Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues

Expression profiling with DNA microarrays has been used to examine the transcriptome of a wide spectrum of vertebrate cells and tissues. The sensitivity and accuracy of the data generated is dependent on the quality and composition of the input RNA. In this report, we examine the quality and array performance of over 200 total RNA samples extracted from ocular tissues and cells that have been processed in a microarray core laboratory over a 7-year period. Total RNA integrity and cRNA target size distribution were assessed using the 2100 Bioanalyzer. We present Affymetrix GeneChip array performance metrics for different ocular samples processed according to a standard microarray assay workflow including several quality control checkpoints. Our review of ocular sample performance in the microarray assay demonstrates the value of considering tissue-specific characteristics in evaluating array data. Specifically, we show that Bioanalyzer electropherograms reveal highly abundant mRNAs in lacrimal gland targets that are correlated with variation in array assay performance. Our results provide useful benchmarks for other gene expression studies of ocular systems

Cytolytic T-cell response against Epstein-Barr virus in lung cancer patients and healthy subjects

<p>Abstract</p> <p>Background</p> <p>This study aimed to examine whether EBV seropositive patients with lung cancer have an altered virus-specific CTL response, as compared to age-matched healthy controls and whether any variation in this response could be attributed to senescence.</p> <p>Methods</p> <p>Peripheral blood mononuclear cells from lung cancer patients, age-matched and younger healthy individuals were used to measure EBV-specific CTLs after in vitro amplification with the GLCTLVAML and RYSIFFDYM peptides followed by HLA-multimer staining.</p> <p>Results</p> <p>Lung cancer patients and aged-matched controls had significantly lesser EBV-specific CTL than younger healthy individuals. Multimer positive populations from either group did not differ with respect to the percentage of multimer positive CTLs and the intensity of multimer binding.</p> <p>Conclusions</p> <p>This study provides evidence that patients with lung cancer exhibit an EBV-specific CTL response equivalent to that of age-matched healthy counterparts. These data warrant the examination of whether young individuals have a more robust anti-tumor response, as is the case with the anti-EBV response.</p

Doing politics in the recent Arab uprisings: Towards a political discourse analysis of the Arab Spring slogans

The present paper aims to analyse a number of those slogans collected from the sit-in quarters in Egypt, Libya and Yemen. Using political discourse analysis, it unravels various typical discourse structures and strategies that are used in slogans in the construction of a sub-genre of political discourse in the Arab world. Drawing data from several mediums, including banners, wall graffiti, audio-visual instruments, chanting, speeches and songs, this paper tries to show the extent to which the slogans serve as a medium by which political complaints and comments are dispensed and consumed. This paper draws on a rhetorical analysis to find out their persuasive effect on shaping the Arab intellect and on the change of the political atmosphere in the region. Lastly, this paper attempts to show to what extent the slogans meet the standards of political discourse and whether they can be considered as a sub-genre of political discourse or not.IS

Flash Spectroscopy: Emission Lines from the Ionized Circumstellar Material Around &lt;10-Day-Old Type II Supernovae

The American Astronomical Society. All rights reserved.Supernovae (SNe) embedded in dense circumstellar material (CSM) may show prominent emission lines in their early-time spectra (≤10 days after the explosion), owing to recombination of the CSM ionized by the shock-breakout flash. From such spectra ("flash spectroscopy"), we can measure various physical properties of the CSM, as well as the mass-loss rate of the progenitor during the year prior to its explosion. Searching through the Palomar Transient Factory (PTF and iPTF) SN spectroscopy databases from 2009 through 2014, we found 12 SNe II showing flash-ionized (FI) signatures in their first spectra. All are younger than 10 days. These events constitute 14% of all 84 SNe in our sample having a spectrum within 10 days from explosion, and 18% of SNe II observed at ages <5 days, thereby setting lower limits on the fraction of FI events. We classified as "blue/featureless" (BF) those events having a first spectrum that is similar to that of a blackbody, without any emission or absorption signatures. It is possible that some BF events had FI signatures at an earlier phase than observed, or that they lack dense CSM around the progenitor. Within 2 days after explosion, 8 out of 11 SNe in our sample are either BF events or show FI signatures. Interestingly, we found that 19 out of 21 SNe brighter than an absolute magnitude MR = -18.2 belong to the FI or BF groups, and that all FI events peaked above MR = -17.6 mag, significantly brighter than average SNe II

HPRT Deficiency Coordinately Dysregulates Canonical Wnt and Presenilin-1 Signaling: A Neuro-Developmental Regulatory Role for a Housekeeping Gene?

We have used microarray-based methods of global gene expression together with quantitative PCR and Western blot analysis to identify dysregulation of genes and aberrant cellular processes in human fibroblasts and in SH-SY5Y neuroblastoma cells made HPRT-deficient by transduction with a retrovirus stably expressing an shRNA targeted against HPRT. Analysis of the microarray expression data by Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) as well as significant pathway analysis by GeneSpring GX10 and Panther Classification System reveal that HPRT deficiency is accompanied by aberrations in a variety of pathways known to regulate neurogenesis or to be implicated in neurodegenerative disease, including the canonical Wnt/β-catenin and the Alzheimer's disease/presenilin signaling pathways. Dysregulation of the Wnt/β-catenin pathway is confirmed by Western blot demonstration of cytosolic sequestration of β-catenin during in vitro differentiation of the SH-SY5Y cells toward the neuronal phenotype. We also demonstrate that two key transcription factor genes known to be regulated by Wnt signaling and to be vital for the generation and function of dopaminergic neurons; i.e., Lmx1a and Engrailed 1, are down-regulated in the HPRT knockdown SH-SY5Y cells. In addition to the Wnt signaling aberration, we found that expression of presenilin-1 shows severely aberrant expression in HPRT-deficient SH-SY5Y cells, reflected by marked deficiency of the 23 kDa C-terminal fragment of presenilin-1 in knockdown cells. Western blot analysis of primary fibroblast cultures from two LND patients also shows dysregulated presenilin-1 expression, including aberrant proteolytic processing of presenilin-1. These demonstrations of dysregulated Wnt signaling and presenilin-1 expression together with impaired expression of dopaminergic transcription factors reveal broad pleitropic neuro-regulatory defects played by HPRT expression and suggest new directions for investigating mechanisms of aberrant neurogenesis and neuropathology in LND and potential new targets for restoration of effective signaling in this neuro-developmental defect

Dissecting a supernova impostor's circumstellar medium: MUSEing about the SHAPE of eta Carinae's outer ejecta

Aims. The role of episodic mass loss is one of the outstanding questions in massive star evolution. The structural inhomogeneities and kinematics of their nebulae are tracers of their mass-loss history. We conduct a three-dimensional morpho-kinematic analysis of the ejecta of η Car outside its famous Homunculus nebula. Methods. We carried out the first large-scale integral field unit observations of η Car in the optical, covering a field of view of 1′× 1′ centered on the star. Observations with the Multi Unit Spectroscopic Explorer (MUSE) at the Very Large Telescope (VLT) reveal the detailed three-dimensional structure of η Car’s outer ejecta. Morpho-kinematic modeling of these ejecta is conducted with the code SHAPE. Results. The largest coherent structure in η Car’s outer ejecta can be described as a bent cylinder with roughly the same symmetry axis as the Homunculus nebula. This large outer shell is interacting with the surrounding medium, creating soft X-ray emission. Doppler velocities of up to 3000 km s-1 are observed. We establish the shape and extent of the ghost shell in front of the southern Homunculus lobe and confirm that the NN condensation can best be modeled as a bowshock in the orbital/equatorial plane. Conclusions. The SHAPE modeling of the MUSE observations provides a significant gain in the study of the three-dimensional structure of η Car’s outer ejecta. Our SHAPE modeling indicates that the kinematics of the outer ejecta measured with MUSE can be described by a spatially coherent structure, and that this structure also correlates with the extended soft X-ray emission associated with the outer debris field. The ghost shell immediately outside the southern Homunculus lobe hints at a sequence of eruptions within the time frame of the Great Eruption from 1837–1858 or possibly a later shock/reverse shock velocity separation. Our 3D morpho-kinematic modeling and the MUSE observations constitute an invaluable dataset to be confronted with future radiation-hydrodynamics simulations. Such a comparison may shed light on the yet elusive physical mechanism responsible for η Car-like eruptions

A Type Ia Supernova at Redshift 1.55 in Hubble Space Telescope Infrared Observations from CANDELS

We report the discovery of a Type Ia supernova (SNIa) at redshift z=1.55 with the infrared detector of the Wide Field Camera 3 (WFC3-IR) on the Hubble Space Telescope (HST). This object was discovered in CANDELS imaging data of the Hubble Ultra Deep Field, and followed as part of the CANDELS+CLASH Supernova project, comprising the SN search components from those two HST multi-cycle treasury programs. This is the highest redshift SNIa with direct spectroscopic evidence for classification. It is also the first SN Ia at z>1 found and followed in the infrared, providing a full light curve in rest-frame optical bands. The classification and redshift are securely defined from a combination of multi-band and multi-epoch photometry of the SN, ground-based spectroscopy of the host galaxy, and WFC3-IR grism spectroscopy of both the SN and host. This object is the first of a projected sample at z>1.5 that will be discovered by the CANDELS and CLASH programs. The full CANDELS+CLASH SN Ia sample will enable unique tests for evolutionary effects that could arise due to differences in SN Ia progenitor systems as a function of redshift. This high-z sample will also allow measurement of the SN Ia rate out to z~2, providing a complementary constraint on SN Ia progenitor models.Comment: 10 pages, 6 figures, accepted for publication in Ap

Progenitor mass constraints for core-collapse supernovae from correlations with host galaxy star formation

Using H-alpha emission as a tracer of on-going (<16 Myr old) and near-UV emission as a tracer of recent (16-100 Myr old) star formation (SF), we present constraints on core-collapse (CC) supernova (SN) progenitors through their association with SF regions. We present statistics of a large sample of SNe; 163.5 type II (58 IIP, 13 IIL, 13.5 IIb, 19 IIn and 12 'impostors') and 96.5 type Ib/c (39.5 Ib and 52 Ic). Using pixel statistics our main findings and conclusions are: 1) An increasing progenitor mass sequence is observed, implied from an increasing association of SNe to host galaxy H-alpha emission. This commences with the type Ia (SNIa) showing the weakest association, followed by the SNII, then the SNIb, with the SNIc showing the strongest correlation to SF regions. Thus our progenitor mass sequence runs Ia-II-Ib-Ic. 2) Overall SNIbc are found to occur nearer to bright HII regions than SNII. This implies that the former have shorter stellar lifetimes thus arising from more massive progenitor stars. 3) While SNIIP do not closely follow the on-going SF, they accurately trace the recent formation. This implies that their progenitors arise from stars at the low end of the CC SN mass sequence, consistent with direct detections of progenitors in pre-explosion imaging. 4) Similarly SNIIn trace recent but not the on-going SF. This implies that, contrary to the general consensus, the majority of these SNe do not arise from the most massive stars. Results and constraints are also presented for the less numerous SNIIL, IIb, and 'impostors'. Finally we present analysis of possible biases in the data, the results of which argue strongly against any selection effects that could explain the relative excess of SNIbc within bright HII regions. Thus intrinsic progenitor differences in the sense of the mass sequence we propose remain the most plausible explanation of our findings.Comment: 22 pages, 13 figures. Accepted for publication in MNRAS. The abstract has been edited to fit within arXiv.org submission requirement