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At least 1,063 records · Page 59

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

ABSTRACT Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS − ). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS 2 ). Recently, paradigm-shifting studies indicate that Fe and S in FeS 2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS 2 , as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS 2 , Fe(II)/HS − , or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS − , either as a component of the growth medium [Fe(II)/HS − ] or generated through reduction of FeS 2 , were likely a major factor underpinning these phenotypic differences. IMPORTANCE The methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life’s origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.

59 BASIC BIOLOGICAL SCIENCES↗

Model of Operation-and-Maintenance Costs for Photovoltaic Systems

This article presents a method for calculating costs associated with operation and maintenance (O&M) of photovoltaic (PV) systems. It compiles details regarding the cost and frequency of multiple O&M services to estimate annual O&M costs ($\$$/year) for each year of an analysis period, the net present value ($\$$) of life cycle costs accumulated over the analysis period, and the reserve account amount ($\$$). Here we show that this method is an improvement over the previous averaged or levelized per-unit ($\$$/kW/year) valuations for estimating PV O&M costs, because it allows a detailed selection of services to perform based on system size, market served (e.g., residential, commercial, or utility), type and configuration of system components (e.g., micro-, string or central inverter) and site and environmental conditions (e.g., snow, pollen, bird populations). This model also distinguishes costs that vary from year to year and increase at different rates over time because of heuristic failure distributions (e.g. Weibull or Lognormal distribution) based on actuarial data for many of the services. This cost model was created by the PV O&M Working Group of researchers and industry, sponsored by DOE Solar Energy Technologies Office, and has been published in an on-line version hosted by SunSpec Alliance at apsuite.sunspec.org. A spreadsheet version is included with this paper as supplementary material.

14 SOLAR ENERGY↗

Analysis of dynamic capacity of low-contact-ratio spur gears using Lundberg-Palmgren theory

A concise mathematical model is developed for surface fatigue life of low-contact-ratio spur gears. The expected fatigue life of the pinion, gear, or gear sets may be calculated from the model. An equation for the dynamic capacity of the gear set was also derived in terms of the transmitted tangential tooth load which will give a 10-percent fatigue life of one million pinion revolutions. The theoretical life was compared with experimental data for a set of VAR AISI 9310 gears operating at a Hertz stress of 1.71X10 to the 9th power newtons per square meter (248,000 psi) and 10 000 revolutions per minute. Good agreement was obtained between the experimental and theoretical surface fatigue life of the gears.

Coy, J. J.↗

Methods for the culture of C. elegans and S. cerevisiae in microgravity

To support the study of the effects of microgravity on biological systems, our group is developing and testing methods that allow the cultivation of C. elegans and S. cerevisiae in microgravity. Our aim is to develop the experimental means by which investigators may conduct peer reviewed biological experiments with C. elegans or S. cerevisiae in microgravity. Our protocols are aimed at enabling investigators to grow these organisms for extended periods during which samples may be sub-cultured, collected, preserved, frozen, and/or returned to earth for analysis. Data presented include characterization of the growth phenotype of these organisms in liquid medium in OptiCells(TM) (Biocrystal, LTD).

NASA Center ARC↗

Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System

Root systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes and cis -regulatory elements for further functional validations and root growth improvements in grasses.

59 BASIC BIOLOGICAL SCIENCES↗

Space shuttle nonmetallic materials age life prediction

The chemiluminescence from samples of polybutadiene, Viton, Teflon, Silicone, PL 731 Adhesive, and SP 296 Boron-Epoxy composite was measured at temperatures from 25 to 150 C. Excellent correlations were obtained between chemiluminescence and temperature. These correlations serve to validate accelerated aging tests (at elevated temperatures) designed to predict service life at lower temperatures. In most cases, smooth or linear correlations were obtained between chemiluminescence and physical properties of purified polymer gums, including the tensile strength, viscosity, and loss tangent. The latter is a complex function of certain polymer properties. Data were obtained with far greater ease by the chemiluminescence technique than by the conventional methods of study. The chemiluminescence from the Teflon (Halon) samples was discovered to arise from trace amounts of impurities, which were undetectable by conventional, destructive analysis of the sample.

Mendenhall, G. D.↗

multiplex gas chromatography: A novel analytical technique for future planetary studies

Determination of molecular species comprised of the biogenic elements in the atmospheres of planets and moons of the solar system is one the foremost requirements of the exobiologist studying chemical evolution and the origin of life. Multiplex chromatography is a technique where many samples are pseudo-randomly introduced to the chromatograph without regard to elution of preceding components. The resulting data are then reduced using mathematical techniques such as cross correlation or Fourier Transforms. To demonstrate the utility of this technique for future solar system exploration, chemical modulators were developed. Several advantages were realized from this technique in combination with these modulators: improvement in detection limits of several orders of magnitude, improvement in the analysis of complex mixtures by selectively modulating some of the components present in the sample, increase in the number of analyses that can be conducted in a given period of time, and reduction in the amount of expendables needed to run an analysis. In order to apply this technique in a real application, methane in ambient air was monitored continuously over a period of one week. By using ambient air as its own carrier all expendables beyond power were eliminated.

Valentin, J. R.↗

Configuring the Orion Guidance, Navigation, and Control Flight Software for Automated Sequencing

The Orion Crew Exploration Vehicle is being designed with greater automation capabilities than any other crewed spacecraft in NASA s history. The Guidance, Navigation, and Control (GN&C) flight software architecture is designed to provide a flexible and evolvable framework that accommodates increasing levels of automation over time. Within the GN&C flight software, a data-driven approach is used to configure software. This approach allows data reconfiguration and updates to automated sequences without requiring recompilation of the software. Because of the great dependency of the automation and the flight software on the configuration data, the data management is a vital component of the processes for software certification, mission design, and flight operations. To enable the automated sequencing and data configuration of the GN&C subsystem on Orion, a desktop database configuration tool has been developed. The database tool allows the specification of the GN&C activity sequences, the automated transitions in the software, and the corresponding parameter reconfigurations. These aspects of the GN&C automation on Orion are all coordinated via data management, and the database tool provides the ability to test the automation capabilities during the development of the GN&C software. In addition to providing the infrastructure to manage the GN&C automation, the database tool has been designed with capabilities to import and export artifacts for simulation analysis and documentation purposes. Furthermore, the database configuration tool, currently used to manage simulation data, is envisioned to evolve into a mission planning tool for generating and testing GN&C software sequences and configurations. A key enabler of the GN&C automation design, the database tool allows both the creation and maintenance of the data artifacts, as well as serving the critical role of helping to manage, visualize, and understand the data-driven parameters both during software development and throughout the life of the Orion project.

Odegard, Ryan G.↗

Study of Fallout Metrics for Contamination Analysis

A challenge present in assessing contamination accumulation on many missions is predicting fallout during ground processing given the multiple and various orientations possible for surfaces such as optics and instruments. The best practice assumption has been to quantify particle build up on vertical surfaces as approximately 1/10 that of horizontal surfaces. This fractional relation is important when considering contamination allocations necessary to meet cleanliness requirements since spacecraft can be in many orientations during integration and testing. There is insufficient data to provide confidence in the 1/10 approximation, yet its use can have a significant effect on mission end of life contamination level predictions, leading to expenditures of precious resources to meet mission requirements. A study was conducted to compare and analyze the fallout in horizontal and vertical orientations. Silicon wafers were deployed in four different facilities. Data sets from a long term deployment of wafers were analyzed from a cleanroom facility housing integration of the James Webb Space Telescope (JWST) as well as from a shorter term deployment of wafers in three cleanroom facilities at Goddard Space Flight Center with lower activity. There are many variables influencing the relationship between fallout on vertical and horizontal wafers, including wafer position with respect to air flow, air changes in the facility, duration of exposure, and activity workload. The goal of this continuing study is to develop a tool to inform particulate accumulation predictions for future projects.

Contamination↗

Development of the ARM Lagrangian Large-Scale Forcing Data (ARMLAGTRAJ) Value-Added Product Based on the lagtraj Framework

The Atmospheric Radiation Measurement (ARM) large-scale forcing data developed based on the constrained variational analysis (VARANAL) value-added product (VAP) (Zhang and Lin 1997, Zhang et al. 2001, Xie et al. 2004, Tang et al. 2019) has been widely used for single-column models (SCMs), cloud-resolving models (CRMs), and large-eddy simulation models (LESs) to understand and improve physical processes in models. Recently, the U.S. Department of Energy (DOE) ARM user facility conducted several major field campaigns using ship-based moving observational platforms. For example, the Marine ARM GPCI Investigation of Clouds (MAGIC) field campaign focused on the role of subtropical marine-boundary layer (MBL) clouds, and the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) field campaign aimed to improve understanding of the coupled climate systems in the Arctic. Observations from moving platforms are critical to provide a comprehensive characterization of coupled-system processes associated with all stages of the cloud and/or sea-ice life cycle. Traditional ARM large-scale forcing data have been developed at fixed locations. They need to be extended to include these moving platforms to address data needs for ship-based field campaigns or to support LES modeling in a Lagrangian framework. With these considerations in mind, we develop ARM-type Lagrangian large-scale forcing data sets based on the lagtraj framework (Boeing et al. 2020) with notable enhancements in generating forcings that are more suitable for ARM field campaigns. The lagtraj is a novel tool that generates forcings for LES and SCM simulation in both Lagrangian and Eulerian perspective. This technical report focuses on the major changes we performed on the lagtraj algorithm and provides an overview of the ARM Lagrangian Large-Scale Forcing Data (ARMLAGTRAJ) value-added products.

54 ENVIRONMENTAL SCIENCES↗

Exploring Secondary Markets to Improve Circularity: A Comparative Case Study of Photovoltaics and Hard-Disk Drives

Each year renewable energy generation increases notably with solar panel installations, but these panels have a limited lifespan and will produce between 2 and 4 million metric tons of waste by 2040. Similarly, there are currently between 20 to 70 million hard-disk drives (HDDs) reaching end-of-life (EOL) annually. The circular economy (CE) strives to recycle and reuse materials that are rare and expensive to obtain, minimizing waste. However, studying the potential circularity of photovoltaics (PV) and HDDs requires various data, for instance, on the maturity of the secondhand markets. In this context, the objective of the present study is to identify the current state of secondhand PV and HDD markets. After conducting a literature review, an automated data collection process was set up for that purpose. The analysis of the literature and collected data assess the maturity of the secondhand PV modules and HDDs markets and highlight differences between them.

agent-based modelling↗

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↗

ProvLight: Efficient Workflow Provenance Capture on the Edge-to-Cloud Continuum

Modern scientific workflows require hybrid infrastructures combining numerous decentralized resources on the IoT/Edge interconnected to Cloud/HPC systems (aka the Computing Continuum) to enable their optimized execution. Understanding and optimizing the performance of such complex Edge-to-Cloud workflows is challenging. Capturing the provenance of key performance indicators, with their related data and processes, may assist in understanding and optimizing workflow executions. However, the capture overhead can be prohibitive, particularly in resource-constrained devices, such as the ones on the IoT/Edge.To address this challenge, based on a performance analysis of existing systems, we propose ProvLight, a tool to enable efficient provenance capture on the IoT/Edge. We leverage simplified data models, data compression and grouping, and lightweight transmission protocols to reduce overheads. We further integrate ProvLight into the E2Clab framework to enable workflow provenance capture across the Edge-to-Cloud Continuum. This integration makes E2Clab a promising platform for the performance optimization of applications through reproducible experiments.We validate ProvLight at a large scale with synthetic workloads on 64 real-life IoT/Edge devices in the FIT IoT LAB testbed. Evaluations show that ProvLight outperforms state-of-the-art systems like ProvLake and DfAnalyzer in resource-constrained devices. ProvLight is 26—37x faster to capture and transmit provenance data; uses 5—7x less CPU; 2x less memory; transmits 2x less data; and consumes 2—2.5x less energy. ProvLight [1] and E2Clab [2] are available as open-source tools.

Rosendo, Daniel↗

An Adaptive Tracking Algorithm for Convection in Simulated and Remote Sensing Data

A robust and computationally efficient object tracking algorithm is developed by incorporating various tracking techniques. Physical properties of the objects, such as brightness temperature or reflectivity, are not considered. Therefore, the algorithm is adaptable for tracking convection-like features in simulated data and remotely sensed two-dimensional images. In this algorithm, a first guess of the motion, estimated using the Fourier phase shift, is used to predict the candidates for matching. A disparity score is computed for each target–candidate pair. The disparity also incorporates overlapping criteria in the case of large objects. Then the Hungarian method is applied to identify the best pairs by minimizing the global disparity. The high-disparity pairs are unmatched, and their target and candidate are declared expired and newly initiated objects, respectively. They are tested for merger and split on the basis of their size and overlap with the other objects. The sensitivity of track duration is shown for different disparity and size thresholds. The report highlights the algorithm’s ability to study convective life cycles using radar and simulated data over Darwin, Australia. The algorithm skillfully tracks individual convective cells (a few pixels in size) and large convective systems. The duration of tracks and cell size are found to be lognormally distributed over Darwin. The evolution of size and precipitation types of isolated convective cells is presented in the Lagrangian perspective. This algorithm is part of a vision for a modular platform [viz., TINT is not TITAN (TINT) and Tracking and Object-Based Analysis of Clouds (tobac)] that will evolve into a sustainable choice to analyze atmospheric features.

54 ENVIRONMENTAL SCIENCES↗

Assessing complexity and dynamics in epidemics: geographical barriers and facilitators of foot-and-mouth disease dissemination

Introduction: Physical and non-physical processes that occur in nature may influence biological processes, such as dissemination of infectious diseases. However, such processes may be hard to detect when they are complex systems. Because complexity is a dynamic and non-linear interaction among numerous elements and structural levels in which specific effects are not necessarily linked to any one specific element, cause-effect connections are rarely or poorly observed. Methods: To test this hypothesis, the complex and dynamic properties of geo-biological data were explored with high-resolution epidemiological data collected in the 2001 Uruguayan foot-and-mouth disease (FMD) epizootic that mainly affected cattle. County-level data on cases, farm density, road density, river density, and the ratio of road (or river) length/county perimeter were analyzed with an open-ended procedure that identified geographical clustering in the first 11 epidemic weeks. Two questions were asked: (i) do geo-referenced epidemiologic data display complex properties? and (ii) can such properties facilitate or prevent disease dissemination? Results: Emergent patterns were detected when complex data structures were analyzed, which were not observed when variables were assessed individually. Complex properties–including data circularity–were demonstrated. The emergent patterns helped identify 11 counties as ‘disseminators’ or ‘facilitators’ (F) and 264 counties as ‘barriers’ (B) of epidemic spread. In the early epidemic phase, F and B counties differed in terms of road density and FMD case density. Focusing on non-biological, geographical data, a second analysis indicated that complex relationships may identify B-like counties even before epidemics occur. Discussion: Geographical barriers and/or promoters of disease dispersal may precede the introduction of emerging pathogens. If corroborated, the analysis of geo-referenced complexity may support anticipatory epidemiological policies.

60 APPLIED LIFE SCIENCES↗

Hubble Space Telescope meteoroid-debris protection analysis

A system level failure could occur if the Hubble Space Telescope's (ST) capability to operate as a facility on-orbit is critically reduced or when a significant reduction in the quality of science data is registered. Failure could occur if a meteoroid/debris impact damages a component of a major support subsystem or if a meteoroid/debris penetration causes straylight contamination in the light shield, forward shell, aft shroud, or through the aperture door. The ST was analyzed to find the probability of no critical penetration. This probability value was found to be 92.25% for a two-year service life. A straylight leakage repair technique was recommended for the aft shroud, the region found most likely to be critically penetrated. Fozar tape and multilayer insulation blankets are suggested as posible repair materials.

Horn, J.↗

A Miniaturized Video System for Monitoring Drosophila Behavior

Long-term spaceflight may induce a variety of harmful effects in astronauts, resulting in altered motor and cognitive behavior. The stresses experienced by humans in space - most significantly weightlessness (microgravity) and cosmic radiation - are difficult to accurately simulate on Earth. In fact, prolonged and concomitant exposure to microgravity and cosmic radiation can only be studied in space. Behavioral studies in space have focused on model organisms, including Drosophila melanogaster. Drosophila is often used due to its short life span and generational cycle, small size, and ease of maintenance. Additionally, the well-characterized genetics of Drosophila behavior on Earth can be applied to the analysis of results from spaceflights, provided that the behavior in space is accurately recorded. In 2001, the BioExplorer project introduced a low-cost option for researchers: the small satellite. While this approach enabled multiple inexpensive launches of biological experiments, it also imposed stringent restrictions on the monitoring systems in terms of size, mass, data bandwidth, and power consumption. Suggested parameters for size are on the order of 100 mm3 and 1 kg mass for the entire payload. For Drosophila behavioral studies, these engineering requirements are not met by commercially available systems. One system that does meet many requirements for behavioral studies in space is the actimeter. Actimeters use infrared light gates to track the number of times a fly crosses a boundary within a small container (3x3x40 mm). Unfortunately, the apparatus needed to monitor several flies at once would be larger than the capacity of the small satellite. A system is presented, which expands on the actimeter approach to achieve a highly compact, low-power, ultra-low bandwidth solution for simultaneous monitoring of the behavior of multiple flies in space. This also provides a simple, inexpensive alternative to the current systems for monitoring Drosophila populations in terrestrial experiments, and could be especially useful in field experiments in remote locations. Two practical limitations of the system should be noted: first, only walking flies can be observed - not flying - and second, although it enables population studies, tracking individual flies within the population is not currently possible. The system used video recording and an analog circuit to extract the average light changes as a function of time. Flies were held in a 5-cm diameter Petri dish and illuminated from below by a uniform light source. A miniature, monochrome CMOS (complementary metal-oxide semiconductor) video camera imaged the flies. This camera had automatic gain control, and this did not affect system performance. The camera was positioned 5-7 cm above the Petri dish such that the imaging area was 2.25 sq cm. With this basic setup, still images and continuous video of 15 flies at one time were obtained. To reduce the required data bandwidth by several orders of magnitude, a band-pass filter (0.3-10 Hz) circuit compressed the video signal and extracted changes in image luminance over time. The raw activity signal output of this circuit was recorded on a computer and digitally processed to extract the fly movement "events" from the waveform. These events corresponded to flies entering and leaving the image and were used for extracting activity parameters such as inter-event duration. The efficacy of the system in quantifying locomotor activity was evaluated by varying environmental temperature, then measuring the activity level of the flies.

Bhattacharya, Sharmila↗

Space Algae-2 Ground and Lunar Analog Studies in Preparation for Long-Duration Propagation of Cyanobacteria in Spaceflight

There are numerous applications for microalgae in spaceflight missions and on Earth, such as, oxygen production, carbon dioxide removal, nutrition, wastewater processing, and biofuel production. Space Algae-2 aims to test the genetic stability of Arthrospira platensis, commonly known as spirulina, during six-months of continuous culture in spaceflight on the International Space Station. Long-duration exposure to ionizing radiation and microgravity may impact growth, nutrient composition, and genetic stability. The high protein, vitamin, antioxidant content, and radiation resistance make spirulina a promising candidate for bioregenerative life support systems during long-duration missions. A concept of operations was developed to grow and harvest algal biomass in space. Preflight testing experiments were conducted to optimize conditions for an extended growth period in a gas permeable bioreactor bag. Preflight and post-harvest storage methods were developed in addition to a novel cryopreservation method. After sample return, multi-omics analysis will be conducted to determine the mutation rate, gene expression, and protein and metabolite profile. The concept of operations for Space Algae-2 was tested at HI-SEAS (Hawai’i Space Exploration Analog and Simulation) during a six-day lunar analog mission (EMMIHS23, EuroMoonMars, International MoonBase Alliance, HI-SEAS, 2023). A. platensis was grown in the semi-controlled environment using flight-like hardware and solar powered LED lights. Then, the biomass was harvested and used to supplement bread as an example of A. platensis utilization. Overall, the data collected from Space Algae-2 will inform potential bioengineering of spirulina for space and terrestrial applications.

Algae↗