Adequately representing dynamic characteristics of land use change and forestry in computable gen... more Adequately representing dynamic characteristics of land use change and forestry in computable general equilibrium models is challenging but essential if modellers are to provide credible assessments of policies that directly or indirectly influence these phenomena. In this paper, we show how a dynamic representation of planted or naturally regenerating forests may be integrated within a neoclassical, intertemporal general equilibrium model. We demonstrate the application of such a model to assess the impacts of including forestry within a hypothetical emissions trading scheme in the US, showing the resulting changes in land use and increases in the optimal rotation length.
... Curr Biol 14:21352142 Turner JM, Mahadevaiah SK, Fernandez-Capetillo O, Nussenzweig A, Xu X,... more ... Curr Biol 14:21352142 Turner JM, Mahadevaiah SK, Fernandez-Capetillo O, Nussenzweig A, Xu X, Deng CX, Burgoyne PS (2005) Silencing of ... BioEssays 17:7177 Zechner U, Wilda M, Kehrer-Sawatzki H, Vogel W, Fundele R, Hameister H (2001) A high density of X-linked ...
In mammalian spermatogenesis, the X and Y chromosomes are transcriptionally silenced during the p... more In mammalian spermatogenesis, the X and Y chromosomes are transcriptionally silenced during the pachytene stage of meiotic prophase (meiotic sex chromosome inactivation, MSCI), forming a condensed chromatin domain termed the sex or XY body. The nucleosomal core histone H2AX is phosphorylated within the XY chromatin domain just prior to MSCI, and it has been hypothesized that this triggers the chromatin condensation and transcriptional repression. Here, we show that the kinase ATR localizes to XY chromatin at the onset of MSCI and that this localization is disrupted in mice with a mutant form of the tumor suppressor protein BRCA1. In the mutant pachytene cells, ATR is usually present at nonsex chromosomal sites, where it colocalizes with aberrant sites of H2AX phosphorylation; in these cells, there is MSCI failure. In rare pachytene cells, ATR does locate to XY chromatin, H2AX is then phosphorylated, a sex body forms, and MSCI ensues. These observations highlight an important role fo...
In Neurospora, DNA unpaired in meiosis both is silenced and induces silencing of all DNA homologo... more In Neurospora, DNA unpaired in meiosis both is silenced and induces silencing of all DNA homologous to it. This process, called meiotic silencing by unpaired DNA, is thought to protect the host genome from invasion by transposable elements. We now show that silencing of unpaired (unsynapsed) chromosome regions also takes place in the mouse during both male and female meiosis. The tumor suppressor protein BRCA1 is implicated in this silencing, mirroring its role in the meiotic silencing of the X and Y chromosomes in normal male meiosis. These findings impact on the interpretation of the relationship between synaptic errors and sterility in mammals and extend our understanding of the biology of Brca1.
The toxic acetate analogue monofluoroacetic acid was employed to isolate Arabidopsis tDNA-tagged ... more The toxic acetate analogue monofluoroacetic acid was employed to isolate Arabidopsis tDNA-tagged plants deficient in their ability to utilize or sense acetate. Several tDNA-tagged lines were isolated, including two that were determined to be allelic to an EMS-mutagenized line denoted acn1 for ac non-utilizing. Following conventions, the tDNA-tagged mutants were designated acn1-2 and acn1-3. Both mutants displayed identical behavior to acn1-1 on a variety of fluorinated and nonfluorinated organic acids, indicating that resistance was specific to fluoroacetate. Thermal asymmetric interlaced PCR identified the sites of tDNA insertion in both mutants to be within different exons in a gene, which encoded a protein containing an AMP-binding motif. Reverse transcription-PCR confirmed that the gene was not expressed in the mutants, and quantitative reverse transcription-PCR showed that the gene is expressed in imbibed seeds and increases in amount during establishment. The wild type AMP-bin...
Journal of agricultural and food chemistry, Jan 31, 2002
Molecular modeling was used to propose an "active conformation" for the R-2-phenoxyprop... more Molecular modeling was used to propose an "active conformation" for the R-2-phenoxypropionic acid portion of the aryloxyphenoxypropionic acid series of herbicidal acetyl CoA carboxylase (ACCase) inhibitors. This candidate active conformation is a low-energy conformer with the R-methyl distal to the phenoxy fragment, stabilized by the generalized anomeric effect around the propionate ether bond; the inactive S-enantiomer has difficulty accessing this conformation due to steric interaction of the S-methyl with the o-hydrogen of the phenyl. This candidate conformation was challenged by preparation of a series of novel rigid analogues. ACCase inhibition data suggest that the systems which contain a fused five-membered, but not a six-membered, ring present the necessary pharmacophore to the active site of ACCase, confirming the active conformation hypothesis and demonstrating that the precise placement of the carboxylate relative to the phenyl group is more critical than the pl...
Journal of the American Chemical Society, Jan 2, 2005
It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to... more It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to allow genetic incorporation of unnatural amino acids into proteins in both prokaryotes and eukaryotes. Here we describe the crystal structure of an evolved aminoacyl-tRNA synthetase that charges the unnatural amino acid p-acetylphenylalanine. Molecular recognition is due to altered hydrogen bonding and packing interactions with bound substrate that result from changes in both side-chain and backbone conformation.
The X-ray free-electron laser has opened a new era for photon science, improving the X-ray bright... more The X-ray free-electron laser has opened a new era for photon science, improving the X-ray brightness by ten orders of magnitude over previously available sources. Similar to an optical laser, the spectral and temporal structure of the radiation pulses can be tailored to the specific needs of many experiments by accurately manipulating the lasing medium, that is, the electron beam. Here we report the generation of mJ-level two-colour hard X-ray pulses of few femtoseconds duration with an XFEL driven by twin electron bunches at the Linac Coherent Light Source. This performance represents an improvement of over an order of magnitude in peak power over state-of-the-art two-colour XFELs. The unprecedented intensity and temporal coherence of this new two-colour X-ray free-electron laser enable an entirely new set of scientific applications, ranging from X-ray pump/X-ray probe experiments to the imaging of complex biological samples with multiple wavelength anomalous dispersion.
The GaAsP/GaAs strained superlattice photocathode structure has proven to be a significant advanc... more The GaAsP/GaAs strained superlattice photocathode structure has proven to be a significant advance for polarized electron sources operating with high peak currents per microbunch and relatively low duty factor. This is the characteristic type of operation for SLAC and is also planned for the ILC. This superlattice structure was studied at SLAC [1], and an optimum variation was chosen for the final stage of E-158, a high-energy parity violating experiment at SLAC. Following E-158, the polarized source was maintained on standby with the cathode being re-cesiated about once a week while a thermionic gun, which is installed in parallel with the polarized gun, supplied the linac electron beams. However, in the summer of 2005, while the thermionic gun was disabled, the polarized electron source was again used to provide electron beams for the linac. The performance of the photocathode 24 months after its only activation is described and factors making this possible are discussed.
Physical Review Special Topics - Accelerators and Beams
The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) project presentl... more The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) project presently under construction at SLAC. The injector section, from drive laser and RF photocathode gun through first bunch compressor chicane, was installed in fall 2006. Initial system commissioning with an electron beam was completed in August 2007, with the goal of a 1.2-micron emittance in a 1-nC bunch clearly demonstrated. The second phase of commissioning, including second bunch compressor and full linac, is planned for 2008, with FEL commissioning in 2009. We report experimental results and experience gained in the first phase of commissioning, including the photo-cathode drive laser, RF gun, photocathode, S-band and X-band RF systems, first bunch compressor, and the various beam diagnostics.
Single strained, medium-doped (5×1018 /cm3) GaAs photocathodes show the surface charge limit (SCL... more Single strained, medium-doped (5×1018 /cm3) GaAs photocathodes show the surface charge limit (SCL). The SCL poses a serious problem for operation of polarized electron sources at future linear colliders such as the NLC/JLC. A high-gradient-doping technique has been applied to address this problem. A 5 -7.5 nm p-type surface layer doped to 5×1019/cm3 is found sufficient to overcome the SCL, while maintaining high beam polarization. This technique can be employed to meet the charge requirements of the NLC with a polarization approaching 80%.
We present the design and experimental results for the flashlamp-pumped Ti:Sapphire laser system ... more We present the design and experimental results for the flashlamp-pumped Ti:Sapphire laser system used at the Stanford Linear Accelerator Center (SLAC). This laser system is used in conjunction with the Polarized Electron Source to generate polarized electron beams for fixed target experiments (e.g. the E-158 experiment). The unique capabilities such as high pulse-to-pulse stability, long pulse length and high repetition rate is discussed. Emphasis is placed on recent modifications of the laser system, which allow ultra-stable operation with 0.5% rms intensity jitter.
Future electron-positron linear colliders require a highly polarized electron beam with a pulse s... more Future electron-positron linear colliders require a highly polarized electron beam with a pulse structure that depends primarily on whether the acceleration utilizes warm or superconducting rf structures. The International Linear Collider (ILC) will use cold structures for the main linac. It is shown that a dc-biased polarized photoelectron source such as successfully used for the SLC can meet the charge requirements for the ILC micropulse with a polarization approaching 90%.
The PEP-II B-Factory operated at peak and integrated luminosity several times the original design... more The PEP-II B-Factory operated at peak and integrated luminosity several times the original design values. Its storage rings operated at world-record beam currents with bunch lengths of about 10 mm. Correspondingly significant heat load was imposed on the vacuum system, both due to synchrotron radiation and by energy loss into higher-order modes. The latter in turn would lead to local heating or discharges wherever such energy got absorbed. Over the course of PEP-II running we experienced numerous such effects, which lead to upgrade programs of significant scope. In the following we will describe the most significant of such effects and their mitigation: (1) Upgrades and repairs of RF seals and shields in both rings; (2) Redesign of overheating stripline kicker electrodes to withstand higher powers; and (3) Redesign and replacement of BPM buttons following failure.
Adequately representing dynamic characteristics of land use change and forestry in computable gen... more Adequately representing dynamic characteristics of land use change and forestry in computable general equilibrium models is challenging but essential if modellers are to provide credible assessments of policies that directly or indirectly influence these phenomena. In this paper, we show how a dynamic representation of planted or naturally regenerating forests may be integrated within a neoclassical, intertemporal general equilibrium model. We demonstrate the application of such a model to assess the impacts of including forestry within a hypothetical emissions trading scheme in the US, showing the resulting changes in land use and increases in the optimal rotation length.
... Curr Biol 14:21352142 Turner JM, Mahadevaiah SK, Fernandez-Capetillo O, Nussenzweig A, Xu X,... more ... Curr Biol 14:21352142 Turner JM, Mahadevaiah SK, Fernandez-Capetillo O, Nussenzweig A, Xu X, Deng CX, Burgoyne PS (2005) Silencing of ... BioEssays 17:7177 Zechner U, Wilda M, Kehrer-Sawatzki H, Vogel W, Fundele R, Hameister H (2001) A high density of X-linked ...
In mammalian spermatogenesis, the X and Y chromosomes are transcriptionally silenced during the p... more In mammalian spermatogenesis, the X and Y chromosomes are transcriptionally silenced during the pachytene stage of meiotic prophase (meiotic sex chromosome inactivation, MSCI), forming a condensed chromatin domain termed the sex or XY body. The nucleosomal core histone H2AX is phosphorylated within the XY chromatin domain just prior to MSCI, and it has been hypothesized that this triggers the chromatin condensation and transcriptional repression. Here, we show that the kinase ATR localizes to XY chromatin at the onset of MSCI and that this localization is disrupted in mice with a mutant form of the tumor suppressor protein BRCA1. In the mutant pachytene cells, ATR is usually present at nonsex chromosomal sites, where it colocalizes with aberrant sites of H2AX phosphorylation; in these cells, there is MSCI failure. In rare pachytene cells, ATR does locate to XY chromatin, H2AX is then phosphorylated, a sex body forms, and MSCI ensues. These observations highlight an important role fo...
In Neurospora, DNA unpaired in meiosis both is silenced and induces silencing of all DNA homologo... more In Neurospora, DNA unpaired in meiosis both is silenced and induces silencing of all DNA homologous to it. This process, called meiotic silencing by unpaired DNA, is thought to protect the host genome from invasion by transposable elements. We now show that silencing of unpaired (unsynapsed) chromosome regions also takes place in the mouse during both male and female meiosis. The tumor suppressor protein BRCA1 is implicated in this silencing, mirroring its role in the meiotic silencing of the X and Y chromosomes in normal male meiosis. These findings impact on the interpretation of the relationship between synaptic errors and sterility in mammals and extend our understanding of the biology of Brca1.
The toxic acetate analogue monofluoroacetic acid was employed to isolate Arabidopsis tDNA-tagged ... more The toxic acetate analogue monofluoroacetic acid was employed to isolate Arabidopsis tDNA-tagged plants deficient in their ability to utilize or sense acetate. Several tDNA-tagged lines were isolated, including two that were determined to be allelic to an EMS-mutagenized line denoted acn1 for ac non-utilizing. Following conventions, the tDNA-tagged mutants were designated acn1-2 and acn1-3. Both mutants displayed identical behavior to acn1-1 on a variety of fluorinated and nonfluorinated organic acids, indicating that resistance was specific to fluoroacetate. Thermal asymmetric interlaced PCR identified the sites of tDNA insertion in both mutants to be within different exons in a gene, which encoded a protein containing an AMP-binding motif. Reverse transcription-PCR confirmed that the gene was not expressed in the mutants, and quantitative reverse transcription-PCR showed that the gene is expressed in imbibed seeds and increases in amount during establishment. The wild type AMP-bin...
Journal of agricultural and food chemistry, Jan 31, 2002
Molecular modeling was used to propose an "active conformation" for the R-2-phenoxyprop... more Molecular modeling was used to propose an "active conformation" for the R-2-phenoxypropionic acid portion of the aryloxyphenoxypropionic acid series of herbicidal acetyl CoA carboxylase (ACCase) inhibitors. This candidate active conformation is a low-energy conformer with the R-methyl distal to the phenoxy fragment, stabilized by the generalized anomeric effect around the propionate ether bond; the inactive S-enantiomer has difficulty accessing this conformation due to steric interaction of the S-methyl with the o-hydrogen of the phenyl. This candidate conformation was challenged by preparation of a series of novel rigid analogues. ACCase inhibition data suggest that the systems which contain a fused five-membered, but not a six-membered, ring present the necessary pharmacophore to the active site of ACCase, confirming the active conformation hypothesis and demonstrating that the precise placement of the carboxylate relative to the phenyl group is more critical than the pl...
Journal of the American Chemical Society, Jan 2, 2005
It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to... more It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to allow genetic incorporation of unnatural amino acids into proteins in both prokaryotes and eukaryotes. Here we describe the crystal structure of an evolved aminoacyl-tRNA synthetase that charges the unnatural amino acid p-acetylphenylalanine. Molecular recognition is due to altered hydrogen bonding and packing interactions with bound substrate that result from changes in both side-chain and backbone conformation.
The X-ray free-electron laser has opened a new era for photon science, improving the X-ray bright... more The X-ray free-electron laser has opened a new era for photon science, improving the X-ray brightness by ten orders of magnitude over previously available sources. Similar to an optical laser, the spectral and temporal structure of the radiation pulses can be tailored to the specific needs of many experiments by accurately manipulating the lasing medium, that is, the electron beam. Here we report the generation of mJ-level two-colour hard X-ray pulses of few femtoseconds duration with an XFEL driven by twin electron bunches at the Linac Coherent Light Source. This performance represents an improvement of over an order of magnitude in peak power over state-of-the-art two-colour XFELs. The unprecedented intensity and temporal coherence of this new two-colour X-ray free-electron laser enable an entirely new set of scientific applications, ranging from X-ray pump/X-ray probe experiments to the imaging of complex biological samples with multiple wavelength anomalous dispersion.
The GaAsP/GaAs strained superlattice photocathode structure has proven to be a significant advanc... more The GaAsP/GaAs strained superlattice photocathode structure has proven to be a significant advance for polarized electron sources operating with high peak currents per microbunch and relatively low duty factor. This is the characteristic type of operation for SLAC and is also planned for the ILC. This superlattice structure was studied at SLAC [1], and an optimum variation was chosen for the final stage of E-158, a high-energy parity violating experiment at SLAC. Following E-158, the polarized source was maintained on standby with the cathode being re-cesiated about once a week while a thermionic gun, which is installed in parallel with the polarized gun, supplied the linac electron beams. However, in the summer of 2005, while the thermionic gun was disabled, the polarized electron source was again used to provide electron beams for the linac. The performance of the photocathode 24 months after its only activation is described and factors making this possible are discussed.
Physical Review Special Topics - Accelerators and Beams
The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) project presentl... more The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) project presently under construction at SLAC. The injector section, from drive laser and RF photocathode gun through first bunch compressor chicane, was installed in fall 2006. Initial system commissioning with an electron beam was completed in August 2007, with the goal of a 1.2-micron emittance in a 1-nC bunch clearly demonstrated. The second phase of commissioning, including second bunch compressor and full linac, is planned for 2008, with FEL commissioning in 2009. We report experimental results and experience gained in the first phase of commissioning, including the photo-cathode drive laser, RF gun, photocathode, S-band and X-band RF systems, first bunch compressor, and the various beam diagnostics.
Single strained, medium-doped (5×1018 /cm3) GaAs photocathodes show the surface charge limit (SCL... more Single strained, medium-doped (5×1018 /cm3) GaAs photocathodes show the surface charge limit (SCL). The SCL poses a serious problem for operation of polarized electron sources at future linear colliders such as the NLC/JLC. A high-gradient-doping technique has been applied to address this problem. A 5 -7.5 nm p-type surface layer doped to 5×1019/cm3 is found sufficient to overcome the SCL, while maintaining high beam polarization. This technique can be employed to meet the charge requirements of the NLC with a polarization approaching 80%.
We present the design and experimental results for the flashlamp-pumped Ti:Sapphire laser system ... more We present the design and experimental results for the flashlamp-pumped Ti:Sapphire laser system used at the Stanford Linear Accelerator Center (SLAC). This laser system is used in conjunction with the Polarized Electron Source to generate polarized electron beams for fixed target experiments (e.g. the E-158 experiment). The unique capabilities such as high pulse-to-pulse stability, long pulse length and high repetition rate is discussed. Emphasis is placed on recent modifications of the laser system, which allow ultra-stable operation with 0.5% rms intensity jitter.
Future electron-positron linear colliders require a highly polarized electron beam with a pulse s... more Future electron-positron linear colliders require a highly polarized electron beam with a pulse structure that depends primarily on whether the acceleration utilizes warm or superconducting rf structures. The International Linear Collider (ILC) will use cold structures for the main linac. It is shown that a dc-biased polarized photoelectron source such as successfully used for the SLC can meet the charge requirements for the ILC micropulse with a polarization approaching 90%.
The PEP-II B-Factory operated at peak and integrated luminosity several times the original design... more The PEP-II B-Factory operated at peak and integrated luminosity several times the original design values. Its storage rings operated at world-record beam currents with bunch lengths of about 10 mm. Correspondingly significant heat load was imposed on the vacuum system, both due to synchrotron radiation and by energy loss into higher-order modes. The latter in turn would lead to local heating or discharges wherever such energy got absorbed. Over the course of PEP-II running we experienced numerous such effects, which lead to upgrade programs of significant scope. In the following we will describe the most significant of such effects and their mitigation: (1) Upgrades and repairs of RF seals and shields in both rings; (2) Redesign of overheating stripline kicker electrodes to withstand higher powers; and (3) Redesign and replacement of BPM buttons following failure.
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