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II worked on the identification of mutant genes using GINI analysis.
To distinguish between mRNA accumulations caused by stress response-induced transcription and nonsense-containing mRNA stabilizations is a challenge in identifying mutant genes using GINI.
We then analyzed the enriched subcellular locations of the LoF and GoF mutant genes using a hypergeometric test against the information of the total of 22119 subcellular locations of human proteins.
The major complication in identifying mutant genes using GINI is the fact that too many genes that do not contain nonsense mutations show mRNA accumulation following the blocking of NMD with emetine or small interfering RNA against hUpf1 and hUpf2 genes, the major regulators of NMD.
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EMS-mutagenesis has also been used in a reverse genetics strategy called TILLING, which involves pooling mutagenized lines and screening for mutants in specific genes using enzymes that detect sequence mismatches (Weil and Monde 2007).
With the ever-expanding options for either identifying or generating mutants in desired genes using targeting induced local lesions in genomes (TILLING) [ 23 25] or custom-designed restriction endonucleases (ZFN) [ 26, 27], the field is more regularly turning to a reference mutant phenotype as a validation approach.
A partial transcriptome analysis of the czf1 mutant, conducted on 250 genes using the Nanochip technology, detected very few expression changes in this mutant [ 45].
Given the cross-talk between these important developmental-related phytohormones, we examined their role in regulating transcription of the genes using mutant and chemical treatment studies.
The mutant phenotype would, however, be captured for all relevant genes using SGD's mutant phenotype curation system (12).
For example, two recent studies have suggested that gene therapy could be used to knockdown expression of the mutant ATZ gene using vectors that also encode the wild-type AT and therein would potentially address both gain-of-function proteotoxicity and loss-of-function mechanisms for tissue damage in ATD (Li et al., 2011; Mueller et al., 2012).
We isolated the bona fide loss-of-function mutants in the coding regions of the genes for all the HLH genes using the Salk T-DNA mutant collection (Alonso et al., 2003a).
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