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148 records · Page 9

Biological Insights at the Interface of Multiple Arabidopsis Legacy Datasets

The NASA GeneLab database includes an open-access collection of datasets yielded by space biology experiments. Six Gene Lab Data Sets (GLDS’s) performed in Arabidopsis were selected for analysis (7/17/44/121/205/213), all of which included transcriptome data from spaceflight and ground control environments. Hardware, ecotype, environmental conditions, and other experimental conditions varied, allowing the observations of overarching gene expression impacts of microgravity on plant life without focusing on effects of specific experimental conditions. Using GeneLab pre-processed datasets as the basis for the study, RNA microarray data were analyzed to identify genes that showed altered expression in microgravity when compared to control samples for each individual GLDS. All differentially expressed genes were compared to locate differentially expressed genes common between spaceflight experiments. The most noteworthy result is that not one gene shared differential expression among the six GLDS’s. However, gene expression was not influenced randomly by the microgravity environment, as there were several gene ontology terms that were significantly enriched across all experiments. These included 20 significantly enriched biological processes, and although the genes which enriched each term varied, there were many cases of specific genes common to clusters of multiple GLDS’s. Gene expression such as NAC92 and ERF011 or membrane structural element FFP6 provide insight and direction toward understanding the plant response to spaceflight. Characterizing these common processes and the shared differentially expressed genes has demonstrated potential targets for further study to understand and modulate the biological response of plants in microgravity. Life on Earth has never been subjected to the absence of gravity as a selective pressure, so observing how life forms react to a microgravity environment could provide insight to our shared fundamental biological processes. It is also feasible that the genetic modification of specific genes linked to the microgravity response could improve health and yield of space crops.

Joseph Emhof↗

Statistical and linguistic features of DNA sequences

We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

Non-NASA Center↗

Familial Associations of Prevalence and Cause-Specific Mortality for Thoracic Aortic Disease and Bicuspid Aortic Valve in a Large-Population Database

Thoracic aortic disease and bicuspid aortic valve (BAV) likely have a heritable component, but large population-based studies are lacking. This study characterizes familial associations of thoracic aortic disease and BAV, as well as cardiovascular and aortic-specific mortality, among relatives of these individuals in a large-population database. In this observational case-control study of the Utah Population Database, we identified probands with a diagnosis of BAV, thoracic aortic aneurysm, or thoracic aortic dissection. Age- and sex-matched controls (10:1 ratio) were identified for each proband. First-degree relatives, second-degree relatives, and first cousins of probands and controls were identified through linked genealogical information. Cox proportional hazard models were used to quantify the familial associations for each diagnosis. We used a competing-risk model to determine the risk of cardiovascular-specific and aortic-specific mortality for relatives of probands. The study population included 3,812,588 unique individuals. Familial hazard risk of a concordant diagnosis was elevated in the following populations compared with controls: first-degree relatives of patients with BAV (hazard ratio [HR], 6.88 [95% CI, 5.62–8.43]); first-degree relatives of patients with thoracic aortic aneurysm (HR, 5.09 [95% CI, 3.80–6.82]); and first-degree relatives of patients with thoracic aortic dissection (HR, 4.15 [95% CI, 3.25–5.31]). In addition, the risk of aortic dissection was higher in first-degree relatives of patients with BAV (HR, 3.63 [95% CI, 2.68–4.91]) and in first-degree relatives of patients with thoracic aneurysm (HR, 3.89 [95% CI, 2.93–5.18]) compared with controls. Dissection risk was highest in first-degree relatives of patients who carried a diagnosis of both BAV and aneurysm (HR, 6.13 [95% CI, 2.82–13.33]). First-degree relatives of patients with BAV, thoracic aneurysm, or aortic dissection had a higher risk of aortic-specific mortality (HR, 2.83 [95% CI, 2.44–3.29]) compared with controls. Our results indicate that BAV and thoracic aortic disease carry a significant familial association for concordant disease and aortic dissection. The pattern of familiality is consistent with a genetic cause of disease. Furthermore, we observed higher risk of aortic-specific mortality in relatives of individuals with these diagnoses. In conclusion, this study provides supportive evidence for screening in relatives of patients with BAV, thoracic aneurysm, or dissection.

60 APPLIED LIFE SCIENCES↗

Idaho National Laboratory Integrated Multisite SSHAC Level 3: Probabilistic Volcanic Hazards Assessment

The Idaho National Laboratory (INL) resides on the eastern Snake River Plain (ESRP), part of the Snake River Plain (SRP) with a complex origin and geologic history of volcanism. Much of the Quaternary (last 2.58 million years) volcanism within 400 km of INL is genetically associated with a major thermal anomaly referred to as the Yellowstone hotspot, which is currently located more than 180 km northeast of INL. Near INL, local volcanic sources include silicic domes near its southern border, and numerous dike-fed basaltic vents of the ESRP, some of which are near or within the INL boundaries. Quantitative probabilistic assessments of screened-in volcanic hazardous phenomena for nine different facility complexes at the INL are presented for a Senior Seismic Hazard Analysis Committee (SSHAC) Level 3 (SL3) study. The comprehensive, integrated multisite SSHAC study consists of a single regional Probabilistic Volcanic Hazards Assessment (PVHA) that pertains to all nine INL facility complexes, with site-specific information developed at each respective area of interest (AOI), referred to as the "INL facility AOI" (Figure ES-1). Hazard products are generated for specified INL facility AOIs for use by multiple stakeholders from different agencies in risk-informed decision-making regarding site selection, operations, and design of nuclear facilities at INL, consistent with U.S. Department of Energy (DOE) and U.S. Nuclear Regulatory Commission (NRC) regulatory guidance. The study also serves as the basis for future periodic safety assessments required for existing DOE facilities, such as 10-year evaluations of natural-phenomena hazards. Elements of the INL PVHA including initial characterization, screening, quantitative assessments of eruption and hazard potential, and consideration of facility needs are conducted using the three phases of the SSHAC process: evaluation, integration, and documentation. As per regulatory guidance, the SSHAC framework provided the necessary processes and procedures for the PVHA Technical Integration (TI) team, at three workshops, five formal working meetings and many TI team remote meetings, to conduct initial characterization, screen the volcanic hazards, create PVHA model inputs, exercise those models in the PVHA, consider facility-specific volcanic hazard needs, and perform final hazard calculations. The Participatory Peer Review Panel (PPRP) provided independent oversight and performed process and technical reviews of the PVHA throughout its duration. The study included an extensive New Data Collection and Analyses (NDCA) program developed by the PVHA TI team to reduce uncertainties in hazard-significant elements in the PVHA model. NDCA activities generated 20 reports providing important contributory datasets and results to the project database for characterizing the ESRP. For example, a report compiling the dimensions of ESRP shield volcanoes and lava fields was used to construct volcanic footprints (areas of impact), was compared with data from INL subsurface cores, and was used to validate the results of lava-flow inundation modeling on the contemporary terrain. Another example is the acquisition of aeromagnetic data over INL and its surrounding area, with maps of buried magmatic features (e.g., subsurface volcanoes and swarms of feeder dikes) that informed the PVHA conceptual model of volcanism. The SSHAC evaluation process was used to conduct all elements of the PVHA including initial characterization and screening. Existing data and NDCA activities provided the foundation to develop the tectonomagmatic conceptual model of volcanism for the region of geographical interest in the SRP and Yellowstone hotspot volcanic system, and for considering volcanoes in the western US. Considering Quaternary volcanic sources active during this period, the screening approach identified and evaluated magma compositions, types of eruptive and intrusive phenomena, types of hazardous phenomena, and proximity of sources to INL. The PVHA TI team evaluated 18 types of magmatic sources in terms of 20 potentially hazardous phenomena, resulting in 360 screening decisions. The screening process resulted in 140 screened-in hazardous volcanic phenomena for Quaternary volcanic sources 1) proximal to INL facility complexes in the ESRP (64 basaltic and 54 silicic), 2) regional sources associated with the Yellowstone caldera system and Blackfoot Reservoir volcanic field (7), and 3) more distal sources from thirteen Cascade volcanoes and two volcanoes at Long Valley caldera (CA).

58 GEOSCIENCES↗