347 research outputs found
Fluorescence-based incision assay for human XPF-ERCC1 activity identifies important elements of DNA junction recognition
The structure-specific endonuclease activity of the human XPF–ERCC1 complex is essential for a number of DNA processing mechanisms that help to maintain genomic integrity. XPF–ERCC1 cleaves DNA structures such as stem–loops, bubbles or flaps in one strand of a duplex where there is at least one downstream single strand. Here, we define the minimal substrate requirements for cleavage of stem–loop substrates allowing us to develop a real-time fluorescence-based assay to measure endonuclease activity. Using this assay, we show that changes in the sequence of the duplex upstream of the incision site results in up to 100-fold variation in cleavage rate of a stem-loop substrate by XPF-ERCC1. XPF–ERCC1 has a preference for cleaving the phosphodiester bond positioned on the 3′-side of a T or a U, which is flanked by an upstream T or U suggesting that a T/U pocket may exist within the catalytic domain. In addition to an endonuclease domain and tandem helix–hairpin–helix domains, XPF has a divergent and inactive DEAH helicase-like domain (HLD). We show that deletion of HLD eliminates endonuclease activity and demonstrate that purified recombinant XPF–HLD shows a preference for binding stem–loop structures over single strand or duplex alone, suggesting a role for the HLD in initial structure recognition. Together our data describe features of XPF–ERCC1 and an accepted model substrate that are important for recognition and efficient incision activity
Simulation study of pressure and temperature dependence of the negative thermal expansion in Zn(CN)(2)
12 pages, 16 figures12 pages, 16 figures12 pages, 16 figures12 pages, 16 figure
Low temperature structural phase transition and incommensurate lattice modulation in the spin gap compound BaCuSi2O6
Results of high resolution x-ray diffraction experiments are presented for
single crystals of the spin gap compound BaCuSiO in the temperature
range from 16 to 300 K. The data show clear evidence of a transition from the
room temperature tetragonal phase into an incommensurately modulated
orthorhombic structure below 100 K. This lattice modulation is
characterized by a resolution limited wave vector {\bf
q}=(0,0.13,0) and its 2 and 3 harmonics. The phase
transition is first order and exhibits considerable hysteresis. This
observation implies that the spin Hamiltonian representing the system is more
complex than originally thought.Comment: 4 pages, 4 figure
Roughening of close-packed singular surfaces
An upper bound to the roughening temperature of a close-packed singular
surface, fcc Al (111), is obtained via free energy calculations based on
thermodynamic integration using the embedded-atom interaction model. Roughening
of Al (111) is predicted to occur at around 890 K, well below bulk melting (933
K), and it should therefore be observable, save for possible kinetic hindering.Comment: RevTeX 4 pages, embedded figure
Getting Genetic Ancestry Right for Science and Society
There is a scientific and ethical imperative to embrace a multidimensional,
continuous view of ancestry and move away from continental ancestry categorie
First-principles study of the ferroelastic phase transition in CaCl_2
First-principles density-functional calculations within the local-density
approximation and the pseudopotential approach are used to study and
characterize the ferroelastic phase transition in calcium chloride (CaCl_2). In
accord with experiment, the energy map of CaCl_2 has the typical features of a
pseudoproper ferroelastic with an optical instability as ultimate origin of the
phase transition. This unstable optic mode is close to a pure rigid unit mode
of the framework of chlorine atoms and has a negative Gruneisen parameter. The
ab-initio ground state agrees fairly well with the experimental low temperature
structure extrapolated at 0K. The calculated energy map around the ground state
is interpreted as an extrapolated Landau free-energy and is successfully used
to explain some of the observed thermal properties. Higher-order anharmonic
couplings between the strain and the unstable optic mode, proposed in previous
literature as important terms to explain the soft-phonon temperature behavior,
are shown to be irrelevant for this purpose. The LAPW method is shown to
reproduce the plane-wave results in CaCl_2 within the precision of the
calculations, and is used to analyze the relative stability of different phases
in CaCl_2 and the chemically similar compound SrCl_2.Comment: 9 pages, 6 figures, uses RevTeX
Women\u27s experiences on the path to a career in game development
This chapter seeks to identify whether there is a dominant, presupposed career pipeline to a career in game development and then looks for women and women’s experiences at each stage of that pipeline. It concludes that a dominant pipeline does exist and that this pathway both disadvantages women who attempt it and marginalizes other pathways. Along the way women deal with obstacles that can delegitimize their choices and experiences and/or make the assumed pathway inhospitable. This chapter relies on published literature as well as data from the 2014 and 2015 Developer Satisfaction Surveys (DSS) conducted by the International Game Developers Association (IGDA) in partnership with the authors
Are Vicinal Metal Surfaces Stable?
Quantum Matter and Optic
Antibody Responses against Xenotropic Murine Leukemia Virus-Related Virus Envelope in a Murine Model
Xenotropic murine leukemia virus-related virus (XMRV) was recently discovered to be the first human gammaretrovirus that is associated with chronic fatigue syndrome and prostate cancer (PC). Although a mechanism for XMRV carcinogenesis is yet to be established, this virus belongs to the family of gammaretroviruses well known for their ability to induce cancer in the infected hosts. Since its original identification XMRV has been detected in several independent investigations; however, at this time significant controversy remains regarding reports of XMRV detection/prevalence in other cohorts and cell type/tissue distribution. The potential risk of human infection, coupled with the lack of knowledge about the basic biology of XMRV, warrants further research, including investigation of adaptive immune responses. To study immunogenicity in vivo, we vaccinated mice with a combination of recombinant vectors expressing codon-optimized sequences of XMRV gag and env genes and virus-like particles (VLP) that had the size and morphology of live infectious XMRV.Immunization elicited Env-specific binding and neutralizing antibodies (NAb) against XMRV in mice. The peak titers for ELISA-binding antibodies and NAb were 1:1024 and 1:464, respectively; however, high ELISA-binding and NAb titers were not sustained and persisted for less than three weeks after immunizations.Vaccine-induced XMRV Env antibody titers were transiently high, but their duration was short. The relatively rapid diminution in antibody levels may in part explain the differing prevalences reported for XMRV in various prostate cancer and chronic fatigue syndrome cohorts. The low level of immunogenicity observed in the present study may be characteristic of a natural XMRV infection in humans
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