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In addition to the RNA-based gene expression profiling approach, high throughput analysis at the DNA level, such as genome-wide microarray comparative genomic hybridization (aCGH) and DNA sequencing, has made it possible to decipher the genetic anomalies that drive a particular tumor phenotype.
Because processes operating at the DNA level, such as local mutation rate variation [9], should affect both dS and dN [10: p. 65] while natural selection on the protein should affects dN but not dS, and because protein-level selection is expected to vary across amino acid sites or protein domains, we expect dN to be more variable than dS [see also 3].
As a result, repetitive patterns at the DNA level such as interspersed microsatellites and tandem tri-nucleotide repeats are prevalent.
We do not make use of knowledge of functional elements at the DNA level, such as transcription sites.
CPN labeling might be a potential tool for the tracking of MSCs and therefore can be used to better understand MSCs' differentiation and homing mechanisms without any manipulations performed at the DNA level such as GFP or luciferase labeling.
This ultimately can lead to the formation of adducts at lipids, proteins and DNA level such as 4-hydroxy-nonenal (4-HNE) and lipid peroxidation products [ 150– 152], protein carbonyls [ 153, 154] and DNA adducts [ 150, 155] respectively.
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However, little variation has been detected at the DNA level using techniques such as RAPDs (Random Amplified Polymorphic DNAs), AFLPs (Amplified Fragment Length Polymorphisms) and RFLPs (Restriction Fragment Length Polymorphisms) [ 5, 8- 15].
It is known that many cellular regulatory mechanisms are encoded on the DNA level as regulatory motifs, such as promoters, repressors, oscillators etc. Gene activity, including transcriptional control and also post-transcriptional mechanisms, can be closely regulated by intrinsic and external signals.
This is quite evident in senior biology classes that require mastery of many concepts at the microbiological level, such as DNA replication, transcription and translation, and cell respiration/photosynthesis, and yet remain poorly rooted to fundamental units taught at lower grade levels, like the principles of evolution and the diversity of life.
Entities of biomedical data cover broad levels from the molecular level such as DNA or chemical, to the phenotypic level such as symptom or disease.
In figure 4, we propose molecular mechanisms at the DNA level that may have driven such loss in genome synteny, refining mechanisms previously proposed in the literature (Bzymek et al. 1999; Chantret et al. 2005; Wicker et al. 2010; Woodhouse, Pedersen, et al. 2010).
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