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DOE OSTI2013

Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data

The advent of high throughput technologies capable of comprehensive analysis of genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification of molecular markers of disease processes. However, it has simultaneously complicated the problem of extracting meaningful signatures of biological processes from these complex datasets. The process of biomarker discovery and characterization provides opportunities both for purely statistical and expert knowledge-based approaches and would benefit from improved integration of the two. Areas covered In this review we will present examples of current practices for biomarker discovery from complex omic datasets and the challenges that have been encountered. We will then present a high-level review of data-driven (statistical) and knowledge-based methods applied to biomarker discovery, highlighting some current efforts to combine the two distinct approaches. Expert opinion Effective, reproducible and objective tools for combining data-driven and knowledge-based approaches to biomarker discovery and characterization are key to future success in the biomarker field. We will describe our recommendations of possible approaches to this problem including metrics for the evaluation of biomarkers.

bioinformatics↗

DOE OSTI2023

Task 2.1: Adsorption-Based ISPR for BETO-Relevant Bioproducts

This task focuses on the development of adsorption-based in situ product recovery (ISPR) integrated with simulated moving bed chromatography for the recovery and purification of carboxylate products that are relevant to BETO. ISPR has been pursued previously in the Separations Consortium to recover carboxylic acids near or below their pKa values with liquid-liquid extraction coupled to downstream distillation. However, there are many acid products in the BETO portfolio that require neutralization well above their pKa values wherein ISPR could still be a major benefit to the bioprocess performance, including muconic acid, beta-ketoadipic acid, 3-hydroxypropionic acid, itaconic acid, butyric acid, and others. In this task, we are combining dynamic filtration with a rotating ceramic disk, resin capacity measurements, tailored resin synthesis, and simulated moving bed chromatography into an ISPR system that can be used to recover BETO-relevant carboxylates from bioreactor cultivations. We are working across process scales and using computational modeling where applicable alongside techno-economic analysis and life cycle assessment to understand major cost, energy, and GHG emissions drivers. The impact of this project will be a bench-scale integrated approach to recover carboxylate products in situ, which will reduce the waste generation from biological carboxylate production processes and improve the productivities of biological systems.

bio-based acid↗

DOE OSTI2019

In Situ Liquid Secondary Ion Mass Spectrometry: A Surprisingly Soft Ionization Process for Investigation of Halide Ion Hydration

The understanding of ion solvation phenomenon is of significance due to their influences on many important chemical, biological and environmental processes. Mass spectrometry (MS) based methods have been used to investigate this topic with molecular insights. As ion-solvent interactions are weak, ionization processes should be as soft as possible in order to retain solvation structures. An in situ liquid secondary ion MS (SIMS) approach developed in our group has been recently utilized in investigations of Li ion solvation in non-aqueous solution and detected a series of solvated Li ions. As traditionally SIMS has long been recognized as a hard ionization process with strong damage occurring at the sputtering interface, it is very interesting to study further how soft in situ liquid SIMS can be. In this work, we used halide ion hydration as an example to compare the ionization performance of in situ liquid SIMS approach with regular electrospray ionization MS (ESI-MS). Results show that although ESI has been recognized as a soft ionization method, nearly no solvated halide ions were detected by ESI-MS analysis, which acquired only strong signals of salt ion clusters. In contrast, in liquid SIMS spectra, a series of obvious hydrated halide ion compositions could be observed. We further evaluated the hydration numbers of halide ions and revealed the effects of the ion size, charge density and polarizability on the hydration phenomenon. Our findings demonstrated that the in situ liquid SIMS approach is surprisingly soft, and expected to have very broad applications on investigation of various ion-solvent interactions and many other interesting chemical processes (e.g., the initial nucleation of nanoparticle formation) in liquid environment.

Zhang, Yanyan↗

DOE OSTI2013

Advanced Self-Potential Inversion. Development and Use for Investigating Natural Recharge Processes at the ORNL IFC

Understanding the influence of coupled biological, chemical, and hydrological processes on subsurface contaminant behavior at multiple scales is a prerequisite for developing effective remedial approaches, whether they are active remediation or natural attenuation strategies. To develop this understanding, methods are needed that can measure critical components of the natural system in real time. The self-potential method corresponds to the passive measurement of the distribution of the electrical potential at the surface of the Earth or in boreholes. This method is very complemetary to other geophysical methods like DC resistivity and induced polarization. In this report, we summarize of research efforts to advance the theory of low-frequency geoelectrical methods and their applications to the contaminant plumes in the vicinity of the former S-3 settling basins at Oak Ridge, TN.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Roadmap on semiconductor–cell biointerfaces

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Bioinspired synthesis and self-assembly of hybrid organic–inorganic nanomaterials

Nature is replete with complex organic–inorganic hierarchical materials of diverse yet specific functions. These materials are intricately designed under physiological conditions through biomineralization and biological self-assembly processes. Tremendous efforts have been devoted to investigating mechanisms of such biomineralization and biological self-assembly processes as well as gaining inspiration to develop biomimetic methods for synthesis and self-assembly of functional nanomaterials. In this work, we focus on the bioinspired synthesis and self-assembly of functional inorganic nanomaterials templated by specialized macromolecules including proteins, DNA and polymers. The in vitro biomineralization process of the magnetite biomineralizing protein Mms6 has been investigated using small-angle X-ray scattering. Templated by Mms6, complex magnetic nanomaterials can be synthesized on surfaces and in the bulk. DNA and synthetic polymers have been exploited to construct macroscopic two- and three-dimensional (2D and 3D) superlattices of gold nanocrystals. Employing X-ray scattering and spectroscopy techniques, the self-assembled structures and the self-assembly mechanisms have been studied, and theoretical models have been developed. Our results show that specialized macromolecules including proteins, DNA and polymers act as effective templates for synthesis and self-assembly of nanomaterials. These bottom-up approaches provide promising routes to fabricate hybrid organic–inorganic nanomaterials with rationally designed hierarchical structures, targeting specific functions.

36 MATERIALS SCIENCE↗

DOE OSTI2015

A microfluidic platform for precision small-volume sample processing and its use to size separate biological particles with an acoustic microdevice [Precision size separation of biological particles in small-volume samples by an acoustic microfluidic system]

Here, a major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15–1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection, system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing.

42 ENGINEERING↗

DOE OSTI2018

Reversal of Increasing Tropical Ocean Hypoxia Trends With Sustained Climate Warming

Dissolved oxygen (O 2 ) is essential for the survival of marine animals. Climate change impacts on future oxygen distributions could modify species biogeography, trophic interactions, biodiversity, and biogeochemistry. The Coupled Model Intercomparison Project Phase 5 models predict a decreasing trend in marine O 2 over the 21st century. Here we show that this increasing hypoxia trend reverses in the tropics after 2100 in the Community Earth System Model forced by atmospheric CO 2 from the Representative Concentration Pathway 8.5 and Extended Concentration Pathway 8.5. In tropical intermediate waters between 200 and 1,000 m, the model predicts a steady decline of O 2 and an expansion of oxygen minimum zones (OMZs) during the 21st century. By 2150, however, the trend reverses with oxygen concentration increasing and OMZ volume shrinking through 2300. A novel five-box model approach in conjunction with output from the full Earth system model is used to separate the contributions of biological and physical processes to the trends in tropical oxygen. The tropical O 2 recovery is caused mainly by reductions in tropical biological export, coupled with a modest increase in ventilation after 2200. The time-evolving oxygen distribution impacts marine nitrogen cycling, with potentially important climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1982

Controlled ecological life support system - biological problems

The general processes and controls associated with two distinct experimental paradigms are examined. Specific areas for research related to biotic production (food production) and biotic decomposition (waste management) are explored. The workshop discussions were directed toward Elemental cycles and the biological factors that affect the transformations of nutrients into food, of food material into waste, and of waste into nutrients were discussed. To focus on biological issues, the discussion assumed that (1) food production would be by biological means (thus excluding chemical synthesis), (2) energy would not be a limiting factor, and (3) engineering capacity for composition and leak rate would be adequate.

Moore, B., III↗

NASA NTRS1972

Bosch CO2 reduction unit research and development.

Development of Bosch CO2 reduction units for manned spacecraft application has been in progress for a decade. The Bosch process catalytically reacts CO2 with H2 to produce water and carbon. The water may then be electrolyzed to close the biological oxygen and process hydrogen loops. A critical problem has been to confine the reaction so that carbon does not block flow and stop the process. Reaction isolation within a replaceable catalyst cartridge has been successfully demonstrated. Objectives of the current development program are a 25% reduction in operating power, an 80% reduction in expendable weight, and minimized resupply volume.

Holmes, R. F.↗

NASA NTRS1984

Biological Oceanography

Within the framework of global biogeochemical cycles and ocean productivity, there are two areas that will be of particular interest to biological oceanography in the 1990s. The first is the mapping in space time of the biomass and productivity of phytoplankton in the world ocean. The second area is the coupling of biological and physical processes as it affects the distribution and growth rate of phytoplankton biomass. Certainly other areas will be of interest to biological oceanographers, but these two areas are amenable to observations from satellites. Temporal and spatial variability is a regular feature of marine ecosystems. The temporal and spatial variability of phytoplankton biomass and productivity which is ubiquitous at all time and space scales in the ocean must be characterized. Remote sensing from satellites addresses these problems with global observations of mesocale (2 to 20 days, 10 to 200 km) features over a long period of time.

Abbott, M. R.↗

NASA NTRS2017

Sample Processor for Life on Icy Worlds (SPLIce): Design and Test Results

We report the design, development, and testing of the Sample Processor for Life on Icy Worlds (SPLIce) system, a microfluidic sample processor to enable autonomous detection of signatures of life and measurements of habitability parameters in Ocean Worlds. This monolithic fluid processing-and-handling system (Figure 1; mass 0.5 kg) retrieves a 50-L-volume sample and prepares it to supply a suite of detection instruments, each with unique preparation needs. SPLIce has potential applications in orbiter missions that sample ocean plumes, such as found in Saturns icy moon Enceladus, or landed missions on the surface of icy satellites, such as Jupiters moon Europa. Answering the question Are we alone in the universe? is captivating and exceptionally challenging. Even general criteria that define life very broadly include a significant role for water [1,2]. Searches for extinct or extant life therefore prioritize locations of abundant water whether in ancient (Mars), or present (Europa and Enceladus) times. Only two previous planetary missions had onboard fluid processing: the Viking Biology Experiments [3] and Phoenixs Wet Chemistry Laboratory (WCL) [4]. SPLIce differs crucially from those systems, including its capability to process and distribute L-volume samples and the integration autonomous control of a wide range of fluidic functions, including: 1) retrieval of fluid samples from an evacuated sample chamber; 2) onboard multi-year storage of dehydrated reagents; 3) integrated pressure, pH, and conductivity measurement; 4) filtration and retention of insoluble particles for microscopy; 5) dilution or vacuum-driven concentration of samples to accommodate instrument working ranges; 6) removal of gas bubbles from sample aliquots; 7) unidirectional flow (check valves); 8) active flow-path selection (solenoid-actuated valves); 9) metered pumping in 100 nL volume increments. The SPLIce manifold, made of three thermally fused layers of precision-machined cyclo-olefin polymer, supports all fluidic components (Figure 1) and integrated microchannels (125 x 250 m). Fluid is pumped by a stepper-motor-driven pump (Lee Co.). The functionality of the integrated MEMS pressure sensor (Honeywell) and passive check valves (Figure 2) were tested in conjunction with our newly designed integral bubble traps (Figure 3) and hydrophobic membrane-based concentrator (Figure 4). The concentrator (initially tested as a standalone component) demonstrated 5-fold vacuum-evaporative concentration. Polyethylene fused bead beds (PEFBBs; 50 porosity) store drylyophilized buffers, calibrants, and fluorescent dyes, and also promote mixing of sample with calibrant, dye, or H2O. Software-controlled automated tests demonstrated successful 1) fluid delivery to each component 2) valve and pump synchronization 3) sample aliquot delivery to instrument interface ports, and 4) rehydration of vacuum-dried fluorescent dye. In Figure 5, fluorescein on PEFBBs was rehydrated for 15 min using a pump-delivered water aliquot; it is displaced as H2O enters the bottom of the channel and pushes the dye into a check valve. Ultimately, SPLIce will fluorescently label amino acids in the sample for microchip-based electrophoretic (MCE) chiral separation and detection to seek and quantify key organic bio-signatures [5]; it will also deliver sample to a microfluidic version of WCL (mWCL) to measure soluble ions and redox-active species.

Life detection↗

DOE OSTI2019

Tailoring diesel bioblendstock from integrated catalytic upgrading of carboxylic acids: a “fuel property first” approach

Abstract Lignocellulosic biomass offers the potential to produce renewable fuels at a scale commensurate with petroleum consumption. Hybrid approaches that combine biological and chemocatalytic processes have garnered increasing attention due to their flexibility for feedstock utilization and diversity of potential products. Of note, lignocellulosic sugars can be converted biologically to short-chain carboxylic acids, while subsequent chemocatalytic upgrading can elongate the carbon backbone and remove oxygen from the structure to produce drop-in hydrocarbon fuels. However, hybrid conversion processes are typically not designed with the fuel properties in mind a priori . In this work, we apply a “fuel property first” design approach to produce a tailored hydrocarbon bioblendstock with lower intrinsic sooting and drop-in diesel fuel potential. Initially, model predictions for six fuel properties critical to diesel applications (physicochemical requirements, energy content, safety considerations, autoignition ability, and sooting tendency) were used to screen an array of hydrocarbons accessible from upgrading individual and mixed C 2 /C 4 acids. This screening step allowed for down-selection to a non-cyclic branched C 14 hydrocarbon (5-ethyl-4-propylnonane) that can be synthesized from butyric acid through sequential catalytic reactions of acid ketonization, ketone condensation, and hydrodeoxygenation. Following evaluation of each conversion step with model compounds, butyric acid was then converted through an integrated catalytic process scheme to achieve >80% overall carbon yield to a hydrocarbon mixture product containing >60% of the target C 14 hydrocarbon. The potential of this conversion strategy to produce a hydrocarbon diesel bioblendstock from lignocellulosic biomass was then demonstrated using corn stover-derived butyric acid produced from Clostridium butyricum fermentation. Experimental fuel property testing of the purified C 14 blendstock validated the majority of the fuel property model predictions, including <50% of the intrinsic sooting tendency when compared to conventional diesel. Meanwhile, the crude conversion product met fuel property target metrics, validating conversion process development. When the C 14 bioblendstock was blended into a petroleum diesel at 20 vol.%, the blend maintained low cloud point, high energy density, and cetane number. Notably, the blend reduced sooting tendency by more than 10%, highlighting the potential of the tailored bioblendstock to reduce particulate emissions.

09 BIOMASS FUELS↗

NASA NTRS2006

Closure of Regenerative Life Support Systems: Results of the Lunar-Mars Life Support Test Project

Future long duration human exploration missions away from Earth will require closed-loop regenerative life support systems to reduce launch mass, reduce dependency on resupply and increase the level of mission self sufficiency. Such systems may be based on the integration of biological and physiocochemical processes to produce potable water, breathable atmosphere and nutritious food from metabolic and other mission wastes. Over the period 1995 to 1998 a series of ground-based tests were conducted at the National Aeronautics and Space Administration, Johnson Space Center, to evaluate the performance of advanced closed-loop life support technologies with real human metabolic and hygiene loads. Named the Lunar-Mars Life Support Test Project (LMLSTP), four integrated human tests were conducted with increasing duration, complexity and closure. The first test, LMLSTP Phase I, was designed to demonstrate the ability of higher plants to revitalize cabin atmosphere. A single crew member spent 15 days within an atmospherically closed chamber containing 11.2 square meters of actively growing wheat. Atmospheric carbon dioxide and oxygen levels were maintained by control of the rate of photosynthesis through manipulation of light intensity or the availability of carbon dioxide and included integrated physicochemical systems. During the second and third tests, LMLSTP Phases II & IIa, four crew members spent 30 days and 60 days, respectively, in a larger sealed chamber. Advanced physicochemical life support hardware was used to regenerate the atmosphere and produce potable water from wastewater. Air revitalization was accomplished by using a molecular sieve and a Sabatier processor for carbon dioxide absorption and reduction, respectively, with oxygen generation performed by water hydrolysis. Production of potable water from wastewater included urine treatment (vapor compression distillation), primary treatment (ultrafiltration/reverse osmosis and multi-filtration) and post processing. For the Phase II test the water recovery rate ranged from 95 to 98%, depending on the processor. LMLSTP Phase III, the fourth test of the series, had a duration of 91 days and included four crew members. The test demonstrated an integration of physicochemical and biological technologies for air revitalization, water recovery and waste processing. Wheat supplemented the physicochemical air revitalization systems by providing approximately 25% of the oxygen required for the 4-person crew. The water recovery system included immobilized cell and trickling filter bioreactors for primary water treatment, reverse osmosis and air evaporation systems for secondary water treatment, followed by post processing. The 8 day initial supply of water was recycled through the chamber and crew 10 times over the course of the test. Grain from the wheat together with fresh lettuce from a small growth chamber within the crew chamber provided supplementation to the stored food system, but at a level less than 5% of the crew s caloric requirement. An incinerator was used to demonstrate mineralization of the crew s solid waste, with the combustion products (mainly carbon dioxide) returned to the wheat for conversion to oxygen.

Barta, Daniel↗

DOE OSTI2016

Highly-defective nanocrystals of ZnS formed via dissimilatory bacterial sulfate reduction: A comparative study with their abiogenic analogues

The physicochemical properties of a (nano)mineral are strongly affected by its formation processes, and thus, may indicate the (nano)mineral’s formation environment and mechanism. This correlation, although relevant to a myriad of geological, environmental, and material-science processes, has not yet been fully appreciated and systematically explored. In this study, using the Zn–S system, we demonstrate that biological and abiotic processes at similar experimental conditions can produce distinctive particle size, morphology, and crystal structure in the formed ZnS. Specifically, bacterial sulfate reduction led to the formation of highly-defective nanocrystals of mixed sphalerite and wurtzite in a range of ~4–12 nm. By comparison, the abiotic procedures of titration- or diffusion-controlled precipitation resulted in the formation of polycrystalline aggregates that contained randomly-oriented, ultrafine crystals below ~2–3 nm. The poor crystallinity in the abiogenic samples, regardless of the sulfide addition rates, reveals an overall nucleation-dominated, crystal growth-restricted pathway for the formation of ZnS from low-temperature aqueous solutions. The difficulty in the ZnS crystallization likely stems from the intrinsic surface instability of the ZnS growth units (i.e., in the form of nanoclusters) resulting from the dipole–dipole interactions of the unit with surrounding water molecules. In the biogenic samples, the ZnS crystallinity was significantly improved, indicating that the presence of bacterial metabolites somehow promoted the crystallization process. With evidence for the enlarged {1 1 1} planes in the biogenic nanocrystals, we attribute this enhancement mainly to the selective interaction of the bacterial metabolites with polar faces of the ZnS growth units, which might have effectively screened the dipole moments in the growth units and enabled their crystallographic assembly. By revealing the intrinsic difficulty and specific pathways for the ZnS crystallization, we also present viable explanations for the exclusive occurrence of structural defects in {1 1 1} planes of the biogenic nanocrystals. The findings of our study provide insight into the origin and fate of metal sulfide nanoparticles in the environment, and have implications for biomineralization, bioremediation of metal-contaminated sites, and bacterial production of functional nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Abstract Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1989

Gravity receptors and responses

The overall process of gravity sensing and response processes in plants may be divided conveniently into at least four components or stages: Stimulus susception (a physical event, characteristically the input to the G receptor system of environmental information about the G force magnitude, its vector direction, or both); information perception (an influence of susception on some biological structure or process that can be described as the transformation of environmental information into a biologicallly meaningful change); information transport (the export, if required, of an influence (often chemical) to cells and organs other than those at the sensor location); and biological response (almost always (in plants) a growth change of some kind). Some analysts of the process identify, between information perception and information transport, an additional stage, transduction, which would emphasize the importance of a transformation from one form of information to another, for example from mechanical statolith displacement to an electric, chemical, or other alteration that was its indirect result. These four (or five) stages are temporally sequential. Even if all that occurs at each stage can not be confidently identified, it seems evident that during transduction and transport, matters dealt with are found relatively late in the information flow rather than at the perception stage. As more and more is learned about the roles played by plant hormones which condition the G responses, the mechanism(s) of perception which should be are not necessarily better understood. However, if by asking the right questions and being lucky with experiments perhaps the discovery of how some process (such as sedimentation of protoplasmic organelles) dictates what happens down stream in the information flow sequence may be made.

Brown, Allan H.↗

DOE OSTI2014

Using High Performance Computing to Examine the Processes of Neurogenesis Underlying Pattern Separation and Completion of Episodic Information

Adult neurogenesis in the hippocampus region of the brain is a neurobiological process that is believed to contribute to the brain's advanced abilities in complex pattern recognition and cognition. Here, we describe how realistic scale simulations of the neurogenesis process can offer both a unique perspective on the biological relevance of this process and confer computational insights that are suggestive of novel machine learning techniques. First, supercomputer based scaling studies of the neurogenesis process demonstrate how a small fraction of adult-born neurons have a uniquely larger impact in biologically realistic scaled networks. Second, we describe a novel technical approach by which the information content of ensembles of neurons can be estimated. Finally, we illustrate several examples of broader algorithmic impact of neurogenesis, including both extending existing machine learning approaches and novel approaches for intelligent sensing.

Aimone, James Bradley↗