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The other strain, named SG61-1L, was pursued further because of its ability to completely degrade 200 μM GGE in 75 h (Fig. 1C).
The analysis identified polymorphic sequence variants as risk factors for the combined cohorts (focal and GGE) in SCN1A perhaps the most well known epilepsy gene and in protocadherin 7 (PCHD7), a gene not yet known to be associated with epilepsy.
LC-MS monitoring of enzymatic transformation from GGE to MPHPV was performed under the following reaction conditions: 50 μM purified enzyme SG61-1L 724, 20 mM Tris (pH 7.5), 5 mM NAD+, and 100 μM GGE in a final volume of 100 μl.
Bacterial growth under conditions where vanillin (a catabolic intermediate of GGE in both strains) was used as the sole carbon source were comparable (per mole of carbon) to those observed for growth on GGE as the sole carbon source (Fig. S2 in the supplemental material), indicating that bacterial growth rates with GGE were real and not an artifact of growth from cellular reserves.
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A genome-wide scan for significant QTL expression was performed using the single interval mapping procedure and each predicted marker position fitted as a fixed environment-specific QTL effect while maintaining the best variance-covariance structure based on Schwarz information criterion (Schwarz 1978) set in the Genstat GGE model determined in G×E interaction analysis.
Chromosome microarrays should be considered in severe cases and in GGE with co-morbid features, where the likelihood of finding a disease-associated CNV is highest.
In GGE growth experiments, SG61-1L cells were pelleted following the disappearance of GGE and resuspended in the same volume of fresh MM supplemented with 200 μM GGE, and both degradation and growth were again monitored over time at 28°C.
The percent composition of each stereoisomer in GGE was as follows: 39.5% (αS,βR -GGE,βR -GGE(αR,βS)-GGE, 10.5% (αS,βS)-GGE, and 10.5% (αR,βR)-GGE (see Fig. S1 in the supplemental material).
Exome-sequencing studies in GGE have been less successful at identifying clear genetic risk factors or high-penetrance mutations.
Very large cohorts may be required to make progress in GGE due to the complex genetic architecture that likely underlies this class of epilepsy.
Three additional uncharacterized SYK-6 genes are also present in the GGE dehydrogenase clade, but it seems unlikely that they play a larger role in GGE oxidation than those already characterized.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com