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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data for Propagation Method and Planting Density Influence Canopy Developmental Transition and Biomass Productivity in Miscanthus × giganteus

Understanding how establishment practices influence the mechanisms underlying Miscanthus × giganteus (miscanthus) productivity and canopy development is critical for optimizing management. Data was collected during the juvenile (2011–2013) and mature (2024) phases of a long-term field experiment established in Urbana, Illinois, to evaluate the effects of propagation method (plug propagation [PP] and rhizome propagation [RP]), planting density (1.0, 0.75, and 0.25 plants m⁻²), and nitrogen application (0 and 67 kg N ha⁻¹) on end-of-season biomass yield, tiller mass, tiller density, and tiller height. Linear regression models identified the dominant predictors of yield across stand ages and management regimes. Planting density, nitrogen (N) application, and propagation method significantly influenced early yield and canopy development. During the juvenile phase, biomass yield was driven by tiller density due to canopy expansion; in the mature phase, yield became driven by tiller mass. The PP plots produced higher tiller density than the RP plots, resulting in faster canopy closure and higher juvenile-phase yields. Rhizome-propagated (RP) plots produced lower tiller density, but individual tillers were 3.3–6.4 g tiller−1 heavier than PP tillers. After the canopy reached equilibrium, the PP and RP yields were similar because greater RP tiller mass compensated for its lower tiller density. Higher planting density resulted in greater yield and tiller density during the second year (2012), but this effect was absent from the third year (2013) onward. In the juvenile phase, N fertilization enhanced yield by 1.6–3.4 Mg ha−1. Initiating fertilization in 2013 on unfertilized plots produced biomass similar to that in fertilized plots, suggesting yield recovery in the mature phase. These findings revealed that establishment strategies, including propagation method and planting density, influence juvenile miscanthus canopy development and productivity, transitioning from tiller-density- to mass-dominated yields, but not mature phase productivity.

Miscanthus↗
DOE OSTI2021

SEM petrography of dispersed organic matter in black shales: A review

Organic matter (OM)-hosted pores are important constituents of the pore system of black shales and play a crucial role in determining their methane adsorption capacity and porosity. OM-hosted pores are generally observed and described with scanning electron microscope (SEM) on Ar ion-milled surfaces. However, SEM imaging is not able to reliably distinguish OM types and relate the observed pores to specific macerals. Partly because of this inability to relate organic pores to macerals, the evolution of organic porosity during thermal maturation remains poorly understood. In this paper, we review the petrographic characteristics of dispersed organic matter (DOM) in black shales under the SEM. Organic petrographic classification of DOM developed for reflected-light microscopy is so far the most practical method when describing DOM in black shales under the SEM because this classification has information on the origin of DOM. Therefore, correlative microscopy (combination of reflected-light and electron microscopy) is the most effective method to identify both OM types and OM-hosted pores. This method, however, is not readily available to most researchers. Although identifying OM on the basis of SEM observations is a challenging task, it is achievable provided there is a good understanding of the studied shales, especially their thermal maturity and original OM composition. Therefore, the overall objective of this paper is to review petrographic characteristics of DOM in black shales under the SEM to provide some guidelines for identifying DOM from SEM observations. We also review factors that control the formation and preservation of OM-hosted pores. OM-hosted pores consist of primary and secondary organic pores. Primary organic pores are pores inherited from the biological structure of the original OM. Secondary organic pores develop during hydrocarbon generation and expulsion from oil-prone OM and are hosted by solid bitumen or pyrobitumen. The development of secondary organic pores is controlled by thermal maturity and OM type, and their preservation is subject to thermal maturity, OM content, and mineralogical composition. The presented view of the evolution of micropore and mesopore characteristics of OM with thermal maturity is based on data from the literature. The specific surface area and pore volume of OM in black shales follow a parabolic pattern with increasing thermal maturity (quantified via vitrinite reflectance, R o ). The initial increase reflects development of OM-hosted pores, and the subsequent decrease is due to denser stacking of aromatic units in the macromolecular structure of OM, with maximum values (specific surface area ~ 300 m 2 /g and pore volume ~ 0.3 cm 3 /g) reached at R o values in the 2.5-3.5% range. The contribution of OM-hosted pores to the pore characteristics of black shales depends on OM content, OM type, and thermal maturity.

03 NATURAL GAS↗
DOE OSTI2022

Assembly of ordered DNA-curli fibril complexes during Salmonella biofilm formation correlates with strengths of the type I interferon and autoimmune responses

Deposition of human amyloids is associated with complex human diseases such as Alzheimer’s and Parkinson’s. Amyloid proteins are also produced by bacteria. The bacterial amyloid curli, found in the extracellular matrix of both commensal and pathogenic enteric bacterial biofilms, forms complexes with extracellular DNA, and recognition of these complexes by the host immune system may initiate an autoimmune response. Here, we isolated early intermediate, intermediate, and mature curli fibrils that form throughout the biofilm development and investigated the structural and pathogenic properties of each. Early intermediate aggregates were smaller than intermediate and mature curli fibrils, and circular dichroism, tryptophan, and thioflavin T analyses confirmed the establishment of a beta-sheet secondary structure as the curli conformations matured. Intermediate and mature curli fibrils were more immune stimulatory than early intermediate fibrils in vitro . The intermediate curli was cytotoxic to macrophages independent of Toll-like receptor 2. Mature curli fibrils had the highest DNA content and induced the highest levels of Isg15 expression and TNFα production in macrophages. In mice, mature curli fibrils induced the highest levels of anti-double-stranded DNA autoantibodies. The levels of autoantibodies were higher in autoimmune-prone NZBWxF/1 mice than wild-type C57BL/6 mice. Chronic exposure to all curli forms led to significant histopathological changes and synovial proliferation in the joints of autoimmune-prone mice; mature curli was the most detrimental. In conclusion, curli fibrils, generated during biofilm formation, cause pathogenic autoimmune responses that are stronger when curli complexes contain higher levels of DNA and in mice predisposed to autoimmunity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Raman Microscopy Analysis of Wyoming CarbonSAFE Pilot Well Thin Sections for Mineralogy and Organic Matter Characterization

Scanning confocal Raman microspectroscopy (RMS) was used to analyze thin sections for inorganic mineral content and for evaluation of organic material (OM). Thin sections were selected from a stratigraphic test well core in the Powder River Basin, Wyoming under the Wyoming CarbonSAFE project. The well was analyzed with a variety of rock and fluid characterization techniques to determine the feasibility of a commercial-scale CO2 storage site. RMS complements other analyses, including traditional petrography, SEM, porosity and permeability, and XRD For this aspect of the study, RMS is especially important in the evaluation of OM in sealing lithologies. At prospective geologic CO2 storage sites, it is imperative to assess the unconventional oil and gas potential of seals to ensure that any future development would not compromise the integrity of the seals. Whole-slide mineralogical surveys were performed on thin sections from various shale and sandstone formations. Surveys were analyzed with Direct Classical Least Squares to identify and quantify minerals. The location and concentration of minerals was color-coded and overlaid on optical images for visualization of the distribution of minerals. Dense hyperspectral Raman mapping of OM was performed on five thin sections. Eleven spectral parameters diagnostic of organic type and thermal maturity were used to train a Partial Least Squares (PLS) calibration against a set of artificially matured samples spanning the pre- to mid-oil window. The PLS was applied to the study set and a post-mature set. Additionally, the PLS was applied to each point in hyperspectral maps for visualization of trends in maturity across sample sets and discrimination of organic matter types within a given map. In inorganic surveys on thin sections, a total of 14 unique inorganic minerals were identified in Raman spectra including quartz, dolomite, calcite, hematite and anhydrite. Shale thin sections tended to be dominated by organic material. OM was often observed mixed with inorganic minerals. Sand- and mudstones were dominated by inorganic minerals. The PLS extrapolated the post-mature set to reflectances >1.2%. The study set ranged from very immature to postmature in the median of map fit-peak parameters. However, point maturity maps indicate that matrix OM in all study samples is immature and that discreet organic particles selected for mapping, which may be inertinites, bias medians towards more-mature. The work demonstrates the capabilities of RMS to perform both whole-slide mineralogy and OM analysis with applications to formation evaluation in oil & gas, carbon sequestration and mining. Here, analysis of sealing formations in the well indicates high levels of immature organic matter that would not be a viable target for future oil production that could compromise the CO2 storage site. The work brings together diverse disciplines from geology and petrography to analytical chemistry, big data and microscopy.

Myers, Grant↗
DOE OSTI2022

Cybersecurity vulnerability mitigation framework

Systems, methods, and computer media for mitigating cybersecurity vulnerabilities of systems are provided herein. A current cybersecurity maturity of a system can be determined based on maturity criteria. The maturity criteria can be ranked based on importance. Solution candidates for increasing the cybersecurity maturity of the system can be determined based on the ranking. The solution candidates specify cybersecurity levels for the maturity criteria. A present state value reflecting the current cybersecurity maturity of the system can be calculated. For the solution candidates, an implementation state value and a transition state value can be determined. The implementation state value represents implementation of the maturity levels of the solution candidate, and the transition state value represents a transition from the present state value to the implementation state value. Based on the transition state values, a solution candidate can be selected for the system, and the system can be modified accordingly.

Gourisetti, Sri Nikhil Gupta↗
DOE OSTI2020

Controls on reservoir properties in organic-matter-rich shales: Insights from MICP analysis

Mercury injection capillary pressure (MICP) analysis was used to study organic-matter-rich Devonian shales varying in maturity from marginally mature to postmature to discuss controls on drainage and imbibition in shale reservoirs. Six samples come from the New Albany Shale; their total organic carbon (TOC) ranged from 3.3–8.4 % and vitrinite reflectance (R o ) from 0.54–1.42 %. One Marcellus Shale sample with R o 2.50 % was used to extend the maturity range to the advanced dry gas window. Three coal samples of varying rank were also included for comparison. Porosity of the shales ranges from 1.5–5.0 %, and MICP-derived permeability ranges from 0.17–9.9 mD. Injection capillary pressure curves have a range of entry pressures from 0.055 to0.421 MPa, and no relationship of entry pressure with maturity was revealed. Maturity, however, has an influence on pore size distribution, with the higher-maturity samples having significantly lower volumes of pores with throats less than 10 nm in diameter. Withdrawal capillary pressure curves document a wide range of withdrawal efficiencies from 55 % to almost 100 %, and pores having throats between 3–50 nm in diameter play a major role in the ability of mercury to be released from the pore system. The obtained data provide valuable information about shale properties and their behavior not only in the air-mercury system but also under reservoir conditions.

02 PETROLEUM↗
DOE OSTI2022

Comparing Life Histories of the Shortest-Lived Turtle Known (Chicken Turtles, Deirochelys reticularia ) with Long-Lived Blanding's Turtles ( Emydoidea blandingii )

Evolutionary theories predict major differences in life-history trait values of long- and short-lived organisms. Such comparisons have not been possible for chelonians because no shortlived turtle was known until research revealed that chicken turtles (Deirochelys reticularia; DR) have a maximum longevity of 21 yrs. Life-history trait values of DR females are 1) age at maturity of females = 5–6 yrs; 2) clutches per season = 1.6; 3) annual fecundity = 6–8 female eggs per female; 4) average juvenile survivorship from age 1 to maturity = 0.60; and 5) low average annual adult survivorship = 0.66. We compared DR with the very long-lived Blanding’s turtles (Emydoidea blandingii; EB) in Michigan. Over 14 yrs with no mortality (the minimum age at maturity of EB), the maximum potential fecundity produced by a single female embryo and her mature female offspring was 5 female eggs for EB and 1040 eggs for DR. Comparisons of life table output for approximately stable populations of DR and EB resulted in cohort generation times of 7 and 37 yrs, respectively. The life-history prediction that short-lived organisms should produce smaller offspring was not supported. Average wet mass of eggs is 10 g (8.4–11.3 g) for DR and 12 g (10–14 g) for EB; and average wet mass of hatchlings is 7.3 g (6–9 g) for DR and 9.3 g (6–13 g) for EB. Both differences are smaller than expected based on the difference in longevity. Here, short-lived female DR have an unusual tactic of investing in high fecundity and making substantial body sizespecific investment in large eggs, which may reflect why juvenile survivorship had greater influence on population change rates than did adult survivorship. In contrast, adult survivorship had the greatest influence on population change rates of EB. Comparison of cohorts of 1000 female DR and EB hatchlings highlights the differences in life histories of short- and long-lived turtles: all DR would be dead by the time the last female EB had reached maturity at 21 yrs of age.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Functional and transcriptional characterization of complex neuronal co-cultures

Brain-on-a-chip systems are designed to simulate brain activity using traditional in vitro cell culture on an engineered platform. It is a noninvasive tool to screen new drugs, evaluate toxicants, and elucidate disease mechanisms. However, successful recapitulation of brain function on these systems is dependent on the complexity of the cell culture. In this study, we increased cellular complexity of traditional (simple) neuronal cultures by co-culturing with astrocytes and oligodendrocyte precursor cells (complex culture). We evaluated and compared neuronal activity (e.g., network formation and maturation), cellular composition in long-term culture, and the transcriptome of the two cultures. Compared to simple cultures, neurons from complex co-cultures exhibited earlier synapse and network development and maturation, which was supported by localized synaptophysin expression, up-regulation of genes involved in mature neuronal processes, and synchronized neural network activity. Also, mature oligodendrocytes and reactive astrocytes were only detected in complex cultures upon transcriptomic analysis of age-matched cultures. Functionally, the GABA antagonist bicuculline had a greater influence on bursting activity in complex versus simple cultures. Collectively, the cellular complexity of brain-on-a-chip systems intrinsically develops cell type-specific phenotypes relevant to the brain while accelerating the maturation of neuronal networks, important features underdeveloped in traditional cultures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Photosynthetic decline in aging perennial grass is not fully explained by leaf nitrogen

Abstract Aging in perennial plants is traditionally observed in terms of changes in end-of-season biomass; however, the driving phenological and physiological changes are poorly understood. We found that 3-year-old (mature) stands of the perennial grass Miscanthus×giganteus had 19–30% lower Anet than 1-year-old M.×giganteus (juvenile) stands; 10–34% lower maximum carboxylation rates of Rubisco and 34% lower light-saturated Anet (Asat). These changes could be related to nitrogen (N) limitations, as mature plants were larger and had 14–34% lower leaf N on an area basis (Na) than juveniles. However, N fertilization restored Na to juvenile levels but compensated only 50% of the observed decline in leaf photosynthesis with age. Comparison of leaf photosynthesis per unit of leaf N (PNUE) showed that mature stands had at least 26% lower PNUE than juvenile stands across all N fertilization rates, suggesting that other factors, besides N, may be limiting photosynthesis in mature stands. We hypothesize that sink limitations in mature stands could be causing feedback inhibition of photosynthesis which is associated with the age-related decline in photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots

The composition of biomass determines its suitability for different applications within a biorefinery system. The proportion of the major biomass fractions (sugar, cellulose, hemicellulose and lignin) may vary in different sugarcane genotypes and growth environments and different parts of the plant. This study investigated the composition of mature and immature internodes, roots and mature leaves of sugarcane. Internodes were found to have a significantly larger alcohol-soluble component than leaves and roots. The primary difference between the immature and mature internodes was the ratio of soluble sugars. In mature tissues, sucrose content was significantly higher, whereas in immature internodal tissues there was lower sucrose and heightened concentrations of reducing sugars. Carbon (C) partitioning in leaf tissues was characterised by low levels of soluble components and high “other” and cell wall fractions. Root tissue had low ratios of soluble fractions relative to their cell wall contents, indicating a lack of storage of soluble carbon. There was no significant difference in the ratio of the major cell wall fractions between the major organ types. Characterisation of individual non-cellulosic monomers indicated leaf and root tissues had significantly higher arabinose and galactose fractions. Significantly larger proportions of syringyl lignin compounds and the hydroxycinnamic compound, p-coumaric acid were observed in mature internodal tissues compared to the other tissue types. Tissue-specific differences in composition were shown to greatly affect the recalcitrance of the cell wall to enzymatic saccharification. Overall, this study displayed clear evidence of the differential partitioning of C throughout the sugarcane plant in specific organs. These organ-specific differences have major implications in their utility as a bioproduct feedstock. For example, the inclusion of trash (leaves) with the culms (internodes) may alter processing efficiency.

09 BIOMASS FUELS↗
DOE OSTI2020

Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. In this work, we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism

Anaerobic gut fungi of the phylum Neocallimastigomycota are microbes proficient in valorizing low-cost but difficult-to-breakdown lignocellulosic plant biomass. Characterization of different fungal life stages and how they contribute to biomass breakdown are critical for biotechnological applications, yet we lack foundational knowledge about the transcriptional, metabolic, and enzyme secretion behavior of different life stages of anaerobic gut fungi: zoospores, germlings, immature thalli, and mature zoosporangia. A Miracloth-based technique was developed to enrich cell pellets with zoospores - the free-swimming, flagellated, young life stage of anaerobic gut fungi. By contrast, fungal mats contained relatively more vegetative, encysted, mature sporangia that form films. Global gene expression profiles were compared from two sample types (zoospore-enriched cell pellets vs. mature mats) harvested from the anaerobic gut fungal strain Neocallimastix californiae G1. Despite cultures being grown on glucose, the fungal zoospore-enriched samples were transcriptionally primed to encounter plant matter substrate, as evidenced by upregulation of catabolic carbohydrate-active enzymes and putative carbohydrate transporters. Furthermore, we report significant differential gene expression for gene annotation groups, including putative secondary metabolites and transcription factors. Understanding global gene expression differences between the fungal zoospore-enriched cells and mature fungi aid in characterizing fungal development, unmasking gene function, and guiding cultivation conditions and engineering targets to promote enzyme secretion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Propagation method and planting density influence canopy developmental transition and biomass productivity in Miscanthus × giganteus

Understanding how establishment practices influence the mechanisms underlying Miscanthus × giganteus (miscanthus) productivity and canopy development is critical for optimizing management. Data was collected during the juvenile (2011–2013) and mature (2024) phases of a long-term field experiment established in Urbana, Illinois, to evaluate the effects of propagation method (plug propagation [PP] and rhizome propagation [RP]), planting density (1.0, 0.75, and 0.25 plants m⁻²), and nitrogen application (0 and 67 kg N ha⁻¹) on end-of-season biomass yield, tiller mass, tiller density, and tiller height. Linear regression models identified the dominant predictors of yield across stand ages and management regimes. Planting density, nitrogen (N) application, and propagation method significantly influenced early yield and canopy development. During the juvenile phase, biomass yield was driven by tiller density due to canopy expansion; in the mature phase, yield became driven by tiller mass. The PP plots produced higher tiller density than the RP plots, resulting in faster canopy closure and higher juvenile-phase yields. Rhizome-propagated (RP) plots produced lower tiller density, but individual tillers were 3.3–6.4 g tiller −1 heavier than PP tillers. After the canopy reached equilibrium, the PP and RP yields were similar because greater RP tiller mass compensated for its lower tiller density. Higher planting density resulted in greater yield and tiller density during the second year (2012), but this effect was absent from the third year (2013) onward. In the juvenile phase, N fertilization enhanced yield by 1.6–3.4 Mg ha −1 . Initiating fertilization in 2013 on unfertilized plots produced biomass similar to that in fertilized plots, suggesting yield recovery in the mature phase. These findings revealed that establishment strategies, including propagation method and planting density, influence juvenile miscanthus canopy development and productivity, transitioning from tiller-density- to mass-dominated yields, but not mature phase productivity.

09 BIOMASS FUELS↗
DOE OSTI2021

Dl-3-n-butylphthalide promotes neurite outgrowth of primary cortical neurons by Sonic Hedgehog signaling via upregulating Gap43

Highlights: • NBP promoted neurite outgrowth in immature primary cortical neurons. • NBP increased axon and dendrite extension in mature primary cortical neurons. • NBP promoted neuritogenesis and neuronal plasticity via Shh signaling pathway. • The Shh signaling pathway increased Gap43 expression in primary cortical neuron. • NBP promoted neurite outgrowth by Shh signaling via upregulating Gap43 expression. Neurite outgrowth is the basis for wiring during the development of the nervous system. Dl-3-n-butylphthalide (NBP) has been recognized as a promising treatment to improve behavioral, neurological and cognitive outcomes in ischemic stroke. However, little is known about the effect and mechanism of NBP on the neurite outgrowth. In this study, we used different methods to investigate the potential effects of NBP on the neurite extension and plasticity of immature and mature primary cortical neurons and explored the underlying mechanisms. Our results demonstrated that in immature and mature cortical neurons, NBP promoted the neurite length and intersections, increased neuritic arborization, elevated numbers of neurite branch and terminal points and improved neurite complexity and plasticity of neuronal development processes. Besides, our data revealed that NBP promoted neurite extension and branching partly by activating Shh signaling pathway via increasing Gap43 expression both in immature and mature primary cortical neurons. The present study provided new insights into the contribution of NBP in neuronal plasticity and unveiled a novel pathway to induce Gap43 expression in primary cortical neurons.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Updraft and Downdraft Core Size and Intensity as Revealed by Radar Wind Profilers: MCS Observations and Idealized Model Comparisons

This study explores the updraft and downdraft properties of mature stage mesoscale convective systems (MCSs) in terms of draft core width, shape, intensity, and mass flux characteristics. The observations use extended radar wind profiler (RWP) and surveillance radar datasets from the U.S. Department of Energy Atmospheric Radiation Measurement program for midlatitude (Oklahoma, USA) and tropical (Amazon, Brazil) sites. MCS drafts behave qualitatively similar to previous aircraft and RWP cloud summaries. The Oklahoma MCSs indicate larger and more intense convective up- and downdraft cores, and greater mass flux than Amazon MCS counterparts. However, similar size-intensity relationships and draft vertical profile behaviors are observed for both regions. Additional similarities include weak positive correlations between core intensity and core width (correlation coefficient r ~ 0.5), and increases in draft intensity with altitude. A model-observational intercomparison for draft properties (core width, intensity, mass flux) is also performed to illustrate the potential usefulness of statistical observed draft characterizations. Idealized simulations with the Weather Research and Forecasting model aligned with midlatitude MCS conditions are performed at model grid spacings (?x) that range from 4 km to 250 m. It is shown that the simulations performed at ?x = 250 m at similar mature MCS lifecycle stages are those that exhibit draft intensity, width, mass flux, and shape parameter performances best matching with observed properties.

radar, arm, wind profiler, goamazon↗
DOE OSTI2021

Probing the subcellular nanostructure of engineered human cardiomyocytes in 3D tissue

Abstract The structural and functional maturation of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) is essential for pharmaceutical testing, disease modeling, and ultimately therapeutic use. Multicellular 3D-tissue platforms have improved the functional maturation of hiPSC-CMs, but probing cardiac contractile properties in a 3D environment remains challenging, especially at depth and in live tissues. Using small-angle X-ray scattering (SAXS) imaging, we show that hiPSC-CMs matured and examined in a 3D environment exhibit a periodic spatial arrangement of the myofilament lattice, which has not been previously detected in hiPSC-CMs. The contractile force is found to correlate with both the scattering intensity ( R 2 = 0.44) and lattice spacing ( R 2 = 0.46). The scattering intensity also correlates with lattice spacing ( R 2 = 0.81), suggestive of lower noise in our structural measurement than in the functional measurement. Notably, we observed decreased myofilament ordering in tissues with a myofilament mutation known to lead to hypertrophic cardiomyopathy (HCM). Our results highlight the progress of human cardiac tissue engineering and enable unprecedented study of structural maturation in hiPSC-CMs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage

Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Iron-molybdenum cofactor synthesis by a thermophilic nitrogenase devoid of the scaffold NifEN

The maturation and installation of the active site metal cluster (FeMo-co, Fe 7 S 9 CMo- R -homocitrate) in Mo-dependent nitrogenase requires the protein product of the nifB gene for production of the FeS cluster precursor (NifB-co, [Fe 8 S 9 C]) and the action of the maturase complex composed of the protein products from the nifE and nifN genes. However, some putative diazotrophic bacteria, like Roseiflexus sp. RS-1, lack the nifEN genes, suggesting an alternative pathway for maturation of FeMo-co that does not require NifEN. In this study, the Roseiflexus NifH, NifB, and apo-NifDK proteins produced in Escherichia coli are shown to be sufficient for FeMo-co maturation and insertion into the NifDK protein to achieve active nitrogenase. The E. coli expressed NifDK RS contained P-clusters but was devoid of FeMo-co (referred to as apo-NifDK RS ). Apo-NifDK RS could be activated for N 2 reduction by addition of preformed FeMo-co. Further, it was found that apo-NifDK RS plus E. coli produced NifB RS and NifH RS were sufficient to yield active NifDK RS when incubated with the necessary substrates (homocitrate, molybdate, and S -adenosylmethionine [SAM]), demonstrating that these proteins can replace the need for NifEN in maturation of Mo-nitrogenase. The E. coli produced NifH RS and NifB RS proteins were independently shown to be functional. The reconstituted NifDK RS demonstrated reduction of N 2 , protons, and acetylene in ratios observed for Azotobacter vinelandii NifDK. These findings reveal a distinct NifEN-independent pathway for nitrogenase activation involving NifH RS , NifB RS , and apo-NifDK RS .

Payá-Tormo, Lucía↗