Method and tool for machining a transverse slot about a bore

A method and apparatus for cutting a transverse slot about a bore of smaller diameter than that of the slot are disclosed. The invention consists of introducing a cutting head facing transversely to the bore, through the bore opening its distance from the mill shaft being progressively extended by the addition of spacers between the head and the shaft until the desired slot depth is obtained. The spacers are held in position by a cable passing from the cutting head through the series of spacers and out along the mill shaft. The mill shaft carrying the cutting head is moved transversely into the object wherein the slot is being cut as the object is being rotated thereabout by the mill table to which it is affixed

LINE-1 Retrotransposition Activity in Human Genomes

SummaryHighly active (i.e., “hot”) long interspersed element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s that are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cultured cell retrotransposition assay. Genotyping 26 elements revealed that two L1s are only found in Africa and that two more are absent from the H952 subset of the Human Genome Diversity Panel. Therefore, these results suggest that hot L1s are more abundant in the human population than previously appreciated, and that ongoing L1 retrotransposition continues to be a major source of interindividual genetic variation

Reconstructing complex regions of genomes using long-read sequencing technology

Cataloged from PDF version of article.Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state

Resolving the complexity of the human genome using single-molecule sequencing

The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome - 78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology

Personalized copy number and segmental duplication maps using next-generation sequencing

Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology

A photoresponsive graphene oxide-C60 conjugate

[EN] An all-carbon donor–acceptor hybrid combining graphene oxide (GO) and C60 has been prepared. Laser flash photolysis measurements revealed the occurrence of photoinduced electron transfer from the GO electron donor to the C60 electron acceptor in the conjugate.This research was financially supported by the Spanish Ministry of Economy and Competitiveness of Spain (CTQ2010-17498, MAT2010-20843-C02-01 and PLE-2009-0038) and a Severo Ochoa operating grant from the Spanish Ministry of Economy and Competitiveness. We also acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, Comunidad de Madrid (CAM 09-S2009_MAT-1467), Generalitat Valenciana (PROMETEO program), and VLC/Campus Microcluster "Nanomateriales Funcionales y Nanodispositivos".Barrejón, M.; Vizuete, M.; Gómez Escalonilla, M.; Fierro, J.; Berlanga, I.; Zamora, F.; Abellán, G.... (2014). A photoresponsive graphene oxide-C60 conjugate. Chemical Communications. 50(65):9053-9055. doi:10.1039/C3CC49589BS90539055506

Phthalocyanine-nanocarbon ensembles: From discrete molecular and supramolecular systems to hybrid nanomaterials

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Accounts of Chemical Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ar5004384Conspectus Phthalocyanines (Pcs) are macrocyclic and aromatic compounds that present unique electronic features such as high molar absorption coefficients, rich redox chemistry, and photoinduced energy/electron transfer abilities that can be modulated as a function of the electronic character of their counterparts in donor-acceptor (D-A) ensembles. In this context, carbon nanostructures such as fullerenes, carbon nanotubes (CNTs), and, more recently, graphene are among the most suitable Pc companions. Pc-C60 ensembles have been for a long time the main actors in this field, due to the commercial availability of C60 and the ell-established synthetic methods for its functionalization. As a result, many Pc-C60 architectures have been prepared, featuring different connectivities (covalent or supramolecular), intermolecular interactions (self-organized or molecularly dispersed species), and Pc HOMO/LUMO levels. All these elements provide a versatile toolbox for tuning the photophysical properties in terms of the type of process (photoinduced energy/electron transfer), the nature of the interactions beteen the electroactive units (through bond or space), and the kinetics of the formation/decay of the photogenerated species. Some recent trends in this field include the preparation of stimuli-responsive multicomponent systems ith tunable photophysical properties and highly ordered nanoarchitectures and surface-supported systems shoing high charge mobilities. A breakthrough in the Pc-nanocarbon field as the appearance of CNTs and graphene, hich opened a ne avenue for the preparation of intriguing photoresponsive hybrid ensembles shoing light-stimulated charge separation. The scarce solubility of these 1-D and 2-D nanocarbons, together ith their loer reactivity ith respect to C60 stemming from their less strained sp2 carbon netorks, has not meant an unsurmountable limitation for the preparation of variety of Pc-based hybrids. These systems, hich sho improved solubility and dispersibility features, bring together the unique electronic transport properties of CNTs and graphene ith the excellent light-harvesting and tunable redox properties of Pcs. A singular and distinctive feature of these Pc-CNT/graphene (single- or fe-layers) hybrid materials is the control of the direction of the photoinduced charge transfer as a result of the band-like electronic structure of these carbon nanoforms and the adjustable electronic levels of Pcs. Moreover, these conjugates present intensified light-harvesting capabilities resulting from the grafting of several chromophores on the same nanocarbon platform.In this Account, recent progress in the construction of covalent and supramolecular Pc-nanocarbon ensembles is summarized, ith a particular emphasis on their photoinduced behavior. e believe that the high degree of control achieved in the preparation of Pc-carbon nanostructures, together ith the increasing knoledge of the factors governing their photophysics, ill allo for the design of next-generation light-fueled electroactive systems. Possible implementation of these Pc-nanocarbons in high performance devices is envisioned, finally turning into reality much of the expectations generated by these materialsFinancial support from the Spanish MICINN (CTQ2011-24187/BQU), the Comunidad de Madrid (S2013/MIT-2841 FOTOCARBON) and the EU (“SO2S” FP7-PEOPLE-2012-ITN, no.: 316975) is acknowledge

Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation

The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3–0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested