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At least 289 records · Page 16

Next-Generation Sequencing Data from a CUT&RUN Study of R. toruloides IFO0880 Cse4 and Orc1 Binding Sites

Rhodotorula toruloides has been increasingly explored as a host for bioproduction of lipids, fatty acid derivatives and terpenoids. Various genetic tools have been developed, but neither a centromere nor an autonomously replicating sequence (ARS), both necessary elements for stable episomal plasmid maintenance, has yet been reported. In this study, cleavage under targets and release using nuclease (CUT&RUN), a method used for genome-wide mapping of DNA–protein interactions, was used to identify R. toruloides IFO0880 genomic regions associated with the centromeric histone H3 protein Cse4, a marker of centromeric DNA. Fifteen putative centromeres ranging from 8 to 19 kb in length were identified and analyzed, and four were tested for, but did not show, ARS activity. These centromeric sequences contained below average GC content, corresponded to transcriptional cold spots, were primarily nonrepetitive and shared some vestigial transposon-related sequences but otherwise did not show significant sequence conservation. Future efforts to identify an ARS in this yeast can utilize these centromeric DNA sequences to improve the stability of episomal plasmids derived from putative ARS elements.

Genome Engineering↗

Magnetotelluric Investigations of the Kilauea Volcano, Hawaii

In 2002 and 2003 a collaborative effort was undertaken between Lawrence Berkeley National Laboratory, Sandia National Laboratories, the U.S. Geological Survey (USGS) Menlo Park, the USGS Hawaiian Volcano Observatory, and Electromagnetic Instruments Inc. to study the Kilauea volcano in Hawaii using the magnetotelluric (MT) technique. The work was motivated by a desire to improve understanding of the magma reservoirs and conduits within Kilauea and the East and Southwest Rift zones, which has implications for understanding Kilauea's plumbing system. An improved understanding of the rift zones has implications in understanding large-scale landslides that are generated in the Hilina Slump, which produce significant impacts on coastal communities. Up to eight stations operated simultaneously, with multiple remote reference sites, and data were processed using multi-station robust processing techniques. Data was acquired at 70 sites over the Southwest and East rift zones. Good to excellent quality data were obtained even in the harshest conditions, such as those encountered on the fresh lava flows of the East Rift Zone, where electrical contact resistances are on the order of 100 kΩ. A three-dimensional (3D) MT model study was done to guide interpretation of the observed MT measurements. Synthetic modeling demonstrates that conductive bodies in the upper 3 km can be spatially resolved where MT station sampling is good. Resistivity anomalies in the 3D inversions have a high degree of spatial correlation with previously published seismic velocity anomalies beneath Kilauea. Melt fractions between 0.096 and 0.117 are calculated for the Kilauea and Pu'u'ō'ō low resistivity anomalies, respectively.

58 GEOSCIENCES↗

MAC Europe 1991 campaign: AIRSAR/AVIRIS data integration for agricultural test site classification

During summer 1991, multi-sensor data were acquired over the Italian test site 'Otrepo Pavese', an agricultural flat area in Northern Italy. This area has been the Telespazio pilot test site for experimental activities related to agriculture applications. The aim of the investigation described in the following paper is to assess the amount of information contained in the AIRSAR (Airborne Synthetic Aperture Radar) and AVIRIS (Airborne Visible/Infrared Imaging Spectrometer) data, and to evaluate classification results obtained from each sensor data separately and from the combined dataset. All classifications are examined by means of the resulting confusion matrices and Khat coefficients. Improvements of the classification results obtained by using the integrated dataset are finally evaluated.

Sangiovanni, S.↗

BOREAS TF-6 SSA-YA Surface Energy Flux and Meteorological Data

The BOREAS TF-6 team collected surface energy flux and meteorology data at the SSA-YA site. The data characterize the energy flux and meteorological conditions at the site from 18-Jul to 20-Sep-1994. The data set does not contain any trace gas exchange measurements. The data are available in tabular ASCII files.

Bessemoulin, Pierre↗

Probabilistic Hazard Assessment for Tornadoes, Straight-Line Wind, and Extreme Precipitation at the Savannah River Site

Recent data sets for three meteorological phenomena with the potential to inflict damage on SRS facilities – tornadoes, straight-line winds, and heavy precipitation – are analyzed using appropriate statistical techniques to estimate the occurrence probabilities for these events in the future. Summaries of the results for DOE-mandated return periods and comparisons to similar calculations performed in 2013 by Werth et al. (W2013) are given. Using tornado statistics for i) the combined states of Georgia and South Carolina, and ii) a 2⁰ square area surrounding SRS, we calculated the probability per year of any location at SRS being struck by a tornado (the ‘strike’ probability) and the probability that any point will experience winds above set thresholds. The strike probability was calculated to be 7.04E-4 (1 chance in 1420) per year and tornadic wind speeds for DOE mandated return periods of 50,000 years (corresponding to wind design category 3 (WDC-3), and 125,000 years (meeting WDC-4) (USDOE, 2016) were estimated to be 132 mph and 147 mph, respectively. By contrast, default tornado wind speeds taken from ANSI/ANS-2.3-2011 are somewhat higher: 161 mph for return periods of 50,000 years and 173 mph every 125,000 years (ANS, 2011). Although the ANS and the SRS evaluation used the same basic model (Ramsdell and Rishel, 2007), the region defined in ANS 2.3 that encompasses the SRS also includes areas of the Great Plains and lower Midwest, regions with much higher occurrence frequencies of strong tornadoes. The SRS straight-line wind values associated with various return periods were calculated by fitting existing wind data to a GEV1 distribution and extrapolating the values for any return period from the tail of that function. For the DOE mandated return periods, we expect straight-line winds of 117 mph every 2500 years (the required WDC-3 standard) and 125 mph every 6250 years (WDC-4) at any point within the SRS. These values are similar to those from the ANS-2.3-2011 report, which has wind speeds of 125mph and 133 mph for return periods of 2500 years and 6250 years, respectively. For extreme precipitation, we compared the fits of two different theoretical extreme-value distributions and applied the one that fit the data best for each of several accumulation periods. The DOE mandated 6-hr accumulated rainfall for return periods of 10,000 years (corresponding to precipitation design category 3 (PDC-3) and 25,000 years (PDC-4) were estimated as 9.1 inches and 10.1 inches, respectively. For the 24-hr rainfall return periods of 10,000 years and 25,000 years, total rainfall estimates were 12.02 inches and 13.17 inches, respectively, higher than comparable values provided in the W2013 report.

54 ENVIRONMENTAL SCIENCES↗

Software used with the flux mapper at the solar parabolic dish test site

Software for data archiving and data display was developed for use on a Digital Equipment Corporation (DEC) PDP-11/34A minicomputer for use with the JPL-designed flux mapper. The flux mapper is a two-dimensional, high radiant energy scanning device designed to measure radiant flux energies expected at the focal point of solar parabolic dish concentrators. Interfacing to the DEC equipment was accomplished by standard RS-232C serial lines. The design of the software was dicated by design constraints of the flux-mapper controller. Early attemps at data acquisition from the flux-mapper controller were not without difficulty. Time and personnel limitations result in an alternative method of data recording at the test site with subsequent analysis accomplished at a data evaluation location at some later time. Software for plotting was also written to better visualize the flux patterns. Recommendations for future alternative development are discussed. A listing of the programs used in the anaysis is included in an appendix.

Miyazono, C.↗

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

SITE project. Phase 1: Continuous data bit-error-rate testing

The Systems Integration, Test, and Evaluation (SITE) Project at NASA LeRC encompasses a number of research and technology areas of satellite communications systems. Phase 1 of this project established a complete satellite link simulator system. The evaluation of proof-of-concept microwave devices, radiofrequency (RF) and bit-error-rate (BER) testing of hardware, testing of remote airlinks, and other tests were performed as part of this first testing phase. This final report covers the test results produced in phase 1 of the SITE Project. The data presented include 20-GHz high-power-amplifier testing, 30-GHz low-noise-receiver testing, amplitude equalization, transponder baseline testing, switch matrix tests, and continuous-wave and modulated interference tests. The report also presents the methods used to measure the RF and BER performance of the complete system. Correlations of the RF and BER data are summarized to note the effects of the RF responses on the BER.

Fujikawa, Gene↗

Millinocket Stream, Maine Velocity and Bathymetry Measurements 2021

ORPC staff collected site characterization data on Millinocket Stream, downstream of the hydropower station at the former Great Northern Paper Mill site in Millinocket, Maine. Bathymetry was collected with a SonTek M9 using HydroSurveyor software package and velocity was collected using the SonTek M9 RiverSurveyor software package. Bathymetry only was collected on 9/30/21. Bathymetry and velocity were collected on 10/21/21.

16 TIDAL AND WAVE POWER↗

Performance Audit Report: Automated Meteorological Monitoring Stations, Lawrence Livermore National Laboratory

The Waste and Air Quality Offices Group at the Lawrence Livermore National Laboratory operates two main meteorological monitoring sites near Livermore, California. The primary met tower (Site 200) is located in the northwest corner of the lab and consists of a fifty-two (52) meter tower with vertical wind speed sensors, horizontal wind speed and direction sensors and air temperature sensors at fifty-two (52) meters, twenty-three (23) meters and ten (10) meters. In addition, there is a temperature and humidity probe at ten (10) meters. At two (2) meters there are upward and downward facing solar and infrared radiation sensors, an air temperature sensor, barometric pressure sensor and a temperature and relative humidity probe. At ground level there is a tipping bucket rain gauge located to the southwest of the tower. The datalogger, communication peripherals and the barometric pressure sensor are housed in a small building near the tower. The Site 300 met site is located approximately 10 miles east of Livermore within the boundary of the LLNL blast test site. This site also consists of a 52-meter tower which is configured the same as the 52-meter tower at Site 200. There is also a building at this site that houses the datalogger, communication peripherals and the barometric pressure sensor. At both Site 200 and Site 300, data are collected by Ethernet with telephone modem collection as a backup. The data collection interval for both sites is fifteen (15) minutes via workstations running Loggernet software located at the main lab facility. The audits of the Lawrence Livermore National Laboratory’s two automated meteorological stations located near Livermore, California were performed on October 24 & 25, 2023. These audits were performed under the guidelines of the Quality Assurance Handbook for Air Pollution Measurement Systems, Volume IV, Version 2 and the On-Site Meteorological Program Guidance for Regulatory Modeling Applications, U.S. EPA.

54 ENVIRONMENTAL SCIENCES↗

RHOD Site - Surface Meteorological Station / Processed Data

This dataset contains raw data from the WFIP3 RHOD site supplementary meteorological sensors: T/RH and barometer; 1-sec average. The supplementary meteorological suite was added to PNNL Surface Flux Station to provide independent measurements of air temperature, relative humidity, and atmospheric pressure.

17 WIND ENERGY↗

Situational Lightning Climatologies for Central Florida: Phase V

The AMU added three years of data to the POR from the previous work resulting in a 22-year POR for the warm season months from 1989-2010. In addition to the flow regime stratification, moisture and stability stratifications were added to separate more active from less active lighting days within the same flow regime. The parameters used for moisture and stability stratifications were PWAT and TI which were derived from sounding data at four Florida radiosonde sites. Lightning data consisted of NLDN CG lightning flashes within 30 NM of each airfield. The AMU increased the number of airfields from nine to thirty-six which included the SLF, CCAFS, PAFB and thirty-three airfields across Florida. The NWS MLB requested the AMU calculate lightning climatologies for additional airfields that they support as a backup to NWS TBW which was then expanded to include airfields supported by NWS JAX and NWS MFL. The updated climatologies of lightning probabilities are based on revised synoptic-scale flow regimes over the Florida peninsula (Lambert 2007) for 5-, 10-, 20- and 30-NM radius range rings around the thirty-six airfields in 1-, 3- and 6-hour increments. The lightning, flow regime, moisture and stability data were processed in S-PLUS software using scripts written by the AMU to automate much of the data processing. The S-PLUS data files were exported to Excel to allow the files to be combined in Excel Workbooks for easier data handling and to create the tables and charts for the Gill. The AMU revised the Gill developed in the previous phase (Bauman 2009) with the new data and provided users with an updated HTML tool to display and manipulate the data and corresponding charts. The tool can be used with most web browsers and is computer operating system independent. The AMU delivered two Gills - one with just the PWAT stratification and one with both the PWAT and TI stratifications due to insufficient data in some of the PWATITI stratification combinations. This will allow the forecasters to choose a moisture-only or moisture/stability stratification depending on the flow regime and available data.

Bauman, William H., III↗

BOREAS TF-10 NSA-YJP Tower Flux, Meteorological, and Porometry Data

The BOREAS TF-10 team collected tower flux and meteorological data at two sites, a fen and a young jack pine forest, near Thompson, Manitoba, Canada, as part of BOREAS. A preliminary data set was assembled in August 1993 while field testing the instrument packages, and at both sites data were collected from 15-Aug to 31-Aug. The main experimental period was in 1994, when continuous data were collected from the young jack pine site from 23-May to 20-Sep. Upon examination of the 1994 data set, it became clear that the behavior of the heat, water, and carbon dioxide fluxes throughout the whole growing season was an important scientific question, and that the 1994 data record was not sufficiently long to capture the character of the seasonal behavior of the fluxes. Thus, the young jack pine site was operated from 08-May to 07-Nov in 1996 in order to collect data from spring melt to autumn freeze-up. All variables are presented as 30-minute averages. Supporting data were also collected to describe the surface#s state and to provide the information, in association with the flux data, to build SVAT models. For the young jack pine site, these supporting data included stomatal conductance measurements. The data are stored in tabular ASCII files.

McCaughey, J. Harry↗

Continuous Remote Measurements of Atmospheric O2 Concentrations in Relation to Interannual Variations in Biological Production and Carbon Cycling in the Oceans

We successfully initiated a program to obtain continuous time series of atmospheric O2 concentrations at a semi-remote coastal site, in Trinidad, California. The installation, which was completed in September 1999, consists of a commercially-available O2 and CO2 analyzers interfaced to a custom gas handling system and housed in a dedicated building at the Trinidad site. Ultimately, the data from this site are expected to provide constraints, complementing satellite data, on variations in ocean productivity and carbon exchange on annual and interannual time scales, in the context of human-induced changes in global climate and other perturbations. The existing time-series, of limited duration, have been used in support of studies of the O2/CO2 exchange from a wild fire (which fortuitously occurred nearby in October 1999) and to quantify air-sea N2O and O2 exchanges related to coastal upwelling events. More generally, the project demonstrates the feasibility of obtaining semi-continuous O2 time series at moderate cost from strategic locations globally.

Keeling, Ralph F.↗