Sealed growth chambers can create low-oxygen conditions, altering hypoxia/ROS signaling, which is known to confound microgravity effects. The EMCS hardware (OSD-314) provides a tightly controlled atmosphere (air-tight, regulated N₂/O₂/CO₂, ethylene removal), whereas the CARA plates (OSD-120) were exposed to the ambient ISS atmosphere. Prior analyses found clear hypoxic stress signatures. Starting with OSD-314 and OSD-120, this subgroup aims to compare sealed vs. ambient ISS growth conditions to help separate potential hypoxia responses from broader spaceflight environmental effects. For an overall approach, we’ll be conducting comparative transcriptomic analyses across selected datasets, pathway analyses, and creating a harmonized metadata table.
Research Question
Do sealed (EMCS) vs. ambient-cabin growth conditions produce distinct hypoxia/ROS transcriptional signatures in space-grown Arabidopsis? The hypothesis is that EMCS-grown plants will show stronger enrichment of hypoxia/ROS pathways, whereas a subset of gravitropism/cytoskeleton-related pathways will be consistent across chamber types.
Deliverables
The expected deliverables include a harmonized metadata table and a summarized gene- and pathway-level map distinguishing between the datasets and hardwares (for comparison), with the goal of presenting the results at a conference such as ASGSR or AGU and/or a submission to GSR.
Has anyone done any research on those small Biospheres that people create in jars? There was this one guy that successfully made a small biosphere in a jar that has been sealed away for going on 30 years. Maybe for a sealed plant growth chamber it might need to mirror comparable to a mini-biosphere jar? Spit-balling here…
This is so exciting though!!
@Morgan_Waltz great idea! It would be awesome if any “terrarium” style experiments or any studies with justify billy spaceflight related methods that include analyse volatiles would be of great interest and really cool
Hi & Happy Friday,
I just finished hardening OSD-120 (CARA roots) into a 5-notebook series on Kaggle and thought this group might care about the plant side specifically.
By Day 13 these roots have already gone through the shock of weightlessness and settled into a new program, so the DEGs are basically “how Col-0, phyD, and WS decided to live in space.” The pipeline takes 36 samples and 28k rRNA-removed genes through QC → DESeq2 → DEG overlap → enrichment and lands on a small set of shared circadian genes that stay active no matter which genotype you fly.
I’m not a biologist by training, but the graphs (PCA, DEG patterns, circadian/pathway plots) actually helped me understand the plant biology a lot better, so I figured it might be useful for others too. Next up I’ll be running the same pipeline on OSD-314 sealed-pod data to see how much of this ISS light/circadian story holds. Again the graphs & the pipeline tell the whole story.
Do let me know, if you have anything you want me to zone in while I put the next OSD into my development schedule for the next couple of weeks.
Thx!
Great question, and that’s NoteBook/NB06. Adding a dedicated light × dark interaction model (Earth vs. in-flight, 2x2 contrast) before I move on to the next dataset. I want to make sure OSD-120 is fully covered before forking.
However, the pipeline’s already hardened so it shouldn’t take long to add, I’ll drop it in the series & mention you & the others when it’s live(if you all would like of course). If there are other angles, areas, or specifics that the group wants captured before I move on, now’s the time to mention them.
Also, just a reminder the original goal of this pipeline was to capture the full consciousness of the OSD-120 dataset across all 5 notebooks, not just one angle, but somewhat of a whole story. My plan from the start was to harden these datasets and hand them off, letting the group take them wherever the science leads.
I’m a bit stretched right now so I can’t guarantee I’ll make every meeting, but the notebooks are public, the pipeline is reproducible, and you’re more than welcome to dig in, fork, and build on whatever I introduced here.
