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At least 181 records · Page 10

Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum

The genome of the thermophilic fungus Scytalidium thermophilum (strain CBS 625.91) harbours a wide range of genes involved in carbohydrate degradation, including three genes, abf62A , abf62B and abf62C , predicted to encode glycoside hydrolase family 62 (GH62) enzymes. Transcriptome analysis showed that only abf62A and abf62C are actively expressed during growth on diverse substrates including straws from barley, alfalfa, triticale and canola. The abf62A and abf62C genes were expressed in Escherichia coli and the resulting recombinant proteins were characterized. Calcium-free crystal structures of Abf62C in apo and xylotriose bound forms were determined to 1.23 and 1.48 Å resolution respectively. Site-directed mutagenesis confirmed Asp55, Asp171 and Glu230 as catalytic triad residues, and revealed the critical role of non-catalytic residues Asp194, Trp229 and Tyr338 in positioning the scissile α-L-arabinofuranoside bond at the catalytic site. Further, the +2R substrate-binding site residues Tyr168 and Asn339, as well as the +2NR residue Tyr226, are involved in accommodating long-chain xylan polymers. Overall, our structural and functional analysis highlights characteristic differences between Abf62A and Abf62C, which represent divergent subgroups in the GH62 family.

60 APPLIED LIFE SCIENCES↗

Effect of magnetic field on the character of fluorescence of dense and cold atomic ensembles excited by pulsed radiation

Specific features of fluorescence of dense and cold nondegenerate atomic ensembles in an external constant magnetic field are analyzed theoretically. The angular distribution, polarization properties, as well as the spectral composition of fluorescence radiation are calculated. The time variation of these characteristics after the end of the excitation pulse is analyzed. The dependence of the properties of secondary radiation on the duration and carrier frequency of the pulse is investigated. It is shown that, for dense clouds in which the free path length of quasiresonance photons is commensurate with the interatomic distance, the magnetic field significantly modifies all the observable properties of the radiation. Under these conditions, the trapping time may increase by tens of times. Magnetic field enhances the effect of quantum beats observed on time scales commensurate with the lifetime of the excited states of atoms. For individual polarization channels, this field also intensifies the phenomenon of coherent backscattering (CBS). The phenomena found are explained by the effect of magnetic field on the character of resonance dipole–dipole interaction and, as a result, on the specific features of collective phenomena in dense atomic ensembles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Laboratory tests of laser control of electron beams for future colliders

Laser-driven Compton backscattering (CBS) has been proposed as method for controlling the intensity of colliding bunches in the FCC-ee so as to avoid the flip-flop instability caused by intensity asymmetry in colliding bunches. Laser-based collimation has also been proposed as an indestructible collimator for high-intensity electron beams. We have initiated a laboratory-based test program of these concepts with the E344 experiment at FACET-II. In this paper, we describe simulations of laser–beam interactions at FACET-II and the relevant scaling for FCC-ee. We also describe the experimental setup and diagnostics that will be used to make the measurements at FACET-II.

accelerator physics↗

Erratum to: A molecular genetic toolbox for Yarrowia lipolytica

Shortly after this article was published [1] the authors noticed a few errors which are outlined below: Background paragraph 1, sentence 4, The wild type American CBS number should be: “CBS6124-2.” Background paragraph 1, sentence 5 should be: “The Po1 series, derived directly of successive transformations of W29 [7], has been used for a number of studies.” Background paragraph 1, sentence 6 should be: “CLIB122 or E150, the reference genome strain, is derived of a W29 to YB423-12 cross and brother–sister matings, xpr2 deletion, and introduced auxotrophies [8].” Background paragraph 1, sentence 7 should be: “Genome sequencing efforts have covered some original isolates and their derivatives, including W29 [9], and Po1f, a product of successive transformations [10].” Page 13, Results paragraph 10, sentence 4 should be: “Malate dehydrogenase has been studied for alternative splicing, with one form localized by an N-terminal GFP to the peroxisome matrix by expression from an integrated cassette [107].”

59 BASIC BIOLOGICAL SCIENCES↗

CRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus

Background: 2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material. Results: We work toward this goal by engineering the Shikimate and Ehrlich pathways in the stress-tolerant yeast Kluyveromyces marxianus. First, we develop a multigene integration tool that uses CRISPR-Cas9 induced breaks on the genome as a selection for the one-step integration of an insert that encodes one, two, or three gene expression cassettes. Integration of a 5-kbp insert containing three overexpression cassettes successfully occurs with an efficiency of 51 ± 9% at the ABZ1 locus and was used to create a library of K. marxianus CBS 6556 strains with refactored Shikimate pathway genes. The 3 3 -factorial library includes all combinations of KmARO4, KmARO7, and KmPHA2, each driven by three different promoters that span a wide expression range. Analysis of the refactored pathway library reveals that high expression of the tyrosine-deregulated KmARO4 K221L and native KmPHA2, with the medium expression of feedback insensitive KmARO7 G141S , results in the highest increase in 2-PE biosynthesis, producing 684 ± 73 mg/L. Ehrlich pathway engineering by overexpression of KmARO10 and disruption of KmEAT1 further increases 2-PE production to 766 ± 6 mg/L. The best strain achieves 1943 ± 63 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures. Conclusions: The CRISPR-mediated multigene integration system expands the genome-editing toolset for K. marxianus, a promising multi-stress tolerant host for the biosynthesis of 2-PE and other aromatic compounds derived from the Shikimate pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Model Evaluation Report for Corrective Action Unit 98: Frenchman Flat, Nevada National Security Site, Nye County, Nevada, Revision 1

Model evaluation focused solely on the PIN STRIPE and MILK SHAKE underground nuclear tests’ contaminant boundaries (CBs) because they had the largest extent, uncertainty, and potential consequences. The CAMBRIC radionuclide migration experiment also had a relatively large CB, but because it was constrained by transport data (notably Well UE-5n), there was little uncertainty, and radioactive decay reduced concentrations before much migration could occur. Each evaluation target and the associated data-collection activity were assessed in turn to determine whether the new data support, or demonstrate conservatism of, the CB forecasts. The modeling team—in this case, the same team that developed the Frenchman Flat geologic, source term, and groundwater flow and transport models—analyzed the new data and presented the results to a PER committee. Existing site understanding and its representation in numerical groundwater flow and transport models was evaluated in light of the new data and the ability to proceed to the CR stage of long-term monitoring and institutional control.

54 ENVIRONMENTAL SCIENCES↗

Experiences of Vulnerable Residential Customer Subpopulations with Critical Peak Pricing

DOE decided to co-fund ten utilities to undertake eleven experimentally-designed Consumer Behavior Studies (CBS) that proposed to examine a wide range of the topics of interest to the electric utility industry. Each chosen utility was to design, implement and evaluate their own study in order to address questions of interest both to itself and to its applicable regulatory authority, whose approval was generally necessary for the study to proceed. The DOE Office of Energy Delivery and Electricity Reliability (OE), however, did set guidelines, both in the FOA and subsequently during the contracting period, for what would constitute an acceptable study under the Grant. To assist in ensuring these guidelines were adhered to, OE requested that LBNL act as project manager for these Consumer Behavior Studies to achieve consistency of experimental design and adherence to data collection and reporting protocols across the ten utilities. As part of its role, LBNL formed technical advisory groups (TAG) to separately assist each of the utilities by providing technical assistance in all aspects of the design, implementation and evaluation of their studies. LBNL was also given a unique opportunity to perform a comprehensive, cross-study analysis that uses the customer-level interval meter and demographic data made available by these utilities due to SGIG-imposed reporting requirements, in order to analyze critical policy issues associated with AMI-enabled rates and control/information technology. LBNL will publish the results of these analyses in a series of research reports, of which this is one, that attempt to address critical policy issues relating to a variety of topics including customer acceptance, retention and load response to time-based rates and various forms of enabling control and information technologies. This report extends the existing empirical literature on the experiences of low-income customers exposed to critical peak pricing, and provides the first glimpses into the experiences of the elderly and those who reported being chronically ill. Specifically, we analyzed two of the time-based rate consumer behavior studies, which were co-funded by the Department of Energy as part of the Smart Grid Investment Grant program.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Post-Closure Monitoring Report for Corrective Action Unit 98, Frenchman Flat, Underground Test Area, Nevada National Security Site, Nevada for Calendar Year 2016 (January 2016–December 2016), Revision 0

Corrective Action Unit (CAU) 98: Frenchman Flat on the Nevada National Security Site was the location of 10 underground nuclear tests. CAU 98 underwent a series of investigations and actions in accordance with the Federal Facility Agreement and Consent Order to assess contamination of groundwater by radionuclides from the tests. A Closure Report completed that process in 2016 and called for long-term monitoring, use restrictions (URs), and institutional controls to protect the public and environment from potential exposure to contaminated groundwater. Three types of monitoring are performed for CAU 98: water quality, water level, and institutional control. These are evaluated to determine whether the UR boundaries remain protective of human health and the environment, and to ensure that the regulatory boundary objectives are being met. Additionally, monitoring data are used to evaluate consistency with the groundwater flow and contaminant transport models because the contaminant boundaries (CBs) calculated with the models are the primary basis of the UR boundaries. In summary, the monitoring results from 2016 indicate the regulatory controls on the closure of CAU 98 remain effective in protection of human health and the environment. Recommendations resulting from this first year of monitoring activities include formally incorporating wells UE-5 PW-1, UE-5 PW-2, and UE-5 PW-3 into the groundwater-level monitoring network given their strategic location in the basin; and early development of a basis for trigger levels for the groundwater-level monitoring given the observed trends. Additionally, it is recommended to improve the Real Estate/Operations Permit process for capturing information important for evaluating the impact of activities on groundwater resources, and to shift the reporting requirement for this annual report from the second quarter of the federal fiscal year (end of March) to the second quarter of the calendar year (end of June).

54 ENVIRONMENTAL SCIENCES↗

American Recovery and Reinvestment Act of 2009: Final Report on Customer Acceptance, Retention, and Response to Time-Based Rates from Consumer Behavior Studies

Time-based rate programs, enabled by utility investments in advanced metering infrastructure (AMI), are increasingly being considered by utilities as tools to reduce peak demand and enable customers to better manage consumption and costs. Under the Smart Grid Investment Grant Program (SGIG), the U.S. Department of Energy (DOE) partnered with several electric utilities to conduct consumer behavior studies (CBS). The goals involved applying randomized and controlled experimental designs for estimating customer responses more precisely and credibly to advance understanding of time-based rates and customer systems, and provide new information for improving program designs, implementation strategies, and evaluations. The intent was to produce more robust and credible analysis of impacts, costs, benefits, and lessons learned and assist utility and regulatory decision makers in evaluating investment opportunities involving time-based rates.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Expected condition of concrete exposed to radiation at age 80 years of reactor operation

This report is intended to provide access to information generated by LPI, Inc. on behalf of the US Department of Energy (DOE), Office of Nuclear Energy, Light Water Reactor Sustainability (LWRS) Program and the Electric Power Research Institute (EPRI) in 2013. Specifically, estimates of the fast neutron fluence at 80 years of operation on the outer surface of the concrete biological shield (CBS) of US Nuclear Power Plants (NPPs) operating in 2013 and an estimate of the effects of gamma radiation on the temperature on the biological shield were determined.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Automated Identification of Human Incursion

According to a CBS news report, on April 16, 2013 a San Jose, CA PG&E substation’s security fence was breached, and five transformers were damaged. The damaged transformers had a lead time of several months, leaving the electrical system with reduced capacity through the summer. With the increasing value of copper, the theft of copper electrical lines has also become an issue. Such occurrences highlight the vulnerability of our electrical grid and the need for greater security than fencing.

42 ENGINEERING↗

Groundwater Flow and Contaminant Transport Model of Corrective Action Units 101 and 102: Central and Western Pahute Mesa, Nye County, Nevada (Rev. 1)

This document presents the groundwater flow and transport models along with simulation forecasts needed for the purpose of developing the ensemble of contaminant boundaries (CBs) for the Central and Western Pahute Mesa (PM) corrective action units (CAUs) 101 and 102. The PM CAUs are areas of the Nevada National Security Site (NNSS) that were historically used for underground nuclear testing.

54 ENVIRONMENTAL SCIENCES↗

Study of the Synchrotron Photoionization Oxidation of Alpha-Angelica Lactone (AAL) Initiated by O( 3 P) at 298, 550, and 700 K

In recent years, biofuels have been receiving significant attention because of their potential for decreasing carbon emissions and providing a long-term renewable solution to unsustainable fossil fuels. Currently, lactones are some of the alternatives being produced. Many lactones occur in a range of natural substances and have many advantages over bioethanol. In this study, the oxidation of alpha-angelica lactone initiated by ground-state atomic oxygen, O( 3 P), was studied at 298, 550, and 700 K using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at the Lawrence Berkeley National Lab (LBNL). Photoionization spectra and kinetic time traces were measured to identify the primary products. Ketene, acetaldehyde, methyl vinyl ketone, methylglyoxal, dimethyl glyoxal, and 5-methyl-2,4-furandione were characterized as major reaction products, with ketene being the most abundant at all three temperatures. Possible reaction pathways for the formation of the observed primary products were computed using the CBS–QB3 composite method.

09 BIOMASS FUELS↗

Laboratory Tests of Laser Control of Electron Beams for Future Colliders

Laser-driven Compton backscattering (CBS) has been proposed as method for controlling the intensity of colliding bunches in the FCC-ee so as to avoid the flip-flop instability caused by intensity asymmetry in colliding bunches. Laser-based collimation has also been proposed as an indestructible collimator for high-intensity electron beams. We have initiated a laboratory-based test program of these concepts with the E344 experiment at FACET-II. In this paper, we describe simulations of laser-beam interactions at FACET-II and the relevant scaling for FCC-ee. We also describe the experimental setup and diagnostics that will be used to make the measurements at FACET-II.

Accelerator Physics (physics.acc-ph)↗

Saccharomycopsis sp. strain UFMG-CM-Y6632 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

Amazonian Forest↗

Saccharomycopsis sp. isolate UFMG-CM-Y6632 large subunit ribosomal RNA gene, partial sequence

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

Amazonian Forest↗

Saccharomycopsis sp. KB-2023a isolate UFMG-CM-Y6991, whole genome shotgun sequencing project

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

Amazonian Forest↗