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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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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Open Science Approach to Analyze Climate-Crop Relationships in the US Leveraging GES DISC and Galaxy Workflows

Understanding the intricate relationship between climate variability and agricultural production is crucial for ensuring food security. This study investigates the impact of climate parameters, such as temperature, precipitation, and soil moisture, on major US crop yields. Adopting an open science approach, the study analyzes the impact of climate on agricultural production in the United States. The Galaxy workflow engine serves as the primary tool for integrating climate data from the Goddard Earth Sciences Data and Information Services Center (GES DISC), retrieved via the Giovanni system, with yield statistics from the United States Department of Agriculture’s National Agricultural Statistics Service (USDA NASS). Extensions for reading, preprocessing, and analyzing external data have been developed, enabling the creation of workflows within the Galaxy platform. The development of a reproducible workflow allows for the calculation of seasonal climate averages, which are then assessed for their correlation with crop yields. This methodology ensures the replicability of the research, promoting transparency and collaboration in the scientific community. Correlational and regression analyses have been applied to different sub-zones and crops. The findings from this research offer valuable insights into the relationship between climate parameters and crop yields. These insights contribute to a deeper understanding of climate-crop relationships, providing a solid foundation for informed decision-making in the agricultural sector. The high correlation values indicate a significant relationship between climate parameters and crop yields, underscoring the importance of considering climate factors in agricultural planning and policymaking. This research also exemplifies the power of open science in advancing our understanding of complex environmental and agricultural phenomena. By leveraging open data and services, it provides a robust and replicable framework for future studies in this critical field.

Open science↗
DOE OSTI2020

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo

The 2014–2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was mined to identify emerging mutations and trends in mutations as the outbreak progressed over time. Information on transmission dynamics, prevalence, and persistence of intra-host mutants, and the position of a mutation on a protein were then used to prioritize 544 reported mutations based on their ability to impact ZIKV phenotype. Using this criteria, six mutants (representing naturally occurring mutations) were generated as synthetic infectious clones using a 2015 Puerto Rican epidemic strain PRVABC59 as the parental backbone. The phenotypes of these naturally occurring variants were examined using both cell culture and murine model systems. Mutants had distinct phenotypes, including changes in replication rate, embryo death, and decreased head size. In particular, a NS2B mutant previously detected during in vivo studies in rhesus macaques was found to cause lethal infections in adult mice, abortions in pregnant females, and increased viral genome copies in both brain tissue and blood of female mice. Additionally, mutants with changes in the region of NS3 that interfaces with NS5 during replication displayed reduced replication in the blood of adult mice. This analytical pathway, integrating both bioinformatic and wet lab experiments, provides a foundation for understanding how naturally occurring single mutations affect disease outcome and can be used to predict the of severity of future ZIKV outbreaks. To determine if naturally occurring individual mutations in the Zika virus epidemic genotype affect viral virulence or replication rate in vitro or in vivo, we generated an infectious clone representing the epidemic genotype of stain Puerto Rico, 2015. Using this clone, six mutants were created by changing nucleotides in the genome to cause one to two amino acid substitutions in the encoded proteins. The six mutants we generated represent mutations that differentiated the early epidemic genotype from genotypes that were either ancestral or that occurred later in the epidemic. We assayed each mutant for changes in growth rate, and for virulence in adult mice and pregnant mice. Three of the mutants caused catastrophic embryo effects including increased embryonic death or significant decrease in head diameter. Three other mutants that had mutations in a genome region associated with replication resulted in changes in in vitro and in vivo replication rates. These results illustrate the potential impact of individual mutations in viral phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

A Spatial Classifier for Multispectral Data Using Contextual Information

Connectivity describes the spatial relationship among pixels. A spatial classifier which employs the sigma probability concept of the Gaussian distribution and a type of contextual information connectivity of the pixels, is studied in this paper. This spatial classifier attempts to replicate the kind of spatial synthesis done by the human analyst during visual interpretation or to capture the spatial relationships inherent in an aerial photograph. Several classification results of the Landsat TM data using this classifier with different window sizes for capturing the contextual information are illustrated and compared.

Hung, Chih-Cheng↗
NASA NTRS2001

Band-Moment Compression of AVIRIS Hyperspectral Data and its Use in the Detection of Vegetation Stress

A remote sensing campaign was conducted over a U.S. Department of Agriculture test farm at Shelton, Nebraska. An experimental field was set off in plots that were differentially treated with anhydrous ammonia. Four replicates of 0-kg/ha to 200-kg/ha plots, in 50-kg/ha increments, were set out in a random block design. Low-altitude (GSD of 3 m) Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) hyperspectral data were collected over the site in 224 bands. Simultaneously, ground data were collected to support the airborne imagery. In an effort to reduce data load while maintaining or enhancing algorithm performance for vegetation stress detection, band-moment compression and analysis was applied to the AVIRIS image cube. The results indicated that band-moment techniques compress the AVIRIS dataset significantly while retaining the capability of detecting environmentally induced vegetation stress.

Estep, L.↗
DOE OSTI2015

Murine hematopoietic stem cell dormancy controlled by induction of a novel short form of PSF1 by histone deacetylase inhibitors

Hematopoietic stem cells (HSCs) can survive long-term in a state of dormancy. Little is known about how histone deacetylase inhibitors (HDACi) affect HSC kinetics. Here, we use trichostatin A (TSA), a histone deacetylase inhibitor, to enforce histone acetylation and show that this suppresses cell cycle entry by dormant HSCs. Previously, we found that haploinsufficiency of PSF1, a DNA replication factor, led to attenuation of the bone marrow (BM) HSC pool size and lack of acute proliferation after 5-FU ablation. Because PSF1 protein is present in CD34{sup +} transiently amplifying HSCs but not in CD34{sup −} long-term reconstituting-HSCs which are resting in a dormant state, we analyzed the relationship between dormancy and PSF1 expression, and how a histone deacetylase inhibitor affects this. We found that CD34{sup +} HSCs produce long functional PSF1 (PSF1a) but CD34{sup −} HSCs produce a shorter possibly non-functional PSF1 (PSF1b, c, dominantly PSF1c). Using PSF1a-overexpressing NIH-3T3 cells in which the endogenous PSF1 promoter is suppressed, we found that TSA treatment promotes production of the shorter form of PSF1 possibly by inducing recruitment of E2F family factors upstream of the PSF1 transcription start site. Our data document one mechanism by which histone deacetylase inhibitors affect the dormancy of HSCs by regulating the DNA replication factor PSF1. - Highlights: • Hematopoetic stem cell dormancy is controlled by histone deacetylation inhibitors. • Dormancy of HSCs is associated with a shorter form of non-functional PSF1. • Histone deacetylase inhibitors suppress PSF1 promoter activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Equilibrated Gas and Carbonate Standard‐Derived Dual (Δ 47 and Δ 48 ) Clumped Isotope Values

Abstract Carbonate clumped isotope geochemistry has primarily focused on mass spectrometric determination of m/z 47 CO 2 for geothermometry, but theoretical calculations and recent experiments indicate paired analysis of the m/z 47 ( 13 C 18 O 16 O) and m/z 48 ( 12 C 18 O 18 O) isotopologues (referred to as Δ 47 and Δ 48 ) can be used to study non‐equilibrium isotope fractionations and refine temperature estimates. We utilize 5,448 Δ 47 and 3,400 Δ 48 replicate measurements of carbonate samples and standards, and 183 Δ 47 and 195 Δ 48 replicate measurements of gas standards from 2015 to 2021 from a multi‐year and multi‐instrument data set to constrain Δ 47 and Δ 48 values for 27 samples and standards, including Devils Hole cave calcite, and study equilibrium Δ 47 ‐Δ 48 , Δ 47 ‐temperature, and Δ 48 ‐temperature relationships. We compare results to previously published findings and calculate equilibrium regressions based on data from multiple laboratories. We report acid digestion fractionation factors, Δ* 63‐47 and Δ* 64‐48 , and account for their dependence on the initial clumped isotope values of the mineral.

58 GEOSCIENCES↗
DOE OSTI2023

Genetic control of photoprotection and photosystem II operating efficiency in plants

Summary Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field‐grown crops up to 40%. Using semi‐high‐throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize ( Zea mays ) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome‐wide association studies. For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis ( Arabidopsis thaliana ) were characterized: two thioredoxin genes, and genes encoding a transporter in the chloroplast envelope, an initiator of chloroplast movement, a putative regulator of cell elongation and stomatal patterning, and a protein involved in plant energy homeostasis. Since maize and Arabidopsis are distantly related, we propose that genes involved in photoprotection and PSII function are conserved across vascular plants. The genes and naturally occurring functional alleles identified here considerably expand the toolbox to achieving a sustainable increase in crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Scalable Linked Dynamic Equilibrium (SLiDE)

SLiDE (Scalable Linked Dynamic Equilibrium) replicates the blueNOTE (National Open source Tools for general Equilibrium analysis) datastream from the Wisconsin National Data Consortium. From there, it produces a recursive dynamic computable general equilibrium model of the US states and eventually the global/national economies. The datastream operations have been set up to allow for scalability of both regions and sectors represented. The model has the capability to flexibly define functional forms similar to other general equilibrium model construction software.

Hughes, Caroline↗
DOE OSTI2023

KBase Narrative - Supplemental Data for "Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes"

Here we provide the complete set of circular elements produced by SCAPP from metagenomic data that may represent mobile genetic elements (MGEs). For the publication, these sequences were de-replicated within the high [U] and low [U] sample sets. Additionally, 98 of the circular elements were removed for downstream analysis due to high suspicion of being (1) chloroplast or mitochondrial sequences or (2) erroneously circularized long repeat regions. The complete list of circular elements used for the analysis along with metadata can be found in Tables S5 and S6.

Goff, Jennifer↗
NASA NTRS1991

Issues in the Imprecise Computation Approach to Fault Tolerance

The imprecise computation technique can be used in a natural way to enhance fault tolerance. By providing a usable, approximate result whenever a failure or overload prevent the system from producing the desired, precise result, we can increase the availability of data and services, reduce the need for error-recovery operations, and minimize the costs in replication. This paper describes the domain-specific fault tolerance mechanisms that are needed to support the provision and correct usage of imprecise results for several representative application domains. The elements of an application-domain-independent architecture that can effectively integrate these domain-specific mechanisms are also described.

Liu, Jane W. S.↗
NASA NTRS1992

Crystal structure of an Okazaki fragment at 2-A resolution

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.

Non-NASA Center↗
NASA NTRS2011

Genotoxic Effects of Low- and High-LET Radiation on Human Epithelial Cells Grown in 2-D Versus 3-D Culture

Risk estimation for radiation-induced cancer relies heavily on human epidemiology data obtained from terrestrial irradiation incidents from sources such as medical and occupational exposures as well as from the atomic bomb survivors. No such data exists for exposures to the types and doses of high-LET radiation that will be encountered during space travel; therefore, risk assessment for space radiation requires the use of data derived from cell culture and animal models. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. This work compares the genotoxic effects of radiation on normal human epithelial cells grown in standard 2-D monolayer culture compared to 3-D organotypic co-culture conditions. These 3-D organotypic models mimic the morphological features, differentiation markers, and growth characteristics of fully-differentiated normal human tissue and are reproducible using defined components. Cultures were irradiated with 2 Gy low-LET gamma rays or varying doses of high-LET particle radiation and genotoxic damage was measured using a modified cytokinesis block micronucleus assay. Our results revealed a 2-fold increase in residual damage in 2 Gy gamma irradiated cells grown under organotypic culture conditions compared to monolayer culture. Irradiation with high-LET particle radiation gave similar results, while background levels of damage were comparable under both scenarios. These observations may be related to the phenomenon of "multicellular resistance" where cancer cells grown as 3-D spheroids or in vivo exhibit an increased resistance to killing by chemotherapeutic agents compared to the same cells grown in 2-D culture. A variety of factors are likely involved in mediating this process, including increased cell-cell communication, microenvironment influences, and changes in cell cycle kinetics that may promote survival of damaged cells in 3-D culture that would otherwise die or be rendered reproductively inactive in 2-D culture.

Patel, Z. S.↗
NASA NTRS2012

Accelerated Creep Testing of High Strength Aramid Webbing

A series of preliminary accelerated creep tests were performed on four variants of 12K and 24K lbf rated Vectran webbing to help develop an accelerated creep test methodology and analysis capability for high strength aramid webbings. The variants included pristine, aged, folded and stitched samples. This class of webbings is used in the restraint layer of habitable, inflatable space structures, for which the lifetime properties are currently not well characterized. The Stepped Isothermal Method was used to accelerate the creep life of the webbings and a novel stereo photogrammetry system was used to measure the full-field strains. A custom MATLAB code is described, and used to reduce the strain data to produce master creep curves for the test samples. Initial results show good correlation between replicates; however, it is clear that a larger number of samples are needed to build confidence in the consistency of the results. It is noted that local fiber breaks affect the creep response in a similar manner to increasing the load, thus raising the creep rate and reducing the time to creep failure. The stitched webbings produced the highest variance between replicates, due to the combination of higher local stresses and thread-on-fiber damage. Large variability in the strength of the webbings is also shown to have an impact on the range of predicted creep life.

Jones, Thomas C.↗
NASA NTRS2014

Validation of 3-D Ice Accretion Measurement Methodology for Experimental Aerodynamic Simulation

Determining the adverse aerodynamic effects due to ice accretion often relies on dry-air wind-tunnel testing of artificial, or simulated, ice shapes. Recent developments in ice accretion documentation methods have yielded a laser-scanning capability that can measure highly three-dimensional features of ice accreted in icing wind tunnels. The objective of this paper was to evaluate the aerodynamic accuracy of ice-accretion simulations generated from laser-scan data. Ice-accretion tests were conducted in the NASA Icing Research Tunnel using an 18-inch chord, 2-D straight wing with NACA 23012 airfoil section. For six ice accretion cases, a 3-D laser scan was performed to document the ice geometry prior to the molding process. Aerodynamic performance testing was conducted at the University of Illinois low-speed wind tunnel at a Reynolds number of 1.8 x 10(exp 6) and a Mach number of 0.18 with an 18-inch chord NACA 23012 airfoil model that was designed to accommodate the artificial ice shapes. The ice-accretion molds were used to fabricate one set of artificial ice shapes from polyurethane castings. The laser-scan data were used to fabricate another set of artificial ice shapes using rapid prototype manufacturing such as stereolithography. The iced-airfoil results with both sets of artificial ice shapes were compared to evaluate the aerodynamic simulation accuracy of the laser-scan data. For four of the six ice-accretion cases, there was excellent agreement in the iced-airfoil aerodynamic performance between the casting and laser-scan based simulations. For example, typical differences in iced-airfoil maximum lift coefficient were less than 3% with corresponding differences in stall angle of approximately one degree or less. The aerodynamic simulation accuracy reported in this paper has demonstrated the combined accuracy of the laser-scan and rapid-prototype manufacturing approach to simulating ice accretion for a NACA 23012 airfoil. For several of the ice-accretion cases tested, the aerodynamics is known to depend upon the small, three dimensional features of the ice. These data show that the laser-scan and rapid-prototype manufacturing approach is capable of replicating these ice features within the reported accuracies of the laser-scan measurement and rapid-prototyping method; thus providing a new capability for high-fidelity ice-accretion documentation and artificial ice-shape fabrication for icing research.

Scale Models↗
NASA NTRS2015

Validation of 3-D Ice Accretion Measurement Methodology for Experimental Aerodynamic Simulation

Determining the adverse aerodynamic effects due to ice accretion often relies on dry-air wind-tunnel testing of artificial, or simulated, ice shapes. Recent developments in ice-accretion documentation methods have yielded a laser-scanning capability that can measure highly three-dimensional (3-D) features of ice accreted in icing wind tunnels. The objective of this paper was to evaluate the aerodynamic accuracy of ice-accretion simulations generated from laser-scan data. Ice-accretion tests were conducted in the NASA Icing Research Tunnel using an 18-in. chord, two-dimensional (2-D) straight wing with NACA 23012 airfoil section. For six ice-accretion cases, a 3-D laser scan was performed to document the ice geometry prior to the molding process. Aerodynamic performance testing was conducted at the University of Illinois low-speed wind tunnel at a Reynolds number of 1.8 × 10(exp 6) and a Mach number of 0.18 with an 18-in. chord NACA 23012 airfoil model that was designed to accommodate the artificial ice shapes. The ice-accretion molds were used to fabricate one set of artificial ice shapes from polyurethane castings. The laser-scan data were used to fabricate another set of artificial ice shapes using rapid prototype manufacturing such as stereolithography. The iced-airfoil results with both sets of artificial ice shapes were compared to evaluate the aerodynamic simulation accuracy of the laser-scan data. For five of the six ice-accretion cases, there was excellent agreement in the iced-airfoil aerodynamic performance between the casting and laser-scan based simulations. For example, typical differences in iced-airfoil maximum lift coefficient were less than 3 percent with corresponding differences in stall angle of approximately 1 deg or less. The aerodynamic simulation accuracy reported in this paper has demonstrated the combined accuracy of the laser-scan and rapid-prototype manufacturing approach to simulating ice accretion for a NACA 23012 airfoil. For several of the ice-accretion cases tested, the aerodynamics is known to depend upon the small, three-dimensional features of the ice. These data show that the laser-scan and rapid-prototype manufacturing approach is capable of replicating these ice features within the reported accuracies of the laser-scan measurement and rapid-prototyping method; thus providing a new capability for high-fidelity ice-accretion documentation and artificial ice-shape fabrication for icing research.

Aircraft Icing↗
NASA NTRSDate not supplied

AstroAmpSeq: Microbial Bioinformatics Education with NASA GeneLab’s Amplicon Pipeline

The prevalence and importance of large sequencing datasets in microbiology has led to a movement to share microbial ecology experimental data through open-access databases. This is particularly true of experiments that are difficult to replicate, such as those conducted in the spaceflight environment and shared via NASA GeneLab. It is now possible and indeed valuable for students to access and re-analyze these shared datasets for educational and research purposes. To provide students with experience utilizing microbial bioinformatics tools, GeneLab for Colleges and Universities (GL4U) has designed AstroAmpSeq, a week-long, virtually implemented project-based learning (PBL) minicourse to instruct undergraduate students on 16S amplicon sequencing. AstroAmpSeq was created to be accessible to students without prior bioinformatics or microbial ecology experience. During the minicourse students work in teams to process, analyze, and visualize a subsample of GeneLab dataset GLDS-280 using GeneLab’s standard amplicon processing pipeline, which is based in R. Students develop a hypothesis related to the dataset then generate and analyze figures to evaluate their hypothesis. Formative assessment of student learning is determined via pre- and post-evaluations, peer feedback, and self-reflection. Project and presentation rubrics serve as a summative assessment of student learning. GL4U AstroAmpSeq not only meets American Society for Microbiology Curriculum Guidelines, but also incites student interest in research by an inquiry-based approach and can be made part of a larger semester-long curriculum. GL4U AstroAmpSeq raises awareness of space microbiology and bioinformatics as a field and career path among undergraduates. Further, by using a GeneLab dataset and nesting microbiology techniques into the real-world application of space biology, AstroAmpSeq enforces deeper and longer-lasting student learning.

microbiology↗
DOE OSTI2015

Utilization of GIS technology to support development of flow and contaminant fate and transport models at US DOE sites - 15457

U.S. Department of Energy (DOE) sites have accumulated years of data and millions of spatial and temporal records related to the hydrological cycle, contaminant transport, and parameters of remediation technologies. In addition, numerical models which use field monitoring data to help understand flow and transport produce gigabytes of computed spatial and temporal data for each computation node. There is a need therefore for an advanced spatial data structure that can be used to address the management, processing, and analysis of spatial and temporal numerical modeling data derived from multiple sources. This can be accomplished using a geo-database. The development of an ArcSDE geo-database facilitates the centralized storage, backup, accessibility, organization, and management of model configuration and computed simulation data, putting it into a structured, coherent, and logical computer-supported system. GIS data processing and automation would enable faster and hence more complex analyses of field test data. The Applied Research Center (ARC) at Florida International University (FIU) has provided analysis of flow and transport for several watersheds at DOE's Oak Ridge Reservation (ORR), including East Fork Poplar Creek (EFPC), Upper EFPC in the Y-12 National Security Complex area (Y-12 NSC) and White Oak Creek (WOC). Integrated surface and subsurface flow, fate and transport models were developed to provide analysis of contaminant patterns within each watershed. In addition, digital monitoring data available from the Oak Ridge Environmental Information System (OREIS) related to mercury (Hg) contamination and remediation within these watersheds was used for calibration and verification of the model. Experimental studies were also carried out which provided kinetic and equilibrium data about important parameters related to Hg transport, speciation and methylation/demethylation kinetics within the watershed. Geographic Information Systems (GIS) technology was employed to support the modeling work through storage and geo-processing of spatial and temporal data required by the models and to produce hydrogeological maps for visualization. An ArcGIS geo-database was developed for centralized storage and management of experimental and computed model data and its capabilities were extended over the years using tools such as ModelBuilder combined with Python scripting to automate repetitive tasks, perform statistical analyses and generate maps and reports. The hydrologic geo-database model developed possesses a structure that enables linkage with scalable hydrologic modeling tools/applications to model hydrologic systems, and in this case, enables the testing of the potential impacts of various remediation scenarios on the ORR watersheds. The ArcSDE geo-database can also be used to automate and simplify the process of calling stored GIS and time series data. This geo-database can serve as a tool for contaminant flow and transport analyses which require large amounts of high-quality spatial and temporal data in order to ensure reliability and validity of modeling results. The existing geo-database structure developed for the hydrological modeling at ORR was designed to be replicable for application at other DOE sites. An investigation of downloadable free/open source GIS software along with required security protocols to facilitate online querying of the database was also conducted to determine methods by which project-derived data can be more easily shared with other project stakeholders such as DOE personnel and site contractors. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. Results We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae . Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators ( STE12-TEC1 and RAP1-HAP1-MSN4 ). Conclusion Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗