Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data

Background DNA methylation is an important epigenetic modification involved in many biological processes. Reduced representation bisulfite sequencing (RRBS) is a cost-effective method for studying DNA methylation at single base resolution. Although several tools are available for RRBS data processing and analysis, it is not clear which strategy performs the best and there has not been much attention to the contamination issue from artificial cytosines incorporated during the end repair step of library preparation. To address these issues, we describe a new method, Targeted Alignment and Artificial Cytosine Elimination for RRBS (TRACE-RRBS), which aligns bisulfite sequence reads to MSP1 digitally digested reference and specifically removes the end repair cytosines. We compared this approach on a simulated and a real dataset with 7 other RRBS analysis tools and Illumina 450 K microarray platform. Results TRACE-RRBS aligns sequence reads to a small fraction of the genome where RRBS protocol targets on and was demonstrated as the fastest, most sensitive and specific tool for the simulated dataset. For the real dataset, TRACE-RRBS took about the same time as RRBSMAP, a third to a sixth of time needed for BISMARK and NOVOALIGN. TRACE-RRBS aligned more reads uniquely than other tools and achieved the highest correlation with 450 k microarray data. The end repair artificial cytosine removal increased correlation between nearby CpGs and accuracy of methylation quantification. Conclusions TRACE-RRBS is fast and more accurate tool for RRBS data analysis. It is freely available for academic use at http://​bioinformaticsto​ols.​mayo.​edu/​

Intrathecal long-term gene expression by self-complementary adeno-associated virus type 1 suitable for chronic pain studies in rats

BACKGROUND: Intrathecal (IT) gene transfer is an attractive approach for targeting spinal mechanisms of nociception but the duration of gene expression achieved by reported methods is short (up to two weeks) impairing their utility in the chronic pain setting. The overall goal of this study was to develop IT gene transfer yielding true long-term transgene expression defined as ≥ 3 mo following a single vector administration. We defined "IT" administration as atraumatic injection into the lumbar cerebrospinal fluid (CSF) modeling a lumbar puncture. Our studies focused on recombinant adeno-associated virus (rAAV), one of the most promising vector types for clinical use. RESULTS: Conventional single stranded rAAV2 vectors performed poorly after IT delivery in rats. Pseudotyping of rAAV with capsids of serotypes 1, 3, and 5 was tested alone or in combination with a modification of the inverted terminal repeat. The former alters vector tropism and the latter allows packaging of self-complementary rAAV (sc-rAAV) vectors. Combining both types of modification led to the identification of sc-rAAV2/l as a vector that performed superiorly in the IT space. IT delivery of 3 × 10e9 sc-rAAV2/l particles per animal led to stable expression of enhanced green fluorescent protein (EGFP) for ≥ 3 mo detectable by Western blotting, quantitative PCR, and in a blinded study by confocal microscopy. Expression was strongest in the cauda equina and the lower sections of the spinal cord and only minimal in the forebrain. Microscopic examination of the SC fixed in situ with intact nerve roots and meninges revealed strong EGFP fluorescence in the nerve roots. CONCLUSION: sc-rAAVl mediates stable IT transgene expression for ≥ 3 mo. Our findings support the underlying hypothesis that IT target cells for gene transfer lack the machinery for efficient conversion of the single-stranded rAAV genome into double-stranded DNA and favor uptake of serotype 1 vectors over 2. Experiments presented here will provide a rational basis for utilizing IT rAAV gene transfer in basic and translational studies on chronic pain

Biological predictors of chemotherapy-induced peripheral neuropathy (CIPN): MASCC neurological complications working group overview.

Chemotherapy-induced peripheral neuropathy (CIPN) is a common and debilitating condition associated with a number of chemotherapeutic agents. Drugs commonly implicated in the development of CIPN include platinum agents, taxanes, vinca alkaloids, bortezomib, and thalidomide analogues. As a drug response can vary between individuals, it is hypothesized that an individual's specific genetic variants could impact the regulation of genes involved in drug pharmacokinetics, ion channel functioning, neurotoxicity, and DNA repair, which in turn affect CIPN development and severity. Variations of other molecular markers may also affect the incidence and severity of CIPN. Hence, the objective of this review was to summarize the known biological (molecular and genomic) predictors of CIPN and discuss the means to facilitate progress in this field

Preclinical toxicity evaluation of AAV for pain: evidence from human AAV studies and from the pharmacology of analgesic drugs

Abstract Gene therapy with adeno-associated virus (AAV) has advanced in the last few years from promising results in animal models to >100 clinical trials (reported or under way). While vector availability was a substantial hurdle a decade ago, innovative new production methods now routinely match the scale of AAV doses required for clinical testing. These advances may become relevant to translational research in the chronic pain field. AAV for pain targeting the peripheral nervous system was proven to be efficacious in rodent models several years ago, but has not yet been tested in humans. The present review addresses the steps needed for translation of AAV for pain from the bench to the bedside focusing on pre-clinical toxicology. We break the potential toxicities into three conceptual categories of risk: First, risks related to the delivery procedure used to administer the vector. Second, risks related to AAV biology, i.e., effects of the vector itself that may occur independently of the transgene. Third, risks related to the effects of the therapeutic transgene. To identify potential toxicities, we consulted the existing evidence from AAV gene therapy for other nervous system disorders (animal toxicology and human studies) and from the clinical pharmacology of conventional analgesic drugs. Thereby, we identified required preclinical studies and charted a hypothetical path towards a future phase I/II clinical trial in the oncology-palliative care setting

Genetic variation in EPHA contributes to sensitivity to paclitaxel‐induced peripheral neuropathy

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154957/1/bcp14192.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154957/2/bcp14192_am.pd

Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue

DNA methylation can control some CpG-poor genes but unbiased studies have not found a consistent genome-wide association with gene activity outside of CpG islands or shores possibly due to use of cell lines or limited bioinformatics analyses. We performed reduced representation bisulfite sequencing (RRBS) of rat dorsal root ganglia encompassing postmitotic primary sensory neurons (n = 5, r > 0.99; orthogonal validation p < 10−19). The rat genome suggested a dichotomy of genes previously reported in other mammals: low CpG content (< 3.2%) promoter (LCP) genes and high CpG content (≥ 3.2%) promoter (HCP) genes. A genome-wide integrated methylome-transcriptome analysis showed that LCP genes were markedly hypermethylated when repressed, and hypomethylated when active with a 40% difference in a broad region at the 5′ of the transcription start site (p < 10−87 for -6000 bp to -2000 bp, p < 10−73 for -2000 bp to +2000 bp, no difference in gene body p = 0.42). HCP genes had minimal TSS-associated methylation regardless of transcription status, but gene body methylation appeared to be lost in repressed HCP genes. Therefore, diametrically opposite methylome-transcriptome associations characterize LCP and HCP genes in postmitotic neural tissue in vivo

The Eleventh and Twelfth data releases of the Sloan Digital Sky Survey: Final data from SDSS-III

The third generation of the Sloan Digital Sky Survey (SDSS-III) tookdata from 2008 to 2014 using the original SDSS wide-field imager, theoriginal and an upgraded multi-object fiber-fed optical spectrograph, anew near-infrared high-resolution spectrograph, and a novel opticalinterferometer. All of the data from SDSS-III are now made public. Inparticular, this paper describes Data Release 11 (DR11) including alldata acquired through 2013 July, and Data Release 12 (DR12) adding dataacquired through 2014 July (including all data included in previous datareleases), marking the end of SDSS-III observing. Relative to ourprevious public release (DR10), DR12 adds one million new spectra ofgalaxies and quasars from the Baryon Oscillation Spectroscopic Survey(BOSS) over an additional 3000 deg2 of sky, more than triplesthe number of H-band spectra of stars as part of the Apache PointObservatory (APO) Galactic Evolution Experiment (APOGEE), and includesrepeated accurate radial velocity measurements of 5500 stars from theMulti-object APO Radial Velocity Exoplanet Large-area Survey (MARVELS).The APOGEE outputs now include the measured abundances of 15 differentelements for each star. In total, SDSS-III added 5200 deg2 ofugriz imaging; 155,520 spectra of 138,099 stars as part of the SloanExploration of Galactic Understanding and Evolution 2 (SEGUE-2) survey;2,497,484 BOSS spectra of 1,372,737 galaxies, 294,512 quasars, and247,216 stars over 9376 deg2; 618,080 APOGEE spectra of156,593 stars; and 197,040 MARVELS spectra of 5513 stars. Since itsfirst light in 1998, SDSS has imaged over 1/3 of the Celestial sphere infive bands and obtained over five million astronomical spectra.Fil: Alam, Shadab. University of Carnegie Mellon; Estados UnidosFil: Albareti, Franco D.. Universidad Autónoma de Madrid; EspañaFil: Prieto, Carlos Allende. Universidad de La Laguna; EspañaFil: Anders, F.. Leibniz Institute For Astrophysics Potsdam; AlemaniaFil: Anderson, Scott F.. University of Utah; Estados UnidosFil: Anderton, Timothy. University of Utah; Estados UnidosFil: Andrews, Brett H.. Ohio State University; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Armengaud, Eric. Service de Physique Des Particules; FranciaFil: Aubourg, Éric. Université Paris Diderot - Paris 7; FranciaFil: Bailey, Stephen. Lawrence Berkeley National Laboratory; Estados UnidosFil: Basu, Sarbani. University of Yale; Estados UnidosFil: Bautista, Julian E.. Université Paris Diderot - Paris 7; FranciaFil: Beaton, Rachael L.. University of Virginia; Estados UnidosFil: Beers, Timothy C.. University of Notre Dame; Estados UnidosFil: Bender, Chad F.. Pennsylvania State University; Estados UnidosFil: Berlind, Andreas A.. Vanderbilt University; Estados UnidosFil: Beutler, Florian. Lawrence Berkeley National Laboratory; Estados UnidosFil: Bhardwaj, Vaishali. Lawrence Berkeley National Laboratory; Estados UnidosFil: Bird, Jonathan C.. Vanderbilt University; Estados UnidosFil: Bizyaev, Dmitry. Apache Point Observatory; Estados UnidosFil: Blake, Cullen H.. University of Pennsylvania; Estados UnidosFil: Blanton, Michael R.. New York University; Estados UnidosFil: Blomqvist, Michael. University of California at Irvine; Estados UnidosFil: Bochanski, John J.. University of Washington; Estados UnidosFil: Bolton, Adam S.. University of Utah; Estados UnidosFil: Bovy, Jo. Institute For Advanced Studies; Estados UnidosFil: Shelden, Bradley, A.. Apache Point Observatory; Estados UnidosFil: Brandt, W. N.. Pennsylvania State University; Estados UnidosFil: Brauer, D. E.. Leibniz Institute For Astrophysics Potsdam; AlemaniaFil: Nuza, Sebastian Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; Argentina. Institut Max Planck Fuer Gesellschaft. Max Planck Institute For Extraterrestrial Physics; AlemaniaFil: Scoccola, Claudia Graciela. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentin

Reconstruction and control of a time-dependent two-electron wave packet

The concerted motion of two or more bound electrons governs atomic1 and molecular2,3 non-equilibrium processes including chemical reactions, and hence there is much interest in developing a detailed understanding of such electron dynamics in the quantum regime. However, there is no exact solution for the quantumthree-body problem, and as a result even the minimal system of two active electrons and a nucleus is analytically intractable4. This makes experimental measurements of the dynamics of two bound and correlated electrons, as found in the helium atom, an attractive prospect.However, although the motion of single active electrons and holes has been observed with attosecond time resolution5-7, comparable experiments on two-electron motion have so far remained out of reach. Here we showthat a correlated two-electron wave packet can be reconstructed froma 1.2-femtosecondquantumbeatamong low-lying doubly excited states in helium.The beat appears in attosecond transient-absorption spectra5,7-9 measured with unprecedentedly high spectral resolution and in the presence of an intensity-tunable visible laser field.Wetune the coupling10-12 between the two low-lying quantum states by adjusting the visible laser intensity, and use the Fano resonance as a phase-sensitive quantum interferometer13 to achieve coherent control of the two correlated electrons. Given the excellent agreement with large-scalequantum-mechanical calculations for thehelium atom, we anticipate thatmultidimensional spectroscopy experiments of the type we report here will provide benchmark data for testing fundamental few-body quantumdynamics theory in more complex systems. Theymight also provide a route to the site-specificmeasurement and control of metastable electronic transition states that are at the heart of fundamental chemical reactionsWe thank E. Lindroth for calculating the dipole moment (2p2|r|sp2,3+), and also A. Voitkiv, Z.-H. Loh, and R. Moshammer for helpful discussions. We acknowledge financial support by the Max-Planck Research Group Program of the Max-Planck Gesellschaft (MPG) and the European COST Action CM1204 XLIC. L. A. and F. M. acknowledge computer time from the CCC-UAM and Mare Nostrum supercomputer centers and financial support by the European Research Council under the ERC Advanced Grant no. 290853 XCHEM, the Ministerio de Economía y Competitividad projects FIS2010-15127, FIS2013-42002-R and ERA-Chemistry PIM2010EEC-00751, and the European grant MC-ITN CORIN

Lack of an Antibacterial Response Defect in Drosophila Toll-9 Mutant

Toll and Toll-like receptors represent families of receptors involved in mediating innate immunity response in insects and mammals. Although Drosophila proteome contains multiple Toll paralogs, Toll-1 is, so far, the only receptor to which an immune role has been attributed. In contrast, every single mammalian TLR is a key membrane receptor upstream of the vertebrate immune signaling cascades. The prevailing view is that TLR-mediated immunity is ancient. Structural analysis reveals that Drosophila Toll-9 is the most closely related to vertebrate TLRs and utilizes similar signaling components as Toll-1. This suggests that Toll-9 could be an ancestor of TLR-like receptors and could have immune function. Consistently, it has been reported that over-expression of Toll-9 in immune tissues is sufficient to induce the expression of some antimicrobial peptides in flies. These results have led to the idea that Toll-9 could be a constitutively active receptor that maintain significant levels of antimicrobial molecules and therefore provide constant basal protection against micro-organisms. To test theses hypotheses, we generated and analyzed phenotypes associated with a complete loss-of-function allele of Toll-9. Our results suggest that Toll-9 is neither required to maintain a basal anti-microbial response nor to mount an efficient immune response to bacterial infection

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July