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To determine whether the SCNA-genes from different melanoma cell lines shared membership of one or more cellular pathways, we investigated whether the proteins encoded by the SCNA-genes were connected in known human protein interaction networks (see Materials and Methods).
Among the cellular pathways, we found over-representation of genes related to MAPK signaling pathway, pathways in cancer and metabolic pathways (Table 1).
To induce a complete and selective cell cycle G0/G1 arrest without potentiating other cellular pathways, we used a small molecule cell cycle inhibitor (CCI) to selectively inhibit the kinase activity of CDK4/6 (Fig. 1A).
Underlying proteins were analyzed on potential interactions to uncover responsible deregulated cellular pathways; we could construct a network consisting of nine proteins important for complement activation and immune and inflammatory responses (Fig 6B).
Although these mutants are defective in diverse cellular pathways, we demonstrate below that they fall into three functional groups, each of which interacts with HU through a distinct and previously unearthed function of the drug.
As ROS production could determine the fate of cancer cells through regulating a number of cellular pathways, we examined if ROS accumulation is involved in the activation of JNK/c-Jun pathway in our model system.
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RNAi screens have been widely used in C. elegans to identify genes involved in many different cellular pathways, and we had used this approach in the past to identify novel NMD factors [ 6].
Because CS is known to induce growth factor-related cellular pathways, 57 we examined a specific subnetwork of the cell proliferation network related to growth factor response more closely (Fig. 6 and Supplementary Fig. 1D for a higher resolution view).
This second category likely represents the subset of differentially expressed genes marking dysfunctional cellular pathways, which we hypothesize encompasses the most significant gene expression changes, and includes all the genes from Table 3.
To gain insight into cellular mechanotransduction pathways, we have developed a fluorescence laser tracking microrheometer (FLTM) to measure material rheological features on micrometer length scales using fluorescent microspheres as tracer particles.
In addition to describing the oncogenic role of miR-17 in two cellular senescence pathways, we identified MKP7 as a key mediator of mTOR signaling.
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