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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 325 records · Page 18

Evaluating Protection System Performance for a Real-World Weak Grid Area With High Inverter-Based Resources

This paper evaluates an existing protection scheme implemented in a real-world weak grid area with a high penetration of inverter-based resources (IBRs). The study aims to assess the reliability and adequacy of protection schemes originally designed for traditional synchronous machine systems and determine whether they can continue to operate reliably in systems with high levels of IBRs. Hardware relays are tested using a controller-hardware-in-the-loop setup. PSCAD electromagnetic transient simulation with an IBR original equipment manufacturer black-box model is used to perform fault studies and generate COMTRADE data, which are replayed by a realtime digital simulator (RTDS) to feed input to the hardware relays. Three scenarios are analyzed: normal operation, an N-1 contingency, and an IBR-only scenario. The evaluation results reveal the following: 1) the protection scheme remains reliable under normal conditions and N-1 contingencies and 2) in IBRonly scenarios, differential protection (87L) continues to operate reliably, whereas local protection elements, such as distance and directional elements, fail because of the lack of regulated negative sequence current contributed by IBRs. These findings provide utilities with valuable insights for improving their protection systems in high-IBRs.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Synthetic overlapping genes stabilize genetic systems

Overlapping genes—wherein two different proteins are translated from alternative reading frames of the same DNA sequence—provide a means to stabilize an engineered gene by directly linking its evolutionary fate with that of an overlapping gene. However, creating overlapping gene pairs is challenging, as it requires redesigning both protein products to accommodate overlap constraints. Here, we present a new “overlapping, alternate-frame insertion” (OAFI) method for creating synthetic overlapping genes by inserting an “inner” gene, encoded in an alternate frame, into a flexible region of an “outer” gene. Using OAFI, we create new overlapping gene pairs of genetic reporters and bacterial toxins within an antibiotic resistance gene. We show that both the inner and outer genes retain function despite redesign, with translation of the inner gene influenced by its overlap position in the outer gene. Importantly, we show that, despite these inner gene sequences not contributing to outer gene function, selection for the outer gene alters the permitted inactivating mutations in the inner gene, and that overlapping toxins can restrict horizontal gene transfer of the antibiotic resistance gene. Overall, OAFI offers a versatile tool for synthetic biology, expanding the applications of overlapping genes in gene stabilization and biocontainment.

Biological and medical sciences↗

Human Exploration of Earth's Neighborhood and Mars

The presentation examines Mars landing scenarios, Earth to Moon transfers comparing direct vs. via libration points. Lunar transfer/orbit diagrams, comparison of opposition class and conjunction class missions, and artificial gravity for human exploration missions. Slides related to Mars landing scenarios include: mission scenario; direct entry landing locations; 2005 opportunity - Type 1; Earth-mars superior conjunction; Lander latitude accessibility; Low thrust - Earth return phase; SEP Earth return sequence; Missions - 200, 2007, 2009; and Mission map. Slides related to Earth to Moon transfers (direct vs. via libration points (L1, L2) include libration point missions, expeditionary vs. evolutionary, Earth-Moon L1 - gateway for lunar surface operations, and Lunar mission libration point vs. lunar orbit rendezvous (LOR). Slides related to lunar transfer/orbit diagrams include: trans-lunar trajectory from ISS parking orbit, trans-Earth trajectories, parking orbit considerations, and landing latitude restrictions. Slides related to comparison of opposition class (short-stay) and conjunction class (long-stay) missions for human exploration of Mars include: Mars mission planning, Earth-Mars orbital characteristics, delta-V variations, and Mars mission duration comparison. Slides related to artificial gravity for human exploration missions include: current configuration, NEP thruster location trades, minor axis rotation, and example load paths.

Condon, Gerald↗

The Mars Pathfinder Mission and Science Results

Mars Pathfinder, the first low-cost, quick Discovery class mission to be completed, successfully landed on the surface of Mars on July 4, 1997, deployed and navigated a small rover, and collected data from 3 science instruments and 10 technology experiments. The mission operated on Mars for 3 months and returned 2.3 Gbits of new data, including over 16,500 lander and 550 rover images, 16 chemical analyses of rocks and soil, and 8.5 million individual temperature, pressure and wind measurements. The rover traversed 100 m clockwise around the lander, exploring about 200 square meters of the surface. The mission captured the imagination of the public, and garnered front page headlines during the first week. A total of about 566 million internet "hits" were registered during the first month of the mission, with 47 million "hits" on July 8th alone, making the Pathfinder landing by far the largest internet event in history at the time. Pathfinder was the first mission to deploy a rover on Mars. It carried a chemical analysis instrument, to characterize the rocks and soils in a landing area over hundreds of square meters on Mars, which provided a calibration point or "ground truth" for orbital remote sensing observations. The combination of spectral imaging of the landing area by the lander camera, chemical analyses aboard the rover, and close-up imaging of colors, textures and fabrics with the rover cameras offered the potential of identifying rocks (petrology and mineralogy). With this payload, a landing site in Ares Vallis was selected because it appeared acceptably safe and offered the prospect of analyzing a variety of rock types expected to be deposited by catastrophic floods, which enabled addressing first-order scientific questions such as differentiation of the crust, the development of weathering products, and the nature of the early Martian environment and its subsequent evolution. The 3 instruments and rover allowed seven areas of scientific investigation: the geology and geomorphology of the surface, mineralogy and geochemistry of rocks and soils, physical properties of surface materials, magnetic properties of airborne dust, atmospheric science including aerosols, and rotational and orbital dynamics of Mars. Scientists were assembled into 7 Science Operations Groups that were responsible for requesting measurements by the 3 instruments, rover and engineering subsystems for carrying out their scientific investigations and for analyzing the data and reporting on their findings. The spacecraft was launched on December 4, 1996 and had a 7 month cruise to Mars, with four trajectory correction maneuvers. The vehicle entered the atmosphere directly following cruise stage separation. Parachute deployment, heatshield and lander separation, radar ground acquisition, airbag inflation and rocket ignition all occurred before landing at 2:58 AM true local solar time (9:56:55 AM PDT). The lander bounced at least 15 times up to 12 in high without airbag rupture, demonstrating the robustness of this landing system. Reconstruction of the final landing sequence indicates that the parachute/backshel1/1ander was tilted due to a northwest directed wind and wind shear, which resulted in the lander bouncing about I km to the northwest and initially downhill about 20 m from where the solid rockets fired. Two anomalously bright spots located in the lander scene are likely the heatshield, which continued in a ballistic trajectory about 2 km downrange (west southwest), and the backshell/parachute, which stayed nearer to where the rockets fired. Unconnected disturbed soil patches in the scene indicate that the final few bounces of the lander were from the east-southeast and were followed by a gentle roll to the west before coming to rest on the base petal. The location of the lander away from where the solid rockets fired and considerations of the exhaust products used to inflate the airbags and their fate, indicate that the Pathfinder landing system is one of the cleanest designed leaving the local area essentially contaminant free. The radio signal from the low-=gain antenna was received at 11:34 AM PDT indicating a successful landing.

Golombek, M. P.↗

Monitoring Airspace Complexity and Determining Contributing Factors

The national airspace has evolved over many years to accommodate increased traffic demand [1] while simultaneously maintaining one of the safest forms of transportation [2], [3]. One of the reasons for this success is the ability of the system and the operators to adapt and accommodate to situations that routinely disrupt optimal operations. These situations may include: adverse weather, delays, early arrivals, equipment outages, and other factors that are outside the operators ability to control. These factors can lead to states where automation is unable to properly handle these issues and therefore air traffic controllers and pilots have to intervene, ultimately increasing communication between operators resulting in higher workload. As controller workload increases to handle sub-optimal operating conditions this can be viewed as an increase in complexity. The reasoning for this is because humans are now required to make tactical decisions in response to external factors, resulting in a departure from the strategic plan where operations would be more efficiently managed. Human operators control airspace complexity under rigid regulations that are constantly changing. The airspace is divided into sectors and the number of aircraft assigned to each controller is limited for safe handling. There has been past work that devised airspace complexity metrics in commercial aviation and related these metrics to controller workload (e.g., [4],[5]). The upper bounds on the system load are pre-determined. Such bounds on complexity make for a safe system, but the system cannot scale and adapt to autonomous, dense, and heterogeneous traffic, including the many types of Unmanned Aerial Vehicles (UAVs) envisioned to be added to the operations. We hypothesize that, as traffic density and heterogeneity grow, and other key metrics change, there will be phase transitions at which the way traffic should be managed changes significantly [6]. We offer a method for in-time detection of contributing factors that lead to phase transitions, characterized by increased complexity. To the best of our knowledge, there is no tool similar to our proposed effort that identifies such contributing factors or precursor patterns. To define the scope we are proposing to measure complexity from the viewpoint of the Terminal Radar Approach Control Facilities (TRACON) controller’s perspective. In particular we are analyzing arrivals into KSFO. With safety as the top concern for airspace operators, it is important to recognize that as density and heterogeneity grow, the focus of the system will change. Times of the day when the airspace has low density and heterogeneity, the flights will follow more efficient paths where the aircraft move on established routes that are more or less directly to the destination. However, when density and heterogeneity increases, the system will begin changing focus to avoiding conflicts and collisions and route the flights in a more flexible way. Higher flexibility requires more communication and coordination between controllers and pilots which the current automation is unable to handle. This paper proposes a novel approach that monitors airspace complexity at multiple scales, uses a Machine Learning-based tool that predicts when operations will transition to a regime of greater complexity, and identifies actions that can reduce the complexity while still maintaining efficient and safe operations. We demonstrate our proposed approach using data from multiple complementary sources. This includes, but is not limited to: historical aircraft surveillance data from NASA’s Sherlock Data Warehouse [7], METAR weather data, and airport configuration data from Aviation System Performance Metrics (ASPM). The surveillance data flight paths are sampled at a variable sample rate — increasing as the aircraft approaches the airport. This is due to how Sherlock manages flight track stitching between different radar facilities which have different sampling rates. The weather and performance data are logged at defined intervals throughout the day at a courser refresh rate. In addition to the logged data and metrics, we leverage pre-defined Standard Terminal Arrival Routes (STARs) procedures to characterize the path of each flight. Each flight files for one of these routes in the flight plan well before entering the terminal airspace, and approximately follows the route until it leaves the STAR, typically on the final fix of a runway transition. However, most flights do not always fly the full STAR procedure to completion [8], but the majority do adhere to the fixes within the common route of the procedure. Our approach leverages fixes in the common route of each of the STARs to build a reference path to the airport. This allows us to characterize the flight paths in what we are defining as the “maneuvering area” (the airspace between the STAR and before the flight is lined up on the runway’s final approach) to determine how off nominal the flights are to calculate its complexity score. Determining airspace complexity is a concept that does not have a concrete answer. In designing this metric, we consider what increases the workload for the air traffic controllers. Consequently more specialized vectoring maneuvers results in higher workload. Accordingly, we start with a theory: each flight has a direct path it takes from the STAR’s common route to the final approach’s outer marker fix for the flight’s landing runway. It is important to note that the direct path is only used as a reference. If the majority of the flights have a large consistent offset as compared to other routes it does not necessarily mean that those flights have higher complexity. We are merely building a distribution based on this direct path for that particular STAR and runway pair to determine the normal mode of operations for that route. Flights that are in the upper tail of these distributions will result in higher complexity scores and flights that fly in the median will represent the normal mode of operations and therefore will have lower complexity scores. Since flights following each STAR route take different paths to the airport, we have a different distribution for each STAR route and therefore can model these distributions to compute a complexity score from their respective normalized distributions. To evaluate the effectiveness of our proposed airspace complexity metric we will compare against an established approach based on trajectory clustering [9]. This unsupervised learning technique consists of the following steps: (1) identify the general maneuvering areas (waypoints) by performing $\kappa$-means or DBSCAN clustering on locations where aircraft frequently turn based on the surveillance radar track data, (2) map flight trajectories onto sequences of waypoints, and (3) cluster the sequences based on their common subsequences. From a high-level perspective, this baseline model learns nominal operations in the airspace through the sequence of waypoints that are representative of where aircraft change direction and defines deviations from the nominal operations as “complex.” Therefore, more deviations from the nominal operations correspond to higher complexity values. For our validation, we re-implemented this technique and tune model hyper-parameters to correctly detect waypoints for the arrival traffic into the San Francisco bay area. We will compute the complexity measure over a one-year period using our proposed technique as well as the baseline. Our validation will be based on each technique’s ability to detect a set of undesirable outcomes (e.g., go-arounds, holding patterns, average time in the airspace, etc.). Since our current complexity metric is derived from the offset from the direct reference path, it’s important to understand what causes these offsets. In many of the flights with high offset distance, flights performing holding patterns and S turns can be observed. These maneuvering tactics are utilized to add distance between the aircraft and the destination runway to prevent multiple flights from having conflicting arrival times. In order to predict a rise in complexity (or the precursor to complexity), it’s necessary to be able to identify these potential conflicts (which in turn, result in higher offsets). To do this, we define a “representative flight” for each STAR route and runway pair. This flight is approximately the path the flight would take if there was a clear path with no other flights in the airspace — including the time remaining to the airport. We first identify the flights for a given STAR runway pair using the offset to the reference path distributions that fall between the 44-55 percentiles. This yields the flights that conform to the most normal mode of operation. Each of these flights is partitioned based on the percent complete from the entry point into the maneuvering areas from 0\% – 100\% complete. Then for each percent “bin”, we take the median value of the flight’s latitude/longitude coordinates, airspeed, and (non causal) time remaining to the airport to construct a lookup table for each percent complete bin on a given route. As a flight enters the maneuvering area, we can find the estimated arrival time of a flight to the airport by finding the closest point to the representative path’s percent complete bin (relative to the flight’s current position at any snapshot in the airspace) and therefore retrieve the corresponding remaining time left on the “representative path”. We assume that the flight will follow the representative path to completion when deriving these estimates. We can then compare these estimated arrival times against other flights for the same snapshot in time to identify potential conflicts. If more flights are estimated to arrive within a tolerance window than there are runways available, then we have a potential conflict. We can use this derived measure along with other factors expected to add disruption to the operation such as weather and runway configuration changes as an input to machine learning tools to detect precursors that increases in our complexity measure. This novel method will assist in uncovering insights into the contributing factors that lead to increased complexity that may allow for in-time responses to avoid reaching a high complexity state in the airspace.

complexity↗

Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing [Book Chapter]

Embryonic morphogenesis is strictly dependent on tight spatiotemporal control of developmental gene expression, which is typically achieved through the concerted activity of multiple enhancers driving cell type-specific expression of a target gene. Mammalian genomes are organized in topologically associated domains, providing a preferred environment and framework for interactions between transcriptional enhancers and gene promoters. While epigenomic profiling and three-dimensional chromatin conformation capture have significantly increased the accuracy of identifying enhancers, assessment of subregional enhancer activities via transgenic reporter assays in mice remains the gold standard for assigning enhancer activity in vivo. Once this activity is defined, the ideal method to explore the functional necessity of a transcriptional enhancer and its contribution to target gene dosage and morphological or physiological processes is deletion of the enhancer sequence from the mouse genome. Here we present detailed protocols for efficient introduction of enhancer-reporter transgenes and CRISPR-mediated genomic deletions into the mouse genome, including a step-by-step guide for pronuclear microinjection of fertilized mouse eggs. We provide instructions for the assembly and genomic integration of enhancer-reporter cassettes that have been used for validation of thousands of putative enhancer sequences accessible through the VISTA enhancer browser, including a recently published method for robust site-directed transgenesis at the H11 safe-harbor locus. Together, these methods enable rapid and large-scale assessment of enhancer activities and sequence variants in mice, which is essential to understand mammalian genome function and genetic diseases.

cis-regulatory elements↗

Nulling Data Reduction and On-Sky Performance of the Large Binocular Telescope Interferometer

The Large Binocular Telescope Interferometer (LBTI) is a versatile instrument designed for high angular resolution and high-contrast infrared imaging (1.5-13 micrometers). In this paper, we focus on the mid-infrared (8-13 micrometers) nulling mode and present its theory of operation, data reduction, and on-sky performance as of the end of the commissioning phase in 2015 March. With an interferometric baseline of 14.4 m, the LBTI nuller is specifically tuned to resolve the habitable zone of nearby main-sequence stars, where warm exozodiacal dust emission peaks. Measuring the exozodi luminosity function of nearby main-sequence stars is a key milestone to prepare for future exo-Earth direct imaging instruments. Thanks to recent progress in wavefront control and phase stabilization, as well as in data reduction techniques, the LBTI demonstrated in 2015 February a calibrated null accuracy of 0.05% over a 3 hr long observing sequence on the bright nearby A3V star Beta Leo. This is equivalent to an exozodiacal disk density of 15-30 zodi for a Sun-like star located at 10 pc, depending on the adopted disk model. This result sets a new record for high-contrast mid-infrared interferometric imaging and opens a new window on the study of planetary systems.

circumstellar matter aEuro" techniques: interferom↗

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea , and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus . This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

59 BASIC BIOLOGICAL SCIENCES↗

Mars Interoperability 2008-2015: Options for Relay Orbiter Support to Mars Bound Assets

The current relay orbiter infrastructure at Mars, in support of the user assets presently at Mars and those scheduled for the 2008 to 2015 time frame, only have a need to store-and-forward the returned data collected by an asset to Earth as a single non-prioritized data file. In the forward direction, the relay orbiters are only required to relay the forward link data, i.e., command sequences, software and configuration information assembled on the ground, to the Asset. There are currently no requirements for status/control messages or files to be sent in the return direction from an Asset to an application located on the Relay, nor are there requirements in the forward direction to send status/control messages or files originating on a Relay to an Asset. In addition there are currently no networking requirements at Mars where data originally sent by an Asset is to be delivered to another user asset. However, we foresee the day when standard services for 1) on-board file prioritization of user asset data by a Relay, 2) control/status message transfer between assets and a Relay, and 3) networking between assets i.e., Asset to Asset message/file transfer via a Relay will be required. Each of these services will require the Relay to be capable of understanding the data type and routing needs of the user asset data and be capable of processing it for these purposes. This paper will focus on the innovative enhancements required to the existing communications infrastructure at Mars to enable these future services.

File Transfer↗

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Prior studies have indicated that the transcription factor Creb5 is expressed in the joint interzone, which contains the progenitors for all synovial joint tissues in both mouse and human embryos. In the absence of Creb5 function, most synovial joint interzones fail to form and the cartilage templates in the long bones remain fused. This earlier work did not clarify whether Creb5 initiates a cascade of signaling molecules, such as growth and differentiation factor 5 (Gdf5) and Wnt-family members, that in turn induce the formation of the joint interzone, or instead directly activates the expression of joint interzone markers. In the present study, an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-occupancy in joint progenitors revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of Gdf5 and Sfrp2, each of whose expression in the joint interzone is Creb5-dependent. Functional enhancer analysis indicated that Creb5 binding sites in either the two Creb5 promoters, or in Gdf5 and Sfrp2 regulatory elements are necessary for these sequences to drive transgene expression in the developing synovial joints. While Creb5 directly drives Gdf5 and Sfrp2 expression in the inner joint interzone, Creb5 activates Barx1 expression specifically in the outer joint interzone. Our findings indicate that Creb5 initiates a regulatory network that both promotes the formation of synovial joints, and subsequently activates distinct transcriptional targets in the inner versus the outer regions of the joint interzone, thus regionalizing gene expression in the developing joint.

Zhang, Cheng-Hai↗

Estimation of Airline Benefits from Avionics Upgrade under Preferential Merge Re-sequence Scheduling

Modernization of the airline fleet avionics is essential to fully enable future technologies and procedures for increasing national airspace system capacity. However in the current national airspace system, system-wide benefits gained by avionics upgrade are not fully directed to aircraft/airlines that upgrade, resulting in slow fleet modernization rate. Preferential merge re-sequence scheduling is a best-equipped-best-served concept designed to incentivize avionics upgrade among airlines by allowing aircraft with new avionics (high-equipped) to be re-sequenced ahead of aircraft without the upgrades (low-equipped) at enroute merge waypoints. The goal of this study is to investigate the potential benefits gained or lost by airlines under a high or low-equipped fleet scenario if preferential merge resequence scheduling is implemented.

air traffic management↗

Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes

Abstract Poly(UG) or ‘pUG’ dinucleotide repeats are highly abundant sequences in eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3′ ends to direct gene silencing within Mutator foci, a germ granule condensate. Here, we show that pUG RNAs efficiently self-assemble into gel condensates through quadruplex (G4) interactions. Short pUG sequences form right-handed intermolecular G4s (pUG G4s), while longer pUGs form left-handed intramolecular G4s (pUG folds). We determined a 1.05 Å crystal structure of an intermolecular pUG G4, which reveals an eight stranded G4 dimer involving 48 nucleotides, 7 different G and U quartet conformations, 7 coordinated potassium ions, 8 sodium ions and a buried water molecule. A comparison of the intermolecular pUG G4 and intramolecular pUG fold structures provides insights into the molecular basis for G4 handedness and illustrates how a simple dinucleotide repeat sequence can form complex structures with diverse topologies.

Biochemistry & Molecular Biology↗

CROCUS Sodar Measurements of Lower Atmospheric Wind Profiles at Argonne Testbed for Multiscale Observational Science (ATMOS) Site

The Scintec MFAS Sodar (Multiple-Frequency Acoustic Sounder) is an autonomous, ground-based acoustic remote sensing system designed to measure vertical profiles of horizontal wind speed, wind direction, and vertical velocity in the lower atmosphere. The instrument transmits sequences of acoustic pulses and detects the Doppler-shifted sound waves backscattered by small-scale temperature and velocity fluctuations caused by atmospheric turbulence. From these Doppler shifts, the system derives three-dimensional wind vectors by combining radial velocities from multiple beam orientations.The MFAS Sodar operates with a first usable range gate beginning at approximately 30 m above ground level and a configurable vertical resolution of 10 m. Under favorable acoustic conditions, the system provides wind profiles extending up to 600 m above ground level. Measurements are processed into 15-minute averaged profiles containing wind speed, direction, vertical velocity, and diagnostic quantities such as signal-to-noise ratio and echo strength.This dataset was collected at the Argonne Testbed for Multiscale Observational Science (ATMOS) facility in Lemont, Illinois, as part of DOE's CROCUS Urban Integrated Field Laboratory (UIFL) initiative. The purpose of these observations is to characterize the vertical wind structure and boundary-layer evolution across the urban–suburban gradient of the greater Chicago region. In particular, these data are intended to improve understanding of how local meteorology, such as lake-breeze penetration, nocturnal jets, and daytime mixing, varies between the densely built urban core and the suburban periphery. The MFAS observations provide critical context for evaluating high-resolution model simulations and for integrating with complementary lidar, radar, and in-situ meteorological measurements within the broader CROCUS UIFL network.All data are archived in NetCDF (Network Common Data Form) format and include wind and diagnostic parameters. The files can be accessed and analyzed using standard software that supports NetCDF, such as Python (e.g., xarray, netCDF4), MATLAB, R (e.g., ncdf4, raster), or Panoply (NASA’s NetCDF visualization application).

54 ENVIRONMENTAL SCIENCES↗

Machine learning predicts new anti-CRISPR proteins

The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.

59 BASIC BIOLOGICAL SCIENCES↗

New Approaches for Direct Current (DC) Balanced SpaceWire

Direct Current (DC) line balanced SpaceWire is attractive for a number of reasons. Firstly, a DC line balanced interface provides the ability to isolate the physical layer with either a transformer or capacitor to achieve higher common mode voltage rejection and or the complete galvanic isolation in the case of a transformer. And secondly, it provides the possibility to reduce the number of conductors and transceivers in the classical SpaceWire interface by half by eliminating the Strobe line. Depending on the modulator scheme the clock data recovery frequency requirements may be only twice that of the transmit clock, or even match the transmit clock: depending on the Field Programmable Gate Array (FPGA) decoder design. In this paper, several different implementation scenarios will be discussed. Two of these scenarios are backward compatible with the existing SpaceWire hardware standards except for changes at the character level. Three other scenarios, while decreasing by half the standard SpaceWire hardware components, will require changes at both the character and signal levels and work with fixed rates. Other scenarios with variable data rates will require an additional SpaceWire interface handshake initialization sequence.

Line encoding↗

DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

Significance Microorganisms have evolved transcriptional networks to prioritize utilization of available nutrient sources. For filamentous fungi, such as Neurospora crassa , this entails distinguishing between a variety of organic and inorganic nitrogen sources. Here, we transcriptionally profiled the response of N. crassa to a variety of nitrogen sources and used DNA affinity purification sequencing to characterize the role of regulatory genes and their direct downstream targets. We identified a transcription factor responsible for regulating genes involved in amino acid and mannose metabolism. By comparing the genes regulated by transcription factors that regulate specific nitrogen utilization pathways and transcription factors that regulate utilization of all nitrogen sources that require metabolic processing before utilization, we revealed aspects of the nitrogen regulatory network.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput functional variant screens via in vivo production of single-stranded DNA

Significance We report a methodology for the pooled construction of mutants bearing precise genomic sequence variations and multiplex phenotypic characterization of these mutants using next-generation sequencing (NGS). Unlike existing techniques depending on CRISPR-Cas–directed genomic breaks for genome editing, this strategy instead uses single-stranded DNA produced by a retron element for recombineering. This enables libraries of millions of elements to be constructed and offers relaxed design constraints which permit natural DNA or random variation to be used as inputs.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗