High-Throughput Single-Molecule Telomere Characterization

We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG) n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG) n tract length at the end of each large telomere- terminal DNA segment. The methodology also permits subtelomere and haplotype-resolved analyses of SRE organization and variation, providing a window into the population dynamics and potential functions of these complex and structurally variant telomere-adjacent DNA regions. At its current stage of development, the assay can be used to identify and characterize telomere length distributions of 30-35 discrete telomeres simultaneously and accurately. The assay\u27s utility is demonstrated using early versus late passage and senescent human diploid fibroblasts, documenting the anticipated telomere attrition on a global telomere-by-telomere basis as well as identifying subtelomere-specific biases for critically short telomeres. Similarly, we present the first global single-telomere-resolved analyses of two cancer cell lines

Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome

A Determination of MSH2 and MSH6 Cellular Protein Levels in Saccharomyces Cerevisiae Cells

Genomic mutation rates tend to be very low (~10-10 /generation/base) in a wide variety of organisms and most mutations with a phenotypic effect are deleterious (Drake et al. 1998). This would suggest that increased mutation rates are likely to yield a fitness cost and therefore are likely to face negative selection (Heck et al. 2006). Mismatch repair (MMR) is a DNA repair process that acts to maintain mutation rates at very low levels. In eukaryotes, the Msh2-Msh6 protein complex initiates MMR by binding to base-base and single insertion/deletion DNA mismatches that occur primarily due to DNA polymerase misincorporation errors. MMR proteins also function in genetic recombination and DNA alkylation damage toxicity. Elez, et al. (2007) found that reduced levels of the MMR protein MutL in Escherichia coli affected one type of mitotic recombination but did not affect MMR. To test whether the same could be true for homologous MMR proteins in Saccharomyces cerevisiae, I first measured the levels of MMR proteins in haploid cells grown to mid-log phase. Using a quantitative Western blot analysis, I determined that Msh2p and Msh6p are present at 1600 ± 250 (SEM) and 1300 ± 390 (SEM) per cell, respectively. I then performed a mutational analysis of the MSH2 promoter by mutagenizing its seven putative transcription factor binding sites (MacIsaac et al. 2006). The mutations had little effect on transcription of MSH2 or on cellular Msh2p levels. These data suggest that Msh2p and Msh6p are maintained at similar levels in the cell and that small changes to the MSH2 promoter are insufficient to affect its transcription or cellular Msh2 protein levels

Handling Of Virtual Contact In Immersive Virtual Environments: Beyond Visuals

This paper addresses the issue of improving the perception of contact that users make with purely virtual objects in virtual environments. Because these objects have no physical component, the user's perceptual understanding of the material properties of the object, and of the nature of the contact, is hindered, often limited solely to visual feedback. Many techniques for providing haptic feedback to compensate for the lack of touch in virtual environments have been proposed. These systems have increased our understanding of the nature of how humans perceive contact. However, providing effective, general-purpose haptic feedback solutions has proven elusive. We propose a more-holistic approach, incorporating feedback to several modalities in concert. This paper describes a prototype system we have developed for delivering vibrotactile feedback to the user. The system provides a low-cost, distributed, portable solution for incorporating vibrotactile feedback into various types of systems. We discuss different parameters that can be manipulated in order to provide different sensations, propose ways in which this feedback can be combined with feedback of other modalities to create a better understanding of virtual contact, and describe possible applications. KEY WORDS: haptic feedback; multimodal interaction; vibrotactile feedback 1

Teaching Strategies and Approaches for Pupils with Special Educational Needs: A Scoping Study

Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG)n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. These features make the method a uniquely valuable new tool for improving the quality of genome assemblies in complex DNA regions. Based on single molecule mapping of telomere-terminal DNA fragments, we provide proof of principle for a novel method to estimate telomere lengths linked to distinguishable telomeric haplotypes; this single-telomere genotyping method may ultimately enable delineation of human cis elements involved in telomere length regulation

L'Ordinamento sportivo: caratteri generali Principali testi normativi

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68 % of them missed by sequencing-based callers. Independent experimental validation confirmed the high accuracy of these SVs. The OMSV software is available at http://yiplab.cse.cuhk.edu.hk/omsv/

Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

24 décembre 19361936/12/24 (A37,N13156)