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The content, format, and storage of data bases developed for the Foreign Commodity Production Forecasting project and used to produce normal crop calendars are described. In addition, the data bases may be used for agricultural meteorology, modeling of stage sequences and planting dates, and as indicators of possible drought and famine.
The objectives of NASA's land mobile satellite experiments are discussed. The assigned multiple access protocol combined with a retransmission scheme is to provide reliable transmission of data messages from mobiles to base stations (BSs). The sequences for communication between mobiles and BSs, mobiles and the network management center (NMC), and BSs and NMC are examined, and an example of mobiles/BSs communication is provided. The performance of the retransmission protocol and data message reservation and message channels delays are analyzed. A bit error rate of 0.001 is observed for satellite channels in a mobile environment and the message error probability is between 0-0.1.
The Jet Propulsion Laboratory (JPL) Aircraft Synthetic Aperture Radar (AIRSAR) was deployed to Scotland to obtain radar imagery of ship wakes generated in Loch Linnhe. These observations were part of a joint US and UK experiment to study the internal waves generated by ships under partially controlled conditions. The AIRSAR was mounted on the NASA-Ames DC-8 aircraft. The data acquisition sequence consisted of 8 flights, each about 6 hours in duration, wherein 24 observations of the instrumented site were made on each flight. This Browse File provides the experimenters with a reference of the real time imagery (approximately 100 images) obtained on the 38-deg track. These radar images are copies of those obtained at the time of observation and show the general geometry of the ship wake features. To speed up processing during this flight, the images were all processed around zero Doppler, and thus azimuth ambiguities often occur when the drift angel (yaw) exceeded a few degrees. However, even with the various shortcomings, it is believed that the experimenter will find the Browse File useful in establishing a basis for further investigations.
During replication and transcription, the SV40 control region is subjected to significant levels of DNA unwinding. There are three, alternating purine-pyrimidine tracts within this region that can adopt the Z-DNA conformation in response to negative superhelix density: a single copy of ACACACAT and two copies of ATGCATGC. Since the control region is essential for both efficient transcription and replication, B-DNA to Z-DNA transitions in these vital sequence tracts may have significant biological consequences. We have synthesized DNA minicircles to detect B-DNA to Z-DNA transitions in the SV40 enhancer, and to determine the negative superhelix density required to stabilize the Z-DNA. A variety of DNA sequences, including the entire SV40 enhancer and the two segments of the enhancer with alternating purine-pyrimidine tracts, were incorporated into topologically relaxed minicircles. Negative supercoils were generated, and the resulting topoisomers were resolved by electrophoresis. Using an anti-Z-DNA Fab and an electrophoretic mobility shift assay, Z-DNA was detected in the enhancer-containing minicircles at a superhelix density of -0.05. Fab saturation binding experiments demonstrated that three, independent Z-DNA tracts were stabilized in the supercoiled minicircles. Two other minicircles, each with one of the two alternating purine-pyrimidine tracts, also contained single Z-DNA sites. These results confirm the identities of the Z-DNA-forming sequences within the control region. Moreover, the B-DNA to Z-DNA transitions were detected at superhelix densities observed during normal replication and transcription processes in the SV40 life cycle.
Plants and microbes can be used for biological support of crewed space missions. The radiation and microgravity environment of spaceflight is expected to increase genetic mutation of all organisms. It is essential to understand how spaceflight impacts mutation rates in photosynthetic organisms to enable appropriate countermeasures and ensure productivity during long duration and deep space missions. The Space Algae flight experiments to the International Space Station (ISS) are studying the genomic stability of microalgae that could potentially be used in biological life support systems. Space Algae-1 grew ultraviolet light mutagenized Chlamydomonas reinhardtii in the VEGGIE plant growth chamber for approximately 40 mitotic generations over one month on the ISS. Whole genome sequencing from pooled cell samples every 10 generations revealed that spaceflight cultures had an ~50% increase in DNA polymorphisms relative to ground controls. These mutations had a novel base substitution signature and suggested a risk that microalgae may be unstable for long-term production in space. Space Algae-2 is focusing on the edible cyanobacterium Arthrospira platensis, commonly known as Spirulina. This experiment seeks to grow serial cultures to allow the organism to evolve in long-term spaceflight. Biological responses of the cells to spaceflight will be assessed with multi-omics analyses to determine mutation load, gene/protein expression, metabolic/nutritional composition, and cell morphology.
Plants and microbes can be used for biological support of crewed space missions. The radiation and microgravity environment of spaceflight is expected to increase genetic mutation of all organisms. It is essential to understand how spaceflight impacts mutation rates in photosynthetic organisms to enable appropriate countermeasures and ensure productivity during long duration and deep space missions. The Space Algae flight experiments to the International Space Station (ISS) are studying the genomic stability of microalgae that could potentially be used in biological life support systems. Space Algae-1 grew ultraviolet light mutagenized Chlamydomonas reinhardtii in the VEGGIE plant growth chamber for approximately 40 mitotic generations over one month on the ISS. Whole genome sequencing from pooled cell samples every 10 generations revealed that spaceflight cultures had an ~50% increase in DNA polymorphisms relative to ground controls. These mutations had a novel base substitution signature and suggested a risk that microalgae may be unstable for long-term production in space. Space Algae-2 is focusing on the edible cyanobacterium Arthrospira platensis, commonly known as Spirulina. This experiment seeks to grow serial cultures to allow the organism to evolve in long-term spaceflight. Biological responses of the cells to spaceflight will be assessed with multi-omics analyses to determine mutation load, gene/protein expression, metabolic/nutritional composition, and cell morphology.
The Jet Propulsion Laboratory's (JPL) Telerobot Testbed is an integrated robotic testbed used to develop, implement, and evaluate the performance of advanced concepts in autonomous, tele-autonomous, and tele-operated control of robotic manipulators. Using the Telerobot Testbed, researchers demonstrated several of the capabilities and technological advances in the control and integration of robotic systems which have been under development at JPL for several years. In particular, the Telerobot Testbed was recently employed to perform a near completely automated, end-to-end, satellite grapple and repair sequence. The task of integrating existing as well as new concepts in robot control into the Telerobot Testbed has been a very difficult and timely one. Now that researchers have completed the first major milestone (i.e., the end-to-end demonstration) it is important to reflect back upon experiences and to collect the knowledge that has been gained so that improvements can be made to the existing system. It is also believed that the experiences are of value to the others in the robotics community. Therefore, the primary objective here will be to use the Telerobot Testbed as a case study to identify real problems and technological gaps which exist in the areas of robotics and in particular systems integration. Such problems have surely hindered the development of what could be reasonably called an intelligent robot. In addition to identifying such problems, researchers briefly discuss what approaches have been taken to resolve them or, in several cases, to circumvent them until better approaches can be developed.
Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.
Abstract Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute ( Pf Ago)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology.
Gas-filled plastic spherical shells have been imploded using the 60-beam OMEGA laser. The same laser pulse was used as in a previous experiment, which demonstrated the dynamic formation of a shell by irradiating a homogeneous plastic foam sphere. In the present experiment, the shell initially implodes, bounces, and expands; a new shell then forms and undergoes a second implosion. Analysis of x-ray self-emission-streaked images and sequences of 2D x-ray self-emission framing camera images show shell evolution that is in reasonable agreement with 1D simulations. Shell integrity and symmetry are well maintained until the formation of the new shell. The final implosion, instead, is affected by substantial asymmetries.
In 2021 JET exploited its unique capabilities to operate with T and D–T fuel with an ITER-like Be/W wall (JET-ILW). This second major JET D–T campaign (DTE2), after DTE1 in 1997, represented the culmination of a series of JET enhancements—new fusion diagnostics, new T injection capabilities, refurbishment of the T plant, increased auxiliary heating, in-vessel calibration of 14 MeV neutron yield monitors—as well as significant advances in plasma theory and modelling in the fusion community. DTE2 was complemented by a sequence of isotope physics campaigns encompassing operation in pure tritium at high T-NBI power. Carefully conducted for safe operation with tritium, the new T and D–T experiments used 1 kg of T (vs 100 g in DTE1), yielding the most fusion reactor relevant D–T plasmas to date and expanding our understanding of isotopes and D–T mixture physics. Furthermore, since the JET T and DTE2 campaigns occurred almost 25 years after the last major D–T tokamak experiment, it was also a strategic goal of the European fusion programme to refresh operational experience of a nuclear tokamak to prepare staff for ITER operation. The key physics results of the JET T and DTE2 experiments, carried out within the EUROfusion JET1 work package, are reported in this paper. Progress in the technological exploitation of JET D–T operations, development and validation of nuclear codes, neutronic tools and techniques for ITER operations carried out by EUROfusion (started within the Horizon 2020 Framework Programme and continuing under the Horizon Europe FP) are reported in (Litaudon et al Nucl. Fusion accepted), while JET experience on T and D–T operations is presented in (King et al Nucl. Fusion submitted).
The authors of this review article published in 20131 would like to correct some text and references relating to the first observations and publications on molecular layering. In Sec. II, “Early Years of Atomic Layer Processes” in the original article,1 the first two sentences of the fourth paragraph should instead say “The ALD principle, where surface reactions follow a binary sequence of self-limiting half-reactions, was reported under the name ‘molecular layering’ in the 1960s by S. I. Kol’tsov from Leningrad Technological Institute.2–6 These experiments were conducted under the scientific supervision of V. B. Aleskovskii. The ‘framework hypothesis,’ an antecedent to molecular layering, was proposed by V. B. Aleskovskii in 1952.6” In addition, again in this same section and paragraph, the last two sentences should instead say “In the 1969 article,3 the authors report that the initial reaction between TiCl4 and Si–OH tends to involve 3 Si–OH, forming one Ti–Cl, whereas after the first water step, the second TiCl4 exposure reacts with 2 Ti–OH, forming Ti–Cl2 groups. In the 1969 paper,3 a planar thin film was not produced or evaluated, although nanolayers were prepared by molecular layering at that time.6” These corrections do not affect other sections or the conclusions drawn in the article.
Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.
The purpose of this experiment was to evaluate the human host epigenetic response to Influenza A H5N1 virus and MERS-CoV viral infection from human lung adenocarcinoma cell (Calu-3) high throughput sequencing (MeDIP-Seq) sample data. Host-associated viral downloads contain one or more primary host-pathogen experimental study metadata design workbooks (supporting metadata only).
Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a field grown transgenic poplar engineered with a monolignol 4-O-methyltransferase (MOMT4). The poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR experiments. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (hsqcetgpsisp2.2) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. The NMR spectra provides structural characteristics information about lignin in field grown transgenic MOMT4 poplar. Additional meta data is embedded in the raw spectra figures.
Here we present a curated dataset of a series of 13C nuclear magnetic resonance (NMR) spectra of lignin isolated from transgenic monolignol 4-O-methyltransferase (MOMT4) engineered poplar. The transgenic poplar was collected from a 3-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h. The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR characterization. 13C experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (zgpg) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following conditions: spectra width 229 ppm, 64k data points, 1s pulse delay, and 6k scans. All the data was processed using the Bruker’s TopSpin 3.6 software. Additional meta data is embedded in the raw spectra files.
Here we present a curated dataset of a series of 1H nuclear magnetic resonance (NMR) spectra of lignin isolated from transgenic monolignol 4-O-methyltransferase (MOMT4) engineered poplar. The transgenic poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. Two replicates were collected for each transgenic poplar for the 1H NMR analysis. The poplar samples were Soxhlet-extracted with toluene/ethanol to remove the extractives and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h. The ball-milled materials were subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide and transferred into a 5 mm NMR tube. 1H NMR experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (zg) on a Prodigy platform cryoprobe. The NMR spectra were acquired with 16 ppm spectra width, 32k data points, 3s pulse delay, and 16 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. Additional meta data is embedded in the raw spectra files.
Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from stems of genetically engineered poplar through auxin signaling gene modification. The plants were grown in greenhouse with temperatures between 21 and 23 °C. Plants were harvested and the aboveground stems were cut off an approximately five-inch-long segment from the bottom end of the plant stem, debarked and air-dried for three weeks. The dried stem samples were Wiley milled (mesh size 20), Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extracted biomass was ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was freeze-dried to recover the lignin. The dry stem lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and transferred into a 5 mm tube. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 230 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 2048 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin 3.6 software. Additional meta data is embedded in the raw spectra figures.