bluuebunny/crossref_metadata_2025 huggingface dataset:
Ligand activation leads to regulated intramembrane proteolysis of fibroblast growth factor receptor 3
Authors: Degnin Catherine R. , Laederich Melanie B. , Horton William A.
Published: August 2011

Fibroblast growth factor receptor 3 (FGFR3) is a major negative regulator of bone growth that inhibits the proliferation and differentiation of growth plate chondrocytes. Activating mutations of its c isoform cause dwarfism in humans; somatic mutations can drive oncogenic transformation in multiple myeloma and bladder cancer. How these distinct activities arise is not clear. FGFR3 was previously shown to undergo proteolytic cleavage in the bovine rib growth plate, but this was not explored further. Here, we show that FGF1 induces regulated intramembrane proteolysis (RIP) of FGFR3. The ectodomain is proteolytically cleaved (S1) in response to ligand-induced receptor activation, but unlike most RIP target proteins, it requires endocytosis and does not involve a metalloproteinase. S1 cleavage generates a C-terminal domain fragment that initially remains anchored in the membrane, is phosphorylated, and is spatially distinct from the intact receptor. Ectodomain cleavage is followed by intramembrane cleavage (S2) to generate a soluble intracellular domain that is released into the cytosol and can translocate to the nucleus. We identify the S1 cleavage site and show that γ-secretase mediates the S2 cleavage event. In this way we demonstrate a mechanism for the nuclear localization of FGFR3 in response to ligand activation, which may occur in both development and disease.
Mia40-dependent oxidation of cysteines in domain I of Ccs1 controls its distribution between mitochondria and the cytosol
Authors: Klöppel Christine , Suzuki Yutaka , Kojer Kerstin , Petrungaro Carmelina , Longen Sebastian , Fiedler Sebastian , Keller Sandro , Riemer Jan
Published: August 2011

Superoxide dismutase 1 (Sod1) is an important antioxidative enzyme that converts superoxide anions to hydrogen peroxide and water. Active Sod1 is a homodimer containing one zinc ion, one copper ion, and one disulfide bond per subunit. Maturation of Sod1 depends on its copper chaperone (Ccs1). Sod1 and Ccs1 are dually localized proteins that reside in the cytosol and in the intermembrane space of mitochondria. The import of Ccs1 into mitochondria depends on the mitochondrial disulfide relay system. However, the exact mechanism of this import process has been unclear. In this study we detail the import and folding pathway of Ccs1 and characterize its interaction with the oxidoreductase of the mitochondrial disulfide relay Mia40. We identify cysteines at positions 27 and 64 in domain I of Ccs1 as critical for mitochondrial import and interaction with Mia40. On interaction with Mia40, these cysteines form a structural disulfide bond that stabilizes the overall fold of domain I. Although the cysteines are essential for the accumulation of functional Ccs1 in mitochondria, they are dispensable for the enzymatic activity of cytosolic Ccs1. We propose a model in which the Mia40-mediated oxidative folding of domain I controls the cellular distribution of Ccs1 and, consequently, active Sod1.
Knock-in reconstitution studies reveal an unexpected role of Cys-65 in regulating APE1/Ref-1 subcellular trafficking and function
Authors: Vascotto Carlo , Bisetto Elena , Li Mengxia , Zeef Leo A. H. , D'Ambrosio Chiara , Domenis Rossana , Comelli Marina , Delneri Daniela , Scaloni Andrea , Altieri Fabio , Mavelli Irene , Quadrifoglio Franco , Kelley Mark R. , Tell Gianluca
Published: August 2011

Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1) protects cells from oxidative stress via the base excision repair pathway and as a redox transcriptional coactivator. It is required for tumor progression/metastasis, and its up-regulation is associated with cancer resistance. Loss of APE1 expression causes cell growth arrest, mitochondrial impairment, apoptosis, and alterations of the intracellular redox state and cytoskeletal structure. A detailed knowledge of the molecular mechanisms regulating its different activities is required to understand the APE1 function associated with cancer development and for targeting this protein in cancer therapy. To dissect these activities, we performed reconstitution experiments by using wild-type and various APE1 mutants. Our results suggest that the redox function is responsible for cell proliferation through the involvement of Cys-65 in mediating APE1 localization within mitochondria. C65S behaves as a loss-of-function mutation by affecting the in vivo folding of the protein and by causing a reduced accumulation in the intermembrane space of mitochondria, where the import protein Mia40 specifically interacts with APE1. Treatment of cells with (E)-3-(2-[5,6-dimethoxy-3-methyl-1,4-benzoquinonyl])-2-nonyl propenoic acid, a specific inhibitor of APE1 redox function through increased Cys-65 oxidation, confirm that Cys-65 controls APE1 subcellular trafficking and provides the basis for a new role for this residue.
The functionally distinct fission yeast formins have specific actin-assembly properties
Authors: Scott Bonnie J. , Neidt Erin M. , Kovar David R.
Published: August 2011

Fission yeast expresses three formins required for distinct actin cytoskeletal processes: Cdc12 (cytokinesis), For3 (polarization), and Fus1 (mating). We propose that in addition to differential regulation, key actin-assembly properties tailor formins for a particular role. In direct comparison to the well-studied Cdc12, we report the first in vitro characterization of the actin-assembly properties of For3 and Fus1. All three share fundamental formin activities; however, particular reaction rates vary significantly. Cdc12 is an efficient nucleator (one filament per approximately 3 Cdc12 dimers) that processively elongates profilin-actin at a moderate rate of 10 subunits s−1μM−1, but lacks filament-bundling activity. Fus1 is also an efficient nucleator, yet processively elongates profilin-actin at one-half the rate of and dissociates 10-fold more rapidly than Cdc12; it also bundles filaments. For3 nucleates filaments 100-fold less well than Fus1, but like Cdc12, processively elongates profilin-actin at a moderate rate and lacks filament-bundling activity. Additionally, both the formin homology FH1 and FH2 domains contribute to the overall rate of profilin-actin elongation. We also confirmed the physiological importance of the actin-assembly activity of the fission yeast formins. Point mutants that disrupt their ability to stimulate actin assembly in vitro do not function properly in vivo.
The Economic Returns to U.S. Public Agricultural Research
Authors: Alston Julian M. , Andersen Matthew A. , James Jennifer S. , Pardey Philip G.
Published: August 2011

We use newly constructed state‐specific data to explore the implications of common modeling choices for measures of research returns. Our results indicate that state‐to‐state spillover effects are important, that the research and development lag is longer than many studies have allowed, and that misspecification can give rise to significant biases. Across states, the average of the own‐state benefit‐cost ratios is 21:1, or 32:1 when the spillover benefits to other states are included. These ratios correspond to real internal rates of return of 9% or 10% per annum, much smaller than those typically reported in the literature, partly because we have corrected for a methodological flaw in computing rates of return.
Estimating Free-Riding Behavior: The StratAM Model
Authors: Steinwand Martin C.
Published: August 2011

Spatial statistical methods in political science provide a tool to deal with spatial and other forms of interdependence in observational data. In this article, I derive a statistical model from a game of impure public goods provision. The resulting strategic autoregressive model (StratAM) allows the researcher to systematically explore the sources of free-riding behavior in the provision of public goods. The StratAM model is tightly related to the well-known spatial autoregressive (SAR) model and can be estimated in a maximum likelihood framework. I demonstrate the use of the StratAM model by analyzing free riding in the provision of foreign aid. Indicators of developmental needs and good governance strongly increase free-riding during the 1990s. Free-riding patterns in the 2000s are more similar to Cold War patterns.
A role for heterochromatin protein 1γ at human telomeres
Authors: Canudas Silvia , Houghtaling Benjamin R. , Bhanot Monica , Sasa Ghadir , Savage Sharon A. , Bertuch Alison A. , Smith Susan
Published: August 2011

Human telomere function is mediated by shelterin, a six-subunit complex that is required for telomere replication, protection, and cohesion. TIN2, the central component of shelterin, has binding sites to three subunits: TRF1, TRF2, and TPP1. Here we identify a fourth partner, heterochromatin protein 1γ (HP1γ), that binds to a conserved canonical HP1-binding motif, PXVXL, in the C-terminal domain of TIN2. We show that HP1γ localizes to telomeres in S phase, where it is required to establish/maintain cohesion. We further demonstrate that the HP1-binding site in TIN2 is required for sister telomere cohesion and can impact telomere length maintenance by telomerase. Remarkably, the PTVML HP1-binding site is embedded in the recently identified cluster of mutations in TIN2 that gives rise to dyskeratosis congenita (DC), an inherited bone marrow failure syndrome caused by defects in telomere maintenance. We show that DC-associated mutations in TIN2 abrogate binding to HP1γ and that DC patient cells are defective in sister telomere cohesion. Our data indicate a novel requirement for HP1γ in the establishment/maintenance of cohesion at human telomeres and, furthermore, may provide insight into the mechanism of pathogenesis in TIN2-mediated DC.
Biosynthesis of the Major Tetrahydroxystilbenes in Spruce, Astringin and Isorhapontin, Proceeds via Resveratrol and Is Enhanced by Fungal Infection
Authors: Hammerbacher Almuth , Ralph Steven G. , Bohlmann Joerg , Fenning Trevor M. , Gershenzon Jonathan , Schmidt Axel
Published: August 2011

Stilbenes are dibenzyl polyphenolic compounds produced in several unrelated plant families that appear to protect against various biotic and abiotic stresses. Stilbene biosynthesis has been well described in economically important plants, such as grape (Vitis vinifera), peanut (Arachis hypogaea), and pine (Pinus species). However, very little is known about the biosynthesis and ecological role of stilbenes in spruce (Picea), an important gymnosperm tree genus in temperate and boreal forests. To investigate the biosynthesis of stilbenes in spruce, we identified two similar stilbene synthase (STS) genes in Norway spruce (Picea abies), PaSTS1 and PaSTS2, which had orthologs with high sequence identity in sitka (Picea sitchensis) and white (Picea glauca) spruce. Despite the conservation of STS sequences in these three spruce species, they differed substantially from angiosperm STSs. Several types of in vitro and in vivo assays revealed that the P. abies STSs catalyze the condensation of p-coumaroyl-coenzyme A and three molecules of malonyl-coenzyme A to yield the trihydroxystilbene resveratrol but do not directly form the dominant spruce stilbenes, which are tetrahydroxylated. However, in transgenic Norway spruce overexpressing PaSTS1, significantly higher amounts of the tetrahydroxystilbene glycosides, astringin and isorhapontin, were produced. This result suggests that the first step of stilbene biosynthesis in spruce is the formation of resveratrol, which is further modified by hydroxylation, O-methylation, and O-glucosylation to yield astringin and isorhapontin. Inoculating spruce with fungal mycelium increased STS transcript abundance and tetrahydroxystilbene glycoside production. Extracts from STS-overexpressing lines significantly inhibited fungal growth in vitro compared with extracts from control lines, suggesting that spruce stilbenes have a role in antifungal defense.
Improvement of rotary encoders in human-machine-interfaces through optimized acoustic feedback
Authors: Treiber Alexander S. , Gruhler Gerhard , Rozinaj Gregor
Published: August 2011

This work investigates the effect of the acoustic feedback of rotary encoders that are common in current human-machine-interfaces. The results are based on subjective trials in which the probands had to complete generic tasks using an encoder with programmable electro acoustic feedback. The tasks had to be performed with individually optimized feedback and two reference conditions. The results of the investigation showed the advantage of well-defined acoustic feedback on both accuracy and speed of task fulfillment.
Sensitivity of vocal fold vibratory modes to their three-layer structure: Implications for computational modeling of phonation
Authors: Xue Q. , Zheng X. , Bielamowicz S. , Mittal R.
Published: August 2011

The sensitivity of the eigenmodes and eigenfrequencies of the human vocal fold to its three-layer structure is studied using finite-element modeling. The study covers a variety of three-dimensional vocal fold models ranging from an idealized, longitudinally uniform structure to a physiologically more realistic, longitudinally varying structure. Geometric parameters including the thickness of the ligament and cover layers as well as the ligament length are varied systematically. The results indicate that vocal fold vibratory modes are quite insensitive to the longitudinal variation in the thickness of the three layers as well as the variation in ligament length. However, significant overall changes in thickness of each layer can produce noticeable changes in these modes. The implications of these findings on computational modeling of phonation are discussed.
Influence of static compression on mechanical parameters of acoustic foams
Authors: Geslain A. , Dazel O. , Groby J.-P. , Sahraoui S. , Lauriks W.
Published: August 2011

The modification of elastic properties of compressed acoustic foams is investigated. The porous sample is first submitted to a static compression and then to a dynamic excitation of smaller amplitude, corresponding to acoustical applications. The static compression induces the modification of the dynamic elastic parameters of the material. This work focuses on Young’s modulus. The variation is measured with two different experimental methods: The classical rigidimeter and an absorption measurement. The effective Young’s modulus is directly measured with the first method and is indirectly determined through the quarter-wave length resonance of the frame with the second one. The results of the two measurements are compared and give similar tendencies. The variation of the dynamic Young’s modulus as a function of the degree of compression of the sample is shown to be separated in several zones. In the zones associated with weak compression (those usually zones encountered in practice), the variation of the effective Young’s modulus can be approximated by a simple affine function. The results are compared for different foams. A simple model of the dependency of the Young’s modulus with respect to the static degree of compression is finally proposed for weak compressions.
Computation of physiological human vocal fold parameters by mathematical optimization of a biomechanical model
Authors: Yang Anxiong , Stingl Michael , Berry David A. , Lohscheller Jörg , Voigt Daniel , Eysholdt Ulrich , Döllinger Michael
Published: August 2011

With the use of an endoscopic, high-speed camera, vocal fold dynamics may be observed clinically during phonation. However, observation and subjective judgment alone may be insufficient for clinical diagnosis and documentation of improved vocal function, especially when the laryngeal disease lacks any clear morphological presentation. In this study, biomechanical parameters of the vocal folds are computed by adjusting the corresponding parameters of a three-dimensional model until the dynamics of both systems are similar. First, a mathematical optimization method is presented. Next, model parameters (such as pressure, tension and masses) are adjusted to reproduce vocal fold dynamics, and the deduced parameters are physiologically interpreted. Various combinations of global and local optimization techniques are attempted. Evaluation of the optimization procedure is performed using 50 synthetically generated data sets. The results show sufficient reliability, including 0.07 normalized error, 96% correlation, and 91% accuracy. The technique is also demonstrated on data from human hemilarynx experiments, in which a low normalized error (0.16) and high correlation (84%) values were achieved. In the future, this technique may be applied to clinical high-speed images, yielding objective measures with which to document improved vocal function of patients with voice disorders.
Absolute backscatter coefficient estimates of tissue-mimicking phantoms in the 5–50 MHz frequency range
Authors: McCormick Matthew M. , Madsen Ernest L. , Deaner Meagan E. , Varghese Tomy
Published: August 2011

Absolute backscatter coefficients in tissue-mimicking phantoms were experimentally determined in the 5–50 MHz frequency range using a broadband technique. A focused broadband transducer from a commercial research system, the VisualSonics Vevo 770, was used with two tissue-mimicking phantoms. The phantoms differed regarding the thin layers covering their surfaces to prevent desiccation and regarding glass bead concentrations and diameter distributions. Ultrasound scanning of these phantoms was performed through the thin layer. To avoid signal saturation, the power spectra obtained from the backscattered radio frequency signals were calibrated by using the signal from a liquid planar reflector, a water-brominated hydrocarbon interface with acoustic impedance close to that of water. Experimental values of absolute backscatter coefficients were compared with those predicted by the Faran scattering model over the frequency range 5–50 MHz. The mean percent difference and standard deviation was 54% ± 45% for the phantom with a mean glass bead diameter of 5.40 μm and was 47% ± 28% for the phantom with 5.16 μm mean diameter beads.
Assessment of local vocal fold deformation characteristics in an in vitro static tensile test
Authors: Döllinger M. , Berry D. A. , Hüttner B. , Bohr C.
Published: August 2011

Voice quality is strongly dependent on vocal fold dynamics, which in turn are dependent on lung pressure and vocal fold biomechanics. Numerical and physical models are often used to investigate the interactions of these different subsystems. However, the utility of numerical and physical models is limited unless appropriately validated with data from physiological models. Hence a method that enables analysis of local vocal fold deformations along the entire surface is presented. In static tensile tests, forces are applied to distinctive working points being located in cover and muscle, respectively, so that specific layer properties can be investigated. The forces are directed vertically upward and are applied along or above the vocal fold edge. The resulting deformations are analyzed using multiple perspectives and three-dimensional reconstruction. Deformation characteristics of four human vocal folds were investigated. Preliminary results showed two phases of deformation: a range with a small slope for small deformations fading into a significant nonlinear deformation trend with a high slope. An increase of tissue stiffness from posterior to anterior was detected. This trend is more significant for muscle and in the mid-anterior half of the vocal fold.
A first-principles model for estimating the prevalence of annoyance with aircraft noise exposure
Authors: Fidell Sanford , Mestre Vincent , Schomer Paul , Berry Bernard , Gjestland Truls , Vallet Michel , Reid Timothy
Published: August 2011

Numerous relationships between noise exposure and transportation noise-induced annoyance have been inferred by curve-fitting methods. The present paper develops a different approach. It derives a systematic relationship by applying an a priori, first-principles model to the findings of forty three studies of the annoyance of aviation noise. The rate of change of annoyance with day-night average sound level (DNL) due to aircraft noise exposure was found to closely resemble the rate of change of loudness with sound level. The agreement of model predictions with the findings of recent curve-fitting exercises (cf. Miedma and Vos, 1998) is noteworthy, considering that other analyses have relied on different analytic methods and disparate data sets. Even though annoyance prevalence rates within individual communities consistently grow in proportion to duration-adjusted loudness, variability in annoyance prevalence rates across communities remains great. The present analyses demonstrate that 1) community-specific differences in annoyance prevalence rates can be plausibly attributed to the joint effect of acoustic and non-DNL related factors and (2) a simple model can account for the aggregate influences of non-DNL related factors on annoyance prevalence rates in different communities in terms of a single parameter expressed in DNL units—a “community tolerance level.”
Binaural benefit for speech recognition with spectral mismatch across ears in simulated electric hearing
Authors: Yoon Yang-soo , Liu Aiguo , Fu Qian-Jie
Published: August 2011

The present study investigated the effects of binaural spectral mismatch on binaural benefits in the context of bilateral cochlear implants using acoustic simulations. Binaural spectral mismatch was systematically manipulated by simulating changes in the relative insertion depths across ears. Sentence recognition, presented unilaterally and bilaterally, were measured in normal-hearing listeners in quiet and noise at +5 dB signal-to-noise ratio. Significant binaural benefits were observed when the interaural difference in insertion depth was 1 mm or less. This result suggests a dependence of the binaural benefit on redundant speech information, rather than on similarity in performance across ears.
Response to Comments on “Drought-Induced Reduction in Global Terrestrial Net Primary Production from 2000 Through 2009”
Authors: Zhao Maosheng , Running Steven W.
Published: August 2011

Samanta
et al
. and Medlyn challenge our report of reduced global terrestrial net primary production (NPP) from 2000 through 2009. Our new tests show that other vegetation indices had even stronger negative changes through the decade, and weakening temperature controls on water stress and respiration still did not produce a positive trend in NPP. These analyses strengthen the conclusion of drought-induced reduction in global NPP over the past decade.
Chaperonins Facilitate KNOTTED1 Cell-to-Cell Trafficking and Stem Cell Function
Authors: Xu Xianfeng Morgan , Wang Jing , Xuan Zhenyu , Goldshmidt Alexander , Borrill Philippa G. M. , Hariharan Nisha , Kim Jae Yean , Jackson David
Published: August 2011

Active transfer of a transcription factor between plant cells is required for stem cell maintenance.
Unraveling the Perplexing Structure of the Zeolite SSZ-57
Authors: Baerlocher Christian , Weber Thomas , McCusker Lynne B. , Palatinus Lukas , Zones Stacey I.
Published: August 2011

X-ray analysis reveals a zeolite structure in which 10-sided channels are periodically disrupted by 12-sided channels.
Incipient Space Weathering Observed on the Surface of Itokawa Dust Particles
Authors: Noguchi T. , Nakamura T. , Kimura M. , Zolensky M. E. , Tanaka M. , Hashimoto T. , Konno M. , Nakato A. , Ogami T. , Fujimura A. , Abe M. , Yada T. , Mukai T. , Ueno M. , Okada T. , Shirai K. , Ishibashi Y. , Okazaki R.
Published: August 2011

Laboratory analysis of samples returned from an asteroid establishes a direct link between asteroids and meteorites and provides clues to the complex history of the asteroid and its surface.
Three-Dimensional Structure of Hayabusa Samples: Origin and Evolution of Itokawa Regolith
Authors: Tsuchiyama Akira , Uesugi Masayuki , Matsushima Takashi , Michikami Tatsuhiro , Kadono Toshihiko , Nakamura Tomoki , Uesugi Kentaro , Nakano Tsukasa , Sandford Scott A. , Noguchi Ryo , Matsumoto Toru , Matsuno Junya , Nagano Takashi , Imai Yuta , Takeuchi Akihisa , Suzuki Yoshio , Ogami Toshihiro , Katagiri Jun , Ebihara Mitsuru , Ireland Trevor R. , Kitajima Fumio , Nagao Keisuke , Naraoka Hiroshi , Noguchi Takaaki , Okazaki Ryuji , Yurimoto Hisayoshi , Zolensky Michael E. , Mukai Toshifumi , Abe Masanao , Yada Toru , Fujimura Akio , Yoshikawa Makoto , Kawaguchi Junichiro
Published: August 2011

Laboratory analysis of samples returned from an asteroid establishes a direct link between asteroids and meteorites and provides clues to the complex history of the asteroid and its surface.
Lively Notes on Nocturnal Singers
Cricket Radio
Tuning In the Night-Singing Insects

by John Himmelman

Harvard University Press, Cambridge, MA, 2011. 316 pp. $22.95, £16.95, €20.70. ISBN 9780674046900.
Authors: Berenbaum May
Published: August 2011

Introducing night songs and the crickets and katydids that make them, Himmelman aims to help people appreciate these extraordinary singers.
U.S. to Leave Consortium and Go It Alone After 2013
Authors: Kerr Richard A. , Normile Dennis
Published: August 2011

Pleading poverty, the U.S. National Science Foundation is ending a decade-long era of international collaboration in ocean drilling, leaving Japan and Europe to fend for themselves.
Cambridge Seeks Global Reach, Says University Head
Authors: Macilwain Colin
Published: August 2011

Leszek Borysiewicz, vice-chancellor of the University of Cambridge, sat down with
Science
for a frank discussion of the future of Cambridge and other U.K. universities.
Who Were the Denisovans?
Authors: Gibbons Ann
Published: August 2011

At an unusual meeting at a Siberian cave, researchers find that these mysterious archaic humans lived in the same place as both modern humans and Neandertals—though not necessarily at the same time—and their range probably stretched into east Asia.
Europe's Innovation Engine, Eager to Grow, Faces Criticism
Authors: Macilwain Colin
Published: August 2011

A European attempt to remain competitive by boosting innovation is off to a shaky start.
LIFE SCIENCE TECHNOLOGIES: Protein Chemistry: Getting Above The Fold
Authors: Dove Alan
Published: August 2011

Fifty years ago, biochemist Christian Anfinsen denatured some pure globular proteins, and observed that they refolded into their proper three-dimensional shapes without assistance, demonstrating that the amino acid sequence alone provides all of the information necessary to direct the folding of at least certain proteins. All researchers had to do was figure out the rules for that process, and they would be able to predict any structure from the protein's sequence.
Genome Sequence of the Halotolerant Marine Bacterium Myxococcus fulvus HW-1
Authors: Li Zhi-Feng , Li Xia , Liu Hong , Liu Xin , Han Kui , Wu Zhi-Hong , Hu Wei , Li Fei-fei , Li Yue-Zhong
Published: August 2011

Myxococcus fulvus
HW-1 (ATCC BAA-855) is a halotolerant marine myxobacterium. This strain exhibits complex social behaviors in the presence of low concentrations of seawater but adopts an asocial living pattern under oceanic conditions. The whole genome of
M. fulvus
HW-1 will enable us to further investigate the details of its evolution.
Draft Genome Sequence of Lactobacillus zeae KCTC 3804
Authors: Kim Dong-Wook , Choi Sang-Haeng , Kang Aram , Nam Seong-Hyeuk , Kim Dae-Soo , Kim Ryong Nam , Kim Aeri , Park Hong-Seog
Published: August 2011

We announce the draft genome sequence of the type strain
Lactobacillus zeae
KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).
Complete Genome Sequence of the Chloromethane-Degrading Hyphomicrobium sp. Strain MC1
Authors: Vuilleumier Stéphane , Nadalig Thierry , Farhan Ul Haque Muhammad , Magdelenat Ghislaine , Lajus Aurélie , Roselli Sandro , Muller Emilie E. L. , Gruffaz Christelle , Barbe Valérie , Médigue Claudine , Bringel Françoise
Published: August 2011

Hyphomicrobium
sp. strain MC1 is an aerobic methylotroph originally isolated from industrial sewage. This prosthecate bacterium was the first strain reported to grow with chloromethane as the sole carbon and energy source. Its genome, consisting of a single 4.76-Mb chromosome, is the first for a chloromethane-degrading bacterium to be formally reported.
Clinical and Molecular Characteristics of Invasive and Noninvasive Skin and Soft Tissue Infections Caused by Group A Streptococcus
Authors: Lin Jiun-Nong , Chang Lin-Li , Lai Chung-Hsu , Lin Hsi-Hsun , Chen Yen-Hsu
Published: August 2011

The severity of skin and soft tissue infections caused by group A
Streptococcus
(GAS) is variable, and there are only a limited number of studies evaluating the characteristics of these infections in the literature. From May 2005 to November 2007, 73 patients with skin and soft tissue infections caused by group A
Streptococcus
were included in this study. Among these patients, 34 (46.6%) had invasive diseases. Diabetes mellitus, alcoholism, and hypertension were the most common underlying disorders. The overall mortality rate was 6.8%, and the elderly were predisposed to invasive infections (
P
< 0.001). Neutrophil percentages of ≥80, serum creatinine levels of ≥2 mg/dl, and high serum C-reactive protein levels were noted more frequently in patients with invasive infections than in patients with noninvasive infections, as were bacteremia and a high mortality rate. Of the 73 isolates, 93.2%, 97.3%, and 37% exhibited susceptibility to erythromycin, clindamycin, and tetracycline, respectively. The five most prevalent
emm
types were
emm
106 (24.7%),
emm
11 (12.3%),
emm
102 (9.6%),
emm
4 (8.2%), and
emm
12 (8.2%). Compared to other types, the
emm
106 type was significantly more likely to be associated with invasive diseases (
P
= 0.012). Dendrogram analysis showed a unique SmaI-digested pulsed-field gel electrophoresis pattern of the
emm
106 type that was particularly prone to cause invasive skin and soft tissue infections (
P
< 0.001). The results of this study suggest that isolates with the
emm
106 gene may be an emerging group A
Streptococcus
strain that causes invasive skin and soft tissue infections. Further surveillance study to understand the significance of this invasive strain is critical.
Visual Detection of High-Risk Human Papillomavirus Genotypes 16, 18, 45, 52, and 58 by Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye
Authors: Luo Le , Nie Kai , Yang Meng-Jie , Wang Miao , Li Jin , Zhang Chen , Liu Hong-Tu , Ma Xue-Jun
Published: August 2011

A simple, rapid, sensitive, qualitative, colorimetric loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue dye (HNB) was established to detect high-risk human papillomavirus (HPV) genotypes 16, 18, 45, 52, and 58. All initial validation studies with the control DNA proved to be type specific. The colorimetric type-specific LAMP assay could achieve a sensitivity of 10 to 100 copies at 63°C for 65 min, comparable to that of real-time PCR. In order to evaluate the reliability of HPV type-specific LAMP, the assay was further evaluated with HPV DNAs from a panel of 294 clinical specimens whose HPV status was previously determined with a novel one-step typing method with multiplex PCR. The tested panel comprised 108 HPV DNA-negative samples and 186 HPV-DNA-positive samples of 14 genotypes. The results showed that the sensitivity of HPV type-specific LAMP for HPV types 16, 18, 45, 52, and 58 was 100%, 100%, 100%, 100%, and 100%, respectively, and the specificity was 100%, 98.5%, 100%, 98.8%, and 99.2%, respectively, compared with a novel one-step typing method with multiplex PCR. No cross-reactivity with other HPV genotypes was observed. In conclusion, this qualitative and colorimetric LAMP assay has potential usefulness for the rapid screening of HPV genotype 16, 18, 45, 52, and 58 infections, especially in resource-limited hospitals or rural clinics of provincial and municipal regions in China.
Predictors of Relapse of Methicillin-Resistant Staphylococcus aureus Bacteremia after Treatment with Vancomycin
Authors: Welsh Kerry J. , Skrobarcek Kimberly A. , Abbott April N. , Lewis Cole T. , Kruzel Mark C. , Lewis Evan M. , Gardiner Jeanelle M. , Mohr John F. , Armitige Lisa Y. , Wanger Audrey
Published: August 2011

The risk factors for relapse of methicillin-resistant
Staphylococcus aureus
(MRSA) bacteremia after vancomycin treatment are unknown. Diversilab typing was used to classify recurrent bacteremia as relapse or reinfection. Bacteremia for >7 days and staphylococcal cassette chromosome
mec
element (SCC
mec
) type II were independently associated with relapse of MRSA bacteremia after vancomycin treatment.
MyD88 Plays an Essential Role in Inducing B Cells Capable of Differentiating into Antibody-Secreting Cells after Vaccination
Authors: Kang Sang-Moo , Yoo Dae-Goon , Kim Min-Chul , Song Jae-Min , Park Min-Kyung , O Eunju , Quan Fu-Shi , Akira Shizuo , Compans Richard W.
Published: August 2011

We investigated the roles of MyD88, an innate adaptor signaling molecule, in inducing protective humoral immunity after vaccination with influenza virus-like particles (VLPs). MyD88 knockout C57BL/6 mice (MyD88−/−mice) vaccinated with influenza VLPs showed significant defects in inducing IgG2a/c isotype antibodies and in generating splenic recall memory B cell responses and antibody-secreting plasma cells in the bone marrow. The protective efficacy of influenza VLP vaccination was lower in MyD88−/−mice than in the wild-type mice. Our findings indicate that MyD88-mediated innate signaling pathways are important for effectively inducing primary and boost immune responses, T helper type 1 isotype-switched antibodies, and gamma interferon (IFN-γ)-secreting T cell responses. In particular, the results in this study demonstrated for the first time that MyD88-mediated immune activation is likely an essential pathway for effective generation of long-lived antibody-secreting plasma cells and highly protective immunity after vaccination with influenza VLPs. This study provides insight into mechanisms by which recombinant viral vaccines induce protective immunity via the MyD88-mediated innate immune signaling pathway.
Inhibition of Hepatitis B Virus Replication by cIAP2 Involves Accelerating the Ubiquitin-Proteasome-Mediated Destruction of Polymerase
Authors: Wang Zekun , Ni Jinjing , Li Jianhua , Shi Bisheng , Xu Yang , Yuan Zhenghong
Published: August 2011

Cellular inhibitor of apoptosis protein 2 (cIAP2) is a potent suppressor of apoptotic cell death. We have shown previously that cIAP2 is involved in the tumor necrosis factor alpha (TNF-α)-induced anti-hepatitis B virus (HBV) response; however, the mechanism for this antiviral effect remains unclear. In the present study, we demonstrate that cIAP2 can significantly reduce the levels of HBV DNA replication intermediates but not the total viral RNA or core protein levels. Domain-mapping analysis revealed that the carboxy-terminal domains of cIAP2 were indispensable for this anti-HBV ability and that an E3 ligase-deficient mutant of cIAP2 (termed cIAP2*) completely lost its antiviral activity. We further identified HBV polymerase as the target of cIAP2. Overexpression of cIAP2 but not cIAP2* reduced polymerase protein levels, while cIAP2 knockdown increased polymerase expression. In addition, we observed that cIAP2 promoted the degradation of the viral polymerase through a proteasome-dependent pathway. Further experiments demonstrated that cIAP2 can bind to polymerase and promote its polyubiquitylation. Finally, we found that cIAP2 downregulated the encapsidation of HBV pregenomic RNA. Taken together, these data reveal a novel mechanism for the inhibition of HBV replication by cIAP2 via acceleration of the ubiquitin-proteasome-mediated decay of polymerase and reduction of the encapsidation of HBV pregenomic RNA, making this mechanism a novel strategy for HBV therapy.
Determinants of Bluetongue Virus Virulence in Murine Models of Disease
Authors: Caporale Marco , Wash Rachael , Pini Attilio , Savini Giovanni , Franchi Paola , Golder Matthew , Patterson-Kane Janet , Mertens Peter , Di Gialleonardo Luigina , Armillotta Gisella , Lelli Rossella , Kellam Paul , Palmarini Massimo
Published: August 2011

Bluetongue is a major infectious disease of ruminants that is caused by bluetongue virus (BTV). In this study, we analyzed virulence and genetic differences of (i) three BTV field strains from Italy maintained at either a low (L strains) or high (H strains) passage number in cell culture and (ii) three South African “reference” wild-type strains and their corresponding live attenuated vaccine strains. The Italian BTV L strains, in general, were lethal for both newborn NIH-Swiss mice inoculated intracerebrally and adult type I interferon receptor-deficient (IFNAR−/−) mice, while the virulence of the H strains was attenuated significantly in both experimental models. Similarly, the South African vaccine strains were not pathogenic for IFNAR−/−mice, while the corresponding wild-type strains were virulent. Thus, attenuation of the virulence of the BTV strains used in this study is not mediated by the presence of an intact interferon system. No clear distinction in virulence was observed for the South African BTV strains in newborn NIH-Swiss mice. Full genomic sequencing revealed relatively few amino acid substitutions, scattered in several different viral proteins, for the strains found to be attenuated in mice compared to the pathogenic related strains. However, only the genome segments encoding VP1, VP2, and NS2 consistently showed nonsynonymous changes between all virulent and attenuated strain pairs. This study established an experimental platform for investigating the determinants of BTV virulence. Future studies using reverse genetics will allow researchers to precisely map and “weight” the relative influences of the various genome segments and viral proteins on BTV virulence.
H5N1 Virus-Like Particle Vaccine Elicits Cross-Reactive Neutralizing Antibodies That Preferentially Bind to the Oligomeric Form of Influenza Virus Hemagglutinin in Humans
Authors: Khurana Surender , Wu Jian , Verma Nitin , Verma Swati , Raghunandan Ramadevi , Manischewitz Jody , King Lisa R. , Kpamegan Eloi , Pincus Steven , Smith Gale , Glenn Gregory , Golding Hana
Published: August 2011

Transmission of pathogenic avian influenza viruses (AIV) from wild birds to domestic poultry and humans is continuing in multiple countries around the world. In preparation for a potential AIV pandemic, multiple vaccine candidates are under development. In the case of H5N1 AIV, a clear shift in transmission from clade 1 to clade 2 viruses occurred in recent years. The virus-like particle (VLP) represents an economical approach to pandemic vaccine development. In the current study, we evaluated the humoral immune response in humans vaccinated with H5N1 A/Indonesia/05/2005 (clade 2.1) VLP vaccine manufactured in Sf9 insect cells. The VLPs were comprised of the influenza virus hemagglutinin (HA), neuraminidase (NA), and matrix 1 (M1) proteins. In an FDA-approved phase I/II human clinical study, two doses of H5N1 VLPs at 15, 45, or 90 μg HA/dose resulted in seroconversion and production of functional antibodies. Moreover, cross-reactivity against other clade 2 subtypes was demonstrated using virus neutralization assays. H5N1 whole-genome fragment phage display libraries (GFPDL) were used to elucidate the antibody epitope repertoire in postvaccination human sera. Diverse epitopes in HA1/HA2 and NA were recognized by postvaccination sera from the two high-dose groups, including large segments spanning the HA1 receptor binding domain. Importantly, the vaccine elicited sera that preferentially bound to an oligomeric form of recombinant HA1 compared with monomeric HA1. The oligomeric/monomeric HA1 binding ratios of the sera correlated with the virus neutralizing titers. Additionally, the two high-dose VLP vaccine groups generated NA-inhibiting antibodies that were associated with binding to a C-terminal epitope close to the sialic acid binding site. These findings represent the first report describing the quality of the antibody responses in humans following AIV VLP immunization and support further development of such vaccines against emerging influenza virus strains.
A Duck Enteritis Virus-Vectored Bivalent Live Vaccine Provides Fast and Complete Protection against H5N1 Avian Influenza Virus Infection in Ducks
Authors: Liu Jinxiong , Chen Pucheng , Jiang Yongping , Wu Li , Zeng Xianying , Tian Guobin , Ge Jinying , Kawaoka Yoshihiro , Bu Zhigao , Chen Hualan
Published: August 2011

Ducks play an important role in the maintenance of highly pathogenic H5N1 avian influenza viruses (AIVs) in nature, and the successful control of AIVs in ducks has important implications for the eradication of the disease in poultry and its prevention in humans. The inactivated influenza vaccine is expensive, labor-intensive, and usually needs 2 to 3 weeks to induce protective immunity in ducks. Live attenuated duck enteritis virus (DEV; a herpesvirus) vaccine is used routinely to control lethal DEV infections in many duck-producing areas. Here, we first established a system to generate the DEV vaccine strain by using the transfection of overlapping fosmid DNAs. Using this system, we constructed two recombinant viruses, rDEV-ul41HA and rDEV-us78HA, in which the hemagglutinin (HA) gene of the H5N1 virus A/duck/Anhui/1/06 was inserted and stably maintained within the ul41 gene or between the us7 and us8 genes of the DEV genome. Duck studies indicated that rDEV-us78HA had protective efficacy similar to that of the live DEV vaccine against lethal DEV challenge; importantly, a single dose of 10
6
PFU of rDEV-us78HA induced complete protection against a lethal H5N1 virus challenge in as little as 3 days postvaccination. The protective efficacy against both lethal DEV and H5N1 challenge provided by rDEV-ul41HA inoculation in ducks was slightly weaker than that provided by rDEV-us78HA. These results demonstrate, for the first time, that recombinant DEV is suitable for use as a bivalent live attenuated vaccine, providing rapid protection against both DEV and H5N1 virus infection in ducks.
Inhibition of Dengue Virus by Targeting Viral NS4B Protein
Authors: Xie Xuping , Wang Qing-Yin , Xu Hao Ying , Qing Min , Kramer Laura , Yuan Zhiming , Shi Pei-Yong
Published: August 2011

We report a novel inhibitor that selectively suppresses dengue virus (DENV) by targeting viral NS4B protein. The inhibitor was identified by screening a 1.8-million-compound library using a luciferase replicon of DENV serotype 2 (DENV-2). The compound specifically inhibits all four serotypes of DENV (50% effective concentration [EC
50
], 1 to 4 μM; and 50% cytotoxic concentration [CC
50
], >40 μM), but it does not inhibit closely related flaviviruses (West Nile virus and yellow fever virus) or nonflaviviruses (Western equine encephalomyelitis virus, Chikungunya virus, and vesicular stomatitis virus). A mode-of-action study suggested that the compound inhibits viral RNA synthesis. Replicons resistant to the inhibitor were selected in cell culture. Sequencing of the resistant replicons revealed two mutations (P104L and A119T) in the viral NS4B protein. Genetic analysis, using DENV-2 replicon and recombinant viruses, demonstrated that each of the two NS4B mutations alone confers partial resistance and double mutations confer additive resistance to the inhibitor in mammalian cells. In addition, we found that a replication defect caused by a lethal NS4B mutation could be partially rescued through
trans
complementation. The ability to complement NS4B in
trans
affected drug sensitivity when a single cell was coinfected with drug-sensitive and drug-resistant viruses. Mechanistically, NS4B was previously shown to interact with the viral NS3 helicase domain; one of the two NS4B mutations recovered in our resistance analysis—P104L—abolished the NS3-NS4B interaction (I. Umareddy, A. Chao, A. Sampath, F. Gu, and S. G. Vasudevan, J. Gen. Virol. 87:2605-2614, 2006). Collectively, the results suggest that the identified inhibitor targets the DENV NS4B protein, leading to a defect in viral RNA synthesis.
Improved Knockout Methodology Reveals That Frog Virus 3 Mutants Lacking either the
18K
Immediate-Early Gene or the Truncated
vIF-2
α Gene Are Defective for Replication and Growth
In Vivo
Authors: Chen Guangchun , Ward Brian M. , Yu Kwang H. , Chinchar V. Gregory , Robert Jacques
Published: August 2011

To better assess the roles of frog virus 3 (FV3; genus
Ranavirus
, family
Iridoviridae
) genes in virulence and immune evasion, we have developed a reliable and efficient method to systematically knock out (KO) putative virulence genes by site-specific integration into the FV3 genome. Our approach utilizes a dual selection marker consisting of the puromycin resistance gene fused in frame with the enhanced green fluorescent protein (EGFP) reporter (Puro-EGFP cassette) under the control of the FV3 immediate-early (IE)
18K
promoter. By successive rounds of selection for puromycin resistance and GFP expression, we have successfully constructed three recombinant viruses. In one, a “knock-in” mutant was created by inserting the Puro-EGFP cassette into a noncoding region of the FV3 genome (FV3-Puro/GFP). In the remaining two, KO mutants were constructed by replacement of the truncated viral homolog of
eIF-2α
(FV3-ΔvIF-2α) or the
18K
IE gene (FV3-Δ18K) with the Puro-EGFP cassette. The specificity of recombination and the clonality of each mutant were confirmed by PCR, sequencing, and immunofluorescence microscopy. Viral replication of each recombinant in cell culture was similar to that of parental FV3; however, infection in
Xenopus laevis
tadpoles revealed that FV3-ΔvIF-2α and FV3-Δ18K replicated less and resulted in lower mortality than did GFP-FV3 and wild-type FV3. Our results suggest that
18K
, which is conserved in all ranaviruses, and the truncated
vIF-2α
gene contribute to virulence. In addition, our study describes a powerful methodology that lays the foundation for the discovery of potentially new ranaviral genes involved in virulence and immune escape.