69 Results
for term "sites"
- High-Resolution Specificity from DNA Sequencing Highlights Alternative Modes of Lac Repressor Binding.... Details of its binding interaction and its selection of an asymmetric binding site have been controversial. We employed a new method to accurately determine relative binding afnities to thousands of sequences simultaneously, requiring only sequencing of bound and unbound fractions. An analysis of 2560 ~~~
- Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast...leading to a 6 kb expansion was veried on a 1% agarose gel. PCR verication of the insertion failed in three clones, YMD2681, YMD2683, and YMD2697. The PCR reactions were cleaned using a Zymo DNA Clean and Concentrator kit, and eluted in 100 ml of water. Ty1 contains two EcoRI sites not shared with Ty2 ~~~
- A New Method, “Reverse Yeast Two-Hybrid Array” (RYTHA), Identifies Mutants that Dissociate the Physical Interaction Between Elg1 and Slx5... and prey proteins interact, then the AD and BD of the transcription factor are indirectly connected, bringing the AD in proximity to the transcription start site, and the transcription of a reporter gene (e.g.,HIS3) can occur (Fields and Song 1989). In this way, a successful interaction between the fused ~~~
- A Biophysical Approach to Predicting Protein–DNA Binding Energetics...this degeneracy into account, we have developed a graphical representation of parameter uncertainties called IntervalLogo. We nd that our simplest model, in which each nucleotide in the binding site is treated independently, performs better than previous biophysical approaches. The extensions of this model ~~~
- The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length...independent simulation sets. Of the 100,000 sites chosen in each simulation set, bamsurgeon successfully inserted an average of 95,172 SNVs. Using these 10 simulated variant sets, we tested two different methods of grouping our strains for variant calling: calling strains individually (comparing sequences ~~~
- Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria...rearrangements are compared through the relationship Figure 2 (A) Loss of gene order conservation (GOC250) with time (time is estimated through 16S rRNA distance, in nucleotide substitutions per site). Different data sets are shown in different colors and have different rates of GOC250 change, implying different ~~~
- Transcript Isoform Variation Associated with Cytosine Modification in Human Lymphoblastoid Cell Lines...detected cytosine modication-specic TIVs for 17% of the analyzed genes at a 5% false discovery rate. Forty-ve percent of the TIV-associated cytosine modications correlated with the overall gene expression levels as well, with the corresponding CpG sites overrepresented in transcript initiation sites ~~~
- Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856...). A study of chemoreceptor gene families uncovered functional genes in CB4856 that are defective in N2 (Stewart et al. 2005). Recent genomic analyses of CB4856 and N2, alongside other isolates, again found the Hawaiian strain to be among the most divergent, either by using sequencing restriction-site ~~~
- Integration Profiling of Gene Function With Dense Maps of Transposon Integration...of 360,513 insertions in the genome of Schizosaccharomyces pombe. On average, we obtained one insertion for every 29 bp of the genome. Hermes integrated more often into nucleosome free sites and 33% of the insertions occurred in ORFs. We found that ORFs with low integration densities successfully ~~~
- Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays...of the structural variation within 8 kb, making this a novel and efcient approach to whole-genome structural variation analysis. Furthermore, our maps pinpoint the EpsteinBarr Virus (EBV) integration sites in the lymphoblastoid cell lines used and provide size estimates of two-thirds of the large N-base gaps ~~~