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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Machine‐Learning‐Driven Exploration of Surface Reconstructions of Reduced Rutile TiO 2

Titanium dioxide (TiO 2 ) is widely used as a catalyst support due to its stability, tunable electronic properties, and surface oxygen vacancies, which are crucial for catalytic processes such as the reverse water-gas shift (RWGS) reaction. Reduced TiO 2 surfaces undergo complex surface reconstructions that endow unique properties but are computationally challenging to describe. In this study, we utilize machine-learning interatomic potentials (MLIPs) integrated with an active-learning workflow to efficiently explore reduced rutile TiO 2 surfaces. This approach enabled the prediction of a phase diagram as a function of oxygen chemical potential, revealing a variety of reconstructed phases, including a previously unreported subsurface shear plane structure. We further investigate the electronic properties of these surfaces and validate our results by comparing experimental and theoretical high-resolution transmission electron microscopy (HRTEM). Our findings provide new insights into how extreme surface reductions influence the structural and electronic properties of TiO 2 , with potential implications for catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2024

Irreversible Catalyst Deactivation Mechanisms of PdO/γ-Al 2 O 3 Catalysts for Lean Methane Oxidation

PdO/γ-Al 2 O 3 catalysts suffer from gradual and irreversible catalyst deactivation under lean CH 4 oxidation conditions, especially in a wet feed. Here, time-resolved CO chemisorption DRIFTS measurements are conducted systematically on a series of PdO/γ-Al 2 O 3 catalysts to probe the surface reactivity of PdO nanoparticles after various in situ pretreatments. At 80 °C, CO barely adsorbs on fully oxidized PdO surfaces but interacts with coordinatively unsaturated Pd sites, causing gradual reduction of the PdO surfaces. This results in the formation of characteristic IR bands on various metallic Pd 0 sites. By monitoring and comparing the formation kinetics of these IR bands on samples before and after CH 4 oxidation, we theorize that the irreversible catalyst deactivation during CH 4 oxidation is caused by PdO surface reconstruction, in which coordinatively unsaturated Pd sites gradually become fully coordinated by oxygen. Effectively, the surface reconstruction leads to the formation of a passivation layer on the PdO nanoparticles, which hinders their ability in activating CH 4 , and hence the subsequent oxidation reaction. Temperature-programmed reduction with CO as the reductant (CO-TPR) reveals that the passivation layer formed during CH 4 oxidation is significant enough to increase the reduction temperature of PdO nanoparticles of the 3.0% PdO/γ-Al 2 O 3 samples, although such an effect is less obvious for the 0.4% PdO/γ-Al 2 O 3 samples. On the other hand, it is also discovered that the passivation layer is not completely inert. Under certain reaction conditions, with some being relatively mild, such as low-temperature CO oxidation in a net lean atmosphere and in the presence of H 2 O, the passivation layer can undergo structure change which results in regeneration or even activation of CH 4 oxidation activity of an already deactivated catalyst. Additionally, it is discovered that the fully coordinated Pd–O surface is a metastable phase under CH 4 oxidation conditions. In the presence of H 2 O and at ambient temperatures, surfaces with coordinatively unsaturated Pd sites are thermodynamically more favorable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1981

Applied tagmemics: A heuristic approach to the use of graphic aids in technical writing

In technical report writing, two needs which must be met if reports are to be useable by an audience are the language needs and the technical needs of that particular audience. A heuristic analysis helps to decide the most suitable format for information; that is, whether the information should be presented verbally or visually. The report writing process should be seen as an organic whole which can be divided and subdivided according to the writer's purpose, but which always functions as a totality. The tagmemic heuristic, because it itself follows a process of deconstructing and reconstructing information, lends itself to being a useful approach to the teaching of technical writing. By applying the abstract questions this heuristic asks to specific parts of the report. The language and technical needs of the audience are analyzed by examining the viability of the solution within the givens of the corporate structure, and by deciding which graphic or verbal format will best suit the writer's purpose. By following such a method, answers which are both specific and thorough in their range of application are found.

Brownlee, P. P.↗
DOE OSTI2020

Effects of Extended Aqueous Processing on Structure, Chemistry, and Performance of Polycrystalline LiNi x Mn y Co z O 2 Cathode Powders

The prospect of aqueous processing of LiNi x Mn y Co z O 2 (NMC) cathodes has significant appeal to battery manufacturers for the reduction in materials cost, toxicological risk, and environmental impact compared to conventional N -methyl-2-pyrrolidone (NMP)-based processing. However, the effects of aqueous processing of NMC powders at industrial timescales are not well studied, with prior studies mostly focusing on relatively brief water washing processes. Here, we investigate the bulk and surface impacts of extended aqueous processing of polycrystalline NMC powders with different compositions. We demonstrate that at timescales of several hours, polycrystalline NMC is susceptible to intergranular fracture, with the severity of fracture scaling with the NMC nickel content. While bulk crystallinity and composition are unchanged, surface sensitive techniques such as X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) indicate that the exposure of water leads to a level of delithiation, nickel reduction, and reconstruction from the layered to rock-salt structure at the surface of individual grains. Dynamic single NMC microparticle compression testing suggests that the resulting mechanical stresses weaken the integrity of the polycrystalline particle and increases susceptibility of intergranular fracture. The initially degraded surfaces along with the increased surface area lead to faster capacity fade and impedance growth during electrochemical cycling. From this work, it is demonstrated that NMC powders require surface or grain boundary modifications to make industrial-scale aqueous cathode processing viable, especially for next-generation nickel-rich NMC chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Calibration of the ProtoDUNE Horizontal-Drift position reconstruction using a laser system

Forthcoming in the next decade of neutrino physics advancements is the construction of the Deep Underground Neutrino Experiment (DUNE), a long baseline neutrino oscillation experiment which has the potential to answer fundamental questions such as why there is more matter than antimatter in the universe, and ultimately why we exist at all. A prototype of this experiment, ProtoDUNE, sits in a charged particle test beam at the European Organization for Nuclear Research (CERN) and uses Liquid Argon time projection chambers to image interactions of these particles. ProtoDUNE Single-Phase (ProtoDUNESP) had positively charged hadrons as well as positrons in its initial 2018 beam data run. Because ProtoDUNE is a surface-based time projection chamber, it experiences a constant influx of cosmic rays. These cosmic rays ionize the liquid argon within the detector, resulting in an accumulation of slow moving positive ions towards the cathode. This local charge distribution results in electric field non uniformities, which can have a significant effect on the accuracy of the event reconstruction. This paper outlines a monte carlo simulation study which adapts methodology from the MicroBooNE experiment, another neutrino oscillation experiment, to derive electric field correction maps which can correct for distortions of the electric field within the detector. These correction maps accurately estimate the electric field throughout the detector volume and correct for uncertainties in reconstructed event data enabling for physics discoveries.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1997

Three-dimensional analysis of vestibular efferent neurons innervating semicircular canals of the gerbil

Anterograde labeling techniques were used to examine peripheral innervation patterns of vestibular efferent neurons in the crista ampullares of the gerbil. Vestibular efferent neurons were labeled by extracellular injections of biocytin or biotinylated dextran amine into the contralateral or ipsilateral dorsal subgroup of efferent cell bodies (group e) located dorsolateral to the facial nerve genu. Anterogradely labeled efferent terminal field varicosities consist mainly of boutons en passant with fewer of the terminal type. The bouton swellings are located predominately in apposition to the basolateral borders of the afferent calyces and type II hair cells, but several boutons were identified close to the hair cell apical border on both types. Three-dimensional reconstruction and morphological analysis of the terminal fields from these cells located in the sensory neuroepithelium of the anterior, horizontal, and posterior cristae were performed. We show that efferent neurons densely innervate each end organ in widespread terminal fields. Subepithelial bifurcations of parent axons were minimal, with extensive collateralization occurring after the axons penetrated the basement membrane of the neuroepithelium. Axonal branching ranged between the 6th and 27th orders and terminal field collecting area far exceeds that of the peripheral terminals of primary afferent neurons. The terminal fields of the efferent neurons display three morphologically heterogeneous types: central, peripheral, and planum. All cell types possess terminal fields displaying a high degree of anisotropy with orientations typically parallel to or within +/-45 degrees of the longitudinal axis if the crista. Terminal fields of the central and planum zones predominately project medially toward the transverse axis from the more laterally located penetration of the basement membrane by the parent axon. Peripheral zone terminal fields extend predominately toward the planum semilunatum. The innervation areas of efferent terminal fields display a trend from smallest to largest for the central, peripheral, and planum types, respectively. Neurons that innervate the central zone of the crista do not extend into the peripheral or planum regions. Conversely, those neurons with terminal fields in the peripheral or planum regions do not innervate the central zone of the sensory neuroepithelium. The central zone of the crista is innervated preferentially by efferent neurons with cell bodies located in the ipsilateral group e. The peripheral and planum zones of the crista are innervated preferentially by efferent neurons with cell bodies located in the contralateral group e. A model incorporating our anatomic observations is presented describing an ipsilateral closed-loop feedback between ipsilateral efferent neurons and the periphery and an open-loop feed-forward innervation from contralateral efferent neurons. A possible role for the vestibular efferent neurons in the modulation of semicircular canal afferent response dynamics is proposed.

Non-NASA Center↗
DOE OSTI2021

Linear Combination of Atomic Dipoles to Calculate the Bond and Molecular Dipole Moments of Molecules and Molecular Liquids

Here we report a linear combination of atomic dipole (LCAD) method for calculating the bond dipole moments of molecules. We show that the LCAD method reproduces the known molecular dipole moments of small to large molecules with a small error with respect to experimental and benchmark ab initio calculations, and molecular dipole distributions of bulk water that agree with maximally localized Wannier functions. The bond dipole moments derived from LCAD are also chemically interpretable in terms of the trend in bond ionicity in going from neutral to charged molecules. Moreover, the LCAD method accurately captures the influence of electric fields, supported by the correct trend in the change of the dipole moment under a uniform external electric field. The better grounding of bond dipole calculations indicates that it should also serve as a useful approach to bond dipole-field models used in catalysis or to reconstruct the small dipole of a H-terminated graphene flake.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Continuous Family of Conformal Field Theories and Exactly Marginal Operators

Does a conformal manifold imply the existence of exactly marginal operators? We answer this question affirmatively under the assumption that there exists a conformal interface with certain properties connecting nearby conformal field theories. We show that the exactly marginal operator that connects the conformal field theories can be reconstructed from the interface displacement operator. Our construction is model independent and based on the general principles of conformal symmetry.

conformal field theory↗
DOE OSTI2021

Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

The last common bilaterian ancestor

Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution.

Review↗
NASA NTRS2020

Assessment of Holographic Microscopy for Quantifying Marine Particle Size and Concentration

Holographic microscopy has emerged as a tool for in situ imaging of microscopic organisms and other particles in the marine environment: appealing because of relatively larger sampling volumes and simpler optical configurations compared to similar imaging systems. However, its quantitative capabilities have remained uncertain, in part because hologram reconstruction and image recognition have required manual operation. Here we assess the quantitative skill of our automated hologram processing pipeline, the CCV Pipeline, to evaluate the size and concentration measurements of environmental and cultured assemblages of marine plankton particles, and microspheres. Over one-million particles, ranging from 10-200 microns equivalent spherical diameter (ESD), imaged by the 4-Deep HoloSea digital inline holographic microscope (DIHM) are analyzed. These measurements were collected in parallel with FlowCam, Imaging FlowCytobot, and manual microscope identification. Once corrections for particle location and nonuniform illumination were developed and applied, the DIHM showed an underestimate in ESD of about 3-10%, but successfully reproduced the size-spectral-slope from environmental samples, and the size distribution of monocultures and microspheres. DIHM concentrations (order 1-1000 particles~ml-1) showed linear agreement (r^2=0.73) with the other instruments, but individual comparisons at times had large uncertainty.

holograpy↗
NASA NTRS1981

Organic compounds in meteorites and their origins

The current investigation represents an extensively updated version of a review conducted by Anders et al. (1973). The investigation takes into account the literature through mid-1980. It is pointed out that Type 1 carbonaceous chondrites (C1) contain 6% of their cosmic complement of carbon, mainly in the form of organic matter. Most authors now agree that this material represents primitive prebiotic matter. The principal questions remaining are what abiotic processes formed the organic matter, and to what extent these processes took place in locales other than the solar nebula, such as interstellar clouds or meteorite parent bodes. The problem is approached in three stages. It is attempted to reconstruct the physical conditions during condensation from the clues contained in the inorganic matrix of the meteorite. The condensation behavior of carbon under these conditions is determined on the basis of thermodynamic calculations. Model experiments on the condensation of carbon are performed, and the synthesized compounds are compared with those actually found in meteorites.

Hayatsu, R.↗
DOE OSTI2025

AAPM Truth‐based CT (TrueCT) reconstruction grand challenge

Background: This Special Report summarizes the 2022, AAPM grand challenge on Truth-based CT image reconstruction. Purpose: To provide an objective framework for evaluating CT reconstruction methods using virtual imaging resources consisting of a library of simulated CT projection images of a population of human models with various diseases. Methods: Two hundred unique anthropomorphic, computational models were created with varied diseases consisting of 67 emphysema, 67 lung lesions, and 66 liver lesions. The organs were modeled based on clinical CT images of real patients. The emphysematous regions were modeled using segmentations from patient CT cases in the COPDGene Phase I dataset. For the lung and liver lesion cases, 1–6 malignant lesions were created and inserted into the human models, with lesion diameters ranging from 5.6 to 21.9 mm for lung lesions and 3.9 to 14.9 mm for liver lesions. The contrast defined between the liver lesions and liver parenchyma was 82 ± 12 HU, ranging from 50 to 110 HU. Similarly, the contrast between the lung lesions and the lung parenchyma was defined as 781 ± 11 HU, ranging from 725 to 805 HU. For the emphysematous regions, the defined HU values were −950 ± 17 HU ranging from −918 to −979 HU. The developed human models were imaged with a validated CT simulator. The resulting CT sinograms were shared with the participants. The participants reconstructed CT images from the sinograms and sent back their reconstructed images. Further, the reconstructed images were then scored by comparing the results against the corresponding ground truth values. The scores included both task-generic (root mean square error [RMSE] and structural similarity matrix [SSIM]), and task-specific (detectability index [d’] and lesion volume accuracy) metrics. For the cases with multiple lesions, the measured metric was averaged across all the lesions. To combine the metrics with each other, each metric was normalized to a range of 0 to 1 per disease type, with “0” and “1” being the worst and best measured values across all cases of the disease type for all received reconstructions. Results: The True-CT challenge attracted 52 participants, out of which 5 successfully completed the challenge and submitted the requested 200 reconstructions. Across all participants and disease types, SSIM absolute values ranged from 0.22 to 0.90, RMSE from 77.6 to 490.5 HU, d’ from 0.1 to 64.6, and volume accuracy ranged from 1.2 to 753.1 mm3. The overall scores demonstrated that participant “A” had the best performance in all categories, except for the metrics of d’ for lung lesions and RMSE for liver lesions. Participant “A” had an average normalized score of 0.41 ± 0.22, 0.48 ± 0.32, and 0.42 ± 0.33 for the emphysema, lung lesion, and liver lesion cases, respectively. Conclusions: The True-CT challenge successfully enabled objective assessment of CT reconstructions with the unique advantage of access to a diverse population of diseased human models with known ground truth. This study highlights the significant potential of virtual imaging trials in objective assessment of medical imaging technologies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Support Effect and Surface Reconstruction in In 2 O 3 / m- ZrO 2 Catalyzed CO 2 Hydrogenation

Here, we investigate the chemical and structural dynamics at the interface of In 2 O 3 /m-ZrO 2 and their consequences on the CO 2 hydrogenation reaction (CO 2 HR) under reaction conditions. While acting to enrich CO 2 , monoclinic zirconia (m-ZrO 2 ) was also found to serve as a chemical and structural modifier of In 2 O 3 that directly governs the outcome of the CO 2 HR. These modifying effects include the following: (1) Under reaction conditions (above 623 K), partially reduced In 2 O 3 , i.e., InO x (0 < x < 1.5), was found to migrate in and out of the subsurface of m-ZrO 2 in a semireversible manner, where m-ZrO 2 accommodates and stabilizes InO x by serving as a reservoir. The decreased concentration of surface InO x under elevated temperatures coincides with significantly decreased selectivity toward methanol and a sharp increase of the reverse water–gas shift reaction. The reconstruction-induced variation of InO x concentration appears to be one of the most important factors contributing to the altered catalytic performance of CO 2 HR at different reaction conditions. (2) The strong interactions and reactions between m-ZrO 2 and In 2 O 3 result in the activation of a pool of In–O bonds at the In 2 O 3 /m-ZrO 2 interface to form oxygen vacancies. On the other hand, the high dispersity of In 2 O 3 nanostructures onto m-ZrO 2 prevents their over-reduction under catalytically relevant conditions (up to 673 K), when bare In 2 O 3 is unavoidably reduced into the metallic phase (In 0 ). The relationship between the extent of reduction of In 2 O 3 and catalytic performance (CO 2 conversion, CH 3 OH selectivity, or yield of CH 3 OH) suggests the presence of an optimum coverage of surface InO x and oxygen vacancies under reaction conditions. The conventional model that links catalytic performance solely to the coverage of oxygen vacancies appears invalid in the present case. In situ analysis also allows the observation of surface reaction intermediates and their interconversions, including the reduction of CO 3 * into formate, a precursor for the formation of methanol and CO. The combinative ex situ and in situ study sheds light on the reaction mechanism of the CO 2 HR on In 2 O 3 /m-ZrO 2 -based catalysts. Our findings on the large-scale surface reconstructions, support effect, and the reaction mechanism of In 2 O 3 /m-ZrO 2 for CO 2 HR may apply to other related metal oxide catalyzed CO 2 reduction reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A consensus-based ensemble approach to improve transcriptome assembly

Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes. In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble. Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Spatiotemporal analysis of 3D human iPSC-derived neural networks using a 3D multi-electrode array

While there is a growing appreciation of three-dimensional (3D) neural tissues (i.e., hydrogel-based, organoids, and spheroids), shown to improve cellular health and network activity to mirror brain-like activity in vivo , functional assessment using current electrophysiology techniques (e.g., planar multi-electrode arrays or patch clamp) has been technically challenging and limited to surface measurements at the bottom or top of the 3D tissue. As next-generation MEAs, specifically 3D MEAs, are being developed to increase the spatial precision across all three dimensions (X, Y, Z), development of improved computational analytical tools to discern region-specific changes within the Z dimension of the 3D tissue is needed. In the present study, we introduce a novel computational analytical pipeline to analyze 3D neural network activity recorded from a “bottom-up” 3D MEA integrated with a 3D hydrogel-based tissue containing human iPSC-derived neurons and primary astrocytes. Over a period of ~6.5 weeks, we describe the development and maturation of 3D neural activity (i.e., features of spiking and bursting activity) within cross sections of the 3D tissue, based on the vertical position of the electrode on the 3D MEA probe, in addition to network activity (identified using synchrony analysis) within and between cross sections. Then, using the sequential addition of postsynaptic receptor antagonists, bicuculline (BIC), 2-amino-5-phosphonovaleric acid (AP-5), and 6-cyano-5-nitroquinoxaline-2,3-dione (CNQX), we demonstrate that networks within and between cross sections of the 3D hydrogel-based tissue show a preference for GABA and/or glutamate synaptic transmission, suggesting differences in the network composition throughout the neural tissue. The ability to monitor the functional dynamics of the entire 3D reconstructed neural tissue is a critical bottleneck; here we demonstrate a computational pipeline that can be implemented in studies to better interpret network activity within an engineered 3D neural tissue and have a better understanding of the modeled organ tissue.

3D culture↗