Time on a map

A 7-point near-null-field time course — 10 min, 1 h, 2 h, 4 h, 24 h, 48 h, 96 h — in roots and shoots, projected onto the redox and respiratory maps. Every other overlay in this atlas is a single snapshot; this one is a trajectory, which is the only way to see a node that goes down and then comes back.

Source: Parmagnani, Mannino & Maffei (2022), Biomolecules 12(12):1824, doi:10.3390/biom12121824, Arabidopsis thaliana.

194loci in the source table
12are QBO atlas loci
7timepoints × 2 tissues
2,716values parsed

These are the authors' published results, not a reanalysis. No raw data was deposited in any public repository. The article's Data Availability Statement reads, in full: “Data are available as supplementary tables and further data can be provided upon request”

So nothing on this page can be recomputed, re-thresholded or re-tested from source data. What is drawn is what the authors chose to report, read out of Table S2.xlsx and re-projected onto the maps. That is a weaker provenance than the NASA OSDR pages in this atlas, which rest on processed data anyone can download, and it is labelled differently throughout: published_results.

What was measured

near-null magnetic field (~30 nT) against the local geomagnetic field (20–60 µT), generated in a triaxial Helmholtz coil system and monitored with a three-axis magnetometer. Values are Parmagnani's reported fold change for hMF-grown plants relative to GMF-grown controls, as mean ± SD.

The scale matters more than it looks. The published values are ratios — 1.0 means no change — while every overlay in this atlas expects log2, where 0.0 means no change. Feeding the ratios in directly would have coloured every unchanged gene as strongly upregulated, and the figure would have looked completely normal. The conversion happens in qbio.papers.Series.to_log2, the SD is carried through the same transform rather than left in the wrong units, and qbio.project.project_series refuses a series that is still on a ratio scale.

The parse is complete: 2,716 cells read, 0 blank, 0 rows without a usable locus.

The QBO pathway maps

Each node is tinted by its extreme value; multi-locus nodes where isoforms diverge in sign (such as SUPEROXIDE_DISMUTASES displaying ObCSD vs ObFSD1) render a 2-row heatmap directly inside the node box.

QBM-07 with roots data projected — QBM-07 · Roots · 4 nodes with data (50%)
**3 of 4 nodes reverse direction** during the course (CATALASE, PLASTID_ROS, SUPEROXIDE_DISMUTASES) — behaviour no single-contrast overlay can represent.
**2-Row Heatmap (Isoform Divergence) on ASCORBATE_PEROXIDASE, PLASTID_ROS, SUPEROXIDE_DISMUTASES:** `AT1G08830` (ObCSD, Cu/Zn-SOD) is downregulated (`-1.45`, blue) while `AT4G25100` (ObFSD1, Fe-SOD) is upregulated (`+1.15`, vermillion).

Values are the authors' published results from Parmagnani, Mannino & Maffei (2022), Biomolecules 12(12):1824 (doi:10.3390/biom12121824), not a reanalysis: NNMF-grown plants relative to GMF-grown controls. No raw data was deposited — the Data Availability Statement reads “Data are available as supplementary tables and further data can be provided upon request”. Reported as fold change; the authors treat a gene as regulated only outside their own thresholds of ≥2 and ≤0.5, which this page preserves rather than re-thresholding. roots, 7 timepoints (10 min, 1 h, 2 h, 4 h, 24 h, 48 h, 96 h). 4 of 8 identifier-bearing nodes received a series (50%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. values were published as fold change and converted to log2 for display; the reported SD is carried through the same transform. 3 node(s) have loci that disagree in direction at the same timepoint (PLASTID_ROS, SUPEROXIDE_DISMUTASES, ASCORBATE_PEROXIDASE), so their single trace is the aggregator choosing between genes that are doing different things — read those per locus, not as a node. 3 node(s) reverse direction during the course (PLASTID_ROS, SUPEROXIDE_DISMUTASES, CATALASE), which no single-contrast overlay can show.

SVG · PNG

QBM-07 with shoots data projected — QBM-07 · Shoots · 4 nodes with data (50%)
**4 of 4 nodes reverse direction** during the course (ASCORBATE_PEROXIDASE, CATALASE, PLASTID_ROS, SUPEROXIDE_DISMUTASES) — behaviour no single-contrast overlay can represent.
**2-Row Heatmap (Isoform Divergence) on ASCORBATE_PEROXIDASE, PLASTID_ROS, SUPEROXIDE_DISMUTASES:** `AT1G08830` (ObCSD, Cu/Zn-SOD) is downregulated (`-1.45`, blue) while `AT4G25100` (ObFSD1, Fe-SOD) is upregulated (`+1.15`, vermillion).

Values are the authors' published results from Parmagnani, Mannino & Maffei (2022), Biomolecules 12(12):1824 (doi:10.3390/biom12121824), not a reanalysis: NNMF-grown plants relative to GMF-grown controls. No raw data was deposited — the Data Availability Statement reads “Data are available as supplementary tables and further data can be provided upon request”. Reported as fold change; the authors treat a gene as regulated only outside their own thresholds of ≥2 and ≤0.5, which this page preserves rather than re-thresholding. shoots, 7 timepoints (10 min, 1 h, 2 h, 4 h, 24 h, 48 h, 96 h). 4 of 8 identifier-bearing nodes received a series (50%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. values were published as fold change and converted to log2 for display; the reported SD is carried through the same transform. 3 node(s) have loci that disagree in direction at the same timepoint (PLASTID_ROS, SUPEROXIDE_DISMUTASES, ASCORBATE_PEROXIDASE), so their single trace is the aggregator choosing between genes that are doing different things — read those per locus, not as a node. 4 node(s) reverse direction during the course (PLASTID_ROS, SUPEROXIDE_DISMUTASES, ASCORBATE_PEROXIDASE, CATALASE), which no single-contrast overlay can show.

SVG · PNG

QBM-01 with roots data projected — QBM-01 · Roots · 2 nodes with data (20%)
**Coverage is below the atlas's own 25% threshold** (20%). It is shown anyway, with the number stated, because the map's remaining nodes are respiratory complexes the source table does not cover at all — not nodes that were measured and found unchanged.
**2 of 2 nodes reverse direction** during the course (ALT_NADH_DH, AOX) — behaviour no single-contrast overlay can represent.
**2-Row Heatmap (Isoform Divergence) on AOX:** `AT1G08830` (ObCSD, Cu/Zn-SOD) is downregulated (`-1.45`, blue) while `AT4G25100` (ObFSD1, Fe-SOD) is upregulated (`+1.15`, vermillion).

Values are the authors' published results from Parmagnani, Mannino & Maffei (2022), Biomolecules 12(12):1824 (doi:10.3390/biom12121824), not a reanalysis: NNMF-grown plants relative to GMF-grown controls. No raw data was deposited — the Data Availability Statement reads “Data are available as supplementary tables and further data can be provided upon request”. Reported as fold change; the authors treat a gene as regulated only outside their own thresholds of ≥2 and ≤0.5, which this page preserves rather than re-thresholding. roots, 7 timepoints (10 min, 1 h, 2 h, 4 h, 24 h, 48 h, 96 h). 2 of 10 identifier-bearing nodes received a series (20%); 7 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. values were published as fold change and converted to log2 for display; the reported SD is carried through the same transform. 1 node(s) have loci that disagree in direction at the same timepoint (AOX), so their single trace is the aggregator choosing between genes that are doing different things — read those per locus, not as a node. 2 node(s) reverse direction during the course (ALT_NADH_DH, AOX), which no single-contrast overlay can show.

SVG · PNG

QBM-01 with shoots data projected — QBM-01 · Shoots · 2 nodes with data (20%)
**Coverage is below the atlas's own 25% threshold** (20%). It is shown anyway, with the number stated, because the map's remaining nodes are respiratory complexes the source table does not cover at all — not nodes that were measured and found unchanged.
**1 of 2 nodes reverse direction** during the course (AOX) — behaviour no single-contrast overlay can represent.
**2-Row Heatmap (Isoform Divergence) on AOX:** `AT1G08830` (ObCSD, Cu/Zn-SOD) is downregulated (`-1.45`, blue) while `AT4G25100` (ObFSD1, Fe-SOD) is upregulated (`+1.15`, vermillion).

Values are the authors' published results from Parmagnani, Mannino & Maffei (2022), Biomolecules 12(12):1824 (doi:10.3390/biom12121824), not a reanalysis: NNMF-grown plants relative to GMF-grown controls. No raw data was deposited — the Data Availability Statement reads “Data are available as supplementary tables and further data can be provided upon request”. Reported as fold change; the authors treat a gene as regulated only outside their own thresholds of ≥2 and ≤0.5, which this page preserves rather than re-thresholding. shoots, 7 timepoints (10 min, 1 h, 2 h, 4 h, 24 h, 48 h, 96 h). 2 of 10 identifier-bearing nodes received a series (20%); 7 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. values were published as fold change and converted to log2 for display; the reported SD is carried through the same transform. 1 node(s) have loci that disagree in direction at the same timepoint (AOX), so their single trace is the aggregator choosing between genes that are doing different things — read those per locus, not as a node. 1 node(s) reverse direction during the course (AOX), which no single-contrast overlay can show.

SVG · PNG

Every value behind the figures

The numbers on the maps, in full, so the figures can be checked rather than taken on trust. Values are log2 fold change (hMF vs GMF); multi-locus nodes display their 2-row per-locus heatmap.

QBM-07 · Roots

Node	Tier	Loci	10 min	1 h	2 h	4 h	24 h	48 h	96 h	Peak
PLASTID_ROS (reverses) (isoforms diverge: 2-row heatmap)	T2	`AT4G25100` `AT2G28190`	-0.27	+0.03	+0.11	+0.04	+0.21	+0.12	+0.20	-0.27 @ 10 min
SUPEROXIDE_DISMUTASES (reverses) (isoforms diverge: 2-row heatmap)	T4	`AT1G08830` `AT2G28190` `AT4G25100`	-0.27	+0.15	+0.12	+0.06	+0.21	+0.12	+0.20	-0.27 @ 10 min
ASCORBATE_PEROXIDASE (isoforms diverge: 2-row heatmap)	T3	`AT1G07890` `AT3G09640`	-0.76	-0.29	-0.76	-0.38	-1.09	-0.12	-0.22	-1.09 @ 24 h
CATALASE (reverses)	T3	`AT1G20630`	+0.04	-0.22	+0.58	-0.40	-0.62	-0.23	+0.34	-0.62 @ 24 h

Scroll the table sideways to see every timepoint.

QBM-07 · Shoots

Node	Tier	Loci	10 min	1 h	2 h	4 h	24 h	48 h	96 h	Peak
PLASTID_ROS (reverses) (isoforms diverge: 2-row heatmap)	T2	`AT4G25100` `AT2G28190`	+0.19	+0.03	-0.14	+0.25	+0.50	-0.09	-0.29	+0.50 @ 24 h
SUPEROXIDE_DISMUTASES (reverses) (isoforms diverge: 2-row heatmap)	T4	`AT1G08830` `AT2G28190` `AT4G25100`	+0.19	+0.11	-0.14	+0.25	+0.50	-0.12	-0.29	+0.50 @ 24 h
ASCORBATE_PEROXIDASE (reverses) (isoforms diverge: 2-row heatmap)	T3	`AT1G07890` `AT3G09640`	-0.45	+0.03	-0.40	+0.80	-0.56	+0.23	-0.67	+0.80 @ 4 h
CATALASE (reverses)	T3	`AT1G20630`	+0.01	-0.25	+0.46	+0.94	-0.25	-0.60	-0.40	+0.94 @ 4 h

Scroll the table sideways to see every timepoint.

QBM-01 · Roots

Node	Tier	Loci	Trace / 2-Row Heatmap	10 min	1 h	2 h	4 h	24 h	48 h	96 h	Peak
ALT_NADH_DH (reverses)	T3	`AT4G28220`		-0.09	-0.15	-0.09	-0.29	+0.01	-0.10	-0.14	-0.29 @ 4 h
AOX (reverses) (isoforms diverge: 2-row heatmap)	T4	`AT3G22370` `AT3G22360` `AT1G32350` `AT5G64210`		-1.22	-1.18	+0.31	+0.96	-0.43	-0.10	+0.29	-1.22 @ 10 min

Scroll the table sideways to see every timepoint.

QBM-01 · Shoots

Node	Tier	Loci	Trace / 2-Row Heatmap	10 min	1 h	2 h	4 h	24 h	48 h	96 h	Peak
ALT_NADH_DH	T3	`AT4G28220`		-0.09	-0.12	-0.10	-0.07	+0.00	-0.06	-0.03	-0.12 @ 1 h
AOX (reverses) (isoforms diverge: 2-row heatmap)	T4	`AT3G22370` `AT3G22360` `AT1G32350` `AT5G64210`		-0.22	+0.94	+0.82	+0.74	+1.13	+1.41	+1.29	+1.41 @ 48 h

Scroll the table sideways to see every timepoint.

What this does not show

Coverage is partial by construction. The source table was filtered by its authors to genes involved in oxidative reactions, so it reaches the redox map well and the respiratory map barely. 12 of the atlas's QBO loci appear in it: AT1G07890, AT1G08830, AT1G15550, AT1G20630, AT1G32350, AT2G28190, AT3G09640, AT3G22360, AT3G22370, AT4G25100, AT4G28220, AT5G64210.
No significance is shown. The source reports mean ± SD with no per-gene adjusted p-value, so there is no threshold to mark and none is invented. The atlas's other overlays carry an asterisk for significance; this one deliberately has none.
A tier is not a result. The border style still reports how much is known about each node's field sensitivity, which is independent of how far it moved here. A T3 node that responds strongly is still a node with no measured magnetic mechanism.
One experiment. Replication across the near-null-field literature is what the atlas's pre-registered test addresses, and that test's result was null with a minimum detectable effect of 4.0 — this page does not change that.

Reproducing it

PYTHONPATH=src python3 scripts/build_paper_showcase.py --paper Parmagnani2022
PYTHONPATH=src python3 scripts/build_paper_page.py --paper Parmagnani2022

The supplementary archive is fetched from EuropePMC and cached under data/external/papers/; the parsed values, per-node series and coverage are written to results/papers/Parmagnani2022/record.json, and this page is generated from that record.