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Search Results: 1 - 10 of 302642 matches for " Kenneth J Evans "
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Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression
Kenneth J Evans
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-16
Abstract: The mouse genome is shown to have a segmented structure defined by strand bias. Transcription is known to cause a strand bias and numerous analyses are presented to show that the strand bias in question is not caused by transcription. However, these strand bias segments influence the position of genes and their unspliced length. The position of genes within the strand bias structure affects the probability that a gene is switched on and its expression level. Transcription has a highly directional flow within this structure and the peak volume of transcription is around 20 kb from the A-rich/T-rich segment boundary on the T-rich side, directed away from the boundary. The A-rich/T-rich boundaries are SATB1 binding regions, whereas the T-rich/A-rich boundary regions are not.The direct cause of the strand bias structure may be DNA replication. The strand bias segments represent a further biological feature, the chromatin structure, which in turn influences the ease of transcription.Because of the Watson-Crick structure of DNA – A paired with T and C with G – the number of As must equal the number of Ts when the bases on both strands are counted. Although this equality does not have to be true for a single strand, Chargaff's second law refers to the equality of A/T and C/G bases on a single strand [1] and broadly speaking eukaryote genomes are free of intrastrand bias [2].Early work on strand bias analysed prokaryote and viral genomes where strand biases have been observed and associated with origins of replication: the leading strand is found to be G-rich and T-rich, with the G-C bias often being found to be more consistent than the A-T bias [3-6].Strand bias has been discovered at transcription start sites in plants and fungi [7], animals [8,9], and splice sites [10]. Strand bias has been found for long regions of DNA around actual and putative origins of replication [11]. An analysis of nearby divergent genes concluded that both replication and transcription effects w
Genomic DNA from animals shows contrasting strand bias in large and small subsequences
Kenneth J Evans
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-43
Abstract: For a typical mammal, for example mouse or human, there is a small strand bias throughout the genomic DNA: there is a correlation between (G - C) and (A - T) on the same strand, (that is between the difference in the number of guanine and cytosine bases and the difference in the number of adenine and thymine bases). For small subsequences – up to 1 kb – this correlation is weak but positive; but for large windows – around 50 kb to 2 Mb – the correlation is strong and negative. This effect is largely independent of GC%. Transcribed and untranscribed regions give similar correlations both for small and large subsequences, but there is a difference in these regions for intermediate sized subsequences. An analysis of the human genome showed that position within the isochore structure did not affect these correlations. An analysis of available genomes of different species shows that this contrast between large and small windows is a general feature of mammals and birds. Further down the evolutionary tree, other organisms show a similar but smaller effect. Except for the nematode, all the animals analysed showed at least a small effect.The correlations on the large scale may be explained by DNA replication. Transcription may be a modifier of these effects but is not the fundamental cause. These results cast light on how DNA mutations affect the genome over evolutionary time. At least for vertebrates, there is a broad relationship between body temperature and the size of the correlation. The genome of mammals and birds has a structure marked by strand bias segments.Because of the Watson-Crick structure of DNA – A paired with T and C with G – it is necessary that the number of As must equal the number of Ts when the bases on both strands are counted. Although, this equality does not have to be true for a single strand, Chargaff's second law refers to the equality of A/T and C/G bases on a single strand [1] and broadly speaking eukaryote genomes are free of intrastrand bias
Most transcription factor binding sites are in a few mosaic classes of the human genome
Kenneth J Evans
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-286
Abstract: We find that the human genome may be described by 19 pairs of mosaic classes, each defined by its base frequencies, (or more precisely by the frequencies of doublets), so that typically a run of 10 to 100 bases belongs to the same class. Most experimentally verified binding sites are in the same four pairs of classes. In our sample of seventeen transcription factors — taken from different families of transcription factors — the average proportion of sites in this subset of classes was 75%, with values for individual factors ranging from 48% to 98%. By contrast these same classes contain only 26% of the bases of the genome and only 31% of occurrences of the motifs of these factors — that is places where one might expect the factors to bind. These results are not a consequence of the class composition in promoter regions.This method of analysis will help to find transcription factor binding sites and assist with the problem of false positives. These results also imply a profound difference between the mosaic classes.The DNA sequence has no landmarks to guide the search for transcription factor binding sites: these binding sites may be near the transcription start site but may also be far from it [1,2]. Many papers have examined how these sites might be found computationally [3]. Some methods use a comparison between orthologous regions of different species [4], often treating the problem as one of multiple alignment [5,6]. Other algorithms use a collection of subsequences containing a binding site (for example the promoter regions of coregulated genes or subsequences derived from ChIp-chip experiments) to deduce the form or motif of the binding site which is then used to identify sites in other sequences — reviews of these methods are given in [7,8]. These methods include Weeder [9], MEME [10], ANN-SPEC [11], MORPH [12] and GLAM [13]. Some authors have proposed a statistical test to decide whether a region of DNA is a regulatory region: two methods [14,15] tested on f
Variable structure motifs for transcription factor binding sites
John E Reid, Kenneth J Evans, Nigel Dyer, Lorenz Wernisch, Sascha Ott
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-30
Abstract: We re-analysed binding sites from the TRANSFAC database and found motivating examples where our new variable length model provides a better fit. We analysed several ChIP-seq data sets with a novel motif search algorithm and compared the results to one of the best standard PWM finders and a recently developed alternative method for finding motifs of variable structure. All the methods performed comparably in held-out cross validation tests. Known motifs of variable structure were recovered for p53, Stat5a and Stat5b. In addition our method recovered a novel generalised version of an existing PWM for Sp1 that allows for variable length binding. This motif improved classification performance.We have presented a new gapped PWM model for variable length DNA binding sites that is not too restrictive nor over-parameterised. Our comparison with existing tools shows that on average it does not have better predictive accuracy than existing methods. However, it does provide more interpretable models of motifs of variable structure that are suitable for follow-up structural studies. To our knowledge, we are the first to apply variable length motif models to eukaryotic ChIP-seq data sets and consequently the first to show their value in this domain. The results include a novel motif for the ubiquitous transcription factor Sp1.This paper examines the problem of modelling and discovering sequence motifs for transcription factors that exhibit flexible DNA binding preferences.Transcriptional regulation is an important part of regulatory control in eukaryotes. Experimental techniques to determine which transcription factors bind which loci in particular cell types under specific conditions are improving at a rapid rate. However, we are a long way from determining the binding sites of all transcription factors in all conditions. Until we have this experimental data, mathematical models of binding sites will help us predict TFBSs and in turn help us infer regulatory effects. These mode
Dark plasmons in hot spot generation and polarization in interelectrode nanoscale junctions
Joseph B. Herzog,Mark W. Knight,Yajing Li,Kenneth M. Evans,Naomi J. Halas,Douglas Natelson
Physics , 2013, DOI: 10.1021/nl400363d
Abstract: Nanoscale gaps between adjacent metallic nanostructures give rise to extraordinarily large field enhancements, known as "hot spots", upon illumination. Incident light with the electric field polarized across the gap (along the interparticle axis) is generally known to induce the strongest surface enhanced Raman spectroscopy (SERS) enhancements. However, here we show that for a nanogap located within a nanowire linking extended Au electrodes, the greatest enhancement and resulting SERS emission occurs when the electric field of the incident light is polarized along the gap (transverse to the interelectrode axis). This surprising and counterintuitive polarization dependence results from a strong dipolar plasmon mode that resonates transversely across the nanowire, coupling with dark multipolar modes arising from subtle intrinsic asymmetries in the nanogap. These modes give rise to highly reproducible SERS enhancements at least an order of magnitude larger than the longitudinal modes in these structures.
EPICS for PDAs
Kenneth Evans Jr
Physics , 2001,
Abstract: With the advent of readily available wireless communications and small hand-held computers, commonly known as personal digital assistants (PDAs), it is interesting to consider using these portable devices to access a control system. We have successfully ported the Experimental Physics and Industrial Control System (EPICS) to Windows CE 3.0 (WCE) for the Pocket PC (PPC), and this paper describes the issues involved. The PPC was chosen because the WCE application programming interface (API) for the PPC is a subset of the Win32 API, which EPICS already supports, and because PPC devices tend to have more memory than other PDAs. PDAs provide several ways to connect to a network, using wired or wireless Compact Flash or PCMCIA Ethernet cards and modems. It is the recent advent of readily available wireless networks that makes using the portable PDA interesting. The status and issues surrounding the various kinds of wireless systems available are presented.
A Selectable and Excisable Marker System for the Rapid Creation of Recombinant Poxviruses
Julia L. Rintoul, Jiahu Wang, Don B. Gammon, Nicholas J. van Buuren, Kenneth Garson, Karen Jardine, Michele Barry, David H. Evans, John C. Bell
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024643
Abstract: Background Genetic manipulation of poxvirus genomes through attenuation, or insertion of therapeutic genes has led to a number of vector candidates for the treatment of a variety of human diseases. The development of recombinant poxviruses often involves the genomic insertion of a selectable marker for purification and selection purposes. The use of marker genes however inevitably results in a vector that contains unwanted genetic information of no therapeutic value. Methodology/Principal Findings Here we describe an improved strategy that allows for the creation of marker-free recombinant poxviruses of any species. The Selectable and Excisable Marker (SEM) system incorporates a unique fusion marker gene for the efficient selection of poxvirus recombinants and the Cre/loxP system to facilitate the subsequent removal of the marker. We have defined and characterized this new methodological tool by insertion of a foreign gene into vaccinia virus, with the subsequent removal of the selectable marker. We then analyzed the importance of loxP orientation during Cre recombination, and show that the SEM system can be used to introduce site-specific deletions or inversions into the viral genome. Finally, we demonstrate that the SEM strategy is amenable to other poxviruses, as demonstrated here with the creation of an ectromelia virus recombinant lacking the EVM002 gene. Conclusion/Significance The system described here thus provides a faster, simpler and more efficient means to create clinic-ready recombinant poxviruses for therapeutic gene therapy applications.
Predicting Ground Effects of Omnidirectional Antennas in Wireless Sensor Networks  [PDF]
John F. Janek, Jeffrey J. Evans
Wireless Sensor Network (WSN) , 2010, DOI: 10.4236/wsn.2010.212106
Abstract: Omnidirectional antennas are often used for radio frequency (RF) communication in wireless sensor networks (WSNs). Outside noise, electromagnetic interference (EMI), overloaded network traffic, large obstacles (vegetation and buildings), terrain and atmospheric composition, along with climate patterns can degrade signal quality in the form of data packet loss or reduced RF communication range. This paper explores the RF range reduction properties of a particular WSN designed to operate in agricultural crop fields to collect aggregate data composed of subsurface soil moisture and soil temperature. Our study, using simulation, anechoic and field measurements shows that the effect of antenna placement close to the ground (within 10 cm) signi?cantly changes the omnidirectional transmission pattern. We then develop and propose a prediction method that is more precise than current practices of using the Friis and Fresnel equations. Our prediction method takes into account environmental properties for RF communication range based on the height of nodes and gateways.
Avulsion Dynamics in a River with Alternating Bedrock and Alluvial Reaches, Huron River, Northern Ohio (USA)  [PDF]
Mark J. Potucek, James E. Evans
Open Journal of Modern Hydrology (OJMH) , 2019, DOI: 10.4236/ojmh.2019.91002
Abstract: The Huron River consists of alternating bedrock reaches and alluvial reaches. Analysis of historical aerial photography from 1950-2015 reveals six major channel avulsion events in the 8-km study area. These avulsions occurred in the alluvial reaches but were strongly influenced by the properties of the upstream bedrock reach (“inherited characteristics”). The bedrock reaches aligned with the azimuth of joint sets in the underlying bedrock. One inherited characteristic in the alluvial reach downstream is that the avulsion channels diverged only slightly from the orientation of the upstream bedrock channel (range 2 ° - 38 °, mean and standard deviation 12.1 ° ± 13.7 °). A second inherited characteristic is that avulsion channels were initiated from short distances downstream after exiting the upstream bedrock channel reach (range 62 - 266 m, mean and standard deviation 143.7 ± 71.0 m), which is a fraction of the meander wavelength (1.2 km). Field evidence shows that some avulsion channel sites were re-occupied episodically. In addition, two properties were necessary for channel avulsions: 1) avulsion events were triggered by channel-forming hydrologic events (5-year recurrence interval flows), but not every channel-forming hydrologic event resulted in an avulsion, and 2) channel sinuosity (P) increased to 1.72 - 1.77 prior to an avulsion then decreased to 1.65 - 1.70 following an avulsion, suggesting that P ≥ 1.72 is the “critical sinuosity” or triggering value for avulsions on the Huron River. In summary, for this river consisting of alternating bedrock and alluvial reaches, the bedrock reaches impose certain parameters on downstream alluvial reaches (including sediment supply, channel direction and avulsion channel position downstream after exiting a bedrock reach) while adjustments in sinuosity and sediment storage occur in the alluvial reaches.
The MINOS Experiment: Results and Prospects
J. J. Evans
Advances in High Energy Physics , 2013, DOI: 10.1155/2013/182537
Abstract: The MINOS experiment has used the world’s most powerful neutrino beam to make precision neutrino oscillation measurements. By observing the disappearance of muon neutrinos, MINOS has made the world’s most precise measurement of the larger neutrino mass splitting and has measured the neutrino mixing angle . Using a dedicated antineutrino beam, MINOS has made the first direct precision measurements of the corresponding antineutrino parameters. A search for and appearance has enabled a measurement of the mixing angle . A measurement of the neutral-current interaction rate has confirmed oscillation between three active neutrino flavours. MINOS will continue as MINOS+ in an upgraded beam with higher energy and intensity, allowing precision tests of the three-flavour neutrino oscillation picture, in particular a very sensitive search for the existence of sterile neutrinos. 1. Introduction The MINOS experiment, as an idea, was conceived in the late 1990s [1]. This was a very important period in neutrino oscillation physics. For thirty years, results from Homestake [2] and the gallium experiments [3, 4], through to a number of atmospheric neutrino detectors [5–10], had shown that neutrinos behaved in an odd fashion, often showing significant deficits from the expected flux, but none had conclusively determined the mechanism responsible. Then, in 1998, Super-Kamiokande [11] proved decisively that muon neutrinos produced in the Earth’s atmosphere disappeared as they traveled. Around three years later, the SNO experiment showed conclusively that neutrinos, as they propagated, changed between their three flavours [12, 13]. This discovery of neutrino flavour change showed that neutrinos had mass and did not conserve lepton number; it was the first, and still the only, observation of physics beyond the standard model. It was during this period of discovery that the MINOS experiment was proposed, to begin an era of precision measurement of this new phenomenon. The data at the time were well modeled by the theory of neutrino oscillation, in which the rate of oscillation between the three flavours is governed by the differences between the squared neutrino masses, , and . The magnitude of the flavour change is governed by three mixing angles, , , and , and a -violating phase ; these parameters form the PMNS rotation matrix [14–16] that relates the neutrino mass eigenstates to the flavour eigenstates. Nature has decreed that the two mass splittings differ by more than an order of magnitude and that one of the mixing angles, , is small. Therefore, oscillation
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