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This could be a candidate gene that modulates the root and shoot response to drought to ensure yield under stress conditions.
To our knowledge, no other gene expression analyses have been performed on the early stages of iron deficiency examining root and shoot response simultaneously.
The module shown in Figure 6B contains 269 genes dependently co-expressed across shoot response to cold and UV light, and is enriched in GO terms corresponding to the CUL4 RING ubiquitin ligase complex and non-coding RNA processing.
In contrast, there are nine modules spanning B.cinerea infection, root response to cold and shoot response to UV light, making this combination of stresses much more promising for elucidating a common regulatory network.
For example, a researcher interested in unravelling shared regulatory networks between the biotic stress of B.cinerea infection and abiotic stress can see from Figure 5 that only one module spans B.cinerea infection, root response to drought and shoot response to cold.
During B.cinerea infection, senescence and root response to cold genes in the module are upregulated, while they are downregulated during root response to drought and shoot response to UV, consistent with the idea that the mechanism regulating these genes operates in a different mode under different conditions.
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Raising the levels of phosphate and sulphur through strategic fertiliser application may have accentuated the differences found between the PMs in root and shoot responses (van den Driessche 1999; Guillemette and DesRochers 2008), particularly by favouring trees from poles with their larger and more extensive root systems and consequent exploration of greater soil volumes.
Other translocated factors, such as cytokinins, may also originate in roots and modulate ABA signaling to impact shoot responses to drought [ 6, 10].
Other factors, such as cytokinins and small peptides, also originate from roots and may influence shoot responses to drying soils [ 6, 10].
These 4 states allowed us to define 9 classes of gene expression patterns (Table 1), and by comparing root and shoot responses, we were able to observe up to 81 (9rootx9shoot) classes describing organ-specific or -common gene expression patterns.
The promoters of two genes (At3g15210 and At5g05410) from a 26-gene module spanning B.cinerea infection and root and shoot responses to cold (Supplementary Fig. S4a) were screened against a TF library to identify TFs able to bind these DNA sequences.
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