A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

BACKGROUND: Systematic identification and functional characterization of novel types of noncoding (nc)RNA in genomes is more difficult than it is for protein coding mRNAs, since ncRNAs typically do not possess sequence features such as splicing or translation signals, or long open reading frames. Recent "tiling" microarray studies have reported that a surprisingly larger proportion of mammalian genomes is transcribed than was previously anticipated. However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known. RESULTS: To systematically search for functional ncRNAs, we designed microarrays to detect 3,478 intergenic and intronic sequences that are conserved between the human, mouse, and rat genomes, and that score highly by other criteria that characterize ncRNAs. We probed these arrays with total RNA isolated from 16 wild-type mouse tissues. Among 55 candidates for highly-expressed novel ncRNAs tested by northern blotting, eight were confirmed as small, highly-and ubiquitously-expressed RNAs in mouse. Of the eight, five were also detected in rat tissues, but none were detected at appreciable levels in human tissues or cultured cells. CONCLUSION: Since the sequence and expression of most known coding transcripts and functional ncRNAs is conserved between human and mouse, the lack of northern-detectable expression in human cells and tissues of the novel mouse and rat ncRNAs that we identified suggests that they are not functional or possibly have rodent-specific functions. Our results confirm that relatively little of the intergenic sequence conserved between human, mouse and rat is transcribed at high levels in mammalian tissues, possibly suggesting a limited role for transcribed intergenic and intronic sequences as independent functional elements

Considerations in the identification of functional RNA structural elements in genomic alignments

BACKGROUND: Accurate identification of novel, functional noncoding (nc) RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries. RESULTS: We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component) was significantly higher for real than shuffled sequence, while the distribution for coding sequences was lower than that of corresponding shuffles. CONCLUSION: Accurate prediction of novel RNA structural elements in genome sequence remains a difficult problem, and development of an appropriate negative-control strategy for multiple alignments is an important practical challenge. Nonetheless, the general trends we observed for the distributions of predicted ncRNAs across genomic features are biologically meaningful, supporting the presence of secondary structural elements in many 3' UTRs, and providing evidence for evolutionary selection against secondary structures in coding regions

Imaging topologically protected transport with quantum degenerate gases

Ultracold and quantum degenerate gases held near conductive surfaces can serve as sensitive, high resolution, and wide-area probes of electronic current flow. Previous work has imaged transport around grain boundaries in a gold wire by using ultracold and Bose-Einstein condensed atoms held microns from the surface with an atom chip trap. We show that atom chip microscopy may be applied to useful purpose in the context of materials exhibiting topologically protected surface transport. Current flow through lithographically tailored surface defects in topological insulators (TI)---both idealized and with the band-structure and conductivity typical of Bi$_{2}$Se$_{3}$---is numerically calculated. We propose that imaging current flow patterns enables the differentiation of an ideal TI from one with a finite bulk--to--surface conductivity ratio, and specifically, that the determination of this ratio may be possible by imaging transport around trenches etched into the TI's surface.Comment: Extensively rewritten, better introduction. 12 pages, 10 figure

Bestrophin1 Channels are Insensitive to Ethanol and Do not Mediate Tonic GABAergic Currents in Cerebellar Granule Cells

The granule cell layer of the cerebellum functions in spatio-temporal encoding of information. Granule cells (GCs) are tonically inhibited by spillover of GABA released from Golgi cells and this tonic inhibition is facilitated by acute ethanol. Recently, it was demonstrated that a specialized Ca2+-activated anion-channel, bestrophin1 (Best1), found on glial cells, can release GABA that contributes up to 50–75% of the tonic GABAergic current. However, it is unknown if ethanol has any actions on Best1 function. Using whole-cell electrophysiology, we found that recombinant Best1 channels expressed in HEK-293 cells were insensitive to 40 and 80 mM ethanol. We attempted to measure the Best1-mediated component of the tonic current in slices using 5-nitro-2-(3-phenylpropylamino)benzoic acid (NPPB). We confirmed that this agent blocks recombinant Best1 channels. Unexpectedly, we found that NPPB significantly potentiated the tonic current and the area and decay of GABAA-mediated spontaneous inhibitory post-synaptic currents (IPSCs) in GCs in rodent slices under two different recording conditions. To better isolate the Best1-dependent tonic current component, we blocked the Golgi cell component of the tonic current with tetrodotoxin and found that NPPB similarly and significantly potentiated the tonic current amplitude and decay time of miniature IPSCs. Two other Cl−-channel blockers were also tested: 4′-diisothiocyanatostilbene-2,2′-disulfonic acid disodium salt hydrate (DIDS) showed no effect on GABAergic transmission, while niflumic acid (NFA) significantly suppressed the tonic current noise, as well as the mIPSC frequency, amplitude, and area. These data suggest that acute ethanol exposure does not modulate Best1 channels and these findings serve to challenge recent data indicating that these channels participate in the generation of tonic GABAergic currents in cerebellar GCs

Chandra ACIS Survey of M33 (ChASeM33): X-ray Imaging Spectroscopy of M33SNR21, the Brightest X-ray Supernova Remnant in M33

We present and interpret new X-ray data for M33SNR21, the brightest X-ray supernova remnant (SNR) in M33. The SNR is in seen projection against (and appears to be interacting with) the bright HII region NGC592. Data for this source were obtained as part of the Chandra ACIS Survey of M33 (ChASeM33) Very Large Project. The nearly on-axis Chandra data resolve the SNR into a ~5" diameter (20 pc at our assumed M33 distance of 817+/-58 kpc) slightly elliptical shell. The shell is brighter in the east, which suggests that it is encountering higher density material in that direction. The optical emission is coextensive with the X-ray shell in the north, but extends well beyond the X-ray rim in the southwest. Modeling the X-ray spectrum with an absorbed sedov model yields a shock temperature of 0.46(+0.01,-0.02) keV, an ionization timescale of n_e t = $2.1 (+0.2,-0.3) \times 10^{12}$ cm$^{-3}$ s, and half-solar abundances (0.45 (+0.12, -0.09)). Assuming Sedov dynamics gives an average preshock H density of 1.7 +/- 0.3 cm$^{-3}$. The dynamical age estimate is 6500 +/- 600 yr, while the best fit $n_e t$ value and derived $n_e$ gives 8200 +/- 1700 yr; the weighted mean of the age estimates is 7600 +/- 600 yr. We estimate an X-ray luminosity (0.25-4.5 keV) of (1.2 +/- 0.2) times $10^{37}$ ergs s$^{-1}$ (absorbed), and (1.7 +/- 0.3) times $10^{37}$ ergs s$^{-1}$ (unabsorbed), in good agreement with the recent XMM-Newton determination. No significant excess hard emission was detected; the luminosity $\le 1.2\times 10^{35}$ ergs s$^{-1}$ (2-8 keV) for any hard point source.Comment: 27 pages, 6 figures (3 color). ApJ (in press

Genetic variants influence on the placenta regulatory landscape

From genomic association studies, quantitative trait loci analysis, and epigenomic mapping, it is evident that significant efforts are necessary to define genetic-epigenetic interactions and understand their role in disease susceptibility and progression. For this reason, an analysis of the effects of genetic variation on gene expression and DNA methylation in human placentas at high resolution and whole-genome coverage will have multiple mechanistic and practical implications. By producing and analyzing DNA sequence variation (n = 303), DNA methylation (n = 303) and mRNA expression data (n = 80) from placentas from healthy women, we investigate the regulatory landscape of the human placenta and offer analytical approaches to integrate different types of genomic data and address some potential limitations of current platforms. We distinguish two profiles of interaction between expression and DNA methylation, revealing linear or bimodal effects, reflecting differences in genomic context, transcription factor recruitment, and possibly cell subpopulations. These findings help to clarify the interactions of genetic, epigenetic, and transcriptional regulatory mechanisms in normal human placentas. They also provide strong evidence for genotype-driven modifications of transcription and DNA methylation in normal placentas. In addition to these mechanistic implications, the data and analytical methods presented here will improve the interpretability of genome-wide and epigenome-wide association studies for human traits and diseases that involve placental functions

Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ lymphocyte counts greater than 350 cells/mm3: a phase II, multi-centre, double-blind, randomized, placebo-controlled trial.

BACKGROUND: Novel tuberculosis vaccines should be safe, immunogenic, and effective in various population groups, including HIV-infected individuals. In this phase II multi-centre, double-blind, placebo-controlled trial, the safety and immunogenicity of the novel H1/IC31 vaccine, a fusion protein of Ag85B-ESAT-6 (H1) formulated with the adjuvant IC31, was evaluated in HIV-infected adults. METHODS: HIV-infected adults with CD4+ T cell counts >350/mm3 and without evidence of active tuberculosis were enrolled and followed until day 182. H1/IC31 vaccine or placebo was randomly allocated in a 5:1 ratio. The vaccine was administered intramuscularly at day 0 and 56. Safety assessment was based on medical history, clinical examinations, and blood and urine testing. Immunogenicity was determined by a short-term whole blood intracellular cytokine staining assay. RESULTS: 47 of the 48 randomised participants completed both vaccinations. In total, 459 mild or moderate and 2 severe adverse events were reported. There were three serious adverse events in two vaccinees classified as not related to the investigational product. Local injection site reactions were more common in H1/IC31 versus placebo recipients (65.0% vs. 12.5%, p = 0.015). Solicited systemic and unsolicited adverse events were similar by study arm. The baseline CD4+ T cell count and HIV viral load were similar by study arm and remained constant over time. The H1/IC31 vaccine induced a persistent Th1-immune response with predominately TNF-α and IL-2 co-expressing CD4+ T cells, as well as polyfunctional IFN-γ, TNF-α and IL-2 expressing CD4+ T cells. CONCLUSION: H1/IC31 was well tolerated and safe in HIV-infected adults with a CD4+ Lymphocyte count greater than 350 cells/mm3. The vaccine did not have an effect on CD4+ T cell count or HIV-1 viral load. H1/IC31 induced a specific and durable Th1 immune response. TRIAL REGISTRATION: Pan African Clinical Trials Registry (PACTR) PACTR201105000289276