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Search Results: 1 - 10 of 380861 matches for " J Peter W Young "
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Genes: an Open Access Journal
J. Peter W. Young
Genes , 2010, DOI: 10.3390/genes1010001
Abstract: Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any hypothesis" [1], but others were already pointing to chromosomes as the likely location of genes. The science of genetics was born at that time, and genes were rapidly connected with mutations, with patterns of inheritance, with development, with quantitative traits, with evolution and with biochemical pathways. All this was achieved without knowledge of the physical nature of genes, but this changed in mid-century with the discoveries of molecular biology. DNA was revealed as the genetic material, and the mechanisms were elucidated by which the information was encoded, and propagated, and linked to the phenotype. However, the concept of a "gene" did not become clearer. Quite the reverse, as the units of mutation, of recombination, of inheritance, of expression, of regulation, etc. did not necessarily coincide. [...]
Slipins: ancient origin, duplication and diversification of the stomatin protein family
Jasper B Green, J Peter W Young
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-44
Abstract: We have constructed a comprehensive phylogeny of all 'stomatin-like' sequences that share a 150 amino acid domain. We show these proteins comprise an ancient family that arose early in prokaryotic evolution, and we propose a new nomenclature that reflects their phylogeny, based on the name "slipin" (stomatin-like protein). Within prokaryotes there are two distinct subfamilies that account for the two different origins of the eight eukaryotic stomatin subfamilies, one of which gave rise to eukaryotic SLP-2, renamed here "paraslipin". This was apparently acquired through the mitochondrial endosymbiosis and is widely distributed amongst the major kingdoms. The other prokaryotic subfamily gave rise to the ancestor of the remaining seven eukaryotic subfamilies. The highly diverged "alloslipin" subfamily is represented only by fungal, viral and ciliate sequences. The remaining six subfamilies, collectively termed "slipins", are confined to metazoa. Protostome stomatin, as well as a newly reported arthropod subfamily slipin-4, are restricted to invertebrate groups, whilst slipin-1 (previously SLP-1) is present in nematodes and higher metazoa. In vertebrates, the stomatin family expanded considerably, with at least two duplication events giving rise to podocin and slipin-3 subfamilies (previously SLP-3), with the retained ancestral sequence giving rise to vertebrate stomatin.Stomatin-like proteins have their origin in an ancient duplication event that occurred early on in the evolution of prokaryotes. By constructing a phylogeny of this family, we have identified and named a number of orthologous groups: these can now be used to infer function of stomatin subfamilies in a meaningful way.Human stomatin (hstomatin) was first identified as an integral membrane protein in human red blood cells [1-3]. It has since been shown to be expressed in many cell types and organisms, although hstomatin function remains unclear [4]. Loss of stomatin in humans is associated with a condition
Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron
Karyn P Ridgway, Janette M Duck, J Peter W Young
BMC Ecology , 2003, DOI: 10.1186/1472-6785-3-8
Abstract: We show that trnL PCR product length heterogeneity and a maximum of two restriction digests can separate 14 common grassland species. The RFLP key was used to identify root fragments at least to genus level in a field study of upland grassland community diversity. Roots which could not be matched to known types were putatively identified by comparison of the nuclear ribosomal ITS sequence to the GenBank database. Ten taxa were identified among almost 600 root fragments. Additionally, we have employed capillary electrophoresis of fluorescent trnL PCR products (fluorescent fragment length polymorphism, FFLP) to discriminate all taxa identified at the field site.We have developed a molecular database for the identification of some common grassland species based on PCR-RFLP of the plastid transfer RNA leucine (trnL) UAA gene intron. This technique will allow fine-scale studies of the rhizosphere, where root identification by morphology is unrealistic and high throughput is desirable.Plants can be difficult to identify from roots, even for experienced taxonomists. Fine roots often grow deep and intertwined with each other in swards and it is not easy to link above and below ground plant parts for morphological identification. Studies of of below-ground processes are currently hindered by the inability to identify fine roots in soil [1]. To understand nutrient cycling in an upland grassland we are studying the spatial relationship between co-occurring plant roots and their associated microbes, both endomycorrhizal fungi and rhizoplane bacteria. To address the question 'do the roots of different plant species harbour distinct microbial populations?' we first required a method to identify plant species from root fragments.A molecular method for identification must satisfy requirements for specific amplification of plant DNA and reveal enough variability to distinguish species. The trnL UAA intron from plastid DNA shows variability comparable to that of nuclear intergenic re
Underflight calibration of SOHO/CDS and Hinode/EIS with EUNIS-07
Tongjiang Wang,Roger J. Thomas,Jeffrey W. Brosius,Peter R. Young,Douglas M. Rabin,Joseph M. Davila,Giulio Del Zanna
Physics , 2011, DOI: 10.1088/0067-0049/197/2/32
Abstract: Flights of Goddard Space Flight Center's Extreme-Ultraviolet Normal-Incidence Spectrograph (EUNIS) sounding rocket in 2006 and 2007 provided updated radiometric calibrations for SOHO/CDS and Hinode/EIS. EUNIS carried two independent imaging spectrographs covering wavebands of 300-370 A in first order and 170-205 A in second order. After each flight, end-to-end radiometric calibrations of the rocket payload were carried out in the same facility used for pre-launch calibrations of CDS and EIS. During the 2007 flight, EUNIS, SOHO CDS and Hinode EIS observed the same solar locations, allowing the EUNIS calibrations to be directly applied to both CDS and EIS. The measured CDS NIS 1 line intensities calibrated with the standard (version 4) responsivities with the standard long-term corrections are found to be too low by a factor of 1.5 due to the decrease in responsivity. The EIS calibration update is performed in two ways. One is using the direct calibration transfer of the calibrated EUNIS-07 short wavelength (SW) channel. The other is using the insensitive line pairs, in which one member was observed by EUNIS-07 long wavelength (LW) channel and the other by EIS in either LW or SW waveband. Measurements from both methods are in good agreement, and confirm (within the measurement uncertainties) the EIS responsivity measured directly before the instrument's launch. The measurements also suggest that the EIS responsivity decreased by a factor of about 1.2 after the first year of operation. The shape of the EIS SW response curve obtained by EUNIS-07 is consistent with the one measured in laboratory prior to launch. The absolute value of the quiet-Sun He II 304 A intensity measured by EUNIS-07 is consistent with the radiance measured by CDS NIS in quiet regions near the disk center and the solar minimum irradiance obtained by CDS NIS and SDO/EVE recently.
The Effects on Supernova Shock Breakout and Swift Light Curves Due to the Mass of the Hydrogen-Rich Envelope
Amanda J. Bayless,Wesley Even,Lucille H. Frey,Chris L. Fryer,Peter W. A. Roming,Patrick A. Young
Physics , 2014, DOI: 10.1088/0004-637X/805/2/98
Abstract: Mass loss remains one of the primary uncertainties in stellar evolution. In the most massive stars, mass loss dictates the circumstellar medium and can significantly alter the fate of the star. Mass loss is caused by a variety of wind mechanisms and also through binary interactions. Supernovae are excellent probes of this mass loss, both the circumstellar material and the reduced mass of the hydrogen-rich envelope. In this paper, we focus on the effects of reducing the hydrogen-envelope mass on the supernova light curve, studying both the shock breakout and peak light curve emission for a wide variety of mass loss scenarios. Even though the trends of this mass loss will be masked somewhat by variations caused by different progenitors, explosion energies, and circumstellar media, these trends have significant effects on the supernova light-curves that should be seen in supernova surveys. We conclude with a comparison of our results to a few key observations.
Rhizobia with 16S rRNA and nifH Similar to Mesorhizobium huakuii but Novel recA, glnII, nodA and nodC Genes Are Symbionts of New Zealand Carmichaelinae
Heng Wee Tan, Bevan S. Weir, Noel Carter, Peter B. Heenan, Hayley J. Ridgway, Euan K. James, Janet I. Sprent, J. Peter W. Young, Mitchell Andrews
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047677
Abstract: New Zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, Carmichaelia, Clianthus and Montigena in the Carmichaelinae clade, tribe Galegeae, and Sophora, tribe Sophoreae, sub-family Papilionoideae. Ten bacterial strains isolated from NZ Carmichaelinae growing in natural ecosystems grouped close to the Mesorhizobium huakuii type strain in relation to their 16S rRNA and nifH gene sequences. However, the ten strains separated into four groups on the basis of their recA and glnII sequences: all groups were clearly distinct from all Mesorhizobium type strains. The ten strains separated into two groups on the basis of their nodA sequences but grouped closely together in relation to nodC sequences; all nodA and nodC sequences were novel. Seven strains selected and the M. huakuii type strain (isolated from Astragalus sinicus) produced functional nodules on Carmichaelia spp., Clianthus puniceus and A. sinicus but did not nodulate two Sophora species. We conclude that rhizobia closely related to M. huakuii on the basis of 16S rRNA and nifH gene sequences, but with variable recA and glnII genes and novel nodA and nodC genes, are common symbionts of NZ Carmichaelinae.
Analysis of the Association between CIMP and BRAFV600E in Colorectal Cancer by DNA Methylation Profiling
Toshinori Hinoue,Daniel J. Weisenberger,Fei Pan,Mihaela Campan,Myungjin Kim,Joanne Young,Vicki L. Whitehall,Barbara A. Leggett,Peter W. Laird
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008357
Abstract: A CpG island methylator phenotype (CIMP) is displayed by a distinct subset of colorectal cancers with a high frequency of DNA hypermethylation in a specific group of CpG islands. Recent studies have shown that an activating mutation of BRAF (BRAFV600E) is tightly associated with CIMP, raising the question of whether BRAFV600E plays a causal role in the development of CIMP or whether CIMP provides a favorable environment for the acquisition of BRAFV600E. We employed Illumina GoldenGate DNA methylation technology, which interrogates 1,505 CpG sites in 807 different genes, to further study this association. We first examined whether expression of BRAFV600E causes DNA hypermethylation by stably expressing BRAFV600E in the CIMP-negative, BRAF wild-type COLO 320DM colorectal cancer cell line. We determined 100 CIMP-associated CpG sites and examined changes in DNA methylation in eight stably transfected clones over multiple passages. We found that BRAFV600E is not sufficient to induce CIMP in our system. Secondly, considering the alternative possibility, we identified genes whose DNA hypermethylation was closely linked to BRAFV600E and CIMP in 235 primary colorectal tumors. Interestingly, genes that showed the most significant link include those that mediate various signaling pathways implicated in colorectal tumorigenesis, such as BMP3 and BMP6 (BMP signaling), EPHA3, KIT, and FLT1 (receptor tyrosine kinases) and SMO (Hedgehog signaling). Furthermore, we identified CIMP-dependent DNA hypermethylation of IGFBP7, which has been shown to mediate BRAFV600E-induced cellular senescence and apoptosis. Promoter DNA hypermethylation of IGFBP7 was associated with silencing of the gene. CIMP-specific inactivation of BRAFV600E-induced senescence and apoptosis pathways by IGFBP7 DNA hypermethylation might create a favorable context for the acquisition of BRAFV600E in CIMP+ colorectal cancer. Our data will be useful for future investigations toward understanding CIMP in colorectal cancer and gaining insights into the role of aberrant DNA hypermethylation in colorectal tumorigenesis.
Sperm Proteasomes Degrade Sperm Receptor on the Egg Zona Pellucida during Mammalian Fertilization
Shawn W. Zimmerman,Gaurishankar Manandhar,Young-Joo Yi,Satish K. Gupta,Miriam Sutovsky,John F. Odhiambo,Michael D. Powell,David J. Miller,Peter Sutovsky
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017256
Abstract: Despite decades of research, the mechanism by which the fertilizing spermatozoon penetrates the mammalian vitelline membrane, the zona pellucida (ZP) remains one of the unexplained fundamental events of human/mammalian development. Evidence has been accumulating in support of the 26S proteasome as a candidate for echinoderm, ascidian and mammalian egg coat lysin. Monitoring ZP protein degradation by sperm during fertilization is nearly impossible because those few spermatozoa that penetrate the ZP leave behind a virtually untraceable residue of degraded proteins. We have overcome this hurdle by designing an experimentally consistent in vitro system in which live boar spermatozoa are co-incubated with ZP-proteins (ZPP) solubilized from porcine oocytes. Using this assay, mimicking sperm-egg interactions, we demonstrate that the sperm-borne proteasomes can degrade the sperm receptor protein ZPC. Upon coincubation with motile spermatozoa, the solubilized ZPP, which appear to be ubiquitinated, adhered to sperm acrosomal caps and induced acrosomal exocytosis/formation of the acrosomal shroud. The degradation of the sperm receptor protein ZPC was assessed by Western blotting band-densitometry and proteomics. A nearly identical pattern of sperm receptor degradation, evident already within the first 5 min of coincubation, was observed when the spermatozoa were replaced with the isolated, enzymatically active, sperm-derived proteasomes. ZPC degradation was blocked by proteasomal inhibitors and accelerated by ubiquitin-aldehyde(UBAL), a modified ubiquitin protein that stimulates proteasomal proteolysis. Such a degradation pattern of ZPC is consistent with in vitro fertilization studies, in which proteasomal inhibitors completely blocked fertilization, and UBAL increased fertilization and polyspermy rates. Preincubation of intact zona-enclosed ova with isolated active sperm proteasomes caused digestion, abrasions and loosening of the exposed zonae, and significantly reduced the fertilization/polyspermy rates after IVF, accompanied by en-mass detachment of zona bound sperm. Thus, the sperm borne 26S proteasome is a candidate zona lysin in mammals. This new paradigm has implications for contraception and assisted reproductive technologies in humans, as well as animals.
Sunyaev-Zel'dovich clusters in Millennium Gas simulations
Scott T. Kay,Michael W. Peel,C. J. Short,Peter A. Thomas,Owain E. Young,Richard A. Battye,Andrew R. Liddle,Frazer R. Pearce
Physics , 2011, DOI: 10.1111/j.1365-2966.2012.20623.x
Abstract: We have exploited the large-volume Millennium Gas cosmological N-body hydrodynamics simulations to study the SZ cluster population at low and high redshift, for three models with varying gas physics. We confirm previous results using smaller samples that the intrinsic (spherical) Y_{500}-M_{500} relation has very little scatter (sigma_{log_{10}Y}~0.04), is insensitive to cluster gas physics and evolves to redshift one in accord with self-similar expectations. Our pre-heating and feedback models predict scaling relations that are in excellent agreement with the recent analysis from combined Planck and XMM-Newton data by the Planck Collaboration. This agreement is largely preserved when r_{500} and M_{500} are derived using the hydrostatic mass proxy, Y_{X,500}, albeit with significantly reduced scatter (sigma_{log_{10}Y}~0.02), a result that is due to the tight correlation between Y_{500} and Y_{X,500}. Interestingly, this assumption also hides any bias in the relation due to dynamical activity. We also assess the importance of projection effects from large-scale structure along the line-of-sight, by extracting cluster Y_{500} values from fifty simulated 5x5 square degree sky maps. Once the (model-dependent) mean signal is subtracted from the maps we find that the integrated SZ signal is unbiased with respect to the underlying clusters, although the scatter in the (cylindrical) Y_{500}-M_{500} relation increases in the pre-heating case, where a significant amount of energy was injected into the intergalactic medium at high redshift. Finally, we study the hot gas pressure profiles to investigate the origin of the SZ signal and find that the largest contribution comes from radii close to r_{500} in all cases. The profiles themselves are well described by generalised Navarro, Frenk & White profiles but there is significant cluster-to-cluster scatter.
Nonconservative Lagrangian mechanics II: purely causal equations of motion
David W. Dreisigmeyer,Peter M. Young
Physics , 2004, DOI: 10.1007/s10701-015-9892-7
Abstract: This work builds on the Volterra series formalism presented in [D. W. Dreisigmeyer and P. M. Young, J. Phys. A \textbf{36}, 8297, (2003)] to model nonconservative systems. Here we treat Lagrangians and actions as `time dependent' Volterra series. We present a new family of kernels to be used in these Volterra series that allow us to derive a single retarded equation of motion using a variational principle.
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