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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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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Tenuigenin inhibits RANKL-induced osteoclastogenesis by down-regulating NF-κB activation and suppresses bone loss in vivo

Tenuigenin, a major active component of polygala tenuifolia root, has been used to treat patients with insomnia, dementia, and neurosis. In this study, we aimed to investigate the effects of tenuigenin on osteoclastogenesis and clarify the possible mechanism. We showed that tenuigenin inhibited receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast differentiation and bone resorption without cytotoxicity, which was further demonstrated by reduced osteoclast specific gene expression such as TRAP, c-Src, ATP6v0d2, etc. Moreover, the inhibitory effect of tenuigenin was associated with impaired NF-κB activity owing to delayed degradation/regeneration of IkBa and inhibition of p65 nuclear translocation. Consistent with the in vitro results, micro-ct scanning and analysis data showed that tenuigenin suppressed RANKL-induced bone loss in an animal model. Taken together, our data demonstrate that tenuigenin inhibit osteoclast formation and bone resorption both in vitro and in vivo, and comprise a potential therapeutic alternative for osteoclast-related disorders such as osteoporosis and cancer-induced bone destruction. - Highlights: • Tenuigenin suppresses osteoclasts formation, survival and function in vitro. • Tenuigenin impairs NF-κB activation. • Tenuigenin suppresses RANKL-induced bone lose in vivo. • Tenuigenin may be used for treating osteoclast related diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Rifampin suppresses osteoclastogenesis and titanium particle-induced osteolysis via modulating RANKL signaling pathways

Wear particles liberated from the surface of prostheses are considered to be main reason for osteoclast bone resorption and that extensive osteoclastogenesis leads to peri-implant osteolysis and subsequent prosthetic loosening. The aim of this study was to assess the effect of rifampin on osteoclastogenesis and titanium (Ti) particle-induced osteolysis. The Ti particle-induced osteolysis mouse calvarial model and bone marrow-derived macrophages (BMMs) were used. Rifampin, at dose of 10 or 50 mg/kg/day, was respectively given intraperitoneally for 14 days in vivo. The calvariae were removed and processed for Further histological analysis. In vitro, osteoclasts were generated from mouse BMMs with receptor activator of nuclear factor-κB ligand (RANKL) and the macrophage colony stimulating factor. Rifampin at different concentrations was added to the medium. The cell viability, tartrate-resistant acid phosphatase (TRAP) staining, TRAP activity and resorption on bone slices were analysis. Osteoclast-specific genes and RANKL-induced MAPKs signaling were tested for further study of the mechanism. Rifampin inhibited Ti-induced osteolysis and osteoclastogenesis in vivo. In vitro data indicated that rifampin suppressed osteoclast differentiation and bone resorption in a dose-dependent manner. Moreover, rifampin significantly reduced the expression of osteoclast-specific markers, including TRAP, cathepsin K, V-ATPase d2, V-ATPase a3, c-Fos, and nuclear factor of activated T cells (NFAT) c1. Further investigation revealed that rifampin inhibited osteoclast formation by specifically abrogating RANKL-induced p38 and NF-κB signaling. Rifampin had significant potential for the treatment of particle-induced peri-implant osteolysis and other diseases caused by excessive osteoclast formation and function. - Highlights: • Rifampin inhibited Ti-induced osteolysis and osteoclastogenesis in vivo. • Rifampin suppressed osteoclast differentiation and bone resorption in a dose-dependent manner. • Rifampin significantly reduced the expression of osteoclast-specific markers in vitro. • RANKL-induced p38 and NF-κB signaling may be involved behind the effects of rifampin treatment on osteoclastogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria

Comparative genomic studies of the bacterial MFS-type copper importer CcoA, required for cbb 3 -type cytochrome c oxidase (cbb 3 -Cox) biogenesis, revealed a widespread CcoA-like transporters (CalT) family, containing the conserved CcoA Cu-binding MxxxM and HxxxM motifs. Surprisingly, this family also included the RfnT-like proteins, earlier suggested to transport riboflavin. However, presence of the Cu-binding motifs in these proteins raised the possibility that they might be Cu transporters. To test this hypothesis, the genomic context of the corresponding genes was examined, and three of such genes from Ochrobactrum anthropi , Rhodopseudomonas palustris and Agrobacterium tumefaciens were expressed in Escherichia coli (ΔribB) and Rhodobacter capsulatus (ΔccoA) mutants. Copper and riboflavin uptake abilities of these strains were compared with those expressing R. capsulatus CcoA and Rhizobium leguminosarum RibN as bona fide copper and riboflavin importers, respectively. Altogether data demonstrated that the “RfnT-like” CalT proteins are unable to efficiently transport riboflavin, but they import copper like CcoA. Nevertheless, even though expressed and membrane-localized in a R. capsulatus mutant lacking CcoA, these transporters were unable to accumulate Cu or complement for cbb 3 -Cox defect. This lack of functional exchangeability between the different subfamilies of CalT homologs suggests that MFS-type bacterial copper importers might be species-specific.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (~40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. In conclusion, the Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Evaluating two live-attenuated vaccines against Salmonella enterica serovar Reading in turkeys: reduced tissue colonization and cecal tonsil transcriptome responses

Vaccines that cross-protect across serovars ofSalmonella enterica(Salmonella) would be a beneficial intervention against emerging and persistentSalmonellaisolates of concern for the turkey industry. The 2017–2019 foodborne outbreak ofSalmonella entericaserovar Reading (S. Reading) revealed the need for effective control of this serovar in turkey production. This study evaluated two live-attenuatedSalmonellavaccines, an internally developed cross-protective vaccine and a commercially available vaccine, against an outbreak-associated strain ofS. Reading in turkeys. At 1 day and 3 weeks of age, male turkey poults were either mock-vaccinated with phosphate buffered saline (PBS) or given one of the vaccines by oral gavage (primary and booster) or aerosol spray (primary) then drinking water (booster). At 7 weeks of age, poults were challenged with 10 9 colony forming units (CFU) ofS. Reading; a mock-vaccinated group was mock-challenged with PBS. Colonization of the cecal contents and cecal tonsil was 1.5–3 log 10 CFU/g lower in vaccinated birds than mock-vaccinated birds at 7 and/or 14 days post-inoculation (DPI).Salmonelladissemination to the spleen was significantly reduced by both vaccines. Gene expression of intestinal transporters (such asSCNN1BandSLC10A2) and tight junction proteins was significantly decreased in the turkey cecal tonsil transcriptome at 2 DPI withS. Reading. Vaccination with either vaccine mitigated most cecal tonsil gene expression responses toS. Reading challenge. Therefore, both the internally developed vaccine and commercial vaccine were cross-protective against colonization and dissemination, and both were able to limit transcriptional changes from challenge in intestinal health-related genes in the cecal tonsil, thereby providing vaccination efficacy and impact data againstS. Reading in turkeys.

Veterinary Sciences↗
NASA NTRSDate not supplied

Optimizing a Small RNAseq Analysis Pipeline for NASA GeneLab Using Open-Source Tools and Libraries

Small RNA sequencing (small RNAseq) is a powerful tool for studying the regulation of gene expression in various organisms. Small RNAseq has been leveraged in space biology research to study how expression of small RNAs, e.g. micro RNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), change upon exposure to the space environment. NASA GeneLab currently hosts small RNAseq raw data derived from space-relevant experiments on the Open Science Data Repository (OSDR). To maximize the accessibility of these data to the scientific community, in addition to hosting raw data, which is only interpretable by bioinformaticians, GeneLab plans to process all small RNAseq datasets and make those processed data available to the scientific community via the OSDR. In this study, we present the development of the GeneLab standardized pipeline for processing small RNAseq datasets. Using human, plant, and synthetic small RNAseq datasets, we interrogate various open-source software and publicly available databases to evaluate their accuracy and reproducibility in each step of the pipeline. For quality control and adapter detection and trimming, we evaluated TrimGalore!, FASTX, SeqKit, and DNApi methods to optimize alignment to reference genomes. We compared BWA, Bowtie, and Bowtie2 to determine the optimal alignment tool. For each alignment tool we also assessed various reference databases, including Ensembl reference genomes and different types of small RNA reference databases, including genome, hairpin, and miRNA references from the miRbase and MirGeneDB databases. To quantify the aligned data, we compared SAMtools, HTSeq, and RSEM for counting alignment events from each alignment tool used. Finally, we evaluated various tools, including DESeq2 and EdgeR, for data normalization and subsequent differential expression analysis. We will present the results from our comparative analyses for each pipeline step and propose a consensus pipeline for processing small RNAseq data derived from various organisms exposed to the space environment.

SmallRNAseq, NASA GeneLab, quality control, adapte↗
DOE OSTI2016

Studies of the PfkB Family of Proteins in Arabidopsis thaliana

The phosphofructokinase B (PkfB) family of carbohydrate kinases is a large group that includes members with specificity for a diverse array of carbohydrate substrates, including fructose, ribose, fructose‐6‐phosphate, tagatose‐6‐phosphate, adenosine, myo‐inositol, and others. Although there are 21 genes encoding PfkB family members in the higher plant Arabidopsis thaliana , only a few have been studied in detail. Two Arabidopsis proteins with fructokinase activity were identified and characterized via native PAGE and in‐gel assays, though the genes were not identified. Another class of PfkB proteins identified in Arabidopsis lacks demonstrated enzymatic activity, but is necessary for the accumulation of photosynthetic transcripts in chloroplasts. The fructokinase‐like proteins 1 and 2 (FLN1 and FLN2, respectively) and NARA5 all belong to this class, although the mechanism of how NARA5 exerts it's phenotype remains elusive. FLN1 and 2 have been identified in proteomics studies as members of a large protein complex that interacts with, and likely regulates, the prokaryotic‐type plastid RNA polymerase which specifically transcribes photosynthetic genes in the plastid. We have found that FLN1 and FLN2 interact with each other in an ATP‐dependent manner both in vitro and in vivo . Phenotypic analysis suggests that the presence of both proteins is necessary for proper levels of transcription. Our data on the interaction between FLN1 and FLN2 suggests a mechanism where the FLN proteins act as a biochemical switch to activate transcription under conditions that favor their binding to each other. We have also begun characterization of the remainder of the Arabidopsis PfkB family and have identified a group of seven highly similar Arabidopsis PfkB proteins. These seven proteins were expressed in E. coli and enzymatic assays performed. All are active as fructokinases with high specificity for fructose. T‐DNA mediated inactivation of five of the seven genes resulted in no overt phenotype which hints at possible redundancy between some of these gene products. Using GFP fusions, we have determined that all localize to the cytosol except one, which localizes to plastids. Higher order mutants and biochemical analysis, along with expression analysis will allow us to tease apart the differences and the importance of each of these family members. We have characterized another PfkB protein that appears to be the sole Arabidopsis ribokinase (AtRBSK). Its biochemical properties and cofactor requirements are similar to that of known mammalian and prokaryotic RBSKs. T‐DNA insertion into AtRBSK results in the hyper‐accumulation of ribose in both the roots and leaves of 10 day‐old seedlings compared to wild type. Arabidopsis lacking AtRBSK grow poorly on media supplemented with ribose as the only sugar. We are currently dissecting the pathway that leads to the production of ribose in plants to put AtRBSK into a biological context. Our studies of the PfkB family in Arabidopsis are yielding promising results and will continue to further our understanding of many fundamental processes in plant biology ranging from central metabolism to the regulation of transcription in chloroplasts. Support or Funding Information The authors gratefully acknowledge support from the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, US. Department of Energy (contracts DE‐FG02–09ER16077 and DE‐SC0002175) to JC

Riggs, John W.↗
DOE OSTI2023

Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein

IGHV3-33 -encoded antibodies are prevalent in the human humoral response against the Plasmodium falciparum circumsporozoite protein (PfCSP). Among VH3-33 antibodies, cross-reactivity between PfCSP major repeat (NANP), minor (NVDP), and junctional (NPDP) motifs is associated with high affinity and potent parasite inhibition. However, the molecular basis of antibody cross-reactivity and the relationship with efficacy remain unresolved. Here, we perform an extensive structure-function characterization of 12 VH3-33 anti-PfCSP monoclonal antibodies (mAbs) with varying degrees of cross-reactivity induced by immunization of mice expressing a human immunoglobulin gene repertoire. We identify residues in the antibody paratope that mediate cross-reactive binding and delineate four distinct epitope conformations induced by antibody binding, with one consistently associated with high protective efficacy and another that confers comparably potent inhibition of parasite liver invasion. Our data show a link between molecular features of cross-reactive VH3-33 mAb binding to PfCSP and mAb potency, relevant for the development of antibody-based interventions against malaria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effects of Saccharomyces cerevisiae quorum sensing signal molecules on ethanol production in bioethanol fermentation process

Here in this study, the concentrations of Saccharomyces cerevisiae quorum sensing signal molecules (QSMs) were determined, not to mention the exploration of the effects of exogenous S. cerevisiae QSMs on the sole fermentation of S. cerevisiae and co-fermentation of S. cerevisiae and Lactobacillus plantarum. The results showed that the concentrations of three signal molecules (2-phenylethanol (2-PE), tyrosol and tryptophan) produced by S. cerevisiae increased with a higher bacteria density, which tends to become stable up to 118.02, 32.05 and 1.93 mg/L respectively when cultivating for 144 h. Among the three signaling molecules, only 2-PE promoted the ethanol production capacity of S. cerevisiae. The ethanol concentration of the sole fermentation of S. cerevisiae loaded with 120 mg/L 2-PE reached 3.2 g/L in 9 h, which was 58.7% higher than that of the group without 2-PE addition. Moreover, 2-PE reduced the negative impact of L. plantarum on S. cerevisiae. Within 12 h of the co-fermentation of L. plantarum and S. cerevisiae, the ethanol concentration in the co-fermentation group loaded with 2-PE reached 5.6 g/L, similar to that in the group fermenting with sole S. cerevisiae, and the yeast budding rate was also restored to 28.51%. qRT-PCR results of S. cerevisiae which was in sole fermentation with 2-PE addition for 9 h showed that the relative expression levels of ethanol dehydrogenase gene ADH1 in S. cerevisiae decreased by 25% and the relative expression levels of MLS1, CIT2, IDH1,CIT1 decreased by 26%, 30%, 22%,18%, respectively, meant that the glyoxylic and tricarboxylic acid cycles were greatly inhibited, which promotes the accumulation of ethanol. The results of this study provide basic data for using QSMs more than antibiotics in the the prevention of contamination during the industrialized bioethanol production.

2-phenylethanol↗
DOE OSTI2020

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis -element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex

How early sensory experience during “critical periods” of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular profiles of layer 2/3 (L2/3) cell types in the primary visual cortex (V1) are vision-dependent [S. Chenget al.,Cell185, 311–327.e24 (2022)]. Here, we characterize the spatial organization of L2/3 cell types with and without visual experience. Spatial transcriptomic profiling based on 500 genes recapitulates the zonation of L2/3 cell types along the pial–ventricular axis in V1. By applying multitasking theory, we suggest that the spatial zonation of L2/3 cell types is linked to the continuous nature of their gene expression profiles, which can be represented as a 2D manifold bounded by three archetypal cell types. By comparing normally reared and dark reared L2/3 cells, we show that visual deprivation-induced transcriptomic changes comprise two independent gene programs. The first, induced specifically in the visual cortex, includes immediate-early genes and genes associated with metabolic processes. It manifests as a change in cell state that is orthogonal to cell-type-specific gene expression programs. By contrast, the second program impacts L2/3 cell-type identity, regulating a subset of cell-type-specific genes and shifting the distribution of cells within the L2/3 cell-type manifold. Through an integrated analysis of spatial transcriptomics with single-nucleus RNA-seq data, we describe how vision patterns cortical L2/3 cell types during the critical period.

Science & Technology - Other Topics↗
DOE OSTI2015

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints. The algorithm served as the cornerstone for constructing the first global, predictive Environmental Gene Regulatory Influence Network (EGRIN) model for a free-living cell, and has now been applied to many more organisms. However, due to its computational inefficiencies, long run-time and complexity of various input data types, cMonkey was not readily usable by the wider community. To address these primary concerns, we have significantly updated the cMonkey algorithm and refactored its implementation, improving its usability and extendibility. These improvements provide a fully functioning and user-friendly platform for building co-regulated gene modules and the tools necessary for their exploration and interpretation. We show, via three separate analyses of data for E. coli, M. tuberculosis and H. sapiens, that the updated algorithm and inclusion of novel scoring functions for new data types (e.g. ChIP-seq and transcription factor over-expression [TFOE]) improve discovery of biologically informative co-regulated modules. The complete cMonkey2 software package, including source code, is available at https://github.com/baliga-lab/cmonkey2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Optimization of an in Vitro CYP450 Induction Assay Using Cryopreserved Cell Lines

Cytochrome P450 (CYP450) enzymes are responsible for the majority for Phase I metabolism. Induction occurs when a drug increases the rate of CYP450 enzyme production. As a result, the rates of metabolism of subsequent drugs increase, posing concerns for dosing and safety. To further expand the USAMRICD Absorption, Distribution, Metabolism, Excretion, and Toxicity Center of Excellence (ADMET CoE) profiling capabilities, a CYP450 induction assay is being developed using alternative cell lines to primary human hepatocytes to measure changes in gene expression of CYP1A2 and CYP3A4 isoenzymes. Primary human hepatocytes are the gold standard for evaluating P450 induction in vitro ; however, they have inherent limitations such as high costs, fastidious nature, and significant lot‐to‐lot variability. Induction assessments using cryopreserved hepatocytes and two immortalized cell lines, HepaRG and HepatoCells, are being conducted to determine a more robust, cost‐effective alternative model. Each cell line was exposed to the standard inducers rifampicin and omeprazole to assess CYP3A4 and CYP1A2 activity, respectively. Following a 72‐hour incubation period, RNA from the cell cultures was extracted and purified. Fold changes of gene expression were measured using real‐time quantitative PCR (RT‐qPCR). Hepatocytes displayed an average fold change of 92.7 for CYP3A4 and 49.6 for CYP1A2, whereas HepaRG displayed changes of 28.6 and 179.5, respectively. Average values for CYP3A4 and CYP1A2 for HepatoCells were 58.7 and 43.9. Based on the data, HepatoCells most closely mimicked cryopreserved hepatocytes in comparison to HepaRG cells. Additional data on assay parameters and technique optimization will be presented. Support or Funding Information Opinion disclaimer: The views expressed in this abstract are those of the authors and do not reflect the official policy of the Department of the Army, Department of Defense, or the U.S. Government. This project was generously supported in part by an appointment to the Postgraduate Research Participation Program at the U.S. Army Medical Research Institute of Chemical Defense administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and U.S. Army Medical Research and Materiel Command. Support is also provided by the Defense Threat Reduction Agency – Joint Science and Technology Office, Medical S&T Division. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Lim, Tae Young↗
DOE OSTI2021

Redundant roles of four ZIP family members in zinc homeostasis and seed development in Arabidopsis thaliana

Zinc (Zn) is essential for normal plant growth and development. The Zn-regulated transporter, iron-regulated transporter (IRT)-like protein (ZIP) family members are involved in Zn transport and cellular Zn homeostasis throughout the domains of life. In this study, we have characterized four ZIP transporters from Arabidopsis thaliana (IRT3, ZIP4, ZIP6, and ZIP9) to better understand their functional roles. The four ZIP proteins can restore the growth defect of a yeast Zn uptake mutant and are upregulated under Zn deficiency. Single and double mutants show no phenotypes under Zn-sufficient or Zn-limited growth conditions. In contrast, triple and quadruple mutants show impaired growth irrespective of external Zn supply due to reduced Zn translocation from root to shoot. All four ZIP genes are highly expressed during seed development, and siliques from all single and higher-order mutants exhibited an increased number of abnormal seeds and decreased Zn levels in mature seeds relative to wild type. The seed phenotypes could be reversed by supplementing the soil with Zn. Finally, our data demonstrate that IRT3, ZIP4, ZIP6, and ZIP9 function redundantly in maintaining Zn homeostasis and seed development in A. thaliana.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗
DOE OSTI2023

Divergent Metabolic Changes in Rhizomes of Lowland and Upland Switchgrass (Panicum virgatum) from Early Season through Dormancy Onset

High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow—which is a significant source of genetics for yield improvement—was studied over a growing season at a northern site. Metabolite levels and transcript abundances were combined to develop physiological profiles accompanying greening through the onset of dormancy in Kanlow rhizomes. Next, comparisons of the data to rhizome metabolism occurring in the adapted upland cultivar Summer were performed. These data revealed both similarities as well as numerous differences in rhizome metabolism that were indicative of physiological adaptations unique to each cultivar. Similarities included elevated ABA levels and accumulation of starch in rhizomes during dormancy onset. Notable differences were observed in the accumulation of specific metabolites, the expression of genes encoding transcription factors, and several enzymes linked to primary metabolism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Sostdc1 Regulates NK Cell Maturation and Cytotoxicity [Sostdc1 regulates natural killer cell maturation and cytotoxicity]

NK cells are innate-like lymphocytes that eliminate virally infected and cancerous cells, but the mechanisms that control NK cell development and cytotoxicity are incompletely understood. We identified roles for sclerostin domain–containing-1 ( Sostdc1 ) in NK cell development and function. Sostdc1 -knockout ( Sostdc1 –/– ) mice display a progressive accumulation of transitional NK cells (tNKs) (CD27 + CD11b + ) with age, indicating a partial developmental block. The NK cell Ly49 repertoire in Sostdc1 –/– mice is also changed. Lower frequencies of Sostdc1 –/– splenic tNKs express inhibitory Ly49G2 receptors, but higher frequencies express activating Ly49H and Ly49D receptors. Yet, the frequencies of Ly49I + , G2 + , H + , and D + populations were universally decreased at the most mature (CD27 – CD11b + ) stage. We theorized that the Ly49 repertoire in Sostdc1 –/– mice would correlate with NK killing ability and observed that Sostdc1 –/– NK cells are hyporesponsive against MHC class I–deficient cell targets in vitro and in vivo, despite higher CD107a surface levels and similar IFN-γ expression to controls. Consistent with Sostdc1’s known role in Wnt signaling regulation, Tcf7 and Lef1 levels were higher in Sostdc1 –/– NK cells. Expression of the NK development gene Id2 was decreased in Sostdc1 –/– immature NK and tNK cells, but Eomes and Tbx21 expression was unaffected. Reciprocal bone marrow transplant experiments showed that Sostdc1 regulates NK cell maturation and expression of Ly49 receptors in a cell-extrinsic fashion from both nonhematopoietic and hematopoietic sources. Taken together, these data support a role for Sostdc1 in the regulation of NK cell maturation and cytotoxicity, and identify potential NK cell niches.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Radiogenic cell transformation and carcinogenesis

Radiation carcinogenesis is one of the major biological effects considered important in the risk assessment for space travel. Various biological model systems, including both cultured cells and animals, have been found useful for studying the carcinogenic effects of space radiations, which consist of energetic electrons, protons and heavy ions. The development of techniques for studying neoplastic cell transformation in culture has made it possible to examine the cellular and molecular mechanisms of radiation carcinogenesis. Cultured cell systems are thus complementary to animal models. Many investigators have determined the oncogenic effects of ionizing and nonionizing radiation in cultured mammalian cells. One of the cell systems used most often for radiation transformation studies is mouse embryonic cells (C3H10T1/2), which are easy to culture and give good quantitative dose-response curves. Relative biological effectiveness (RBE) for heavy ions with various energies and linear energy transfer (LET) have been obtained with this cell system. Similar RBE and LET relationship was observed by investigators for other cell systems. In addition to RBE measurements, fundamental questions on repair of sub- and potential oncogenic lesions, direct and indirect effect, primary target and lesion, the importance of cell-cell interaction and the role of oncogenes and tumor suppressor genes in radiogenic carcinogenesis have been studied, and interesting results have been found. Recently several human epithelial cell systems have been developed, and ionizing radiation have been shown to transform these cells. Oncogenic transformation of these cells, however, requires a long expression time and/or multiple radiation exposures. Limited experimental data indicate high-LET heavy ions can be more effective than low-LET radiation in inducing cell transformation. Cytogenetic and molecular analyses can be performed with cloned transformants to provide insights into basic genetic mechanism(s) of radiogenic transformation of human epithelial cells.

NASA Discipline Radiation Health↗