Finite Size Analysis of the U(1) Phase Transition using the World-sheet Formulation

We present a high statistics analysis of the pure gauge compact U(1) lattice theory using the the world-sheet or Lagrangian loop representation. We have applied a simulation method that deals directly with (gauge invariant) integer variables on plaquettes. As a result we get a significant amelioration of the simulation that allows to work with large lattices avoiding the metaestability problems that appear using the standard Wilson formulation.Comment: 14 pages, 4 figures. REVTEX and eps

Assembly and structural analysis of a covalently closed nano-scale DNA cage

The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson–Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise are necessary before complex DNA structures can be routinely designed for the use in basal science and/or biotechnology. Here we present the design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron, as defined by the double-stranded DNA helices that assembles from eight oligonucleotides with a yield of ∼30%. As demonstrated by Small Angle X-ray Scattering and cryo-Transmission Electron Microscopy analyses the eight-stranded DNA structure has a central cavity larger than the apertures in the surrounding DNA lattice and can be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures

Molecular Phylogeny of the Astrophorida (Porifera, Demospongiaep) Reveals an Unexpected High Level of Spicule Homoplasy

Background: The Astrophorida (Porifera, Demospongiae(rho)) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. Methodology/Principal Findings: With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 59 end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Conclusion: The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres

Effects of DNA supercoiling on chromatin architecture

Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo

Skeletal remains from St. Peder’s parish church in Randers

Skeletal Remains from St. Peder's parish church in Randers One of Denmarks 17 known Benedictine nunneries was excavated in Randers, Jutland in 1989 (Matthiesen 1989). Although it is not clear when the nunnery was established, it seems that the church, which was part of the nunnery, was built around 1100 A.D. The church, St. Peders, also served as parish church (fig. 1). Two graveyards were located: one south of the church presumably used by the nuns, and a second east of the church which was probably the parish cemetery (Mikkelsen 1990a, Mikkelsen 1990b). The following is a brief account of the preliminary results of the anthropological analyses of the skeletal remains from the parish cemetery excavations. A minimum of 530 individuals were excavated, originating from 252 well defined single graves, several probable mass graves and stray finds (Mikkelsen & Matthiesen 1990). The most frequent type of burial was interment without coffin. Coffin burials were rare, and only six stone lined graves were found. It is assumed that the individuals found in the coffins and stone-lined graves represent people of a higher social status. The skeletons The preservation and completeness of the individual skeletons varied. Most of the large long bones were present. Roughly, one third of the material was well preserved, one third preserved to an average degree, and one third poorly preserved. It is noteworthy that 95 individuals were retrieved with all teeth present (apart from teeth lost ante mortem), and this testifies to the care with which the material was recovered. Age and sex distributions So far only the skeletal material from the single graves has been processed, yielding the following age distribution: 2 fetuses; 60 infants (0 to 12/14 years); 22 adolescents (12/14 to 21 years); and 215 adults (above 21 years) (fig. 2). Only few individuals were found to have an age exceeding 40 years. Subadults make up one third of the total material. Probably the real proportion was higher, up to 50%, due to the high child mortality of the period. However, the delicate bones of infants are not preserved to the same degree as the larger and denser bones of adults. The determination of sex is only possible for the adults, and revealed a fairly balanced distribution. Paleopathology Ordinary and well known pathological conditions affecting bones were found, e.g., many healed or partly healed fractures; inflammations and arthritis. One case of possible tuberculosis was found (see below). Generally, the types and rates of paleopathological changes agree with the results from other Medieval excavations (Møller-Christensen 1958). Although the early Benedictine nunneries to some extent functioned as hospitals (Trabjerg 1993), nothing definite can be deduced from the skeletons in this respect. Dental analyses revealed a low frequency of caries (88 individuals had caries), which is in agreement with results from other contemporary skeletal material (Mellquist & Sandberg 1939; Brinch & Møller­Christensen 1949). There was a clear correlation between caries and periapical abcesses, with half of the individuals with caries having abcesses (fig. 3). The degree of dental wear was moderate (fig. 4). Anthropometry The stature was calculated to be approx. 174 cm. (5' 9») for males and 157 cm. (5' 2») for females, well in accordance with other contemporary finds (Bennike 1985). Several other measurements, especially cranial measurements were taken, and these have since formed part of a large study of cranial morphology of Danish skeletons from the Stone Age to present days (Hjalgrim 1992). Special graves Although the purpose of the anthropological analyses was to reconstruct the population of the period, a few single cases attracted special attention: Grave 13: The skeleton of a young, approx. 18 years old female was found (fig. 5) including the bones of two fetuses (twins, see figure 5) in the pelvic region. From the examination of the fetal bones it appeared that the woman died about 6 months into her pregnancy (fig. 6). The cause of death could not be established. Stray find 510: A male cranium with the facial skeleton completely destroyed. A large iron ball, approx. 30 mm in diameter was found within the calvarium. Analyses at the Institute of Metallurgy at the Danish Engineering College indicated that the ball was made from 99% forged iron (Buchwald 1992, pers. comm.). Historical sources first mention firearms in Denmark in 1360 (Orloff, pers. comm.). The caliber, and the fact that the ball did not exit the skull, i.e. had a low muzzle velocity, indicates that the ball probably was fired from a small cannon (a so-called "skanseboesse"). This is the earliest firearms victim found in Denmark. Grave 202: The skeleton of an approx. 25 years old female yielded an unusal curved vertebral column (fig. 7) and bones with significantly thinner cortical bone mass. Our tentative conclusion is that the woman suffered from tuberculosis. Tuberculosis has been reported both in historical sources and from other Medieval excavations (Møller-Christensen 1958). Conclusion The preliminary results from the excavation of the St. Peder parish cemetery in Randers, show a Medieval (skeletal) population not differing much from other contemporary finds. The results have already formed part of other studies (Hjalgrim 1992). We expect to commence a research programme into Medieval paleothology in cooperation with the Smithsonian Institution of Washington, D.C., U.S.A., and the University of Bradford, England. The Randers skeletal material will then be a valuable contribution. B. Frøhlich, H. Hjalgrim,  J. Littleton, N. Lynnerup og B. Sejrsen.                      &nbsp

Cryptic β-Lactamase Evolution Is Driven by Low β-Lactam Concentrations

Our current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the widespread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to developing clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-MICs of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MICs of ceftazidime, they demonstrated strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies toward ceftazidime. These changes are likely caused by enhanced flexibility of the Ω- and β5-β6 loops and fine-tuning of preexisting active site residues. In conclusion, low-level concentrations of β-lactams can drive the evolution of β-lactamases through cryptic phenotypes which may act as stepping-stones toward clinical resistance

Temperature-controlled encapsulation and release of an active enzyme in the cavity of a self-assembled DNA nanocage

We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage