Executive Abstract
Microgravity aboard the International Space Station (ISS) imposes profound mechanical unloading on plant root systems. In NASA study OSD-615 (APEX-03-1), high-throughput glycome profiling across 155 monoclonal antibodies revealed extensive alterations in cell wall non-cellulosic polysaccharides in Arabidopsis thaliana seedling roots. Here, we present a systems biology framework integrating continuous glycomics matrices with companion spaceflight transcriptomics (OSD-218, OSD-217), the Salk Single-Cell Atlas (Lee et al. 2025, Nature Plants), ggPlantmap vector anatomy, and in situ confocal immunohistochemistry (Nakashima et al. 2023, npj Microgravity). Our multi-scale models reveal that microgravity-induced cell wall remodeling is driven by tissue-specific secondary wall xylan synthesis in metaxylem vessels, coupled to active class XI myosin and kinesin motor dynamics that compensate for microgravity-induced vesicle transport delays.
Study Design (NASA OSD-615 / APEX-03-1)
12 root samples of Arabidopsis thaliana (Col-0 wild-type) harvested at 6-day and 11-day post-germination aboard the ISS Veggie hardware alongside synchronous Kennedy Space Center (KSC) 1g ground controls.
Sequential extraction across 6 chemical fractions: 50mM CDTA, 1M KOH, 4M KOH, 100mM NaClO2, 4M KOHPC, and 0.1M H2SO4.
Multi-Scale Systems Biology Pipeline
Integrated glycomics, transcriptomics, Salk Single-Cell Foundation Model (Lee et al. 2025), ggPlantmap spatial vector anatomy, PMC10444889 confocal microscopy database, and TabPFN cross-study foundation model.
Full FAIR metadata compliance (RO-Crate 1.1, Zenodo schema, and Frictionless Data Tables).
Multi-Scale Experimental & Computational Architecture (Figure 1)
End-to-end integration of spaceflight glycome ELISA profiling, transcriptomics, single-cell atlas mapping, and live biophysical transport simulation.
Monoclonal Antibody Glycome Profiling (155 mAbs)
Interactive clustered heatmap of cell wall glycan epitopes across 12 spaceflight and ground control samples.
Differential Glycan Abundance & Volcano Plots
Statistical screening of Spaceflight vs. Ground controls using two-way ANOVA and Benjamini-Hochberg FDR correction.
Differential Glycomics Volcano Plot
Mean Fold Change by Glycan Class
Multi-Omics Sparse PLS Regression
Cross-correlating 155 glycome epitope vectors with 28 motor protein, MAP, and cell wall synthase transcripts.
sPLS Correlation Circle Plot
Clustered Image Map (CIM) Cross-Correlations
Top Statistically Significant Glycan-Gene Associations
| mAb / Glycan Epitope | Target Polysaccharide | Associated Gene | Gene Family | Correlation (r) | Biological Mechanism |
|---|
Cytoskeleton-to-Cell-Wall Systems Interactome
Interactive high-confidence protein-protein interaction (PPI) network reconstructed from STRING, AraNet v2, and WGCNA co-expression modules.
Gene Biochemical Profile: Click any node in the interactome above
Subcellular Compartmental Interactome & Enzymatic Reaction Reference (Figure 5)
Reconstructed spatial interactome across Golgi, Cytoplasmic Streaming Cables, Cortical MTs, Plasma Membrane, and Apoplast.
Single-Cell Spatial Prediction & ggPlantmap Root Anatomy
Projecting spaceflight-altered cytoskeletal motors and cell wall synthases onto 14 Arabidopsis thaliana root lineages using the Salk Single-Cell Atlas (Lee et al. 2025, Nature Plants) and ggPlantmap vector anatomy.
Root Maturation Cross-Section (ggPlantmap)
Root Tip Longitudinal Map (ggPlantmap)
Salk Atlas Multi-Cell-Type Expression Matrix (Figure 10)
Global dotplot of 15 key spaceflight genes across all 14 root cell types.
Microscopy & In Situ Immunohistochemistry Database
Comprehensive database of seedling morphology, root histology, and confocal laser scanning immunofluorescence from Nakashima et al. (2023, npj Microgravity 9:68 / PMC10444889 ↗ / Supplementary File ESM.pdf ↗).
Multi-Scale Spatial Validation Panel (Figure 11 Composite)
Direct alignment between single-cell spatial transcriptomic predictions (ggPlantmap) and in situ spaceflight confocal IHC.
Dual-Condition Plant Cell Vesicle Transport Simulator
Simultaneous real-time comparative physics simulation of Golgi-derived secretory vesicle transport along cytoskeletal tracks within an Arabidopsis thaliana root cell under 1g Ground Control (Top) vs. 0g Microgravity (Bottom). Modeled with authentic plant cell anatomy: central vacuole, subcortical cytoplasmic streaming sleeve, Golgi/TGN stacks, and layered cell walls.
1g Ground Control (Top Cell)
0g Microgravity (Bottom Cell)
Mechanistic Cell Biology & Trafficking Pathways
Interactive vector pathway diagrams linking motor protein dynamics, intracellular O-GlcNAcylation cascades, and apoplastic polysaccharide assembly.
Mass Spectrometry & Glycomics Workflow Architecture
Comprehensive step-through workflows for O-GlcNAc site mapping on cytoskeletal motor complexes and CCRC sequential glycome ELISA extractions.
Workflow Title
TabPFN Tabular Foundation Model: Cross-Study Meta-Analysis
In-context Bayesian multi-omics inference across spaceflight hardware (ISS Veggie vs. STS-131 BRIC-16) and ecotypes (Col-0 vs. Ler-0) using the landmark TabPFN foundation model (Hollmann et al., 2025, Nature / doi:10.1038/s41586-024-08328-6 ↗).
In-Context Partial Gravity Phenotypic Imputer (Moon, Mars & Microgravity)
Adjust the gravitational field to evaluate TabPFN's zero-shot posterior predictions for cell wall xylan thickening, motor expression, and root skewing.
Zero-Shot Cross-Mission Transfer (ROC Curves)
Bayesian In-Context Feature Importance
Cross-Study Dataset Harmonization (OSD-615 vs. OSD-121)
| Study Accession | Flight Mission & Hardware | Ecotype & Growth | Sample N | Assays Profiled | Key Harmonized Findings |
|---|---|---|---|---|---|
| OSD-615 (APEX-03-1) | ISS Veggie (Light) | A. thaliana Col-0 (6d, 11d) | 12 roots (6 Flight / 6 Ground) | 155-mAb Glycomics, Confocal IHC, RNA-Seq | +192% Xylem Xylan (CCRC-M140), MYA1/XI-K induction, SPR1 repression |
| OSD-121 (BRIC-16) | STS-131 BRIC Canisters (Dark & Light) | A. thaliana Ler-0 (4d) | 16 seedlings (8 Flight / 8 Ground) | Affymetrix ATH1, Cell Wall AIR fractions, Morphometrics | Secondary wall thickening, Root waving (38.5° skew), Myosin motor induction |
TabPFN Cross-Study Machine Learning Meta-Analysis (Figure 12)
Zero-shot cross-hardware ROC evaluation, Bayesian multi-omics feature saliency, and partial gravity dose-response curves.
NASA OSDR VEGGIE Hardware Study Explorer
Query and cross-reference multi-omics spaceflight studies conducted in the Vegetable Production System (Veggie) on the International Space Station.
| Accession | Study Title | Organism | Hardware & Mission | Assay Technology | DOI Link |
|---|
Scientific Manuscript & Peer-Review Package
Prepared for submission to npj Microgravity (Nature Partner Journals format). Includes all 11 high-resolution figures, statistical validations, and comprehensive mass spectrometry review.
Systems Biology Integration of Glycomics and Cytoskeletal Transport Networks Reveals Microgravity-Induced Cell Wall Remodeling Mechanisms in Arabidopsis thaliana
Author: Richard Barker (NASA GeneLab / OSDR, NASA Ames & Kennedy Space Centers)