Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the ...process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.
A
bstract
An analysis is presented of events containing jets including at least one
b
-tagged jet, sizeable missing transverse momentum, and at least two leptons including a pair of the same electric ...charge, with the scalar sum of the jet and lepton transverse momenta being large. A data sample with an integrated luminosity of 20.3 fb
−1
of
pp
collisions at
s
=
8
TeV recorded by the ATLAS detector at the Large Hadron Collider is used. Standard Model processes rarely produce these final states, but there are several models of physics beyond the Standard Model that predict an enhanced rate of production of such events; the ones considered here are production of vector-like quarks, enhanced four-top-quark production, pair production of chiral
b
′-quarks, and production of two positively charged top quarks. Eleven signal regions are defined; subsets of these regions are combined when searching for each class of models. In the three signal regions primarily sensitive to positively charged top quark pair production, the data yield is consistent with the background expectation. There are more data events than expected from background in the set of eight signal regions defined for searching for vector-like quarks and chiral
b
′-quarks, but the significance of the discrepancy is less than two standard deviations. The discrepancy reaches 2.5 standard deviations in the set of five signal regions defined for searching for four-top-quark production. The results are used to set 95% CL limits on various models.
A
bstract
Measurements of fiducial and differential cross sections are presented for Higgs boson production in proton-proton collisions at a centre-of-mass energy of
s
=
8
TeV. The analysis is ...performed in the
H
→
γγ
decay channel using 20.3 fb
−1
of data recorded by the ATLAS experiment at the CERN Large Hadron Collider. The signal is extracted using a fit to the diphoton invariant mass spectrum assuming that the width of the resonance is much smaller than the experimental resolution. The signal yields are corrected for the effects of detector inefficiency and resolution. The
pp
→
H
→
γγ
fiducial cross section is measured to be 43.2 ±9.4(stat.)
− 2.9
+ 3.2
(syst.) ±1.2(lumi)fb for a Higgs boson of mass 125.4GeV decaying to two isolated photons that have transverse momentum greater than 35% and 25% of the diphoton invariant mass and each with absolute pseudorapidity less than 2.37. Four additional fiducial cross sections and two cross-section limits are presented in phase space regions that test the theoretical modelling of different Higgs boson production mechanisms, or are sensitive to physics beyond the Standard Model. Differential cross sections are also presented, as a function of variables related to the diphoton kinematics and the jet activity produced in the Higgs boson events. The observed spectra are statistically limited but broadly in line with the theoretical expectations.
A
bstract
A measurement of the cross section for the inclusive production of isolated prompt photons in proton-proton collisions at a centre-of-mass energy of
s
=
8
TeV is presented. The measurement ...covers the pseudorapidity ranges |
η
γ
|
<
1
.
37 and 1
.
56 ≤ |
η
γ
|
<
2
.
37 in the transverse energy range 25 <
E
T
γ
< 1500 GeV. The results are based on an integrated luminosity of 20.2 fb
−1
, recorded by the ATLAS detector at the LHC. Photon candidates are identified by combining information from the calorimeters and the inner tracker. The background is subtracted using a data-driven technique, based on the observed calorimeter shower-shape variables and the deposition of hadronic energy in a narrow cone around the photon candidate. The measured cross sections are compared with leading-order and next-to-leading order perturbative QCD calculations and are found to be in a good agreement over ten orders of magnitude.
A
bstract
The production cross sections of top-quark pairs in association with massive vector bosons have been measured using data from
pp
collisions at
s
=
8
TeV. The dataset corresponds to an ...integrated luminosity of 20.3 fb
−1
collected by the ATLAS detector in 2012 at the LHC. Final states with two, three or four leptons are considered. A fit to the data considering the
t
t
¯
W
and
t
t
¯
Z
processes simultaneously yields a significance of 5.0
σ
(4.2
σ
) over the background-only hypothesis for
t
t
¯
W
(
t
t
¯
Z
) production. The measured cross sections are
σ
t
t
¯
W
=
369
−
91
+
100
fb and
σ
t
t
¯
Z
=
176
−
52
+
58
fb. The background-only hypothesis with neither
t
t
¯
W
nor
t
t
¯
Z
production is excluded at 7.1
σ
. All measurements are consistent with next-to-leading-order calculations for the
t
t
¯
W
and
t
t
¯
Z
processes.
Acetyl-CoA carboxylase catalyzes the first committed step in fatty acid synthesis. In Escherichia coli, the enzyme is composed of three distinct protein components: biotin carboxylase, biotin ...carboxyl carrier protein, and carboxyltransferase. The biotin carboxylase component has served for many years as a paradigm for mechanistic studies devoted toward understanding more complicated biotin-dependent carboxylases. The three-dimensional x-ray structure of an unliganded form of E. coli biotin carboxylase was originally solved in 1994 to 2.4-Å resolution. This study revealed the architecture of the enzyme and demonstrated that the protein belongs to the ATP-grasp superfamily. Here we describe the three-dimensional structure of theE. coli biotin carboxylase complexed with ATP and determined to 2.5-Å resolution. The major conformational change that occurs upon nucleotide binding is a rotation of approximately 45o of one domain relative to the other domains thereby closing off the active site pocket. Key residues involved in binding the nucleotide to the protein include Lys-116, His-236, and Glu-201. The backbone amide groups of Gly-165 and Gly-166 participate in hydrogen bonding interactions with the phosphoryl oxygens of the nucleotide. A comparison of this closed form of biotin carboxylase with carbamoyl-phosphate synthetase is presented.
A
bstract
This paper reports the results of a search for strong production of supersymmetric particles in 20.1 fb
−1
of proton-proton collisions at a centre-of-mass energy of 8 TeV using the ATLAS ...detector at the LHC. The search is performed separately in events with either zero or at least one high-
p
T
lepton (electron or muon), large missing transverse momentum, high jet multiplicity and at least three jets identified as originated from the fragmentation of a
b
-quark. No excess is observed with respect to the Standard Model predictions. The results are interpreted in the context of several supersymmetric models involving gluinos and scalar top and bottom quarks, as well as a mSUGRA/CMSSM model. Gluino masses up to 1340 GeV are excluded, depending on the model, significantly extending the previous ATLAS limits.
The Aβ1-42 peptide that is overproduced in Alzheimer's disease (AD) from a large precursor protein has a normal amino acid sequence but, when liberated, misfolds at neutral pH to form "protofibrils" ...and fibrils that are rich in β-sheets. We find that these protofibrils or fibrils are toxic to certain neuronal cells that carry Ca-permeant α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Disrupting the structure of the Aβ1-42 fibrils and protofibrils might lead to the discovery of molecules that would be very useful in the treatment of AD. A high-throughput screen of a library of >3,000 small molecules with known "biological activity" was set up to find compounds that efficiently decrease the β-sheet content of aggregating Aβ1-42. Lead compounds were characterized by using thioflavin T (ThT) as a β-sheet assay. The most effective of six compounds found was 4,5-dianilinophthalimide (DAPH) under the following conditions: DAPH at low micromolar concentrations abolishes or greatly reduces previously existing fully formed Aβ1-42 fibrils, producing instead amorphous materials without fibrils but apparently containing some protofibrils and smaller forms. Coincubation of the Aβ1-42 peptide with DAPH produces either amorphous materials or empty fields. Coincubation of DAPH and Aβ1-42 greatly reduces the β-sheet content, as measured with ThT fluorescence, and produces a novel fluorescent complex with ThT. When the Aβ1-42 peptide was coincubated with DAPH at very low micromolar concentrations, the neuronal toxicity mentioned above ( Ca2+ influx) was eliminated. Clearly, DAPH is a promising candidate for AD therapy.
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