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DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

NASA NTRS1994

Spectral filtering for plant production

Both plants and animals have one general commonality in their perception of light. They both are sensitive primarily to the 400 to 700 nm wavelength portion of the electromagnetic spectrum. This is referred to as the visible spectrum for animals and as the photosynthetically active radiation (PAR) spectrum for plants. Within this portion of the spectrum, animals perceive colors. Relatively recently it has been learned that within this same spectral range plants also demonstrate varying responses at different wavelengths, somewhat analogous to the definition of various colors at specific wavelengths. Although invisible to the human eye, portions of the electromagnetic spectrum on either side of the visible range are relatively inactive photosynthetically but have been found to influence important biological functions. These portions include the ultraviolet (UV approximately equal to 280-400 nm) and the far-red (FR approximately equal to 700-800 nm). The basic photoreceptor of plants for photosynthesis is chlorophyll. It serves to capture radiant energy which combined with carbon dioxide and water produces oxygen and assimulated carbon, used for the synthesis of cell wall polysaccarides, proteins, membrane lipids and other cellular constituents. The energy and carbon building blocks of photosynthesis sustain growth of plants. On the other hand, however, there are other photoreceptors, or pigments, that function as signal transducers to provide information that controls many physiological and morphological responses of how a plant grows. Known photomorphogenic receptors include phytochrome (the red/far-red sensor in the narrow bands of 655-665 nm and 725-735 nm ranges, respectively) and 'cryptochrome' (the hypothetical UV-B sensor in the 280-320 nm range). Since the USDA team of W. L. Butler, S. B. Hendricks, H. A. Borthwick, H. A. Siegleman and K. Norris in Beltsville, MD detected by spectroscopy, extracted and identified phytochrome as a protein in the 1950's, many other investigators have found evidence of its control functions in plants. Considerably less, however, is known about the yet non-isolated cryptochrome. The information-transferring roles of photoreceptors in plants at specific spectral ranges quite naturally stimulated plant scientists and engineers to consider physically manipulating light to achieve desired physiological and morphological characteristics. One way to manipulate light is to filter it through materials that selectively transmit portions of the sun's spectrum in and near the PAR range.

Young, Roy E.↗

NASA NTRS2009

Multi-Mission Suitability of the NASA Ames Modular Common Bus

The obvious advantages of small spacecraft - their lower cost structure and the rapid development schedule - have enabled a large number of missions in the past. However, most of these missions have been focused on Earth observation from low Earth orbits. In 2006, the Small Spacecraft Division at the NASA Ames Research Center began the development of the Modular Common Bus, a spacecraft capable of delivering scientifically and technically useful payloads to a variety of destinations within 0.1 AU around the Earth. The core technologies used in the Common Bus design are a composite structure with body-mounted solar cells, an integrated avionics unit, and a high performance bipropellant propulsion system. Due to its modular approach, the Common Bus can be adapted to fit specific mission needs while still using a standardized and qualified set of components. Additionally a number of low cost launch vehicles are supported, resulting in overall mission costs of around $150M including the launch vehicle but excluding the science payloads. This significant reduction in cost and the shorter development time would enable NASA to conduct more frequent exploration missions within its budget and timeframe constraints, compared to the status quo. In this paper the suitability of the Common Spacecraft Bus for four different exploration scenarios is analyzed. These scenarios include a lunar orbiter, a lunar lander, a mission to a Sun-Earth Libration Point, and a rendezvous mission to a Near Earth Object. For each scenario, a preliminary design reference mission is developed and key design parameters for the spacecraft are determined.

Tietz, Sascha↗

DOE OSTI2019

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1995

Bicycle ergometer instrumentation to determine muscle and bone forces during exercise

It is hypothesized that bone loss experienced by astronauts in zero gravity conditions may be curtailed by appropriate exercise. According to Wolf's law, bone regenerates when muscles produce stresses by pulling on the bone during daily activity and/or exercise on Earth. to use this theory to prevent or decrease bone loss, one needs to quantify musculoskeletal loads and relate them to bone density changes. In the context of the space program, it is desirable to determine musculoskeletal loads during exercise (using the bicycle ergometer in this case) so that one may make similar measurements on Earth and in space. In this manner, load measurements on Earth may be used as reference to generate similar loads during exercise in space. The work reported in this document entails a musculoskeletal load measurement system that, when complete, will provide forces at muscle insertion points and other contact points, on bone. This data will be used by Dr. Beth A. Todd, who is also a SSF working with Dr. Shackelford, as input to a finite element model of bone sections to determine stress distributions. A bicycle ergometer has been instrumented to measure parameters needed to determine musculoskeletal forces during exercise. A primary feature of the system is its compactness. It uses small/light sensors without line-of-sight requirements. The system developed includes sensors, signal processing, a data acquisition system, and software to collect the data. The sensors used include optical encoders to measure position and orientation of the pedal (foot), accelerometers to determine kinematic parameters of the shank and thigh, load cells to measure pedal forces on the sagittal plane, and EMG probes to measure muscle activity. The signals are processed using anti-aliasing filters and amplifiers. The sensors' output is digitized using 30 channels of a board mounted inside a 486 class PC. A program sets the data acquisition parameters and collects data during a time period specified by the user. The data is put directly into a file on the hard disk in binary form. The 30 channels are sampled at 200 KHz, and each 30 channel scan is done at a rate of 1000 Hz. The instrumented ergometer has been flown in the KC-135 zero-gravity (zero-g) flight to collect information needed to determine musculoskeletal forces under these conditions. Similar information has been collected in 1-g conditions for comparision with the results from the zero-g case. At this time, the sets of data from both experiments are being processed. An existing methodology will be used to determine the kinematic parameters of the shank and thigh using accelerometer and encoder data. This methodology was developed during the fellow's previous NASA/ASEE fellowship and thanks to a Director's Grant. In the future, a methodology to determine the musculoskeletal forces using Newton's Law of Motion and optimization techniques will be developed to determine forces exerted by particular muscles.

Figueroa, Fernando↗

DOE OSTI2022

Roll to Roll (R2R) Manufacturing of Electrolysis Electrodes for Low Cost Hydrogen Production: Cooperative Research and Development Final Report, CRADA Number CRD-18-00780

NREL, Argonne National Laboratory (ANL) and Oak Ridge National Laboratory (ORNL), which are also referred to collectively herein as the "Contractors" will perform electrode ink development and characterization, focusing on 1) inks with appropriate properties for R2R (gravure and slot-die) coating onto PFSA membrane and 2) catalysts suitable for electrolysis. Participant will develop acceptance criteria and characterization methods for direct coating on the membrane. The purpose of this project is to show feasibility for cost reduction of the electrode through increased throughput and improved material utilization. Successful completion of this project will result in more affordable hydrogen production via proton exchange membrane (PEM) electrolysis by substantially reducing the anode precious metal content and catalyst-coated membrane processing costs. Assists laboratory in achieving programmatic scope, adds new capability to the laboratory's core competencies. This project uses and enhances the laboratory's core competencies, and enhances U.S. competitiveness by utilizing DOE developed intellectual property and/or capabilities. This project will benefit the Fuel Cell subprogram within the EERE Fuel Cell Technologies Office (FCTO) by actively developing materials, formulations, components, and processes for PEM electrolyzer stacks for overcoming critical technical barriers to widespread hydrogen production for zero-emission transportation applications. Through this JWS, NREL, ANL and ORNL are assisting a key domestic industry partner, Proton Energy Systems, Inc., in the area of low-cost electrolyzer electrode formulation and coating technology. After completion of this project, NREL, ANL and ORNL will be able to verify whether the direct deposit coating processes investigated are suitable for producing CCMs for PEM electrolyzers, which is of great interest and benefit to the DOE EERE Fuel Cell Technologies Office (FCTO) and H2@Scale missions.

08 HYDROGEN↗

DOE OSTI2020

A Systems Biology Approach to Energy Flow in H 2 Producing Microbial Communities: Microbial Mats

This report describes the results of work conducted at NASA Ames Research Center, in collaboration with investigators at Lawrence Livermore National Laboratory, during the time period 12/15/2014 to 12/15/2017. The work was an extension of a collaboration with LLNL that began in 2008. Work this reporting period focused primarily on tasks related to microbial mats from both the Elkhorn Slough and Baja California field sites, including the analysis and publication of data produced prior to 12/15/2014. During this reporting period, in addition to the microbial mat work, we also conducted a series of experiments with a particular algal-bacterial association (C. sorokiniana and A. brasilense). A number of aspects of this well-characterized algal-bacterial association enabled us not only to further our understanding of interactions between these particular organisms, but to apply that knowledge and techniques to our collection of microorganisms isolated from microbial mats. Microbial mat experiments focused both on intact mat communities and on cultures of organisms isolated from the mats (the Microbial Mat Living Library). In a series of co-culture experiments, we documented both positive and negative interactions amongst heterotrophic and autotrophic isolates of microbial mat microorganisms. One particularly important and novel mat cyanobacterium (ESFC-1) was studied in detail. We developed techniques to pursue an investigation of functional redundancy (the idea that closely related organisms perform identical roles in a community) in cyanobacterial autotrophs in the Elkhorn Slough microbial mat. In those experiments, we documented numerous instances of increases in growth rate between co-cultures of two organisms (relative to their growth rate in isolation) performing what would seem to be identical functional roles. Simplified microbial mat communities consisting of organisms from the Microbial Mat Living Library were constructed and studied in laboratory experiments. The “constructed mats” were grown in standard laboratory glassware and plasticware, but cultures were also combined with artificial materials in an effort to re-create the three-dimensional structure of naturally occurring microbial mats. These constructed mats re-created a number of functions attributable to natural microbial mats (N-fixation, H2-production) and simplified their study using molecular ecological techniques due to the smaller number of microbial “species” present. Cyanobacteria which migrated in response to vertical variations in light intensity (irradiance) obtained characteristic positions in constructed mats that were similar to their positions in natural mats. A detailed investigation of nitrogen cycling in both the Baja California and Elkhorn Slough microbial mats was initiated during this reporting period. The nitrogen cycle in the microbial mats has not been studied in depth, despite the fact that nitrogen usually limits growth in marine environments. The organisms conducting nitrogen cycling in both microbial mats were studied using the genomes available from earlier work on these mats, as well as with a targeted approach using molecular ecological methods developed here. Quantitative measurements of rates of nitrogen transformations were made using stable isotopically labeled nitrogen. The processes quantified and examined using molecular ecological methods included: nitrogen fixation, ammonification, ammonium and nitrate assimilation, denitrification, anaerobic oxidation of ammonium, and dissimilatory nitrate reduction to ammonium. In a series of experiments designed to examine a potential application for microbial mats, we demonstrated that both Elkhorn Slough and Baja California microbial mats were very effective in removing large quantities of both nitrate and ammonium from waste streams containing these compounds at levels where they would be considered to be pollutants. Considerable effort was expended during this reporting period to analyze, and prepare for publication, metagenomes and metatranscriptomes collected from two experimental manipulations of microbial mats. The first, a diel study, was conducted in November 2011, while the second, an investigation of the effects of sulfate on community composition, was conducted during this reporting period. For the earlier study, reference-based and reference-free methods were used to assess microbial ecology and genetic partitioning in these complex microbial systems, and that work is available as a pre-print. Four metagenomes from the same experiment were published. In the second, longer (nearly 200 day) manipulation, rRNA iTag libraries for cDNA and DNA were analyzed to determine the effects of sulfate concentration on microbial mat community composition over the course of the experiment. Work on the algal-bacterial association (Chlorella sorokiniana and Azospirillum brasilense) focused initially on demonstrating the transfer of carbon and nitrogen between the partners, using stable isotopic labeling and the LLNL NanoSIMS. Subsequently, the potential role of diazotrophy (nitrogen fixation) by the bacterial partner in supporting the growth of the association was assessed in a series of experiments. It appears to be the case that, although the bacterial partner demonstrably increases the fitness of the algae under nitrogen limitation, and cells of C. sorokiniana receive nitrogen originally fixed from atmospheric nitrogen by A. brasilense, the amount of nitrogen obtained by diazotrophy is too small to explain the increase in fitness.

08 HYDROGEN↗

NASA NTRS1999

Instrumentation and Methods to Measure Dynamic Forces During Exercise Using the Horizontal Exercise Machine

It is hypothesized that bone loss experienced by astronauts in zero gravity conditions may be curtailed by appropriate exercise. According to Wolf's law, bone regenerates when muscles produce stresses by pulling on the bone during daily activity and/or exercise on Earth. To use this theory to prevent or decrease bone loss, one needs to quantify musculoskeletal loads and relate them to bone density changes. In the context of the space program, it is desirable to determine musculoskeletal loads during exercise so that one may make similar measurements on Earth and in space. In this manner, load measurements on Earth may be used as reference to generate similar loads during exercise in space. A research project to investigate the effects of high-resistive exercise to decrease bone density loss underzero-gravity conditions is being carried out in Life Sciences Research Laboratories at NASA JSC. The project consists of a bed-rest study whereby subjects remain in horizontal position for seventeen weeks. During the study, a subset of those subjects executes a regime of resistive exercises in the horizontal exercise machine (HEM). The HEM was designed so that subjects remain horizontal while exercising to minimize gravity loading even during exercise. Bone density of each subject is measured throughout the duration of their participation. The objective of the study is to determine if the resistive exercises are effective in diminishing or eliminating bone loss. My participation in this project relates to instrumentation, measurement, and processing of signals from displacement sensors (optical encoders) and load-cells. Measurement of displacements will be used to determine the motion of the body during exercise, and load measurements will be used (along with displacement data) to determine forces and torques exerted on each section of the body during exercise. Further, I have assisted in specifying new sensors to be added to the HEM and to a new prototype resistive exercise machine called the Interim Resistive Exercise Device (IRED). New load cells and encoders should be mounted in these devices to obtain more complete kineto-dynamic information. This report includes a description of the instrumentation that was built to perform measurements in the HEM and the IRED, along with the software that was developed to collect the measurements. It also includes examples of measurements taken in the HEM. Finally, a plan is laid out that describes how these measurements may be used to determine forces exerted by muscles for each exercise.

Figueroa, Fernando↗

DOE OSTI2019

First Annual Progress Report on the Procurement and Post-Irradiation Examination of the Selected Samples of Alloy 800H and Grade 92 and 91 Steels

Ferritic-martensitic steel Grade 92, with Grade 91 as a reference, together with austenitic stainless steel (or Incoloy Alloy) 800H and its grain-boundary-engineered version 800H-TMP (Thermo-Mechanical Processing), is investigated in this project. A total of fifteen Grade 92 samples from two or three heats, four T91 samples from two heats, and six 800H and six 800H-TMP samples from one heat were selected, which were primarily irradiated in the Advanced Test Reactor (ATR) of Idaho National Laboratory (INL), with the rest in the High Flux Isotope Reactor (HFIR) of Oak Ridge National Laboratory (ORNL), BOR-60 of Russia, and Phénix reactor of France. The samples were irradiated in the temperature range of 241 to 720°C and a dose range of 1.28 to ~70 displacements per atom. All the INL and ORNL samples and part of the LANL (Los Alamos National Laboratory) samples have been received at the Irradiated Materials Examination and Testing (IMET) hot cell facility. The selected ORNL samples include six Grade 92 and two 800H samples, which were irradiated in the HFIR to 0.46–14.66 dpa at 400 to ~720°C. The Grade 92 is an optimized heat and named as G92-2b. The two 800H samples have one sample as the standard solution-annealed condition and the other sample as a TMP condition with a maximized fraction of low-Σ coincidence site lattice (CSL) boundaries. Tensile test of the G92-2b samples were conducted at room temperature in the IMET hot cell. The lower temperature irradiation at 400–496.7°C to 0.52–14.66 dpa resulted in minimal changes in tensile properties. However, the higher temperature irradiation at ~683.3–720°C to 0.46–14.63 dpa tended to reduce yield and tensile strength by about –136 to –311 MPa and plastic elongation by –1 to –3% with the increasing dose. The 800H and 800H-TMP samples were tensile-tested at their irradiation temperature 580°C in the IMET hot cell, which showed >40% increase in yield and tensile strength with nearly 9% reduction in elongation for 800H-TMP compared with 800H. Three of the G92-2b samples, i.e., GB04 (7.44 dpa at ~490°C), GB05 (14.66 dpa at 496.7°C), and GB12 (14.63 dpa at ~720°C), were examined at the LAMDA for Vickers hardness measurements and microstructural characterization by SEM and TEM. Vickers hardness was successfully measured on GB12, which was reduced by is – (112.4 ± 12.3) HV1 from the control sample. However, the Vickers hardness measurements were failed on GB04 and GB05 because the samples were polished too thin to prevent the interference from the substrate (epoxy). The other half of the GB04 and GB05 will be polished for the hardness measurements, as well as nanoindentation studies. Fractography by SEM indicated increased numbers of ductile dimples (or voids) with the increasing irradiation dose, while significantly increased numbers and sizes of dimples with the increasing irradiation temperature. TEM characterization exhibited the presence of Cr 23 C 6 , VN, and Laves precipitates at boundaries and matrix, which showed pronounced precipitate-dislocation interactions (pinning effect). Dense dislocations but limited dislocation loops were observed in the samples, which noticeably reduced in GB12. Additionally, some tiny partially amorphized spherical domains were observed in GB12, which had a normal body-centered cubic lattice parameter of 9Cr steels at the surround regions but ~11% smaller than the lattice parameter of the matrix away from the amorphized spherical domains. Further characterization will be pursued to clarify the new findings.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Abstract An i‐motif is a non‐canonical DNA structure implicated in gene regulation and linked to cancers. The C‐rich strand of the HRAS oncogene, 5′‐CG CCC GTG CCC TGCG CCC GCAA CCC GA‐3′ (herein referred to as iHRAS), forms an i‐motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto‐oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i‐motif dimer capped by two loops on each end and linked by a connecting region. Six C−C + base pairs form each i‐motif core, and the core regions are extended by a G−G base pair and a cytosine stacking. Extensive canonical and non‐canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i‐motif from a human oncogene. This structure sheds light on i‐motifs folding and function in the cell.

Li, Kevin S.↗

DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Li, Kevin S.↗

DOE OSTI2023

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

Abstract Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Replication of Segments of STS-94 as a Lunar Surface Mission

The Artemis program established the goal to land the first woman and first person of color on the Moon, but that is only the beginning of the program. Artemis plans to move towards a sustainable phase, with four crew living on the lunar surface for roughly 30-day annual missions, operating from a Pressurized Rover (PR) and a Surface Habitat (SH). The crew will split up – two living and operating from the PR and the others in the SH, perhaps swapping places halfway through the surface mission. There is a significant degree of maturity surrounding PR operations due to the NASA Desert Research and Technology Studies field tests from 2007-2011. However, there is a degree of uncertainty surrounding activity in the SH, with anecdotal speculation among some Artemis lunar surface engineers that the SH crew might not be fully utilized. Contrary to this belief, there is evidence in US human spaceflight history that the SH crew may instead be extremely busy. In particular, portions of the STS-94 Microgravity Science Lab mission demonstrate a science-based use case for crew activity in the SH. Fifteen Spacelab missions (not including STS-83, which was terminated early due to a fuel cell problem and reflown as STS-94) and eight Spacehab missions used the previously mentioned modules as science labs to expand the science capability of shuttle orbital missions, most flown prior to the assembly of the International Space Station. STS-94 is selected as an example of these flights. STS-94 was a 15.7-day mission with a 7-person crew. The crew operated in split 12-hour shifts, enabling 24-hour science operations. STS-94 used the space shuttle Columbia with the Spacelab module and Extended Duration Orbiter pallet in the cargo bay. The STS-94 physical science investigations were intended to explore various physical aspects of microgravity. These same investigations can be conducted on the Moon to explore 1/6 gravity. The Spacelab module was outfitted with several key facilities to enable this research: Large Isothermal Furnace, Combustion Module-1, Droplet Combustion Experiment, EXPRESS Rack, TEMPUS, Gravity Measurement Devices, and Middeck Glovebox. The current reference concept for the SH is a hybrid inflatable in a vertical orientation. Fairly typical of hybrid inflatables, the SH has an aluminum core pressurized section and a larger inflatable volume, in this case attaching to the top of the core. Two crew will live in the SH at a time, though four can briefly occupy the habitat, such as for contingency or handover activities. This paper will discuss use of the STS-94 physical science equipment in the SH and options for the architectural layout of a resulting physics laboratory. It will also discuss how this laboratory may accompany other science facilities such as biology, human research, and geology. The person hours used by the STS-94 crew to conduct physical science research will be estimated and then mapped to a two-person SH crew, making it possible to determine how many days are required in the SH to complete the lunar gravity physical science investigations at varying levels of crew availability.

STS-94↗

NASA NTRSDate not supplied

Evaluating Long-Term Changes in Atmospheric Ozone

Ozonesondes have made inexpensive, accurate measurements of ozone from the ground to 30km for more than 50 years. The data are used extensively for trend analyses and for evaluation of satellite and model data products, and are also part of climatologies that are used as a priori data for satellite retrievals. They are essential as a transfer standard when merging shorter satellite-derived time series, and are the most important source of trend-quality long-term records below about 18 km. The importance of long-term ozonesonde records as a stable reference has led to increased attention to quantifying uncertainties and changes in ozonesonde data. Based on past intercomparison data, ECC sondes show a modest (~1-5%) high bias with respect to UV-absorption measurements (including MOZAIC-IAGOS) in the troposphere, with an uncertainty of 5%, but no evidence of a change with time. Other sonde types show an increase of 5-20% in sensitivity to tropospheric ozone from 1970-1995. Agreement in the stratosphere is much better. In the past 20 years ozonesonde precision has improved by a factor of 2, primarily through the adoption of strict standard operating procedures. In addition, many of the most important ozonesonde records have been re-evaluated and corrected, and detailed estimates made of their biases and uncertainties. Corrections to historical data for known issues may reduce biases but simultaneously introduce additional uncertainties. The uncertainty budget for the ozone partial pressure reading has contributions from stoichiometry, cell background current, pump efficiency and temperature, sensing solution type and volume. The much-discussed “background current” has recently been shown to be primarily related to reaction stoichiometry. Several quality assurance issues remain, but are tractable problems that can be addressed with further research. This will be required if the present goal of better than 5% overall uncertainty throughout the global ozonesonde network is to be achieved. Finally, the importance of regular sonde intercomparisons, employing UV photometers traceable to the modern UV-absorption standard, and of regular comparison of operational station records with multiple satellite sensors, is emphasized.

Ozonesondes↗

DOE OSTI2022

Microglia are implicated in the development of paclitaxel chemotherapy-associated cognitive impairment in female mice

Chemotherapy remains a mainstay in the treatment of many types of cancer even though it is associated with debilitating behavioral side effects referred to as “chemobrain,” including difficulty concentrating and memory impairment. The predominant hypothesis in the field is that systemic inflammation drives these cognitive impairments, although the brain mechanisms by which this occurs remain poorly understood. Here, we hypothesized that microglia are activated by chemotherapy and drive chemotherapy-associated cognitive impairments. To test this hypothesis, we treated female C57BL/6 mice with a clinically-relevant regimen of a common chemotherapeutic, paclitaxel (6 i.p. doses at 30 mg/kg), which impairs memory of an aversive stimulus as assessed via a contextual fear conditioning (CFC) paradigm. In this work, paclitaxel increased the percent area of IBA1 staining in the dentate gyrus of the hippocampus. Moreover, using a machine learning random forest classifier we identified immunohistochemical features of reactive microglia in multiple hippocampal subregions that were distinct between vehicle- and paclitaxel-treated mice. Paclitaxel treatment also increased gene expression of inflammatory cytokines in a microglia-enriched population of cells from mice. Lastly, a selective inhibitor of colony stimulating factor 1 receptor, PLX5622, was employed to deplete microglia and then assess CFC performance following paclitaxel treatment. PLX5622 significantly reduced hippocampal gene expression of paclitaxel-induced proinflammatory cytokines and restored memory, suggesting that microglia play a critical role in the development of chemotherapy-associated neuroinflammation and cognitive impairments. This work provides critical evidence that microglia drive paclitaxel-associated cognitive impairments, a key mechanistic detail for determining preventative and intervention strategies for these burdensome side effects.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Comprehensive framework for assessing and optimizing existing research networks

Conservation, monitoring, and research networks, or collections of ecological research sites unified under a common mission of data collection or a research mission, are essential infrastructure for understanding large landscapes. However, most networks developed opportunistically over decades rather than through systematic design, creating potential limitations in the ability to address conservation challenges across entire regions. We developed a framework to evaluate how well an existing research network represents the environmental conditions its members study and devised an approach to rank sites of priority for strategic expansion. Our approach measures performance through environmental representativeness, geographic coverage, and adequacy for scientific inference and thus optimizes limited monitoring resources to maximize scientific impact. We demonstrated this approach with the U.S. Department of Agriculture (USDA) Forest Service Experimental Forests and Ranges Network (EFRN), a 79‐site network across the United States that grew opportunistically over a century. At the national scale, the network effectively captured high‐biomass forests important for carbon cycle research; 82% of forest biomass was in well‐represented areas. Some areas in Texas, Florida, the Rocky Mountains, and the West Coast had no relevant EFRN sites, which limits the ability to make regional inferences. A fundamental challenge for the EFRN was that sites improving regional extent coverage sometimes provided minimal national benefits, which can create conflicts between local and global priorities. Adding the highest‐ranked candidate site provided a relevant site for 17% of currently poorly represented 1‐km pixel cells nationally, but regional and national site rankings varied considerably due to nested spatial inference. This framework provides quantitative tools for strategic infrastructure decision‐making, ensures that limited monitoring resources maximize conservation impact, and can be applied broadly to address the widespread challenge of optimizing conservation and monitoring networks worldwide.

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