominated Seyfert galaxies, and namely: 1) the Compton-thick Seyfert 2s NGC1068 and Circinus Galaxy; 2) the Seyfert 1 NGC4051, whose nucleus was observed on May 1998 to have switched off, leaving only a residual reflection component as an echo of its past activity. Our main focus in this paper is on the soft X-ray continuum properties and on the X-ray line spectroscopy.Comment: 6 Latex pages, 5 figures, Accepted for publication in Advances in Space Research, Proceedings of 32nd Sci. Ass. of COSPA

Millimeter-Wave Spectroscopy and Mapping of Quasar Hosts, and the Status of ULIRGs as Quasar 2s

It is becoming possible to detect high redshift quasars in various molecular lines, and to show by mapping lensed objects that the strong dust and molecular emission arises in warm dense ~100 pc-scale "tori." The properties of ULIRGs, at least those with AGN-like narrow line regions, are very similar, as expected in the hidden quasar hypothesis. Several of the latter are in fact confirmed as "Quasar 2s" by spectropolarimetry.Comment: 7 page

Genomic DNA functions as a universal external standard in quantitative real-time PCR

Real-time quantitative PCR (qPCR) is a powerful tool for quantifying specific DNA target sequences. Although determination of relative quantity is widely accepted as a reliable means of measuring differences between samples, there are advantages to being able to determine the absolute copy numbers of a given target. One approach to absolute quantification relies on construction of an accurate standard curve using appropriate external standards of known concentration. We have validated the use of tissue genomic DNA as a universal external standard to facilitate quantification of any target sequence contained in the genome of a given species, addressing several key technical issues regarding its use. This approach was applied to validate mRNA expression of gene candidates identified from microarray data and to determine gene copies in transgenic mice. A simple method that can assist achieving absolute quantification of gene expression would broadly enhance the uses of real-time qPCR and in particular, augment the evaluation of global gene expression studies

The Unified Model & Evolution of Active Galaxies: Implications from a Spectropolarimetric Study

We extend the analysis presented in Tran (2001) of a spectropolarimetric survey of the CfA and 12micron samples of Seyfert 2 galaxies (S2s). We confirm that S2s with hidden broad line regions (HBLRs) tend to have hotter circumnuclear dust temperatures, show mid-IR spectra more characteristic of S1 galaxies, and are intrinsically more luminous than non-HBLR S2s. The level of obscuration and circumnuclear star formation, however, appear to be similar between HBLR and non-HBLR S2 galaxies, based on an examination of various observational indicators. HBLR S2s, on average, share many similar large-scale, presumably isotropic, characteristics with Seyfert 1 galaxies (S1s), as would be expected if the unified model is correct, while non-HBLR S2s generally do not. The active nuclear engines of non-HBLR S2s then, appear to be truly weaker than HBLR S2s, which in turn, are fully consistent with being S1s viewed from another direction. There is also evidence that the fraction of detected HBLR increases with radio power of the AGN. Thus, not all Seyfert 2 galaxies may be intrinsically similar in nature, and we speculate that evolutionary processes may be at work.Comment: 15 pages with embedded figs, ApJ in press, vol. 583, 2003 Feb. 1. v2: minor corrections to text, some typos removed; updated reference list: some added, some remove

VISIR/VLT mid-infrared imaging of Seyfert nuclei: Nuclear dust emission and the Seyfert-2 dichotomy

Half of the Seyfert-2 galaxies escaped detection of broad lines in their polarised spectra observed so far. Some authors have suspected that these non-HBLRs contain real Sy2 nuclei without intrinsic broad line region hidden behind a dust torus. If this were true, then their nuclear structure would fundamentally differ from that of Sy2s with polarised broad lines: in particular, they would not be explained by orientation-based AGN unification. Further arguments for two physically different Sy2 populations have been derived from the warm and cool IRAS F25/F60 ratios. These ratios, however, refer to the entire host galaxies and are unsuitable to conclusively establish the absence of a nuclear dust torus. Instead, a study of the Seyfert-2 dichotomy should be performed on the basis of nuclear properties only. Here we present the first comparison between [OIII] 5007A and mid-infrared imaging at matching spatial resolution. Exploring the Seyfert-2 dichotomy we find that the distributions of nuclear mid-infrared/[OIII] luminosity ratios are indistinguishable for Sy1s and Sy2s with and without detected polarised broad lines and irrespective of having warm or cool IRAS F25/F60 ratios. We find no evidence for the existence of a population of real Sy2s with a deficit of nuclear dust emission. Our results suggest 1) that all Seyfert nuclei possess the same physical structure including the putative dust torus and 2) that the cool IRAS colours are caused by a low contrast of AGN to host galaxy. Then the Seyfert-2 dichotomy is explained in part by unification of non-HBLRs with narrow-line Sy1s and to a larger rate by observational biases caused by a low AGN/host contrast and/or an unfavourable scattering geometry.Comment: 11 pages, 6 figures, accepted by A&

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

An effective tool for the global analysis of both DNA methylation status and protein–chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein–chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements

Longitudinal association between medication adherence and glycaemic control in Type 2 diabetes

Aim Despite the widespread assumption that adherence drives glycaemic control, there is little published support for this in Type 2 diabetes. The study objective was to determine whether self‐reported medication adherence predicts future glycaemic control in Type 2 diabetes, after accounting for baseline control. Methods Medication adherence (4‐item Morisky scale), glycaemic control (HbA 1c %), and other variables were assessed in 287 adult primary care patients prescribed oral medication (40% also on insulin) for Type 2 diabetes. Glycaemic control was reassessed 6 months later. Regression analyses examined concurrent and future glycaemic control as a function of baseline medication adherence after adjustment for baseline glycaemia and other potential confounders. Results Only half of patients reported high adherence. Cross‐sectional adjusted analysis replicated prior reports of an adherence‐HbA 1c association ( P  = 0.011). Even after adjusting for baseline HbA 1c , each one‐point increase in baseline Morisky total score was associated with a 1.8 mmol/mol (or 0.16%) increase in HbA 1c measured 6 months later. Additionally, baseline endorsement of forgetting to take medication was associated with a 4.7 mmol/mol (or 0.43%) increase in 6‐month HbA 1c ( P  = 0.005). This effect persisted after adjusting for psychological distress and did not vary by key demographic and medical features. Conclusions Even after stringent adjustment for baseline glycaemic control, self‐reported adherence to diabetes medication predicts long‐term glycaemic control. The Morisky scale is an easy‐to‐use clinical tool to identify patients whose glycaemic control will subsequently worsen, regardless of age, gender and psychological distress.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96675/1/dme12046.pd