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We did not model these genes, restricting our modeling efforts (and accuracy assessments) to those genes that are regulated.
Consistent with our proposed model, these genes, like Cited2, are also known to control or modulate left right patterning pathways.
In the iJO1366 model, these genes are essential because they are required to produce bmocogdp[c] (bis-molybdopterin guanine dinucleotide), a component of the core biomass formulation.
In the model, these genes are non-essential due to an alternate reaction that produces carbamoyl phosphate, CBMKr (carbamate kinase), catalyzed by the products of yahI (b0323), arcC (b0521), or yqeA (b2874).
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Because the initial mechanism of the pathogenesis should be different between two models, these genes are likely to function during the effector phase of the disease.
We analyzed the expression of the rose B- and C-function gene homologues, as in model plants these genes were shown to be implicated in petal and stamen (B-function) and stamen and carpel (C-function) identity.
Thus, we are effectively removing highly discriminatory genes from the data, and forming a new model without these genes.
These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time.
This result is consistent with the model that these genes are expressed in the L4 stage for use in the synthesis or function of the adult cuticle.
It was mentioned previously that regulation of cell cycle genes is difficult to model, as these genes are involved in a complex, post-transcriptional machinery (Cheng et al., 2012).
Previous analyses suggest that GTR is generally the best-fitting model for these genes and that they should be partitioned by gene and codon position [ 16, 17, 19, 20, 36, 81].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com