Characterization of Nucleotide Misincorporation Patterns in the Iceman's Mitochondrial DNA

BACKGROUND: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation ("miscoding lesions") has been the object of extensive investigations. METHODOLOGY/PRINCIPAL FINDINGS: To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350-5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Otzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences. CONCLUSIONS/SIGNIFICANCE: This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine-->thymine/guanine-->adenine) transitions and that type 1 transitions are essentially PCR artifacts

Virtual reality interfaces for feature-based computer-aided design systems

A computer-aided design (CAD) system with a virtual reality (VR) interface simplifies the design of complex mechanical parts. To add a design feature (e.g., a hole,slot, or protrusion), the designer can navigate in the part to the appropriate face of the part where he/she wishes to attach the feature, and sketch directly on that face.Besides convenience, this method of feature specification implicitly enforces feature accessibility constraints, and also provides hints to the process-planner regarding the order in which the features may be manufactured. We detail the design of a VR-based prototype CAD system. The system maintains the knowledge of part cavities and their adjacencies, and a triangulated boundary-representation of an approximating polyhedron. We present incremental provably correct algorithms for updatingthis representation as the user edits the part. We also show how this representation supports real-time displays, navigation, and collision detection. The user-interface of the CAD system relies on these capabilities to provide the above-mentioned advantages

Morphology and substructure of lath martensites in dilute Zr---Nb alloys

The morphology and substructure of lath martensites formed in ß quenched dilute Zr---Nb alloys are described. The laths are arranged in a nearly parallel manner within any given colony or packet. Packets of alternately twin related laths and clusters of three mutually twin related lath martensite variants have been observed and the twinning plane is of {1I̅01}<SUB>H</SUB> type. With increasing niobium content a continuous transition from large colonies of lath martensites, through smaller lath colonies, to individual plates of the acicular martensites occurs. The lath-lath interface consists of regularly spaced parallel arrays of dislocations of &lt;2I̅I̅3&gt;type. The habit plane traces of lath martensite lie close to {334} type poles and the operating lattice invariant shear mode is {I̅101}<SUB>H</SUB>&lt;2 I̅I̅3&gt;<SUB>H</SUB> shear system. This result is consistent with results predicted by the phenomenological theory. The preferred two and three habit plane variant grouping clustering is explained on the basis of self-accommodation effects

Bat-mouse bone marrow chimera: a novel animal model for dissecting the uniqueness of the bat immune system

Bats are an important animal model with long lifespans, low incidences of tumorigenesis and an ability to asymptomatically harbour pathogens. Currently, in vivo studies of bats are hampered due to their low reproduction rates. To overcome this, we transplanted bat cells from bone marrow (BM) and spleen into an immunodeficient mouse strain NOD-scid IL-2R−/− (NSG), and have successfully established stable, long-term reconstitution of bat immune cells in mice (bat-mice). Immune functionality of our bat-mouse model was demonstrated through generation of antigen-specific antibody response by bat cells following immunization. Post-engraftment of total bat BM cells and splenocytes, bat immune cells survived, expanded and repopulated the mouse without any observable clinical abnormalities. Utilizing bat’s remarkable immunological functions, this novel model has a potential to be transformed into a powerful platform for basic and translational research