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Search Results: 1 - 10 of 380980 matches for " Andrew D. L. Nelson? "
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A Transposable Element within the Non-canonical Telomerase RNA of Arabidopsis thaliana Modulates Telomerase in Response to DNA Damage
Hengyi Xu?,Andrew D. L. Nelson,Dorothy E. Shippen
PLOS Genetics , 2015, DOI: 10.1371/journal.pgen.1005281
Abstract: Long noncoding RNAs (lncRNAs) have emerged as critical factors in many biological processes, but little is known about how their regulatory functions evolved. One of the best-studied lncRNAs is TER, the essential RNA template for telomerase reverse transcriptase. We previously showed that Arabidopsis thaliana harbors three TER isoforms: TER1, TER2 and TER2S. TER1 serves as a canonical telomere template, while TER2 is a novel negative regulator of telomerase activity, induced in response to double-strand breaks (DSBs). TER2 contains a 529 nt intervening sequence that is removed along with 36 nt at the RNA 3’ terminus to generate TER2S, an RNA of unknown function. Here we investigate how A. thaliana TER2 acquired its regulatory function. Using data from the 1,001 Arabidopsis genomes project, we report that the intervening sequence within TER2 is derived from a transposable element termed DSB responsive element (DRE). DRE is found in the TER2 loci of most but not all A. thaliana accessions. By analyzing accessions with (TER2) and without DRE (TER2Δ) we demonstrate that this element is responsible for many of the unique properties of TER2, including its enhanced binding to TERT and telomerase inhibitory function. We show that DRE destabilizes TER2, and further that TER2 induction by DNA damage reflects increased RNA stability and not increased transcription. DRE-mediated changes in TER2 stability thus provide a rapid and sensitive switch to fine-tune telomerase enzyme activity. Altogether, our data shows that invasion of the TER2 locus by a small transposon converted this lncRNA into a DNA damage sensor that modulates telomerase enzyme activity in response to genome assault.
Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae
Christopher L Parkinson, Jeffrey P Mower, Yin-Long Qiu, Andrew J Shirk, Keming Song, Nelson D Young, Claude W dePamphilis, Jeffrey D Palmer
BMC Evolutionary Biology , 2005, DOI: 10.1186/1471-2148-5-73
Abstract: We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, ~10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent ~10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history.The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and – consistent with the lack of RNA editing – exceptionally high levels of "mutagenic" retroprocessing. That the mitocho
Development of the Preterm Gut Microbiome in Twins at Risk of Necrotising Enterocolitis and Sepsis
Christopher J. Stewart, Emma C. L. Marrs, Andrew Nelson, Clare Lanyon, John D. Perry, Nicholas D. Embleton, Stephen P. Cummings, Janet E. Berrington
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073465
Abstract: The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC) and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM) microbiome. Stool samples (n = 173) from 27 infants (12 twin pairs and 1 triplet set) and EBM (n = 18) from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis) analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics.
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome
Andrew J Severin, Jenna L Woody, Yung-Tsi Bolon, Bindu Joseph, Brian W Diers, Andrew D Farmer, Gary J Muehlbauer, Rex T Nelson, David Grant, James E Specht, Michelle A Graham, Steven B Cannon, Gregory D May, Carroll P Vance, Randy C Shoemaker
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-160
Abstract: The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome.This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq webcite.Early hybridization-based studies indicated that the soybean genome has undergone at least one round of large-scale duplication [1]. This finding was supported by analyses of Expressed Sequence Tags (ESTs) [2,3], which suggested an additional duplication event, with estimated times of approximately 14 and 44 mya. The generation of so many duplicated genes likely gave rise to a large number of new, novel and perhaps unique gene functions [4,5]. It is possible to gain insight into their gene function through the exploration of transcriptome data.With the release of a high-quality draft of the G. max genomic sequence [6], we are in a position to significantly improve our understandi
From attention to memory along the dorsal-ventral axis of the medial prefrontal cortex: some methodological considerations
Helen J. Cassaday,Andrew J. D. Nelson,Marie A. Pezze
Frontiers in Systems Neuroscience , 2014, DOI: 10.3389/fnsys.2014.00160
Abstract: Distinctions along the dorsal-ventral axis of medial prefrontal cortex (mPFC), between anterior cingulate (AC), prelimbic (PL), and infralimbic (IL) sub-regions, have been proposed on a variety of neuroanatomical and neurophysiological grounds. Conventional lesion approaches (as well as some electrophysiological studies) have shown that these distinctions relate to function in that a number behavioral dissociations have been demonstrated, particularly using rodent models of attention, learning, and memory. For example, there is evidence to suggest that AC has a relatively greater role in attention, whereas IL is more involved in executive function. However, the well-established methods of behavioral neuroscience have the limitation that neuromodulation is not addressed. The neurotoxin 6-hydroxydopamine has been used to deplete dopamine (DA) in mPFC sub-regions, but these lesions are not selective anatomically and noradrenalin is typically also depleted. Microinfusion of drugs through indwelling cannulae provides an alternative approach, to address the role of neuromodulation and moreover that of specific receptor subtypes within mPFC sub-regions, but the effects of such treatments cannot be assumed to be anatomically restricted either. New methodological approaches to the functional delineation of the role of mPFC in attention, learning and memory will also be considered. Taken in isolation, the conventional lesion methods which have been a first line of approach may suggest that a particular mPFC sub-region is not necessary for a particular aspect of function. However, this does not exclude a neuromodulatory role and more neuropsychopharmacological approaches are needed to explain some of the apparent inconsistencies in the results.
Light Stops and Observation of Supersymmetry at LHC RUN-II
Bryan Kaufman,Pran Nath,Brent D Nelson,Andrew Spisak
Physics , 2015, DOI: 10.1103/PhysRevD.92.095021
Abstract: Light stops consistent with the Higgs boson mass of $\sim126\,{\rm GeV}$ are investigated within the framework of minimal supergravity. It is shown that models with light stops which are also consistent with the thermal relic density constraints require stop coannihilation with the neutralino LSP. The analysis shows that the residual set of parameter points with light stops satisfying both the Higgs mass and the relic density constraints lie within a series of thin strips in the $m_0-m_{1/2}$ plane for different values of $A_0/m_0$. Consequently, this region of minimal supergravity parameter space makes a number of very precise predictions. It is found that light stops of mass down to 400~GeV or lower can exist consistent with all constraints. A signal analysis for this class of models at LHC RUN-II is carried out and the dominant signals for their detection identified. Also computed is the minimum integrated luminosity for $5\sigma$ discovery of the models analyzed. If supersymmetry is realized in this manner, the stop masses can be as low as 400~GeV or lower, and the mass gap between the lightest neutralino and lightest stop will be approximately 30-40~GeV. We have optimized the ATLAS signal regions specifically for stop searches in the parameter space and find that a stop with mass $\sim 375\,{\rm GeV}$ can be discovered with as little as $\sim$ 60~fb$^{-1}$ of integrated luminosity at RUN-II of the LHC; the integrated luminosity needed for discovery could be further reduced with more efficient signature analyses. The direct detection of dark matter in this class of models is also discussed. It is found that dark matter cross sections lie close to, but above, coherent neutrino scattering and would require multi-ton detectors such as LZ to see a signal of dark matter for this class of models.
The Panchromatic Hubble Andromeda Treasury I: Bright UV Stars in the Bulge of M31
Philip Rosenfield,L. Clifton Johnson,Léo Girardi,Julianne J. Dalcanton,Alessandro Bressan,Dustin Lang,Benjamin F. Williams,Puragra Guhathakurta,Kirsten M. Howley,Tod R. Lauer,Eric F. Bell,Luciana Bianchi,Nelson Caldwell,Andrew Dolphin,Claire E. Dorman,Karoline M. Gilbert,Jason Kalirai,S?ren S. Larsen,Knut A. G. Olsen,Hans-Walter Rix,Anil C. Seth,Evan D. Skillman,Daniel R. Weisz
Physics , 2012, DOI: 10.1088/0004-637X/755/2/131
Abstract: As part of the Panchromatic Hubble Andromeda Treasury (PHAT) multi-cycle program, we observed a 12' \times 6.5' area of the bulge of M31 with the WFC3/UVIS filters F275W and F336W. From these data we have assembled a sample of \sim4000 UV-bright, old stars, vastly larger than previously available. We use updated Padova stellar evolutionary tracks to classify these hot stars into three classes: Post-AGB stars (P-AGB), Post-Early AGB (PE-AGB) stars and AGB-manqu\'e stars. P-AGB stars are the end result of the asymptotic giant branch (AGB) phase and are expected in a wide range of stellar populations, whereas PE-AGB and AGB-manqu\'e (together referred to as the hot post-horizontal branch; HP-HB) stars are the result of insufficient envelope masses to allow a full AGB phase, and are expected to be particularly prominent at high helium or {\alpha} abundances when the mass loss on the RGB is high. Our data support previous claims that most UV-bright sources in the bulge are likely hot (extreme) horizontal branch stars (EHB) and their progeny. We construct the first radial profiles of these stellar populations, and show that they are highly centrally concentrated, even more so than the integrated UV or optical light. However, we find that this UV-bright population does not dominate the total UV luminosity at any radius, as we are detecting only the progeny of the EHB stars that are the likely source of the UVX. We calculate that only a few percent of MS stars in the central bulge can have gone through the HP-HB phase and that this percentage decreases strongly with distance from the center. We also find that the surface density of hot UV-bright stars has the same radial variation as that of low-mass X-ray binaries. We discuss age, metallicity, and abundance variations as possible explanations for the observed radial variation in the UV-bright population.
The Panchromatic Hubble Andromeda Treasury III. Measuring Ages and Masses of Partially Resolved Stellar Clusters
Lori C. Beerman,L. Clifton Johnson,Morgan Fouesneau,Julianne J. Dalcanton,Daniel R. Weisz,Anil C. Seth,Ben F. Williams,Eric F. Bell,Luciana C. Bianchi,Nelson Caldwell,Andrew E. Dolphin,Dimitrios A. Gouliermis,Jason S. Kalirai,S?ren S. Larsen,Jason L. Melbourne,Hans-Walter Rix,Evan D. Skillman
Physics , 2012, DOI: 10.1088/0004-637X/760/2/104
Abstract: The apparent age and mass of a stellar cluster can be strongly affected by stochastic sampling of the stellar initial mass function, when inferred from the integrated color of low mass clusters (less than ~10^4 solar masses). We use simulated star clusters to show that these effects are minimized when the brightest, rapidly evolving stars in a cluster can be resolved, and the light of the fainter, more numerous unresolved stars can be analyzed separately. When comparing the light from the less luminous cluster members to models of unresolved light, more accurate age estimates can be obtained than when analyzing the integrated light from the entire cluster under the assumption that the initial mass function is fully populated. We show the success of this technique first using simulated clusters, and then with a stellar cluster in M31. This method represents one way of accounting for the discrete, stochastic sampling of the stellar initial mass function in less massive clusters and can be leveraged in studies of clusters throughout the Local Group and other nearby galaxies.
Fractional Quantum Hall Physics in Jaynes-Cummings-Hubbard Lattices
Andrew L. C. Hayward,Andrew M. Martin,Andrew D. Greentree
Physics , 2012,
Abstract: Jaynes-Cummings-Hubbard arrays provide unique opportunities for quantum emulation as they exhibit convenient state preparation and measurement, and in-situ tuning of parameters. We show how to realise strongly correlated states of light in Jaynes-Cummings-Hubbard arrays under the introduction of an e?ective magnetic ?eld. The e?ective ?eld is realised by dynamic tuning of the cavity resonances. We demonstrate the existence of Fractional Quantum Hall states by com- puting topological invariants, phase transitions between topologically distinct states, and Laughlin wavefunction overlap.
Pablo L. Freyre y Nelson Díaz.
Revista Investigación Operacional , 2007,
Abstract: In this work we present a new algorithm that allows, given an invertible matrix defined over Z2 (boolean matrix), obtain their inverse. The algorithm transforms the matrix written in its classical form into polynomials and elements the field Z2, starting from which the inverse of the matrix is calculated. The advantage of this algorithm is that it allows to solve equations system in the form X = YA-1, with known Y and A, where A ∈ GLn (Z2) and Y, X ∈ (Z2)n, with no need to calculate explicitely the inverted matrix, but using instead the inverted polynomials associated with to matrix A. The algorithm is implemented on Mathematica language (Version 4.0).
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