Results for “Sequence Function Data” — Page 13

NASA NTRS1989

Assessment of autonomic response by broad-band respiration

We present a technique for introducing broad-band respiratory perturbations so that the response characteristics of the autonomic nervous system can be determined noninvasively over a wide range of physiologically relevant frequencies. A subject's respiratory bandwidth was broadened by breathing on cue to a sequence of audible tones spaced by Poisson intervals. The transfer function between the respiratory input and the resulting instantaneous heart rate was then computed using spectral analysis techniques. Results using this method are comparable to those found using traditional techniques, but are obtained with an economy of data collection.

NASA Discipline Cardiopulmonary↗

NASA NTRS2014

Ames Culture Chamber System: Enabling Model Organism Research Aboard the international Space Station

Understanding the genetic, physiological, and behavioral effects of spaceflight on living organisms and elucidating the molecular mechanisms that underlie these effects are high priorities for NASA. Certain organisms, known as model organisms, are widely studied to help researchers better understand how all biological systems function. Small model organisms such as nem-atodes, slime mold, bacteria, green algae, yeast, and moss can be used to study the effects of micro- and reduced gravity at both the cellular and systems level over multiple generations. Many model organisms have sequenced genomes and published data sets on their transcriptomes and proteomes that enable scientific investigations of the molecular mechanisms underlying the adaptations of these organisms to space flight.

culture chamber system↗

DOE OSTI2024

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

favela3/Maize.N-cycle.Function

Supplemental sequence processing and R statistical analysis for publication which compares the microbiome of 27 Zea cultivars: 12 Inbred maize genotypes, 9 hybrids, and 6 wild teosinte. The project contains amplicon data for various genes: 16S rRNA, ITS, bacterial amoA, Archeal amoA, nirS, nirK, and nosZ. In addition to functional potential assay data, and N2O flux.

Favela, Alonso↗

DOE OSTI2025

GenomeDepot v1.0

GenomeDepot is a web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, BLAST search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools.

Kazakov, Alexey [Lawrence Berkeley National Labora↗

NASA NTRS2008

VML Sequencing: Growing Capabilities over Multiple Missions

Virtual Machine Language (VML) is an award-winning advanced procedural sequencing language in use on NASA deep-space missions since 1997. Missions featuring VML include Spitzer Space Telescope, Mars Odyssey, Stardust, Genesis, Mars Reconnaissance Orbiter, Phoenix, Dawn and Juno. The latest deployed version, VML 2.0, features parameterized functions, conditionals, polymorphism, a rich set of control directives and data types, event detection and response, and on-the-fly creation of spacecraft commands. This feature set is used to simplify spacecraft operations and science gathering activities. A new 2.1 version is being prototyped for use as an executive within flight instruments, and may be deployed on Juno.

Dawn↗

NASA NTRS2018

Radio-hosted Flight / Ground Interface for Operations Standardization

The interface between a spacecraft and its ground operations segment includes the flow of commands, configuration, and sequencing elements to the spacecraft, and the flow of telemetry and data products from the spacecraft. Creating and implementing a complete definition of this interface simplifies and standardizes mission operations, allowing easy sharing of operations personnel across missions. Early spacecraft featured a simple flight / ground interface (FGI) using hardware command decoding in the radio, driven by technological limitations of the time. Modern spacecraft use command and data handling (CDH) avionics on which flight software executes, which in turn controls and configures the mission, executes subsystem and instrument instructions, and implements critical fault protection actions. Deep space missions feature advanced operations software for running sequenced activities over a period of weeks, which allows them to function with only infrequent ground contact. This approach comes at the cost of increased complexity in the FGI, requiring expensive modifications to heritage flight software and ground systems. By hosting the interface in the radio instead of the CDH avionics, modern missions can approximate the FGI design simplicity of early spacecraft, with significant advantages for vendor competition, lowered costs, standardization of operations, and reduction of implementation risk.

Lock, Patricia D.↗

DOE OSTI2026

Discovery of additional ancient genome duplications in yeasts

Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi. The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species, including the baker’s yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery. Some studies have suggested that fungal lineages that experience chromosome and genome duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales. In conclusion, our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.

convergent evolution↗

NASA NTRS1978

Design representation and consistency maintenance needs

Two major issues of data base support for large-scale engineering design are considered. The first deals with the need to support multidisciplinary, hierarchical and interactive design without imposing a priori constraints on the sequence of design decisions. An abstract logical model of the data base capable of such support is outlined. The second issue deals with the role the data base must play in maintaining integrity and consistency among the data representing the emerging design. A tentative model implementing a number of consistency management functions is presented.

Eastman, C. M.↗

NASA NTRS1987

Stochastic nature of Landsat MSS data

A multiple series generalization of the ARIMA models is used to model Landsat MSS scan lines as sequences of vectors, each vector having four elements (bands). The purpose of this work is to investigate if Landsat scan lines can be described by a general multiple series linear stochastic model and if the coefficients of such a model vary as a function of satellite system and target attributes. To accomplish this objective, an exploratory experimental design was set up incorporating six factors, four representing target attributes - location, cloud cover, row (within location), and column (within location) - and two factors representing system attributes - satellite number and detector bank. Each factor was included in the design at two levels and, with two replicates per treatment, 128 scan lines were analyzed. The results of the analysis suggests that a multiple AR(4) model is an adequate representation across all scan lines. Furthermore, the coefficients of the AR(4) model vary with location, particularly changes in physiography (slope regimes), and with percent cloud cover, but are insensitive to changes in system attributes.

Labovitz, M. L.↗

NASA NTRS1991

Evaluation of an efficient statistical transport model for turbulent droplet dispersion in dilute combusting sprays

Evaluation of an efficient statistical transport model for turbulent droplet dispersion is made for a dilute spray of methanol droplets injected into a turbulent, axisymmnetric methane-fuelled diffusion flame burning in stagnant air. In the dispersion model, a computational parcel representing a group of physical particles (droplets) is considered to have a normal probability density function (pdf) in space. The mean is determined by Lagrangian tracking through a sequence of stochastically generated turbulent eddies and the variance is evaluated from a statistical formulation based on the linearized particle equations of motion. The basic validity of this model is established through comparison with available experimental data and with theoretical predictions using a conventional stochastic direct modeling approach. The conclusion of the evaluation is that the proposed dispersion model compares favorably with experimental data and provides a valid technique for simulating turbulent combusting sprays with significant computational savings over conventional methods.

Litchford, Ron J.↗

NASA NTRS1993

A packet-based concept for spacecraft command planning

The current generation of spacecraft being developed and operated by the Applied Physics Laboratory provides users with access to a broad spectrum of scientific instruments on maneuverable platforms that can be oriented for observation of both moving and stationary targets of interest. The capability of these increasingly complex spacecraft to perform data collection operations is approaching one observation per orbit. To enable both rapid configuration and generation of complex spacecraft command sequences, as well as reusability of command sequences among data collection operations, a packet-based concept for spacecraft command planning has been developed. The configuration of the spacecraft for any operation is designed using 'packets' where a packet represents a set of commands that is reusable. The packets can be combined in varying levels of functionality, and in varying time relationships, to create an observation timeline. At the lowest packet level are primitives. Primitives relate the details of command generation for a particular spacecraft to a 'message template.' Thus the packet concept itself is reusable from one spacecraft to the next.

Barnes, Valerie B.↗

NASA NTRS1971

Experiment S051: Daytime sodium cloud

Daytime wind velocity measurements of the upper atmosphere as function of altitude were supposed to be gathered by Gemini 12 sequential photography of rocket made sodium clouds. Evaluation of the film was indicative that all 26 photographs were overexposed during the photographic sequences. The overexposures were caused by a camera shutter locked in the open position. Therefore, useful photographic data were not obtained for analysis.

Blamont, J. E.↗

NASA NTRS1993

Network command processing system overview

The Network Command Processing System (NCPS) developed for the National Aeronautics and Space Administration (NASA) Ground Network (GN) stations is a spacecraft command system utilizing a MULTIBUS I/68030 microprocessor. This system was developed and implemented at ground stations worldwide to provide a Project Operations Control Center (POCC) with command capability for support of spacecraft operations such as the LANDSAT, Shuttle, Tracking and Data Relay Satellite, and Nimbus-7. The NCPS consolidates multiple modulation schemes for supporting various manned/unmanned orbital platforms. The NCPS interacts with the POCC and a local operator to process configuration requests, generate modulated uplink sequences, and inform users of the ground command link status. This paper presents the system functional description, hardware description, and the software design.

Nam, Yon-Woo↗

NASA NTRS2024

ISS External Microorganisms: A Planetary Protection Experiment to Inform Requirements for Crewed Missions to Mars

We have developed, tested, and flown a caddy capable of collecting aseptic samples from external surfaces of the ISS (International Space Station). The sampling caddy is certified for use during US EVA (extra vehicular activity) and was launched to ISS in the summer of 2023. We are scheduled to collect samples from 6 locations outside ISS during an EVA in May of 2024. We will freeze these samples at -80°C on orbit and return them to Earth. We will then extract and sequence any DNA collected during the EVA using next generation sequencing technologies to characterize the community composition and function of each sample. Measuring the type and quantity of microbes present on the exterior of ISS will allow us to address knowledge gap 2B, “Acceptable levels of microbial/organic releases from humans and support systems” described in a 2019 COSPAR report. Collecting data about microbial release from current crewed vehicles will inform requirements for acceptable leak rates for future crewed missions to Mars. The sampling kit consists of eight commercially available, sterile, DNA free, macrofoam swabs ( 23 mm. diameter ) installed in custom aluminum end effectors. Each end effector is housed in and individual aluminum canister. Each canister contains a 0.2 μm Teflon filter to allow the interior volume to accommodate pressure changes without permitting microbial contaminants to enter the sterile interior volume. A handle repurposed from the space shuttle tile repair kit is used to remove the end effector from the sample canister, collect a sample by swabbing a surface and then replace the end effector in its canister. The canisters and end effectors were cleaned and assembled on Earth. Prior to installing the sterile swab the canisters and end effectors were sterilized in an autoclave at 134°C, 215 kPA, for 7 min.. The final assembly occurred in a sterilized class II biosafety cabinet. We will collect six samples from the 1) airlock vestibule, 2) airlock thermal cover, 3) a gap in the micrometeorite shielding near the airlock, 4) a handrail near the airlock, 5) the CDRA (Carbon Dioxide Removal Assembly) vent, and 6) the VES (Vacuum Exhaust System) vent. The remaining two swabs will be reserved as controls. One swab will be exposed during the EVA without touching any surfaces to act as a blank. The final swab will remain sealed until the entire sampling kit is returned to earth. Based on previously published results from the Russian segment, we hypothesize that there will be detectable microbes at some or all of these locations. Ground-based testing of this sampling caddy confirms that the swabs remain sterile as the canisters transition in and out of vacuum. We were able to retrieve, viable bacterial and fungal cells as well as DNA from samples collected from US space suits during vacuum chamber tests lasting as long as seven hours. Based on these results and feedback from the test subjects the sampling caddy was modified to improve ergonomics and meet US EVA safety requirements. Bayonet probes were added to the sides of the sample kit as alternate mounting points. Additional locking features were added to the end effector and the filter stack to prevent inadvertent release during use. The opening mechanism was changed from one where the end effector was rocked laterally to defeat a ball detent to a twist-to-open threaded closure for similar reasons. Demonstrating, this sampling caddy’s effectiveness during a US EVA will allow us to address knowledge gaps identified in COSPAR reports and begin to define planetary protection requirements for life support systems on crewed missions to mars. This kit could also be used to collect contamination control samples during Artemis missions to verify requirements and could be easily modified for robotic sample collection.

Planetary Protection↗

NASA NTRSDate not supplied

ISS External Microorganisms: Collecting Planetary Protection Samples During Extravehicular Activity

We have developed, tested, and flown a caddy capable of collecting aseptic samples from external surfaces of the ISS (International Space Station). The sampling caddy is certified for use during US EVA (extra vehicular activity) and was launched to ISS in the summer of 2023. We are scheduled to collect samples from 6 locations outside ISS during an EVA in May of 2024. We will freeze these samples at -80°C on orbit and return them to Earth. We will then extract and sequence any DNA collected during the EVA using next generation sequencing technologies to characterize the community composition and function of each sample. Measuring the type and quantity of microbes present on the exterior of ISS will allow us to address knowledge gap 2B, “Acceptable levels of microbial/organic releases from humans and support systems” described in a 2019 COSPAR report. Collecting data about microbial release from current crewed vehicles will inform requirements for acceptable leak rates for future crewed missions to Mars. The sampling kit consists of eight commercially available, sterile, DNA free, macrofoam swabs ( 23 mm. diameter ) installed in custom aluminum end effectors. Each end effector is housed in and individual aluminum canister. Each canister contains a 0.2 μm Teflon filter to allow the interior volume to accommodate pressure changes without permitting microbial contaminants to enter the sterile interior volume. A handle repurposed from the space shuttle tile repair kit is used to remove the end effector from the sample canister, collect a sample by swabbing a surface and then replace the end effector in its canister. The canisters and end effectors were cleaned and assembled on Earth. Prior to installing the sterile swab the canisters and end effectors were sterilized in an autoclave at 134°C, 215 kPA, for 7 min.. The final assembly occurred in a sterilized class II biosafety cabinet. We will collect six samples from the 1) airlock vestibule, 2) airlock thermal cover, 3) a gap in the micrometeorite shielding near the airlock, 4) a handrail near the airlock, 5) the CDRA (Carbon Dioxide Removal Assembly) vent, and 6) the VES (Vacuum Exhaust System) vent. The remaining two swabs will be reserved as controls. One swab will be exposed during the EVA without touching any surfaces to act as a blank. The final swab will remain sealed until the entire sampling kit is returned to earth. Based on previously published results from the Russian segment, we hypothesize that there will be detectable microbes at some or all of these locations. Ground-based testing of this sampling caddy confirms that the swabs remain sterile as the canisters transition in and out of vacuum. We were able to retrieve, viable bacterial and fungal cells as well as DNA from samples collected from US space suits during vacuum chamber tests lasting as long as seven hours. Based on these results and feedback from the test subjects the sampling caddy was modified to improve ergonomics and meet US EVA safety requirements. Bayonet probes were added to the sides of the sample kit as alternate mounting points. Additional locking features were added to the end effector and the filter stack to prevent inadvertent release during use. The opening mechanism was changed from one where the end effector was rocked laterally to defeat a ball detent to a twist-to-open threaded closure for similar reasons. Demonstrating, this sampling caddy’s effectiveness during a US EVA will allow us to address knowledge gaps identified in COSPAR reports and begin to define planetary protection requirements for life support systems on crewed missions to mars. This kit could also be used to collect contamination control samples during Artemis missions to verify requirements and could be easily modified for robotic sample collection.

Planetary Protection↗

NASA NTRS1984

A dynamic model for plant growth: validation study under changing temperatures

A dynamic simulation model to describe vegetative growth of plants, for which some functions and parameter values have been estimated previously by optimization search techniques and numerical experimentation based on data from constant temperature experiments, is validated under conditions of changing temperatures. To test the predictive capacity of the model, dry matter accumulation in the leaves, stems, and roots of tobacco plants (Nicotiana tabacum L.) was measured at 2- or 3-day intervals during a 5-week period when temperatures in controlled-environment rooms were programmed for changes at weekly and daily intervals and in ascending or descending sequences within a range of 14 to 34 degrees C. Simulations of dry matter accumulation and distribution were carried out using the programmed changes for experimental temperatures and compared with the measured values. The agreement between measured and predicted values was close and indicates that the temperature-dependent functional forms derived from constant-temperature experiments are adequate for modelling plant growth responses to conditions of changing temperatures with switching intervals as short as 1 day.

NASA Discipline Number 60-40↗

NASA NTRS1991

Hidden-Markov-Model Analysis Of Telemanipulator Data

Mathematical model and procedure based on hidden-Markov-model concept undergoing development for use in analysis and prediction of outputs of force and torque sensors of telerobotic manipulators. In model, overall task broken down into subgoals, and transition probabilities encode ease with which operator completes each subgoal. Process portion of model encodes task-sequence/subgoal structure, and probability-density functions for forces and torques associated with each state of manipulation encode sensor signals that one expects to observe at subgoal. Parameters of model constructed from engineering knowledge of task.

Hannaford, Blake↗