429 research outputs found
Structures of an apo and a binary complex of an evolved archeal b family DNA polymerase capable of synthesising highly cy-dye labelled DNA
Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing. Despite this there is a paucity of structural information to guide further engineering of this group of polymerases. Here we report two structures, of the apo form and of a binary complex of a previously described variant (E10) of Pyrococcus furiosus (Pfu) polymerase with an ability to fully replace dCTP with Cyanine dye-labeled dCTP (Cy3-dCTP or Cy5-dCTP) in PCR and synthesise highly fluorescent “CyDNA” densely decorated with cyanine dye heterocycles. The apo form of Pfu-E10 closely matches reported apo form structures of wild-type Pfu. In contrast, the binary complex (in the replicative state with a duplex DNA oligonucleotide) reveals a closing movement of the thumb domain, increasing the contact surface with the nascent DNA duplex strand. Modelling based on the binary complex suggests how bulky fluorophores may be accommodated during processive synthesis and has aided the identification of residues important for the synthesis of unnatural nucleic acid polymers
Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics
We present a study by linear stability analysis and large-scale Monte Carlo
simulations of a simple model of biological coevolution. Selection is provided
through a reproduction probability that contains quenched, random interspecies
interactions, while genetic variation is provided through a low mutation rate.
Both selection and mutation act on individual organisms. Consistent with some
current theories of macroevolutionary dynamics, the model displays
intermittent, statistically self-similar behavior with punctuated equilibria.
The probability density for the lifetimes of ecological communities is well
approximated by a power law with exponent near -2, and the corresponding power
spectral densities show 1/f noise (flicker noise) over several decades. The
long-lived communities (quasi-steady states) consist of a relatively small
number of mutualistically interacting species, and they are surrounded by a
``protection zone'' of closely related genotypes that have a very low
probability of invading the resident community. The extent of the protection
zone affects the stability of the community in a way analogous to the height of
the free-energy barrier surrounding a metastable state in a physical system.
Measures of biological diversity are on average stationary with no discernible
trends, even over our very long simulation runs of approximately 3.4x10^7
generations.Comment: 20 pages RevTex. Minor revisions consistent with published versio
Treatment as Prevention-Provider Knowledge and Counseling Lag Behind Global Campaigns
INTRODUCTION In 2011, the landmark HIV Prevention Trials Network (HPTN) 052 trial found that early initiation of antiretroviral treatment (ART) in persons living with HIV (PLHIV) reduced viral transmission to uninfected partners by 96%. Treatment as prevention (TasP), whereby HIV transmission is prevented by consistent use of HIV treatment and durable viral suppression, has ushered in a new era in worldwide HIV prevention. The combined health benefits of averting new infections and preserving/improving health for PLHIV have translated into rapid scale-up in treatment access across the globe
Probing star formation and ISM properties using galaxy disk inclination: III. Evolution in dust opacity and clumpiness between redshift 0.0 < z < 0.7 constrained from UV to NIR
Interstellar matter and star formatio
ALICE: The Ultraviolet Imaging Spectrograph aboard the New Horizons Pluto-Kuiper Belt Mission
The New Horizons ALICE instrument is a lightweight (4.4 kg), low-power (4.4
Watt) imaging spectrograph aboard the New Horizons mission to Pluto/Charon and
the Kuiper Belt. Its primary job is to determine the relative abundances of
various species in Pluto's atmosphere. ALICE will also be used to search for an
atmosphere around Pluto's moon, Charon, as well as the Kuiper Belt Objects
(KBOs) that New Horizons hopes to fly by after Pluto-Charon, and it will make
UV surface reflectivity measurements of all of these bodies as well. The
instrument incorporates an off-axis telescope feeding a Rowland-circle
spectrograph with a 520-1870 angstroms spectral passband, a spectral point
spread function of 3-6 angstroms FWHM, and an instantaneous spatial
field-of-view that is 6 degrees long. Different input apertures that feed the
telescope allow for both airglow and solar occultation observations during the
mission. The focal plane detector is an imaging microchannel plate (MCP) double
delay-line detector with dual solar-blind opaque photocathodes (KBr and CsI)
and a focal surface that matches the instrument's 15-cm diameter
Rowland-circle. In what follows, we describe the instrument in greater detail,
including descriptions of its ground calibration and initial in flight
performance.Comment: 24 pages, 29 figures, 2 tables; To appear in a special volume of
Space Science Reviews on the New Horizons missio
Ralph: A Visible/Infrared Imager for the New Horizons Pluto/Kuiper Belt Mission
The New Horizons instrument named Ralph is a visible/near infrared
multi-spectral imager and a short wavelength infrared spectral imager. It is
one of the core instruments on New Horizons, NASA's first mission to the
Pluto/Charon system and the Kuiper Belt. Ralph combines panchromatic and color
imaging capabilities with IR imaging spectroscopy. Its primary purpose is to
map the surface geology and composition of these objects, but it will also be
used for atmospheric studies and to map the surface temperature. It is a
compact, low-mass (10.5 kg), power efficient (7.1 W peak), and robust
instrument with good sensitivity and excellent imaging characteristics. Other
than a door opened once in flight, it has no moving parts. These
characteristics and its high degree of redundancy make Ralph ideally suited to
this long-duration flyby reconnaissance mission.Comment: 18 pages, 15 figures, 4 tables; To appear in a special volume of
Space Science Reviews on the New Horizons missio
Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV
Results are presented from a search for a W' boson using a dataset
corresponding to 5.0 inverse femtobarns of integrated luminosity collected
during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV.
The W' boson is modeled as a heavy W boson, but different scenarios for the
couplings to fermions are considered, involving both left-handed and
right-handed chiral projections of the fermions, as well as an arbitrary
mixture of the two. The search is performed in the decay channel W' to t b,
leading to a final state signature with a single lepton (e, mu), missing
transverse energy, and jets, at least one of which is tagged as a b-jet. A W'
boson that couples to fermions with the same coupling constant as the W, but to
the right-handed rather than left-handed chiral projections, is excluded for
masses below 1.85 TeV at the 95% confidence level. For the first time using LHC
data, constraints on the W' gauge coupling for a set of left- and right-handed
coupling combinations have been placed. These results represent a significant
improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe
Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV
A search for a Higgs boson decaying into two photons is described. The
analysis is performed using a dataset recorded by the CMS experiment at the LHC
from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an
integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross
section of the standard model Higgs boson decaying to two photons. The expected
exclusion limit at 95% confidence level is between 1.4 and 2.4 times the
standard model cross section in the mass range between 110 and 150 GeV. The
analysis of the data excludes, at 95% confidence level, the standard model
Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The
largest excess of events above the expected standard model background is
observed for a Higgs boson mass hypothesis of 124 GeV with a local significance
of 3.1 sigma. The global significance of observing an excess with a local
significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is
estimated to be 1.8 sigma. More data are required to ascertain the origin of
this excess.Comment: Submitted to Physics Letters
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