262 research outputs found
Trapped lipopolysaccharide and LptD intermediates reveal lipopolysaccharide translocation steps across the Escherichia coli outer membrane
Lipopolysaccharide (LPS) is a main component of the outer membrane of Gram-negative bacteria, which is essential for the vitality of most Gram-negative bacteria and plays a critical role for drug resistance. LptD/E complex forms a N-terminal LPS transport slide, a hydrophobic intramembrane hole and the hydrophilic channel of the barrel, for LPS transport, lipid A insertion and core oligosaccharide and O-antigen polysaccharide translocation, respectively. However, there is no direct evidence to confirm that LptD/E transports LPS from the periplasm to the external leaflet of the outer membrane. By replacing LptD residues with an unnatural amino acid p-benzoyl-L-phenyalanine (pBPA) and UV-photo-cross-linking in E.coli, the translocon and LPS intermediates were obtained at the N-terminal domain, the intramembrane hole, the lumenal gate, the lumen of LptD channel, and the extracellular loop 1 and 4, providing the first direct evidence and “snapshots” to reveal LPS translocation steps across the outer membrane
Resonances in and
A partial wave analysis is presented of and
from a sample of 58M events in the BES II detector. The
is observed clearly in both sets of data, and parameters of the
Flatt\' e formula are determined accurately: (stat)
(syst) MeV/c, MeV/c, . The data also exhibit a strong peak
centred at MeV/c. It may be fitted with and a
dominant signal made from interfering with a smaller
component. There is evidence that the signal is
resonant, from interference with . There is also a state in with MeV/c and
MeV/c; spin 0 is preferred over spin 2. This state, , is
distinct from . The data contain a strong peak due to
. A shoulder on its upper side may be fitted by interference
between and .Comment: 17 pages, 6 figures, 1 table. Submitted to Phys. Lett.
First Measurements of eta_c Decaying into K^+K^-2(pi^+pi^-) and 3(pi^+pi^-)
The decays of eta_c to K^+K^-2(pi^+pi^-) and 3(pi^+pi^-) are observed for the
first time using a sample of 5.8X10^7 J/\psi events collected by the BESII
detector. The product branching fractions are determined to be B(J/\psi-->gamma
eta_c)*B(eta_c-->K^+K^-pi^+pi^-pi^+pi^-)=(1.21+-0.32+-
0.23)X10^{-4}, and (J/\psi-->gamma eta_c)*
B(eta_c-->pi^+pi^-pi^+pi^-pi^+pi^-)= (2.59+-0.32+-0.48)X10^{-4}. The upper
limit for eta_c-->phi pi^+pi^-pi^+pi^- is also obtained as B(J/\psi-->gamma
eta_c)*B(eta_c--> phi pi^+pi^-pi^+pi^-)< 6.03 X10^{-5} at the 90% confidence
level.Comment: 11 pages, 4 figure
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis
<p>Abstract</p> <p>Background</p> <p>Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences.</p> <p>Results</p> <p>In this paper, a novel building block of proteins called Top-<it>n</it>-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-<it>n</it>-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-<it>n</it>-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-<it>n</it>-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-<it>n</it>-grams and LSA gives significantly better results compared to related methods.</p> <p>Conclusion</p> <p>The method based on Top-<it>n</it>-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-<it>n</it>-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.</p
Measurement of the Branching Fraction of J/psi --> pi+ pi- pi0
Using 58 million J/psi and 14 million psi' decays obtained by the BESII
experiment, the branching fraction of J/psi --> pi+ pi- pi0 is determined. The
result is (2.10+/-0.12)X10^{-2}, which is significantly higher than previous
measurements.Comment: 9 pages, 8 figures, RevTex
Search for K_S K_L in psi'' decays
K_S K_L from psi'' decays is searched for using the psi'' data collected by
BESII at BEPC, the upper limit of the branching fraction is determined to be
B(psi''--> K_S K_L) < 2.1\times 10^{-4} at 90% C. L. The measurement is
compared with the prediction of the S- and D-wave mixing model of the
charmonia, based on the measurements of the branching fractions of J/psi-->K_S
K_L and psi'-->K_S K_L.Comment: 5 pages, 1 figur
First observation of psi(2S)-->K_S K_L
The decay psi(2S)-->K_S K_L is observed for the first time using psi(2S) data
collected with the Beijing Spectrometer (BESII) at the Beijing Electron
Positron Collider (BEPC); the branching ratio is determined to be
B(psi(2S)-->K_S K_L) = (5.24\pm 0.47 \pm 0.48)\times 10^{-5}. Compared with
J/psi-->K_S K_L, the psi(2S) branching ratio is enhanced relative to the
prediction of the perturbative QCD ``12%'' rule. The result, together with the
branching ratios of psi(2S) decays to other pseudoscalar meson pairs
(\pi^+\pi^- and K^+K^-), is used to investigate the relative phase between the
three-gluon and the one-photon annihilation amplitudes of psi(2S) decays.Comment: 5 pages, 4 figures, 2 tables, submitted to Phys. Rev. Let
Study of psi(2S) decays to X J/psi
Using J/psi -> mu^+ mu^- decays from a sample of approximately 4 million
psi(2S) events collected with the BESI detector, the branching fractions of
psi(2S) -> eta J/psi, pi^0 pi^0 J/psi, and anything J/psi normalized to that of
psi(2S) -> pi^+ pi^- J/psi are measured. The results are B(psi(2S) -> eta
J/psi)/B(psi(2S) -> pi^+ pi^- J/psi) = 0.098 \pm 0.005 \pm 0.010, B(psi(2S) ->
pi^0 pi^0 J/psi)/B(psi(2S) -> pi^+ pi^- J/psi) = 0.570 \pm 0.009 \pm 0.026, and
B(psi(2S) -> anything J/psi)/B(psi(2S) -> pi^+ pi^- J/psi) = 1.867 \pm 0.026
\pm 0.055.Comment: 13 pages, 8 figure
Transgenic CHD1L Expression in Mouse Induces Spontaneous Tumors
Background: Amplification of 1q21 is the most frequent genetic alteration in hepatocellular carcinoma (HCC), which was detected in 58-78% of primary HCC cases by comparative genomic hybridization (CGH). Using chromosome microdissection/ hybrid selection approach we recently isolated a candidate oncogene CHD1L from 1q21 region. Our previous study has demonstrated that CHD1L had strong oncogenic ability, which could be effectively suppressed by siRNA against CHD1L. The molecular mechanism of CHD1L in tumorigenesis has been associated with its role in promoting cell proliferation. Methodology/Principal Findings: To further investigate the in vivo oncogenic role of CHD1L, CHD1L ubiquitous-expression transgenic mouse model was generated. Spontaneous tumor formations were found in 10/41 (24.4%) transgenic mice, including 4 HCCs, but not in their 39 wild-type littermates. In addition, alcohol intoxication was used to induce hepatocyte pathological lesions and results found that overexpression of CHD1L in hepatocytes could promote tumor susceptibility in CHD1L-transgenic mice. To address the mechanism of CHD1L in promoting cell proliferation, DNA content between CHD1Ltransgenic and wildtype mouse embryo fibroblasts (MEFs) was compared by flow cytometry. Flow cytometry results found that CHD1L could facilitate DNA synthesis and G1/ S transition through the up-regulation of Cyclin A, Cyclin D1, Cyclin E, CDK2, and CDK4, and down-regulation of Rb, p27Kip1, and p53. Conclusion/Significance: Taken together, our data strongly support that CHD1L is a novel oncogene and plays an important role in HCC pathogenesis. © 2009 Chen et al.published_or_final_versio
RMDAP: A Versatile, Ready-To-Use Toolbox for Multigene Genetic Transformation
Background: The use of transgenes to improve complex traits in crops has challenged current genetic transformation technology for multigene transfer. Therefore, a multigene transformation strategy for use in plant molecular biology and plant genetic breeding is thus needed. Methodology/Principal Findings: Here we describe a versatile, ready-to-use multigene genetic transformation method, named the Recombination-assisted Multifunctional DNA Assembly Platform (RMDAP), which combines many of the useful features of existing plant transformation systems. This platform incorporates three widely-used recombination systems, namely, Gateway technology, in vivo Cre/loxP and recombineering into a highly efficient and reliable approach for gene assembly. RMDAP proposes a strategy for gene stacking and contains a wide range of flexible, modular vectors offering a series of functionally validated genetic elements to manipulate transgene overexpression or gene silencing involved in a metabolic pathway. In particular, the ability to construct a multigene marker-free vector is another attractive feature. The built-in flexibility of original vectors has greatly increased the expansibility and applicability of the system. A proof-ofprinciple experiment was confirmed by successfully transferring several heterologous genes into the plant genome. Conclusions/Significance: This platform is a ready-to-use toolbox for full exploitation of the potential for coordinate regulation of metabolic pathways and molecular breeding, and will eventually achieve the aim of what we call ‘‘one-sto
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