Search NASA⌕ Search

SEARCH · Search NASA

Results for “spatial gene expression”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2016

Using NASA's GeneLab for VESGEN Systems Analysis of Vascular Phenotypes from Stress and Other Signaling Pathways

One fundamental requirement shared by humans with all higher terrestrial life forms, including other vertebrates, insects, and higher land plants, is a complex, fractally branching vascular system. NASA's VESsel GENeration Analysis (VESGEN) software maps and quantifies vascular trees, networks, and tree-network composites according to weighted physiological rules such as vessel connectivity, tapering and bifurcational branching. According to fluid dynamics, successful vascular transport requires a complex distributed system of highly regulated laminar flow. Microvascular branching rules within vertebrates, dicot leaves and the other organisms therefore display many similarities. A unifying perspective is that vascular patterning offers a useful readout of molecular signaling that necessarily integrates these complex pathways. VESGEN has elucidated changes in vascular pattern resulting from inflammatory, developmental and other signaling within numerous tissues and major model organisms studied for Space Biology. For a new VESGEN systems approach, we analyzed differential gene expression in leaves of Arabidopsis thaliana reported by GeneLab (GLDS-7) for spaceflight. Vascularrelated changes in leaf gene expression were identified that can potentially be phenocopied by mutants in ground-based experiments. To link transcriptional, protein and other molecular change with phenotype, alterations in the spatial and dynamic dimensions of vascular patterns for Arabidopsis leaves and other model species are being co-localized with signaling patterns of single molecular expression analyzed as information dimensions. Previously, Drosophila microarray data returned from space suggested significant changes in genes related to wing venation development that include EGF, Notch, Hedghog, Wingless and Dpp signaling. Phenotypes of increasingly abnormal ectopic wing venation in the (non-spaceflight) Drosophila wing generated by overexpression of a Notch antagonist were analyzed by VESGEN. Other VESGEN research applications include the mouse retina, GI and coronary vessels, avian placental analogs and translational studies in the astronaut retina related to health challenges for long-duration missions.

Venation↗
NASA NTRS2002

Ionic signaling in plant responses to gravity and touch

Touch and gravity are two of the many stimuli that plants must integrate to generate an appropriate growth response. Due to the mechanical nature of both of these signals, shared signal transduction elements could well form the basis of the cross-talk between these two sensory systems. However, touch stimulation must elicit signaling events across the plasma membrane whereas gravity sensing is thought to represent transformation of an internal force, amyloplast sedimentation, to signal transduction events. In addition, factors such as turgor pressure and presence of the cell wall may also place unique constraints on these plant mechanosensory systems. Even so, the candidate signal transduction elements in both plant touch and gravity sensing, changes in Ca2+, pH and membrane potential, do mirror the known ionic basis of signaling in animal mechanosensory cells. Distinct spatial and temporal signatures of Ca2+ ions may encode information about the different mechanosignaling stimuli. Signals such as Ca2+ waves or action potentials may also rapidly transfer information perceived in one cell throughout a tissue or organ leading to the systemic reactions characteristic of plant touch and gravity responses. Longer-term growth responses are likely sustained via changes in gene expression and asymmetries in compounds such as inositol-1,4,5-triphosphate (IP3) and calmodulin. Thus, it seems likely that plant mechanoperception involves both spatial and temporal encoding of information at all levels, from the cell to the whole plant. Defining this patterning will be a critical step towards understanding how plants integrate information from multiple mechanical stimuli to an appropriate growth response.

Review↗
DOE OSTI2023

Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass

Abstract Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological—spatial, temporal and phylogenetic—patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Synchrotron Infrared Microspectroscopy Detecting the Evolution of Huntingtons Disease Neuropathology and Suggesting Unique Correlates of Dysfunction in White versus Gray Brain Matter

Huntington's disease (HD), caused by a mutation of the corresponding gene encoding the protein huntingtin (htt), is characterized by progressive deterioration of cognitive and motor functions, paralleled by extensive loss of striatal neurons. At the cellular level, pathogenesis involves an early and prolonged period of neuronal dysfunction followed by neuronal death. Understanding the molecular events driving these deleterious processes is critical to the successful development of therapies to slow down or halt the progression of the disease. Here, we examined biochemical processes in a HD ex vivo rat model, as well as in a HD model for cultured neurons using synchrotron-assisted Fourier transform infrared microspectroscopy (S-FTIRM). The model, based on lentiviral-mediated delivery of a fragment of the HD gene, expresses a mutant htt fragment in one brain hemisphere and a wild-type htt fragment in the control hemisphere. S-FTIRM allowed for high spatial resolution and distinction between spectral features occurring in gray and white matter. We measured a higher content of {beta}-sheet protein in the striatal gray matter exposed to mutant htt as early as 4 weeks following the initiation of mutant htt exposure. In contrast, white matter tracts did not exhibit any changes in protein structure but surprisingly showed reduced content of unsaturated lipids and a significant increase in spectral features associated with phosphorylation. The former is reminiscent of changes consistent with a myelination deficiency, while the latter is characteristic of early pro-apoptotic events. These findings point to the utility of the label-free FTIRM method to follow mutant htt's {beta}-sheet-rich transformation in striatal neurons ex vivo, provide further evidence for mutant htt amyloidogenesis in vivo, and demonstrate novel chemical features indicative of white matter changes in HD. Parallel studies in cultured neurons expressing the same htt fragments showed similar changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Effects of Particle Size on Chemical Speciation and Bioavailability of Copper to Earthworms ( Eisenia fetida ) Exposed to Copper Nanoparticles

To investigate the role of particle size on the oxidation, bioavailability, and adverse effects of manufactured Cu nanoparticles (NPs) in soils, we exposed the earthworm Eisenia fetida to a series of concentrations of commercially produced NPs labeled as 20- to 40-nm or <100-nm Cu in artificial soil media. Effects on growth, mortality, reproduction, and expression of a variety of genes associated with metal homeostasis, general stress, and oxidative stress were measured. We also used X-ray absorption spectroscopy and scanning X-ray fluorescence microscopy to characterize changes in chemical speciation and spatial distribution of the NPs in soil media and earthworm tissues. Exposure concentrations of Cu NPs up to 65 mg kg{sup -1} caused no adverse effects on ecologically relevant endpoints. Increases in metallothionein expression occurred at concentrations exceeding 20 mg kg-1 of Cu NPs and concentrations exceeding 10 mg kg{sup -1} of CuSO{sub 4} Based on the relationship of Cu tissue concentration to metallothionein expression level and the spatial distribution and chemical speciation of Cu in the tissues, we conclude that Cu ions and oxidized Cu NPs were taken up by the earthworms. This study suggests that oxidized Cu NPs may enter food chains from soil but that adverse effects in earthworms are likely to occur only at relatively high concentrations (>65 mg Cu kg{sup -1} soil).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

Nuclear speckles are self-assembled organelles composed of RNAs and proteins. They are proposed to act as structural domains that control distinct steps in gene expression, including transcription, splicing and mRNA export. Earlier studies identified differential localization of a few components within the speckles. It was speculated that the spatial organization of speckle components might contribute directly to the order of operations that coordinate distinct processes. Here, by performing multi-color structured illumination microscopy, we characterized the multilayer organization of speckles at a higher resolution. We found that SON and SC35 (also known as SRSF2) localize to the central region of the speckle, whereas MALAT1 and small nuclear (sn)RNAs are enriched at the speckle periphery. Coarse-grained simulations indicate that the non-random organization arises due to the interplay between favorable sequence-encoded intermolecular interactions of speckle-resident proteins and RNAs. Finally, we observe positive correlation between the total amount of RNA present within a speckle and the speckle size. These results imply that speckle size may be regulated to accommodate RNA accumulation and processing. Accumulation of RNA from various actively transcribed speckle-associated genes could contribute to the observed speckle size variations within a single cell.

Fei, Jingyi↗
DOE OSTI2018

Deficiency of α Calcitonin-gene-related peptide impairs peri-implant angiogenesis and osseointegration via suppressive vasodilative activity

Highlights: • Peri-implant neovasculature in metaphyseal femur increased and then declined within 14 days during healing process. • Deficiency of αCGRP impeded peri-implant angiogenesis and vascular remodeling alongside with osteogenesis. • The osteogenic and angiogenic effect of αCGRP might be a consequence of its vasodilative activity. Blood supply is essential for the bone healing process to obtain successful osseointegration. α Calcitonin gene-related peptide (αCGRP) is osteoanabolic and is the most potent microvascular vasodilator currently known with validated angiogenic effect in vitro. We previously demonstrated that lentiviral αCGRP overexpression vector system could express the gene effectively to enhance titanium implant osseointegration. In this study, we investigated the effect of αCGRP on peri-implant angiogenesis during healing process in vivo. Based on investigation of blood vessel alteration in the peri-implant region of wild-type mice, we found a reduced angiogenesis alongside a decline in bone-implant contact percentage and bone mass in αCGRP {sup −/−} mice. Overexpression of αCGRP could partly rescue the impairment. Alterations were also detected in three-dimensional vascular structural parameters and expression of bone and vessel related genes. The results showed αCGRP increased vascular volume fraction and mean vessel size, as well as spatially relocated vessels approximate to the region of bone formation. And angiogenic and osteogenic genes were significantly upregulated in the transfection and αCGRP{sup +/+} group. These results suggested that αCGRP played a synergic role in angiogenesis and osseointegration, partly as a consequence of its vasodilative activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

A moment-convergence method for stochastic analysis of biochemical reaction networks

Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

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

A modERN resource: identification of Drosophila transcription factor candidate target genes using RNAi

Transcription factors (TFs) play a key role in development and in cellular responses to the environment by activating or repressing the transcription of target genes in precise spatial and temporal patterns. In order to develop a catalog of target genes of Drosophila melanogaster TFs, the modERN consortium systematically knocked down the expression of TFs using RNAi in whole embryos followed by RNA-seq. We generated data for 45 TFs which have 18 different DNA-binding domains and are expressed in 15 of the 16 organ systems. The range of inactivation of the targeted TFs by RNAi ranged from log2fold change -3.52 to +0.49. The TFs also showed remarkable heterogeneity in the numbers of candidate target genes identified, with some generating thousands of candidates and others only tens. We present detailed analysis from five experiments, including those for three TFs that have been the focus of previous functional studies (ERR, sens, and zfh2) and two previously uncharacterized TFs (sens-2 and CG32006), as well as short vignettes for selected additional experiments to illustrate the utility of this resource. The RNA-seq datasets are available through the ENCODE DCC (http://encodeproject.org) and the Sequence Read Archive (SRA). TF and target gene expression patterns can be found here: https://insitu.fruitfly.org. These studies provide data that facilitate scientific inquiries into the functions of individual TFs in key developmental, metabolic, defensive, and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks during embryogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Comparing four heat-inducible promoters in stably transformed sugarcane regarding spatial and temporal control of transgene expression reveals candidates to drive stem-preferred transgene expression

Small heat shock protein (sHSP) promoters contain cis-regulatory elements that facilitate transcription in response to heat stress, making them valuable tools for functional studies through controlled gene expression and the precise regulation of gene-editing tools or morphogenic regulators. To evaluate their utility, GUS reporter gene expression driven by four plant-sourced HSP promoters (p GmHSP17.5 , p HvHSP17 , p ZmHSP17.7 , and p ZmHSP26 ) was compared across various tissues of stably transformed sugarcane before and after heat treatment. At 22°C, all promoters showed minimal activity in leaves and roots, although p ZmHSP17.7 and p HvHSP17 displayed moderate expression in stems. Following heat treatment, all promoters exhibited their highest activity in stems, followed by leaves and roots. In stem tissues, p GmHSP17.5 displayed heat-induced uidA expression comparable to the constitutive p ZmUbi promoter. Notably, heat-induced reporter gene activity in stem middle sections of single-copy transgenic lines containing p ZmHSP17.7 , p HvHSP17 , or p ZmHSP26 exceeded p ZmUbi -derived uidA activity by 9.7-fold, 3.8-fold, and 3.0-fold, respectively, with 346- to 3,672-fold induction compared to control conditions. Most promoters showed peak expression in the middle sections of the stem, while p HvHSP17 was the most active in the stem apices. Histochemical analysis revealed that p ZmHSP17.7 and p HvHSP17 were active in both parenchyma cells and vascular bundles within sugarcane stems. Among leaf tissues, mature leaves exhibited greater expression than senescing or immature leaves, while root activity remained consistently minimal across all promoters. Temperature-course experiments identified distinct activation thresholds: 34°C–36°C for p ZmHSP17.7 , 36°C for p ZmHSP26 , 36°C–38°C for p HvHSP17 , and 40°C–42°C for p GmHSP17.5 . Drought stress also induced reporter gene transcription in stems under HSP promoters, although with lower fold induction than heat treatment. These findings provide valuable tools for gene function studies and biotechnology applications, including heat stress tolerance research, controlled transgene expression in metabolic engineering, precision gene editing, and developmental biology studies.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2005

Linking Archaeal Molecular Diversity and Lipid Biomarker Composition in a Hypersaline Microbial Mat Community

Lipid biomarkers for discrete microbial groups are a valuable tool for establishing links to ancient microbial ecosystems. Lipid biomarkers can establish organism source and function in contemporary microbial ecosystems (membrane lipids) and by analogy, potential relevance to the fossilized carbon skeletons (geolipids) extracted from ancient sedimentary rock. The Mars Exploration Rovers have provided clear evidence for an early wet Mars and the presence of hypersaline evaporitic basins. Ongoing work on an early Earth analog, the hypersaline benthic mats in Guerrero Negro, Baja California Sur, may provide clues to what may have evolved and flourished on an early wet Mars, if only for a short period. Cyanobacterial mats are a pertinent early Earth analog for consideration of evolutionary and microbial processes within the aerobic photosynthetic and adjacent anoxic layers. Fluctuations in physio-chemical parameters associated with spatial and temporal scales are expressed through vast microbial metabolic diversity. Our recent work hopes to establish the dynamic of archaeal diversity, particularly as it relates to methane production in this high sulfate environment, through the use of lipid biomarker and phylogenetic analyses. Archaeal 16s rRNA and mcrA gene assemblages, demonstrated distinct spatial separation over the 130 mm core of at least three distinct genera within the order Methanosarcinales, as well as an abundance of uncultured members of the Thermoplasmales and Crenarchaeota. Ether-bound lipid analysis identified abundant 0-alkyl and 0-isopranyl chains throughout the core, and the presence of sn-2 hydroxyarchaeol, a biomarker for methylotrophic methanogens. A unique ether isoprenoid chain, a C30:1 , possibly related to the geolipid squalane, a paleobiomarker associated with hypersaline environments, was most abundant within the oxic-anoxic transition zone.

Jahnke, Linda↗
DOE OSTI2018

Abiotic stress networks converging on FT2 to control growth in Populus

Regulation of growth, quiescence and dormancy by seasonally recurring and episodic environmental factors is of central importance to the productivity of woody plants. Woody biomass feedstock plants such as Populus show substantial natural variation in growth responses to various environmental conditions; however, the complex genetic nature of these traits slows breeding for optimal biomass production in specific climates and on marginal lands. These growth responses are controlled by complex gene regulatory networks that are poorly understood. Elucidating the mechanisms that determine periods of growth and quiescence will identify specific genes and modules that can be manipulated to maximize growth in different environments. The main goal of the project was to develop transcriptional networks that describe spatially and temporally explicit regulatory relationships for both daylength and nutrient-mediated quiescence. We used next generation sequencing to characterize genome-wide gene expression changes to these two abiotic signals in shoot apices, leaf, root and vascular cambium. Overall, we sequenced 270 mRNAseq libraries and 54 smallRNAseq libraries from Populus trichocarpa and 58 RNAseq libraries from Populus nigra. We found both organ-specific transcriptional responses as well as responses common to multiple organs. Similarly, we uncovered both divergent and convergent gene regulatory networks that control growth responses to changes in daylength and nutrient stress. Thus, this work provides a foundation for developing approaches to optimize tree growth and biomass yield in response to specific as well as multiple abiotic conditions. Finally, we validated the functions of candidate regulators of growth in response to photoperiod and nutrient availability by introducing mutations via gene editing and transgenic methods. This data will be available to the public through journal publications and national/international genomic data archives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks

Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) 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.

cell specificity↗
DOE OSTI2026

Mechanically graded granular scaffolds for osteochondral tissue engineering

Engineered scaffolds designed to approximate the mechanical microenvironment of the osteochondral unit often address this complexity using discrete, two-phase architectures that introduce mechanical discontinuities and interfacial stress concentrations rather than a contiguous stiffness transition. To address this challenge, we created a photoannealed polyethylene glycol (PEG) granular scaffold with a spatially controlled stiffness gradient within a cell-permissive, macroporous architecture. Stiffness was dictated by photoannealing microgels using a photomask. We tuned void volume and available surface area by varying microgel diameter and tested how mesenchymal stromal cells (MSCs) interpret local mechanical environments. MSCs exhibited position-dependent differences in morphology, cytoskeletal structure, matrix deposition, and lineage-specific gene expression within the gradient scaffolds. Softer regions supported rounded cell morphology and deposition of a glycosaminoglycan-rich matrix, whereas stiffer regions promoted cell elongation, increased cytoskeletal tension, and expression of mineral-associated markers. Gradients formed from smaller microgels magnified these spatial responses by increasing cellular confinement and adhesion site availability. Disruption of actomyosin contractility eliminated these regional differences, demonstrating that MSCs rely on tension-dependent mechanotransduction to interpret the gradient. These findings reveal that coupling microgel architecture with continuous stiffness transitions provides a tractable platform to study multiscale mechanobiologic regulation and spatially guide osteochondral tissue formation.

Biological and medical sciences↗
DOE OSTI2018

Generation of regulable EGFRvIII targeted chimeric antigen receptor T cells for adoptive cell therapy of glioblastoma

Adoptive immunotherapy using chimeric antigen receptors-modified T cells (CAR-T) is a promising approach for cancer treatment. However, CARs currently applied in the clinics cannot be effectively regulated and the safety of CAR-T cell therapies remains a major concern. To improve the safety of CAR-T cells, we designed a synthetic splitting CAR (ssCAR) that can regulate T cell functions exogenously. Epidermal growth factor receptor variant III (EGFRvIII) was used as a molecular target for ssCAR. Our results indicate that both EGFRvIII and small molecule are needed for the activation of the ssCAR-T cells. AP21967 dose-dependently increased the expression of T cell activation, production of cytokines and extent of cell lysis. In conclusion, the gene switch designed in this study allows for temporal and spatial control over engineered T cells in a dose-and time-dependent manner by AP21967. Our work demonstrates the feasibility and improved safety profile of this novel treatment approach.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Elongated galactan side chains mediate cellulose–pectin interactions in engineered Arabidopsis secondary cell walls

SUMMARY The plant secondary cell wall is a thickened matrix of polysaccharides and lignin deposited at the cessation of growth in some cells. It forms the majority of carbon in lignocellulosic biomass, and it is an abundant and renewable source for forage, fiber, materials, fuels, and bioproducts. The complex structure and arrangement of the cell wall polymers mean that the carbon is difficult to access in an economical and sustainable way. One solution is to alter the cell wall polymer structure so that it is more suited to downstream processing. However, it remains difficult to predict what the effects of this engineering will be on the assembly, architecture, and properties of the cell wall. Here, we make use of Arabidopsis plants expressing a suite of genes to increase pectic galactan chain length in the secondary cell wall. Using multi‐dimensional solid‐state nuclear magnetic resonance, we show that increasing galactan chain length enhances pectin–cellulose spatial contacts and increases cellulose crystallinity. We also found that the increased galactan content leads to fewer spatial contacts of cellulose with xyloglucan and the backbone of pectin. Hence, we propose that the elongated galactan side chains compete with xyloglucan and the pectic backbone for cellulose interactions. Due to the galactan topology, this may result in comparatively weak interactions and disrupt the cell wall architecture. Therefore, introduction of this strategy into trees or other bioenergy crops would benefit from cell‐specific expression strategies to avoid negative effects on plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

GROWdb US River Systems - Samples

GROW Overview We developed the Genome Resolved Open Watersheds database (GROWdb), which aims to increase genomic sampling and understanding of global river microbiomes. An emphasis of GROWdb is to create a publicly available and ever-expanding microbial genome database that is focused on rivers while being interoperable with databases from other ecosystems. GROWdb is based on a network-of-networks approach to move beyond a small collection of well-studied rivers, towards a spatially distributed, global network of systematic observations. GROWdb represents the first microbial, river-focused resource parsed at various scales from genes to MAGs to community level including expression and potential based measurements that will be of interest to microbiologists, ecologists, geochemists, hydrologists, and modelers. Dataset Acknowledgement GROWdb contains data from various research campaigns, please acknowledge the following data generators, as appropriate: WHONDRS derived genomes or samples - include this statement in your acknowledgements: “This study used data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) under the River Corridor Science Focus Area (SFA) at the Pacific Northwest National Laboratory (PNNL) that was generated at the U.S. Department of Energy (DOE) Joint Genome Institute User Facility. PNNL is operated by Battelle Memorial Institute for the U.S. DOE under Contract No. DE-AC05-76RL01830. The SFA is supported by the U.S. DOE, Office of Biological and Environmental Research (BER), Environmental System Science (ESS) Program.” Total Samples loaded onto this Narrative: 178 Note: Not all GROW samples may be loaded into KBase Data Availability The data underlying GROWdb are accessible across various platforms to ensure all levels of data structure are widely available. First, all reads and MAGs are publicly hosted on National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. Second, all data related data presented here including MAG annotations, extended data tables, phylogenetic tree files, antibiotic resistance gene database files, and MAG abundance tables are available in Zenodo (link). Beyond the flat database files listed above, our aim for GROWdb was to maximize data use by making the data available in searchable and interactive platforms including the National Microbiome Data Collaborative (NMDC) data portal, the Department of Energy’s Systems Biology Knowledgebase (KBase), and a GROW specific user interface released here, GROWdb Explorer. Each platform provides different ways to interact with GROWdb: NMDC GROWdb formed a pilot project for the NMDC. Specifically, individual GROWdb datasets (metagenomes, metatranscriptomes, etc) are easily accessible and searchable through the NMDC data portal, where they are systematically connected to each other and to a rich suite of sample information and standard analysis results, following Findable, Accessible, Interoperable, and Reusable (FAIR) data practices. KBase GROWdb is publicly available within KBase, including samples (this Narrative), MAGs, and corresponding genome scale metabolic models. Access within KBase allows for immediate access and reuse of data, including comparison to private data using KBase’s 500+ analysis tools. Other linked narratives in KBase: GROW Metagenome Assembled Genomes (MAGs) GROW Metabolic Models GROWdb Explorer GROWdb data is also explorable through a graphical user interface built through the Colorado State University Geospatial Centroid (https://geocentroid.shinyapps.io/GROWdatabase/), allowing users to search and graph microbial and spatial data simultaneously. In summary, this microbial genome resource represents the first publicly available genome collection from rivers and offers data that can be leveraged across microbiome studies. GROWdb is an expanding repository to incorporate and unify global river multi-omic data for the future.

59 BASIC BIOLOGICAL SCIENCES↗