SEARCH · Engineering Papers

Results for “Biological Transport”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37

All sources NASA NTRS DOE OSTI

NASA NTRS2010

Proton Lateral Broadening Distribution Comparisons Between GRNTRN, MCNPX, and Laboratory Beam Measurements

Recent developments in NASA s deterministic High charge (Z) and Energy TRaNsport (HZETRN) code have included lateral broadening of primary ion beams due to small-angle multiple Coulomb scattering, and coupling of the ion-nuclear scattering interactions with energy loss and straggling. This new version of HZETRN is based on Green function methods, called GRNTRN, and is suitable for modeling transport with both space environment and laboratory boundary conditions. Multiple scattering processes are a necessary extension to GRNTRN in order to accurately model ion beam experiments, to simulate the physical and biological-effective radiation dose, and to develop new methods and strategies for light ion radiation therapy. In this paper we compare GRNTRN simulations of proton lateral broadening distributions with beam measurements taken at Loma Linda University Proton Therapy Facility. The simulated and measured lateral broadening distributions are compared for a 250 MeV proton beam on aluminum, polyethylene, polystyrene, bone substitute, iron, and lead target materials. The GRNTRN results are also compared to simulations from the Monte Carlo MCNPX code for the same projectile-target combinations described above.

Mertens, Christopher J.↗

NASA NTRSDate not supplied

Modeling Space-Radiation Induced Chromosome Aberrations

Exposure to ionizing radiation is identified as one of the main hazards of space flight. Galactic cosmic rays (GCRs) are composed of energetic protons (87%), helium nuclei (12%) and high-charge and energy (HZE) ions. At the cellular scale, HZE ions have a pattern of energy deposition that depends on the ion linear energy transfer (LET), with high LET ions favoring the formation of complex DNA damages that induce chromosome aberrations (CAs). Understanding how physical (e.g., ion type and energy) and biological (e.g., cell type) parameters impact CA formation is required to assess space radiation risks such as carcinogenesis. The Monte Carlo tool RITCARD/RITRACKS [1,2] developed by NASA allows simulation of the transport of HZE ions and subsequent energy deposition at the cellular scale and models the creation of DNA double strand breaks (DSBs), DNA repair and formation of CAs. We used this radiation transport code to further understand how radiation quality and cell size affects CA formation.

Floriane Poignant↗

DOE OSTI2025

Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery

Nearly one-third of all proteins in eukaryotes are membrane proteins. Moreover, roughly 60% of Food and Drug Adminstration (FDA)-approved small-molecule drugs act on membrane proteins, which includes G protein–coupled receptors (GPCRs), ion channels, and transporters. Here, the vast majority of these membrane proteins are cell-surface accessible and thus amenable to drug discovery. At the same time, they are considerably more challenging to reconstitute and prepare for structure initiatives, antibody discovery, and drug screening. This series of reviews introduces the reader to current reconstitution systems, biophysical characterization of the membrane proteins and associated lipids, and common applications involving nuclear magnetic resonance (NMR), mass spectrometry (MS), and cryo-electron microscopy (cryo-EM).

36 MATERIALS SCIENCE↗

NASA NTRS2001

Polar auxin transport: controlling where and how much

Auxin is transported through plant tissues, moving from cell to cell in a unique polar manner. Polar auxin transport controls important growth and developmental processes in higher plants. Recent studies have identified several proteins that mediate polar auxin transport and have shown that some of these proteins are asymmetrically localized, paving the way for studies of the mechanisms that regulate auxin transport. New data indicate that reversible protein phosphorylation can control the amount of auxin transport, whereas protein secretion through Golgi-derived vesicles and interactions with the actin cytoskeleton might regulate the localization of auxin efflux complexes.

NASA Discipline Plant Biology↗

NASA NTRS1995

Adaptive responses of GLUT-4 and citrate synthase in fast-twitch muscle of voluntary running rats

Glucose transporter (GLUT-4) protein, hexokinase, and citrate synthase (proteins involved in oxidative energy production from blood glucose catabolism) increase in response to chronically elevated neuromuscular activity. It is currently unclear whether these proteins increase in a coordinated manner in response to this stimulus. Therefore, voluntary wheel running (WR) was used to chronically overload the fast-twitch rat plantaris muscle and the myocardium, and the early time courses of adaptative responses of GLUT-4 protein and the activities of hexokinase and citrate synthase were characterized and compared. Plantaris hexokinase activity increased 51% after just 1 wk of WR, whereas GLUT-4 and citrate synthase were increased by 51 and 40%, respectively, only after 2 wk of WR. All three variables remained comparably elevated (+50-64%) through 4 wk of WR. Despite the overload of the myocardium with this protocol, no substantial elevations in these variables were observed. These findings are consistent with a coordinated upregulation of GLUT-4 and citrate synthase in the fast-twitch plantaris, but not in the myocardium, in response to this increased neuromuscular activity. Regulation of hexokinase in fast-twitch muscle appears to be uncoupled from regulation of GLUT-4 and citrate synthase, as increases in the former are detectable well before increases in the latter.

Non-NASA Center↗

DOE OSTI2021

Reactor cell neutron dose for the molten salt breeder reactor conceptual design

The private sector’s interest in the active development of molten salt reactors has led to the need to develop and test advanced modeling and simulation tools to analyze various advanced reactor types under numerous conditions. This paper discusses the effort undertaken to model the Oak Ridge National Laboratory (ORNL) Molten Salt Breeder Reactor (MSBR) design using ORNL’s Shift Monte Carlo code. The MSBR model integrates a Monte Carlo N-Particle (MCNP) MSBR core model with an MCNP model that was generated from a CAD model of the external components and the reactor building, which was subsequently run in Shift. This paper focuses on development of the fully integrated model and its use in performing neutron transport calculations in the reactor cell area. This model is intended to aid in understanding radiological dose conditions during operation, as well as the iron dpa rates in the reactor vessel. The neutron biological dose rates and flux calculated in the reactor cell are much higher in the MSBR than in typical light-water reactors. The implications of these results and future work are also discussed in this paper.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study

The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, for this work, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure–function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Control of Energy Transport and Transduction in Photosynthetic Down-Conversion (Final Technical Report)

The research conducted under this contract focused on three areas related to control of energy transport and transduction in natural and synthetic light harvesting systems: (1) experimental and theoretical studies exploring the use of ultrafast laser pulse shaping to manipulate the initially excited states of multi-chromophore biological light harvesting networks and influence the early time energy transfer and electronic and vibrational relaxation pathways, (2) fundamental theoretical developments aimed at computing and analyzing the dynamics of excitations of complex heterogeneous environments and nano structures, and (3) joint experimental and theoretical design studies of artificial light harvesting materials exploring the influence of incorporating different types of organic layers in low dimensional lead halide perovskite materials on their hot carrier relaxation dynamics, and theoretical studies of the design of nano structured light harvesting antenna systems. These research projects supported the training of three theoretical and computational graduate students, one experimental graduate student, and one experimental post-doctoral researcher. The research has been published in seven peer reviewed papers and presented at several international meetings and workshops.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1999

The microtubule cytoskeleton does not integrate auxin transport and gravitropism in maize roots

The Cholodny-Went hypothesis of gravitropism suggests that the graviresponse is controlled by the distribution of auxin. However, the mechanism of auxin transport during the graviresponse of roots is still unresolved. To determine whether the microtubule (MT) cytoskeleton is participating in auxin transport, the cytoskeleton was examined and the movement of 3H-IAA measured in intact and excised taxol, oryzalin, and naphthylphthalamic acid (NPA)-treated roots of Zea mays cv. Merit. Taxol and oryzalin did not inhibit the graviresponse of roots but the auxin transport inhibitor NPA greatly inhibited both auxin transport and graviresponse. NPA had no effect on MT organization in vertical roots, but caused MT reorientation in horizontally placed roots. Regardless of treatment, the organization of MTs in intact roots differed from that in root segments. The MT inhibitors, taxol and oryzalin had opposite effects on the MTs, namely, depolymerization (oryzalin) and stabilization and thickening (taxol), but both treatments caused swelling of the roots. The data indicate that the MT cytoskeleton does not directly interfere with auxin transport or auxin-mediated growth responses in maize roots.

NASA Discipline Plant Biology↗

NASA NTRS2000

Selected contribution: a three-dimensional model for assessment of in vitro toxicity in balaena mysticetus renal tissue

This study established two- and three-dimensional renal proximal tubular cell cultures of the endangered species bowhead whale (Balaena mysticetus), developed SV40-transfected cultures, and cloned the 61-amino acid open reading frame for the metallothionein protein, the primary binding site for heavy metal contamination in mammals. Microgravity research, modulations in mechanical culture conditions (modeled microgravity), and shear stress have spawned innovative approaches to understanding the dynamics of cellular interactions, gene expression, and differentiation in several cellular systems. These investigations have led to the creation of ex vivo tissue models capable of serving as physiological research analogs for three-dimensional cellular interactions. These models are enabling studies in immune function, tissue modeling for basic research, and neoplasia. Three-dimensional cellular models emulate aspects of in vivo cellular architecture and physiology and may facilitate environmental toxicological studies aimed at elucidating biological functions and responses at the cellular level. Marine mammals occupy a significant ecological niche (72% of the Earth's surface is water) in terms of the potential for information on bioaccumulation and transport of terrestrial and marine environmental toxins in high-order vertebrates. Few ex vivo models of marine mammal physiology exist in vitro to accomplish the aforementioned studies. Techniques developed in this investigation, based on previous tissue modeling successes, may serve to facilitate similar research in other marine mammals.

Whales/genetics/physiology↗

NASA NTRS2000

Cellular Responses to Mechanical Stress Selected Contribution: A Three-Dimensional Model for Assessment of in Vitro Toxicity in Balaena Mysticetus Renal Tissue

Goodwin, T. J.↗

NASA NTRS2019

Updated MISR Over-Water Research Aerosol Retrieval Algorithm - Part 2: A Multi-Angle Aerosol Retrieval Algorithm for Shallow, Turbid, Oligotrophic, and Eutrophic Waters

Coastal waters serve as transport pathways to the ocean for all agricultural and other runoff from terrestrial sources, and many are the sites for upwelling of nutrient rich, deep water; they are also some of the most biologically productive on Earth. Estimating the impact coastal waters have on the global carbon budget requires relating satellite-based remote-sensing retrievals of biological productivity (e.g., chlorophyll alpha concentration) to in situ measurements taken in near-surface waters. The Multi-angle Imaging SpectroRadiometer (MISR) can uniquely constrain the "atmospheric correction" needed to derive ocean color from remote-sensing imagers. Here, we retrieve aerosol amount and type from MISR over all types of water. The primary limitation is an upper bound on aerosol optical depth (AOD), as the algorithm must be able to distinguish the surface. This updated MISR research aerosol retrieval algorithm (RA) also assumes that light reflection by the underlying ocean surface is Lambertian. The RA computes the ocean surface reflectance (R (sub rs)) analytically for a given AOD, aerosol optical model, and wind speed. We provide retrieval examples over shallow, turbid, and eutrophic waters and introduce a productivity and turbidity index (PTI), calculated from retrieved spectral R (sub rs), that distinguished water types (similar to the the normalized difference vegetation index, NDVI, over land). We also validate the new algorithm by comparing spectral AOD and Angstrom exponent (ANG) results with 2419 collocated AErosol RObotic NETwork (AERONET) observations. For AERONET 558 nanometer-interpolated AOD less than 1.0, the root-mean square error (RMSE) is 0.04 and linear correlation coefficient is 0.95. For the 502 cloud-free MISR and AERONET collocations with an AERONET AOD greater than 0.20, the ANG RMSE is 0.25 and r is 0.89. Although MISR RA AOD retrieval quality does not appear to be substantially impacted by the presence of turbid water, the MISR-RA-retrieved Angstrom exponent seems to suffer from increased uncertainty under such conditions. MISR supplements current ocean color sources in regions where sunglint precludes retrievals from single-view-angle instruments. MISR atmospheric correction should also be more robust than that derived from single-view instruments such as the Moderate Resolution Imaging Spectroradiometer (MODIS). This is especially true in regions of shallow, turbid, and eutrophic waters, locations where biological productivity can be high, and single-view-angle retrieval algorithms struggle to separate atmospheric from oceanic features.

Satellite Remote Sensing↗

NASA NTRSDate not supplied

Validation of Multisystem Countermeasures Protocol for Spaceflight during Antarctica Winter-over at Palmer Station (Palmer Countermeasures)

Exploration-class missions beyond the Van Allen belt to the Moon and then Mars will begin soon. Low-Earth orbital spaceflight results in the persistent perturbation of the human immune system, characterized by reductions in T and NK cell function, altered cytokine profiles, and the reactivation of latent herpesviruses. While these alterations have not caused widespread clinical issues, some crewmembers experience immune-related adverse events, including manifestations of symptomatic herpes viral reactivation, allergy, and respiratory distress. Because future deep-space exploration missions will be of unprecedented duration, it is reasonable to hypothesize that the immune perturbations observed aboard International Space Station (ISS) will intensify during longer missions in deep space, thereby placing crewmembers at elevated clinical risk. Thus, it is imperative to preserve the immune vigilance of astronauts by developing a countermeasure strategy. Of all the Earth analogs studied to date, an Antarctica winter-over (AWO) mission most closely reproduces the spaceflight experience: prolonged deployment, extreme environment, circadian misalignment, isolation, station lifestyle, and personal risk. The US maintains three primary stations in Antarctica: South Pole Station, McMurdo, and Palmer. Previous studies suggest that stations located near the interior of Antarctica (South Pole, McMurdo) have confounding effects on the immune system due to persistent hypobaric hypoxia. Thus, it was hypothesized that winter-over at a coastal station (Palmer) would be more akin to spaceflight due to its normoxic but still extreme environment. Therefore, AWO at Palmer Station was chosen as the platform for testing and validating the effectiveness of a NASA multi-system countermeasures protocol designed for deep space missions. The array of countermeasure protocols and monitoring methods deployed for each AWO will consist of diet modifications, nutritional supplementation, prescribed aerobic and resistive exercise, and a protocol of stress relieving virtual reality exercises. A multitude of biological sample types, including blood, saliva, and hair will be collected in tandem with the countermeasures in order to examine the combined effectiveness of the countermeasures. Samples and logs from subjects will be transported from Palmer Station to Johnson Space Center for further processing and distribution to co-investigators at the end of each winter-over. Extracted samples will be analyzed by appropriate testing platforms (Multiplex, qPCR, ELISA, etc.) to monitor alterations in leukocyte distribution, T cell and NK function, cytokine profiles, reactivation of latent herpesviruses, and nutritional factors. The data collected will be compared to a control year in which no countermeasures were deployed to evaluate the overall effectiveness of the analog and to validate the candidate immune countermeasure strategy. With the completion of the Antarctica Winter-Over (WO) 2022 control year, samples for 13 subjects have been successfully returned from Antarctica to NASA/JSC for further processing and distribution to Co-Investigators. WO 2023, the first countermeasure year, has also commenced with 11 subject consenting and performing their base line data collections (BDC) held in Chile. Another 5 subjects, who were already stationed at Palmer Station, Antarctica, joined as participates in the investigation. These 5 subjects were consented, but no BDC was able to be collected due to their joining in-mission. Therefore, there will be a total of 16 subjects participating in Antarctica's 2023 Winter-Over.

Cody L Gutierrez↗

NASA NTRSDate not supplied

Validation of Multisystem Countermeasures Protocol for Spaceflight during Antarctica Winter-over at Palmer Station (Palmer Countermeasures)

Stressors associated with spaceflight induce persistent immune compromise in astronauts which increase subclinical latent virus reactivation. In select crews, adverse clinical events have been documented. Antarctica winter-over (AWO) mission most closely reproduces these mission stressors: prolonged deployment, extreme environment, circadian misalignment, isolation, station lifestyle, and personal risk. The US maintains three primary stations in Antarctica: South Pole Station, McMurdo, and Palmer. Previous studies suggest that stations located near the interior of Antarctica (South Pole, McMurdo) have confounding effects on the immune system due to persistent hypobaric hypoxia. We hypothesized that winter-over at a coastal station (Palmer) would be more akin to spaceflight due to its normoxic but still extreme environment. Therefore, AWO at Palmer Station was selected, and validated in a pilot study [2], as the platform for testing and validating the effectiveness of an immune-restorative countermeasure protocol designed for deep space missions. Specifics include diet modifications, nutritional supplementation (vitamin D, probiotic, etc.), prescribed aerobic and resistive exercise, and a protocol of stress relieving virtual reality exercises. A multitude of biological sample types, including blood, saliva, and hair will be collected in tandem with the countermeasures in order to examine the combined effectiveness of the countermeasures. Samples and logs from subjects will be transported from Palmer Station to Johnson Space Center for further processing and distribution to co-investigators at the end of each winter-over. Extracted samples will be analyzed by appropriate testing platforms (Multiplex, qPCR, ELISA, etc.) to monitor alterations in leukocyte distribution, T cell and NK function, cytokine profiles, reactivation of latent herpesviruses, and nutritional factors. The data collected will be compared to a control year in which no countermeasures were deployed to evaluate the overall effectiveness of the analog and to validate the candidate immune countermeasure strategy. AWO 2023 concluded with the 4th in-mission timepoint conducted in September 2023. Samples for 16 subjects, including blood, saliva, hair, surveys, and PCR data, were all successfully returned from Antarctica to NASA/JSC mid-November 2023. Samples have since been distributed to co-investigators for further processing and analysis. With the completion of the first countermeasure year, preliminary data on the effectiveness of the deep-space protocol is being evaluated, however, no conclusions can be drawn yet until the completion of the second AWO countermeasure year, AWO 2024. AWO 2024 commenced in late-March 2024, with 13 subjects consenting and performing their baseline data collections (BDCs). Unique to the 2024 deployment, NSF lifted certain COVID restrictions and rallied the crewmembers in Punta Arenas, Chile. All NSF activities were transferred to this location and NASA was allowed, for the first time, to perform consent briefings, baseline samplings and training in person. This augment greatly increased the likelihood of success for the overwinter activities.

Cody L Gutierrez↗

NASA NTRSDate not supplied

Validation of Multisystem Countermeasures Protocol for Spaceflight during Antarctica Winter-over at Palmer Station (Palmer Countermeasures)

Stressors associated with spaceflight induce persistent immune compromise in astronauts which increase subclinical latent virus reactivation. In select crews, adverse clinical events have been documented. Antarctica winter-over (AWO) mission most closely reproduces these mission stressors: prolonged deployment, extreme environment, circadian misalignment, isolation, station lifestyle, and personal risk. The US maintains three primary stations in Antarctica: South Pole Station, McMurdo, and Palmer. Previous studies suggest that stations located near the interior of Antarctica (South Pole, McMurdo) have confounding effects on the immune system due to persistent hypobaric hypoxia. We hypothesized that winter-over at a coastal station (Palmer) would be more akin to spaceflight due to its normoxic but still extreme environment. Therefore, AWO at Palmer Station was selected, and validated in a pilot study, as the platform for testing and validating the effectiveness of an immune-restorative countermeasure protocol designed for deep space missions. Specifics include diet modifications, nutritional supplementation (vitamin D, probiotic, etc.), prescribed aerobic and resistive exercise, and a protocol of stress relieving virtual reality exercises. A multitude of biological sample types, including blood, saliva, and hair will be collected in tandem with the countermeasures in order to examine the combined effectiveness of the countermeasures. Samples and logs from subjects will be transported from Palmer Station to Johnson Space Center for further processing and distribution to co-investigators at the end of each winter-over. Extracted samples will be analyzed by appropriate testing platforms (Multiplex, qPCR, ELISA, etc.) to monitor alterations in leukocyte distribution, T cell and NK function, cytokine profiles, reactivation of latent herpesviruses, and nutritional factors. The data collected will be compared to a control year in which no countermeasures were deployed to evaluate the overall effectiveness of the analog and to validate the candidate immune countermeasure strategy. AWO 2023 concluded with the 4th in-mission timepoint conducted in September 2023. Samples for 16 subjects, including blood, saliva, hair, surveys, and PCR data, were all successfully returned from Antarctica to NASA/JSC mid-November 2023. Samples have since been distributed to co-investigators for further processing and analysis. With the completion of the first countermeasure year, preliminary data on the effectiveness of the deep-space protocol is being evaluated, however, no conclusions can be drawn yet until the completion of the second AWO countermeasure year, AWO 2024. AWO 2024 commenced in late-March 2024, with 13 subjects consenting and performing their baseline data collections (BDCs). Unique to the 2024 deployment, NSF lifted certain COVID restrictions and rallied the crewmembers in Punta Arenas, Chile. All NSF activities were transferred to this location and NASA was allowed, for the first time, to perform consent briefings, baseline samplings and training in person. This augment greatly increased the likelihood of success for the overwinter activities.

Cody L Gutierrez↗

DOE OSTI2026

Model‐Based Interpretation of Solute Exports and Carbon Partitioning During Shale Weathering in a Mountainous Hillslope

The weathering of sedimentary rocks in high-elevation catchments influences freshwater quality and the global carbon cycle. While individual biogeochemical mechanisms involved in this process are relatively well understood, quantifying their contributions to solute export and carbon fluxes under natural, transient conditions remains challenging. Here, we implement a numerical multidimensional and multiphase model to simulate coupled hydrological and biogeochemical processes in a shale-underlain, snow-dominated hillslope in the Rocky Mountains, Colorado. The model captures the dynamic interplay between soil respiration, mineral weathering, and climate-driven hydrological forcing, reproducing observed soil CO 2 dynamics, groundwater chemistry, and subsurface flow. Our results reveal that seasonal snowmelt enhances carbonate weathering by promoting the infiltration of CO 2 -rich water to depth, while pyrite oxidation is primarily sensitive to low water saturation that facilitates O 2 diffusion through the regolith. Topography modulates the spatial distribution of shale weathering, as steeper slopes enhance lateral drainage, favoring the delivery of reactants to greater depths. While shale weathering at our site acts as a transient carbon sink, with silicates and carbonates buffering acidity and promoting atmospheric CO 2 consumption (1% of soil-derived CO 2 ), the exported dissolved inorganic carbon is predominantly geogenic (∼73%). Consequently, when accounting for long-term marine carbonate precipitation. The current weathering regime represents a net source of carbon to the atmosphere. The oxidation of pyrite and petrogenic organic carbon together release approximately 0.9 mol·m −2 ·yr −1 of CO 2 . Our findings highlight the role of topography, hydroclimate, and the coupling between acid-base reactions in shaping the carbon balance and the solute exports in mountainous critical zones.

carbon cycling↗

DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2006

The Scientific and Societal Need for Accurate Global Remote Sensing of Marine Suspended Sediments

Population pressure, commercial development, and climate change are expected to cause continuing alteration of the vital oceanic coastal zone environment. These pressures will influence both the geology and biology of the littoral, nearshore, and continental shelf regions. A pressing need for global observation of coastal change processes is an accurate remotely-sensed data product for marine suspended sediments. The concentration, delivery, transport, and deposition of sediments is strongly relevant to coastal primary production, inland and coastal hydrology, coastal erosion, and loss of fragile wetland and island habitats. Sediment transport and deposition is also related to anthropogenic activities including agriculture, fisheries, aquaculture, harbor and port commerce, and military operations. Because accurate estimation of marine suspended sediment concentrations requires advanced ocean optical analysis, a focused collaborative program of algorithm development and assessment is recommended, following the successful experience of data refinement for remotely-sensed global ocean chlorophyll concentrations.

Acker, James G.↗