bluuebunny/crossref_metadata_2025 huggingface dataset:
Piezoelectricity of ZnO Films Prepared by Sol-Gel Method
Authors: Zhang Ke-ming , Zhao Ya-pu , He Fa-quan , Liu Dong-qing
Published: January 2008

ZnO piezoelectric thin films were prepared on crystal substrate Si(111) by sol-gel technology, then characterized by scanning electron microscopy, X-ray diffraction and atomic force microscopy (AFM). The ZnO films characterized by X-ray diffraction are highly oriented in (002) direction with the growing of the film thickness. The morphologies, roughness and grain size of ZnO film investigated by AFM show that roughness and grain size of ZnO piezoelectric films decrease with the increase of the film thickness. The roughness dimension is 2.1880.914 nm. The piezoelectric coefficient d33 was investigated with a piezo-response force microscope (PFM). The results show that the piezoelectric coefficient increases with the increase of thickness and (002) orientation. When the force reference is close to surface roughness of the films, the piezoelectric coefficient measured is inaccurate and fluctuates in a large range, but when the force reference is big, the piezoelectric coefficient d33 changes little and ultimately keeps constant at a low frequency.
Fabrication and Characterization of Micro-Pattern Dandelion-like and Nanobelts of -SrV2O6 via Hydrothermal Process
Authors: Li Zi-an , Yang Huai-xin , Tian Huan-fang , Zhang Ying , Li Jian-qi
Published: January 2008

Dandelion-like micro-crystallites and long belt-like nanostructures of Sr-V-O materials were synthesized under mild hydrothermal reaction conditions in the presence of mineralizer adipic acid at 220C for 60 h and 180C for 60 h, respectively. Scanning electron microscopy measurements show that the Sr-V-O micro-crystallites in general consist of well-arranged microrods with the average length of a few hundred micrometers and diameters ranging from 1 um to 5 m. The long belt-like nanostructures around 100 nm in width exhibit visible twist and waving in shapes, showing high flexibility in nature. Powder X-ray diffraction and electron diffraction measurements both revealed that these micro-/nanometer materials have an orthorhombic structure with the lattice parameter a=9.694 A, b=3.687 A, and c=12.570 A (space group of Pnma) as reported for -SrV2O6 phase. The electron diffraction patterns also indicate that the micro-/nanometer -SrV2O6 crystallites preferentially grow along the 010 crystallographic direction. The effects of the hydrothermal treating temperature and chemical compositions ratio of Sr to V on the morphologies of the final products are extensively investigated. A possible crystallite growth mechanism for the micro-pattern formation is proposed based on the systematic analysis of the experiental results.
Synthesis and Electro-magnetic Properties of Polyaniline-barium Ferrite Nanocomposite
Authors: Li Yuan-xun , Zhang Huai-wu , Liu Ying-li , Q. Xiao John
Published: January 2008

The polyaniline (PANI)-barium ferrite composite with magnetic behavior was synthesized by in situ polymerization of aniline in the presence of BaFe12O19 nanoparticles of 6080 nm in diameters. The structure, morphology and magnetic properties of samples were characterized by powder X-ray diffraction, Fourier transform infrared, scanning electron microscopy, transmission electron microscopy and vibrating sample magnetometer technique. The results of spectroanalysis indicated that there was interaction between PANI chains and ferrite particles. The composite exhibited the hysteresis loops of the ferromagnetic nature. The saturated magnetization of composite was 22.2 emu/g and the conductance was 0.069 S/cm.
Effect of Thermal Treatment on Structure and Catalytic Activity of Supported Fischer-Tropsch Nano-Cobalt Catalysts for Clean Fuels
Authors: Chu Wei , P. Hong J. , Payen E. , Y. Dai X.
Published: January 2008

A series of 15%Co/Al2O3 catalysts were prepared by incipient wetness impregnation under various calcination conditions (90500C), and were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy experiments (XPS), temperature programmed reduction, and catalytic measurements of hydrogenation of carbon monoxide to long-chained hydrocarbons leading to clean fuels (Fischer-Tropsch synthesis). The results of XPS show the presence of incompletely decomposed cobalt nitrate for catalysts calcined at 90200C, and the presence of Co3O4 for catalysts calcined at 200500C. For the four alumina-supported nano-cobalt catalysts with different thermal treatment (200500C), XRD and XPS results illustrated that there were mainly nano Co3O4 crystalite phases of 910 nm and the size of cobalt nano-particles did almost not change with the different temperature of thermal treatment. This was different from that of silica-supported cobalt catalysts. The supported cobalt catalyst (CoAp340 sample) calcinated at 340C presented a better activity for Fischer Tropsch synthesis to clean fuels, at mild conditions like atmospheric pressure (100 kPa), 1800 mL/g/h and 190C; rather than high pressure (2 MPa or more).
Crystallographic Texture and Domain Structure of Nd3.8Dy0.7Pr3.5Fe86Nb1B5 Nanocomposite Prepared by Direct Rapid Solidification
Authors: Diao Shu-lin , Chen Wei , Zhao Xu , Yan Xiu-jun
Published: January 2008

Strong crystallographic texture and high performance of Nd3.8Dy0.7Pr3.5Fe86Nb1B5 (containing 30% -Fe) nanocomposite permanent magnetic material was prepared by direct rapid solidification. X-ray diffraction analysis and magnetic measurement indicated that the ribbons had preferential orientation. The easy magnetization direction switched from perpendicular to the ribbon plane to parallel to the ribbon plane direction as the wheel speed increased from 10 m/s to 30 m/s. The multigrain domains were observed by scan probe microscope (SPM) in the ribbons prepared at wheel speed of 1030 m/s. The Henkel plots were employed to investigate the interactions of the grains in the samples. A very fine and uniform microstructure with the average grain size about 16 nm was obtained in the sample prepared at wheel speed of 30 m/s. The sample consisted of highly oriented hard magnetic phase (Nd,Dy,Pr)2(Fe,Nb)14B and soft magnetic phase -Fe. High performance of Br=1.29 T, Mr/Ms= 0.76 and (BH)max=158.4 kJ/m3 was achieved due to the strong crystallographic texture, fine and homogeneous microstructure and enhancement of the exchange coupling between the soft and hard magnetic phases in this sample. The mechanism of the formation of the crystallographic texture and the multigrain domains was also discussed.
Preparation and Electromagnetic Properties of Composites of Hollow Glass Microspheres Coated with NiFe2O4 Nanoparticles
Authors: Zhao Hai-tao , Ma Rui-ting , Zhang Gang , Xiao Xuan
Published: January 2008

The composites of hollow glass microspheres coated with NiFe2O4 nanoparticles were prepared using poly-acrylamide gel method. The structural characteristics, morphology and electromagnetic properties of the composite powders with different weight percent of glass microspheres (15%, 40%, and 65%) were obtained by X-ray diffraction, scanning electron microscope, infrared spectroscopy and HP8510 network analyzer. The results indicated that the phase structure of composite powders was the mixtures of nickel ferrite, quartz, and mullite. The peak intensity for nickel ferrite decreased rapidly and for mullite increased remarkably with the increasing amount of microspheres. A pure spinel structure of NiFe2O4 formed on the glass microspheres at 600C. A uniform and continuous NiFe2O4-coating was obtained when the content of microspheres was 40%. A great amount of NiFe2O4 particle size is less than 80 nm. The composite with a content of 40% microspheres exhibits better dielectric and magnetic loss properties which are useful to absorb more electromagnetic wave. It can be a kind of good and light electromagnetic wave absorbing material in the X-band.
The Tip Growth Apparatus ofAspergillus nidulans
Authors: Taheri-Talesh Naimeh , Horio Tetsuya , Araujo-Bazán Lidia , Dou Xiaowei , Espeso Eduardo A. , Peñalva Miguel A. , Osmani Stephen A. , Oakley Berl R.
Published: January 2008

Hyphal tip growth in fungi is important because of the economic and medical importance of fungi, and because it may be a useful model for polarized growth in other organisms. We have investigated the central questions of the roles of cytoskeletal elements and of the precise sites of exocytosis and endocytosis at the growing hyphal tip by using the model fungus Aspergillus nidulans. Time-lapse imaging of fluorescent fusion proteins reveals a remarkably dynamic, but highly structured, tip growth apparatus. Live imaging of SYNA, a synaptobrevin homologue, and SECC, an exocyst component, reveals that vesicles accumulate in the Spitzenkörper (apical body) and fuse with the plasma membrane at the extreme apex of the hypha. SYNA is recycled from the plasma membrane by endocytosis at a collar of endocytic patches, 1–2 μm behind the apex of the hypha, that moves forward as the tip grows. Exocytosis and endocytosis are thus spatially coupled. Inhibitor studies, in combination with observations of fluorescent fusion proteins, reveal that actin functions in exocytosis and endocytosis at the tip and in holding the tip growth apparatus together. Microtubules are important for delivering vesicles to the tip area and for holding the tip growth apparatus in position.
APY-1, a NovelCaenorhabditis elegansApyrase Involved in Unfolded Protein Response Signalling and Stress Responses
Authors: Uccelletti D. , Pascoli A. , Farina F. , Alberti A. , Mancini P. , Hirschberg C. B. , Palleschi C.
Published: January 2008

Protein glycosylation modulates a wide variety of intracellular events and dysfunction of the glycosylation pathway has been reported in a variety of human pathologies. Endo-apyrases have been suggested to have critical roles in protein glycosylation and sugar metabolism. However, deciphering the physiological relevance of Endo-apyrases activity has actually proved difficult, owing to their complexity and the functional redundancy within the family. We report here that a UDP/GDPase, homologous to the human apyrase Scan-1, is present in the membranes of Caenorhabditis elegans, encoded by the ORF F08C6.6 and hereinafter-named APY-1. We showed that ER stress induced by tunicamycin or high temperature resulted in increased transcription of apy-1. This increase was not observed in C. elegans mutants defective in ire-1 or atf-6, demonstrating the requirement of both ER stress sensors for up-regulation of apy-1. Depletion of APY-1 resulted in constitutively activated unfolded protein response. Defects in the pharynx and impaired organization of thin fibers in muscle cells were observed in adult worms depleted of APY-1. Some of the apy-1(RNAi) phenotypes are suggestive of premature aging, because these animals also showed accumulation of lipofuscin and reduced lifespan that was not dependent on the functioning of DAF-2, the receptor of the insulin/IGF-1 signaling pathway.
ATP25, a New Nuclear Gene ofSaccharomyces cerevisiaeRequired for Expression and Assembly of the Atp9p Subunit of Mitochondrial ATPase
Authors: Zeng Xiaomei , Barros Mario H. , Shulman Theodore , Tzagoloff Alexander
Published: January 2008

We report a new nuclear gene, designated ATP25 (reading frame YMR098C on chromosome XIII), required for expression of Atp9p (subunit 9) of the Saccharomyces cerevisiae mitochondrial proton translocating ATPase. Mutations in ATP25 elicit a deficit of ATP9 mRNA and of its translation product, thereby preventing assembly of functional F0. Unlike Atp9p, the other mitochondrial gene products, including ATPase subunits Atp6p and Atp8p, are synthesized normally in atp25 mutants. Northern analysis of mitochondrial RNAs in an atp25 temperature-sensitive mutant confirmed that Atp25p is required for stability of the ATP9 mRNA. Atp25p is a mitochondrial inner membrane protein with a predicted mass of 70 kDa. The primary translation product of ATP25 is cleaved in vivo after residue 292 to yield a 35-kDa C-terminal polypeptide. The C-terminal half of Atp25p is sufficient to stabilize the ATP9 mRNA and restore synthesis of Atp9p. Growth on respiratory substrates, however, depends on both halves of Atp25p, indicating that the N-terminal half has another function, which we propose to be oligomerization of Atp9p into a proper size ring structure.
UVB-induced Senescence in Human Keratinocytes Requires a Functional Insulin-like Growth Factor-1 Receptor and p53
Authors: Lewis Davina A. , Yi Qiaofang , Travers Jeffrey B. , Spandau Dan F
Published: January 2008

To cope with the frequent exposure to carcinogenic UV B (UVB) wavelengths found in sunlight, keratinocytes have acquired extensive protective measures to handle UVB-induced DNA damage. Recent in vitro and epidemiological data suggest one these protective mechanisms is dependent on the functional status of the insulin-like growth factor-1 receptor (IGF-1R) signaling network in keratinocytes. During the normal UVB response, ligand-activated IGF-1Rs protect keratinocytes from UVB-induced apoptosis; however, as a consequence, these keratinocytes fail to proliferate. This adaptive response of keratinocytes to UVB exposure maintains the protective barrier function of the epidermis while ensuring that UVB-damaged keratinocytes do not replicate DNA mutations. In contrast, when keratinocytes are exposed to UVB in the absence of IGF-1R activation, the keratinocytes are more sensitive to UVB-induced apoptosis, but the surviving keratinocytes retain the capacity to proliferate. This aberrant UVB response represents flawed protection from UVB damage potentially resulting in the malignant transformation of keratinocytes. Using normal human keratinocytes grown in vitro, we have demonstrated that activation of the IGF-1R promotes the premature senescence of UVB-irradiated keratinocytes through increased generation of reactive oxygen species (ROS) and by maintaining the expression of the cyclin-dependent kinase inhibitor p21CDKN1A. Furthermore, IGF-1R–dependent UVB-induced premature senescence required the phosphorylation of p53 serine 46. These data suggest one mechanism of keratinocyte resistance to UVB-induced carcinogenesis involves the induction of IGF-1R–dependent premature senescence.
Acupuncture: What Underlies Needle Administration?
Authors: Liu Tao
Published: January 2008

Acupuncture is an ancient Chinese therapy with its mode of action unclear and efficacy inconclusive. A lack of attention given to the role of psychosocial context presented in clinical provision of acupuncture may mainly account for the current dilemma in acupuncture research. This psychosocial context induces various cognitive and affective processes in the patient while receiving this treatment. On the basis of the analysis of these psychological factors involved in clinical provision of acupuncture and in light of prior studies on the placebo effect, the author hypothesizes that acupuncture works through potentiation and modulation of a highly organized and somatotopic network of endogenous opioids that links expectation, attention and body schema. This hypothesis, which focuses on the contextual factors involved in clinical provision of acupuncture, has immediate clinical and experimental implications and will take the acupuncture debate much further forward.
No postcopulatory response to inbreeding by male crickets
Authors: Simmons Leigh W , Thomas Melissa L
Published: January 2008

Previous studies of the cricket
Teleogryllus oceanicus
have shown a paternity bias towards non-sibling males. Although non-kin-biased paternity could represent a mechanism of postcopulatory inbreeding avoidance by females, evolutionarily stable strategy (ESS) models of ejaculate evolution also predict that males should reduce their expenditure on the ejaculate when mating with their sisters. Here we provide a test of these models, finding that male crickets invest equally in matings with full-siblings, half-siblings and non-sibling females. The data suggest that in this species, males and females differ in their response to inbreeding.
Quasideterminant solutions of a non-Abelian Toda lattice and kink solutions of a matrix sine-Gordon equation
Authors: Li C.X , Nimmo J.J.C
Published: January 2008

Two families of solutions of a generalized non-Abelian Toda lattice are considered. These solutions are expressed in terms of quasideterminants, constructed by means of Darboux and binary Darboux transformations. As an example of the application of these solutions, we consider the 2-periodic reduction to a matrix sine-Gordon equation. In particular, we investigate the interaction properties of polarized kink solutions.
A Bayesian framework for comparative quantitative genetics
Authors: Ovaskainen Otso , Cano José Manuel , Merilä Juha
Published: January 2008

Bayesian approaches have been extensively used in animal breeding sciences, but similar approaches in the context of evolutionary quantitative genetics have been rare. We compared the performance of Bayesian and frequentist approaches in estimation of quantitative genetic parameters (viz. matrices of additive and dominance variances) in datasets typical of evolutionary studies and traits differing in their genetic architecture. Our results illustrate that it is difficult to disentangle the relative roles of different genetic components from small datasets, and that ignoring, e.g. dominance is likely to lead to biased estimates of additive variance. We suggest that a natural summary statistic forG-matrix comparisons can be obtained by examining how different the underlying multinormal probability distributions are, and illustrate our approach with data on the common frog (Rana temporaria). Furthermore, we derive a simple Monte Carlo method for computation of fraternity coefficients needed for the estimation of dominance variance, and use the pedigree of a natural Siberian jay (Perisoreus infaustus) population to illustrate that the commonly used approximate values can be substantially biased.
Testing evolutionary models of senescence in a natural population: age and inbreeding effects on fitness components in song sparrows
Authors: Keller L.F , Reid J.M , Arcese P
Published: January 2008

Mutation accumulation (MA) and antagonistic pleiotropy (AP) have each been hypothesized to explain the evolution of ‘senescence’ or deteriorating fitness in old age. These hypotheses make contrasting predictions concerning age dependence in inbreeding depression in traits that show senescence. Inbreeding depression is predicted to increase with age under MA but not under AP, suggesting one empirical means by which the two can be distinguished. We use pedigree and life-history data from free-living song sparrows (Melospiza melodia) to test for additive and interactive effects of age and individual inbreeding coefficient (f) on fitness components, and thereby assess the evidence for MA. Annual reproductive success (ARS) and survival (and therefore reproductive value) declined in old age in both sexes, indicating senescence in this short-lived bird. ARS declined withfin both sexes and survival declined withfin males, indicating inbreeding depression in fitness. We observed a significant age×finteraction for male ARS (reflecting increased inbreeding depression as males aged), but not for female ARS or survival in either sex. These analyses therefore provide mixed support for MA. We discuss the strengths and limitations of such analyses and therefore the value of natural pedigreed populations in testing evolutionary models of senescence.
Dispersal as a means of inbreeding avoidance in a wild bird population
Authors: Szulkin Marta , Sheldon Ben C
Published: January 2008

The long-term study of animal populations facilitates detailed analysis of processes otherwise difficult to measure, and whose significance may appear only when a large sample size from many years is available for analysis. For example, inbreeding is a rare event in most natural populations, and therefore many years of data are needed to estimate its effect on fitness. A key behaviour hypothesized to play an important role in avoiding inbreeding is natal dispersal. However, the functional significance of natal dispersal with respect to inbreeding has been much debated but subject to very few empirical tests. We analysed 44 years of data from a wild great titParus majorpopulation involving over 5000 natal dispersal events within Wytham Woods, UK. Individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding; within the class of inbreeding birds, increased inbreeding was associated with reduced dispersal distance, for both males and females. This led to a 3.4-fold increase (2.3–5, 95% CI) in the likelihood of close (f=0.25) inbreeding relative to the population average when individuals dispersed less than 200 m. In the light of our results, and published evidence showing little support for active inbreeding avoidance in vertebrates, we suggest that dispersal should be considered as a mechanism of prime importance for inbreeding avoidance in wild populations.
When fecundity does not equal fitness: evidence of an offspring quantity versus quality trade-off in pre-industrial humans
Authors: Gillespie Duncan O.S , Russell Andrew F , Lummaa Virpi
Published: January 2008

Maternal fitness should be maximized by the optimal division of reproductive investment between offspring number and offspring quality. While evidence for this is abundant in many taxa, there have been fewer tests in mammals, and in particular, humans. We used a dataset of humans spanning three generations from pre-industrial Finland to test how increases in maternal fecundity affect offspring quality and maternal fitness in contrasting socio-economic conditions. For ‘resource-poor’ landless families, but not ‘resource-rich’ landowning families, maternal fitness returns diminished with increased maternal fecundity. This was because the average offspring contribution to maternal fitness declined with increased maternal fecundity for landless but not landowning families. This decline was due to reduced offspring recruitment with increased maternal fecundity. However, in landowning families, recruited offspring fecundity increased with increased maternal fecundity. This suggests that despite decreased offspring recruitment, maternal fitness is not reduced in favourable socio-economic conditions due to an increase in subsequent offspring fecundity. These results provide evidence consistent with an offspring quantity–quality trade-off in the lifetime reproduction of humans from poor socio-economic conditions. The results also highlight the importance of measuring offspring quality across their whole lifespan to estimate reliably the fitness consequences of increased maternal fecundity.
Maturational costs of reproduction due to clutch size and ontogenetic conflict as revealed in the invisible fraction
Authors: Sinervo Barry , McAdam Andrew G
Published: January 2008

Reproduction is thought to entail costs, but assessing survival costs associated with maturation as organisms express reproductive genes for the first time is problematic because many will die prior to expressing a phenotype. We quantified selection acting on this invisible fraction by measuring selection on predicted breeding values for clutch size estimated from a multigenerational pedigree of side-blotched lizards in which clutch size was heritable (h2=0.25±0.04). The survival effects of predicted breeding values for clutch size during maturation, however, differed between males and females indicating ontogenetic conflict. Increased mortality during maturation was associated with lower predicted breeding values for clutch size for females, but higher predicted breeding values for males who do not produce a clutch. Genetic correlations between clutch size and male and female survival were consistent with calculated selection differentials. Experimental yolk removal did not affect progeny survival during maturation, indicating that selection on maturing progeny was not due to confounding yolk-volume maternal effects, and hormone manipulations confirmed clutch size as the target of viability selection during maturation. Such episodes of selection prior to phenotypic expression of the trait will have important consequences for the evolution of reproductive investment.
Critical Depth of Cut and Specific Cutting Energy of a Microscribing Process for Hard and Brittle Materials
Authors: Wang Jiunn-Jyh Junz , Liao Yong-Yuan
Published: January 2008

This paper investigated the scribing process characteristics of the hard and brittle materials including single crystal silicon, STV glass, and sapphire substrate. Under various cutting angles, major process characteristics are examined including the groove geometry, specific cutting energy, and critical depth of cut at the onset of ductile-to-brittle cutting transition. As the cutting depth increases, groove geometry clearly reveals the ductile-to-brittle transition from the plastic deformation to a brittle fracture state. The material size effect in the ductile region as well as the transition in scribing behavior is well reflected by change in the specific cutting energy. Further, it is shown that the change of specific cutting energy as a function of the cutting depth can serve as a criterion for estimating the critical depth of cut. Such estimated critical depth of cut is confirmed by measurement from a 3D confocal microscope. The critical depths of cut for these hard materials are found to be between 0.1μm and 0.5μm depending on the materials and cutting angles.
A Phenomenological Approach for Real-Time Simulation of the Two-Way Shape Memory Effect in NiTi Alloys
Authors: Maletta C. , Falvo A. , Furgiuele F.
Published: January 2008

A phenomenological model to simulate the two-way shape memory effect (TWSME) in nickel-titanium alloys (NiTi) is proposed. The model is based on the Prandtl–Ishlinksii operator and it is able to simulate the hysteretic behavior of the material in the strain-temperature response. Starting from some experimental measurements of well known thermomechanical characteristics of NiTi alloys, the parameters of the phenomenological model are identified by simple and efficient numerical procedures. The model was developed in the commercial software package SIMULINK® and it is able to simulate the effects of applied stresses on the TWSME as well as partial thermal cycles, which generate incomplete martensitic transformations. A systematic comparison between experimental measurements, carried out under different values of applied stress, and numerical predictions are illustrated for both complete and incomplete phase transformations. The results are considered satisfactory both in accuracy and in computational time; therefore, the method is robust and suitable for use in real-time applications.
Spin Conservation Accounts for Aluminum Cluster Anion Reactivity Pattern with O
2
Authors: Burgert R. , Schnöckel H. , Grubisic A. , Li X. , Stokes S. T. , Bowen K. H. , Ganteför G. F. , Kiran B. , Jena P.
Published: January 2008

The reactivity pattern of small (∼10 to 20 atoms) anionic aluminum clusters with oxygen has posed a long-standing puzzle. Those clusters with an odd number of atoms tend to react much more slowly than their even-numbered counterparts. We used Fourier transform ion cyclotron resonance mass spectrometry to show that spin conservation straightforwardly accounts for this trend. The reaction rate of odd-numbered clusters increased appreciably when singlet oxygen was used in place of ground-state (triplet) oxygen. Conversely, monohydride clusters Al

n

H
–
, in which addition of the hydrogen atom shifts the spin state by converting formerly open-shell structures to closed-shell ones (and vice versa), exhibited an opposing trend: The odd-
n
hydride clusters reacted more rapidly with triplet oxygen. These findings are supported by theoretical simulations and highlight the general importance of spin selection rules in mediating cluster reactivity.
Centromeric Aurora-B Activation Requires TD-60, Microtubules, and Substrate Priming Phosphorylation
Authors: Rosasco-Nitcher Sara E. , Lan Weijie , Khorasanizadeh Sepideh , Stukenberg P. Todd
Published: January 2008

The chromosome passenger complex (CPC) controls chromosome congression, kinetochore-microtubule attachments, and spindle checkpoint signaling during mitosis. Aurora-B kinase is the catalytic subunit of the CPC. To understand how a single kinase can regulate such diverse events, we have investigated the activation of Aurora-B and describe two distinct activation mechanisms. First, Aurora-B activation in vitro requires two cofactors, telophase disc–60kD (TD-60) and microtubules. TD-60 is critical to localize both the CPC and Haspin kinase activity to centromeres and thus regulates Aurora-B at several levels. Second, Aurora-B substrates can inhibit kinase activation, and this is relieved by phosphorylation of these substrates by the centromeric kinases Plk1 and Haspin. These regulatory mechanisms suggest models for phosphorylation by Aurora-B of centromeric substrates at unaligned chromosomes and merotelic attachments.
Adaptive Plasticity in Female Mate Choice Dampens Sexual Selection on Male Ornaments in the Lark Bunting
Authors: Chaine Alexis S. , Lyon Bruce E.
Published: January 2008

Theory on the evolution of ornamental male traits by sexual selection assumes consistency in selection over time. Temporal variation in female choice could dampen sexual selection, but scant information exists on the degree to which individual female preferences are flexible. Here we show that in lark buntings sexual selection on male traits varied dramatically across years and, in some cases, exhibited reversals in the direction of selection for a single trait. We show that these shifts are probably because of flexibility in mate choice by individual females and that they parallel shifts in the male traits that predict female reproductive success in a given year. Plasticity in choice and concomitant reversals in mating patterns across time may weaken the strength of sexual selection and could maintain genetic variation underlying multiple sexual ornaments.
The Many Sides of Science
Authors: Laubichler Manfred D.
Published: January 2008

Vienna in the Age of Uncertainty
. Science, Liberalism, and Private Life.
By Deborah R. Coen
. University of Chicago Press, Chicago, 2007. 392 pp. $45, £28.50. ISBN 9780226111728.

Through the story of three generations of the Exner family, the author explores the interactions of science, culture, and society in during the rise and fall of Austrian liberalism.
Alignment Uncertainty and Genomic Analysis
Authors: Wong Karen M. , Suchard Marc A. , Huelsenbeck John P.
Published: January 2008

The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions.
The Frequency Dependence of Osmo-Adaptation in
Saccharomyces cerevisiae
Authors: Mettetal Jerome T. , Muzzey Dale , Gómez-Uribe Carlos , van Oudenaarden Alexander
Published: January 2008

The propagation of information through signaling cascades spans a wide range of time scales, including the rapid ligand-receptor interaction and the much slower response of downstream gene expression. To determine which dynamic range dominates a response, we used periodic stimuli to measure the frequency dependence of signal transduction in the osmo-adaptation pathway of
Saccharomyces cerevisiae
. We applied system identification methods to infer a concise predictive model. We found that the dynamics of the osmo-adaptation response are dominated by a fast-acting negative feedback through the kinase Hog1 that does not require protein synthesis. After large osmotic shocks, an additional, much slower, negative feedback through gene expression allows cells to respond faster to future stimuli.
Steal Away, Music
Authors: Phillips-Silver Jessica
Published: January 2008

Musicophilia
. Tales of Music and the Brain.
By Oliver Sacks
. Knopf, New York, 2007. 397 pp. $26. ISBN 9781400040810.

These stories of the experiences of patients, musicians, and others explore neurological aspects of the power of music.
Bacteria of Dental Caries in Primary and Permanent Teeth in Children and Young Adults
Authors: Aas Jørn A. , Griffen Ann L. , Dardis Sara R. , Lee Alice M. , Olsen Ingar , Dewhirst Floyd E. , Leys Eugene J. , Paster Bruce J.
Published: January 2008

Although
Streptococcus mutans
has been implicated as a major etiological agent of dental caries, our cross-sectional preliminary study indicated that 10% of subjects with rampant caries in permanent teeth do not have detectable levels of
S. mutans
. Our aims were to use molecular methods to detect all bacterial species associated with caries in primary and permanent teeth and to determine the bacterial profiles associated with different disease states. Plaque was collected from 39 healthy controls and from intact enamel and white-spot lesions, dentin lesions, and deep-dentin lesions in each of 51 subjects with severe caries. 16S rRNA genes were PCR amplified, cloned, and sequenced to determine species identities. In a reverse-capture checkerboard assay, 243 samples were analyzed for 110 prevalent bacterial species. A sequencing analysis of 1,285 16S rRNA clones detected 197 bacterial species/phylotypes, of which 50% were not cultivable. Twenty-two new phylotypes were identified. PROC MIXED tests revealed health- and disease-associated species. In subjects with
S. mutans
, additional species, e.g., species of the genera
Atopobium
,
Propionibacterium
, and
Lactobacillus
, were present at significantly higher levels than those of
S. mutans
.
Lactobacillus
spp.,
Bifidobacterium dentium
, and low-pH non-
S. mutans
streptococci were predominant in subjects with no detectable
S. mutans
.
Actinomyces
spp. and non-
S. mutans
streptococci were predominant in white-spot lesions, while known acid producers were found at their highest levels later in disease. Bacterial profiles change with disease states and differ between primary and secondary dentitions. Bacterial species other than
S. mutans
, e.g., species of the genera
Veillonella
,
Lactobacillus
,
Bifidobacterium
, and
Propionibacterium
, low-pH non-
S. mutans
streptococci,
Actinomyces
spp., and
Atopobium
spp., likely play important roles in caries progression.
Diagnostic Evaluation of Multiplexed Reverse Transcription-PCR Microsphere Array Assay for Detection of Foot-and-Mouth and Look-Alike Disease Viruses
Authors: Hindson Benjamin J. , Reid Scott M. , Baker Brian R. , Ebert Katja , Ferris Nigel P. , Tammero Lance F. Bentley , Lenhoff Raymond J. , Naraghi-Arani Pejman , Vitalis Elizabeth A. , Slezak Thomas R. , Hullinger Pamela J. , King Donald P.
Published: January 2008

A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and-mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR assay was evaluated using 287 field samples, including 247 samples (213 true-positive samples and 35 true-negative samples) from suspected cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true-negative samples collected from healthy animals. The mRT-PCR assay results were compared to those of two singleplex rRT-PCR assays, using virus isolation with antigen enzyme-linked immunosorbent assays as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% (95% confidence interval [CI], 89.8 to 96.4%), and the sensitivity was 98.1% (95% CI, 95.3 to 99.3%) for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses, such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (
n
= 2) and bovine viral diarrhea virus (
n
= 2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized by using focused single-target rRT-PCR assays.
Use of Highly Discriminatory Fingerprinting to Analyze Clusters of
Clostridium difficile
Infection Cases Due to Epidemic Ribotype 027 Strains
Authors: Fawley W. N. , Freeman J. , Smith C. , Harmanus C. , van den Berg R. J. , Kuijper E. J. , Wilcox M. H.
Published: January 2008

We compared multilocus variable-number tandem-repeat analysis (MLVA) and macrorestriction endonuclease analysis using pulsed-field gel electrophoresis (PFGE) to determine their utility to identify clusters of
Clostridium difficile
infection (CDI) among 91 isolates of PCR ribotype 027 (NAP1, for
N
orth
A
merican
p
ulsed-field type
1
) from nine hospitals (and 10 general practitioners associated with one institution) in England. We also examined whether mortality in CDI cases was associated with specific MLVA subtypes. PFGE discriminated between ribotype 027 strains at >98% similarity, identifying five pulsovars (I to V) of 1 to 53 isolates. MLVA was markedly more discriminatory, identifying 23 types of 1 to 15 isolates (>71% similarity). PFGE pulsovars I and IV contained 14 and 8 MLVA types, respectively. Twenty-one of twenty-three (91%) of MLVA types were specific to individual PFGE pulsovars. Four CDI clusters were identified in institution A by conventional epidemiological analysis. MLVA typing identified two enlarged and two additional clusters. Thirty of forty-four (68%) patients in institution A with CDI caused by ribotype 027 strains were assigned to seven distinct clusters by a combination of MLVA typing and epidemiological records. Of 33 patients, comprising 14 different MLVA types, nine (27%) died by day 30 (early deaths). Eight of nine (89%) were associated with PFGE type IV
C. difficile
ribotype 027. Five of nine early deaths were associated with MLVA type 16, which was the dominant type in this cohort (10/33 cases); 4 other distinct MLVA types accounted for the other early deaths. MLVA was far superior to PFGE for analyzing clusters of CDI both within and between institutions. Further study is needed to examine whether subtypes of
C. difficile
ribotype 027 affect outcome.
Selection and Validation of a Multilocus Variable-Number Tandem-Repeat Analysis Panel for Typing
Shigella
spp
Authors: Gorgé Olivier , Lopez Stéphanie , Hilaire Valérie , Lisanti Olivier , Ramisse Vincent , Vergnaud Gilles
Published: January 2008

The
Shigella
genus has historically been separated into four species, based on biochemical assays. The classification within each species relies on serotyping. Recently, genome sequencing and DNA assays, in particular the multilocus sequence typing (MLST) approach, greatly improved the current knowledge of the origin and phylogenetic evolution of
Shigella
spp. The
Shigella
and
Escherichia
genera are now considered to belong to a unique genomospecies. Multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses of highly homogeneous bacterial pathogens. Here, we assess the capability of MLVA for
Shigella
typing. Thirty-two potentially polymorphic VNTRs were selected by analyzing in silico five
Shigella
genomic sequences and subsequently evaluated. Eventually, a panel of 15 VNTRs was selected (i.e., MLVA15 analysis). MLVA15 analysis of 78 strains or genome sequences of
Shigella
spp. and 11 strains or genome sequences of
Escherichia coli
distinguished 83 genotypes.
Shigella
population cluster analysis gave consistent results compared to MLST. MLVA15 analysis showed capabilities for
E. coli
typing, providing classification among pathogenic and nonpathogenic
E. coli
strains included in the study. The resulting data can be queried on our genotyping webpage (
http://mlva.u-psud.fr
). The MLVA15 assay is rapid, highly discriminatory, and reproducible for
Shigella
and
Escherichia
strains, suggesting that it could significantly contribute to epidemiological trace-back analysis of
Shigella
infections and pathogenic
Escherichia
outbreaks. Typing was performed on strains obtained mostly from collections. Further studies should include strains of much more diverse origins, including all pathogenic
E. coli
types.
Amino Acid Mutation N348I in the Connection Subdomain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Confers Multiclass Resistance to Nucleoside and Nonnucleoside Reverse Transcriptase Inhibitors
Authors: Hachiya Atsuko , Kodama Eiichi N. , Sarafianos Stefan G. , Schuckmann Matthew M. , Sakagami Yasuko , Matsuoka Masao , Takiguchi Masafumi , Gatanaga Hiroyuki , Oka Shinichi
Published: January 2008

We identified clinical isolates with phenotypic resistance to nevirapine (NVP) in the absence of known nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations. This resistance is caused by N348I, a mutation at the connection subdomain of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Virologic analysis showed that N348I conferred multiclass resistance to NNRTIs (NVP and delavirdine) and to nucleoside reverse transcriptase inhibitors (zidovudine [AZT] and didanosine [ddI]). N348I impaired HIV-1 replication in a cell-type-dependent manner. Acquisition of N348I was frequently observed in AZT- and/or ddI-containing therapy (12.5%;
n
= 48;
P
< 0.0001) and was accompanied with thymidine analogue-associated mutations, e.g., T215Y (
n
= 5/6) and the lamivudine resistance mutation M184V (
n
= 1/6) in a Japanese cohort. Molecular modeling analysis shows that residue 348 is proximal to the NNRTI-binding pocket and to a flexible hinge region at the base of the p66 thumb that may be affected by the N348I mutation. Our results further highlight the role of connection subdomain residues in drug resistance.
Cell Cycle Association of the Retinoblastoma Protein Rb and the Histone Demethylase LSD1 with the Epstein-Barr Virus Latency Promoter Cp
Authors: Chau Charles M. , Deng Zhong , Kang Hyojueng , Lieberman Paul M.
Published: January 2008

The Epstein-Barr virus C promoter (Cp) regulates the major multicistronic transcript encoding the EBNA-LP, 1, 2, and 3 genes required for B-cell proliferation during latency. The growth-transforming potential of these viral genes suggests that they must be tightly regulated with the host cell cycle and differentiation process. To better understand Cp regulation, we used DNA affinity purification to identify cellular and viral proteins that bind to Cp in latently infected cells. Several previously unknown factors were identified, including the cell cycle regulatory proteins E2F1 and Rb. E2F1 bound to a specific site in Cp located in the core Cp region 3′ of the known EBNA2-responsive RBP-Jk (CSL, CBF1) binding site. The histone H3 K4 demethylase LSD1 (BCC110) was also identified by DNA affinity and was shown to form a stable complex with Rb. Coimmunoprecipitation assays demonstrated that E2F1, Rb, and LSD1 bind to Cp in a cell cycle-dependent manner. Rb and LSD1 binding to Cp increased after the S phase, corresponding to a decrease in histone H3 K4 methylation and Cp transcription. Coimmunoprecipitation and immunofluorescence assays reveal that LSD1 interacts with Rb. Surprisingly, LSD1 did not coimmunoprecipitate with E2F1, suggesting that it associates with Rb independently of E2F1. Depletion of LSD1 by small interfering RNAs inhibited Cp basal transcription levels, and overexpression of LSD1 altered the cell cycle profile in p53-positive (p53
+
), but not p53-negative (p53
−
), HCT cells. These findings indicate that Cp is a cell cycle-regulated promoter that is under the control of Rb and the histone demethylase LSD1 in multiple latency types.
The Human Cytomegalovirus Fc Receptor gp68 Binds the Fc CH2-CH3 Interface of Immunoglobulin G
Authors: Sprague Elizabeth R. , Reinhard Henrike , Cheung Evelyn J. , Farley Alexander H. , Trujillo Robin Deis , Hengel Hartmut , Bjorkman Pamela J.
Published: January 2008

Recognition of immunoglobulin G (IgG) by surface receptors for the Fc domain of immunoglobulin G (Fcγ), FcγRs, can trigger both humoral and cellular immune responses. Two human cytomegalovirus (HCMV)-encoded type I transmembrane receptors with Fcγ-binding properties (vFcγRs), gp34 and gp68, have been identified on the surface of HCMV-infected cells and are assumed to confer protection against IgG-mediated immunity. Here we show that Fcγ recognition by both vFcγRs occurs independently of N-linked glycosylation of Fcγ, in contrast with the properties of host FcγRs. To gain further insight into the interaction with Fcγ, truncation mutants of the vFcγR gp68 ectodomain were probed for Fcγ binding, resulting in localization of the Fcγ binding site on gp68 to residues 71 to 289, a region including an immunoglobulin-like domain. Gel filtration and biosensor binding experiments revealed that, unlike host FcγRs but similar to the herpes simplex virus type 1 (HSV-1) Fc receptor gE-gI, gp68 binds to the CH2-CH3 interdomain interface of the Fcγ dimer with a nanomolar affinity and a 2:1 stoichiometry. Unlike gE-gI, which binds Fcγ at the slightly basic pH of the extracellular milieu but not at the acidic pH of endosomes, the gp68/Fcγ complex is stable at pH values from 5.6 to pH 8.1. These data indicate that the mechanistic details of Fc binding by HCMV gp68 differ from those of host FcγRs and from that of HSV-1 gE-gI, suggesting distinct functional and recognition properties.
Single-Cell, Phosphoepitope-Specific Analysis Demonstrates Cell Type- and Pathway-Specific Dysregulation of Jak/STAT and MAPK Signaling Associated with In Vivo Human Immunodeficiency Virus Type 1 Infection
Authors: Lee Andrew W. , Sharp Elizabeth R. , O'Mahony Alison , Rosenberg Michael G. , Israelski Dennis M. , Nolan Garry P. , Nixon Douglas F.
Published: January 2008

Despite extensive evidence of cell signaling alterations induced by human immunodeficiency virus type 1 (HIV-1) in vitro, the relevance of these changes to the clinical and/or immunologic status of HIV-1-infected individuals is often unclear. As such, mapping the details of cell type-specific degradation of immune function as a consequence of changes to signaling network responses has not been readily accessible. We used a flow cytometric-based assay of signaling to determine Janus kinase/signal transducers and activators of transcription (Jak/STAT) signaling changes at the single-cell level within distinct cell subsets from the primary immune cells of HIV-1-infected donors. We identified a specific defect in granulocyte-macrophage colony-stimulating factor (GM-CSF)-driven Stat5 phosphorylation in the monocytes of HIV-1+ donors. This inhibition was statistically significant in a cohort of treated and untreated individuals. Ex vivo Stat5 phosphorylation levels varied among HIV-1+ donors but did not correlate with CD4+T-cell counts or HIV-1 plasma viral load. Low Stat5 activation occurred in HIV-1-infected donors despite normal GM-CSF receptor levels. Investigation of mitogen-activated protein kinase (MAPK) pathways, also stimulated by GM-CSF, led to the observation that lipopolysaccharide-stimulated extracellular signal-regulated kinase phosphorylation is enhanced in monocytes. Thus, we have identified a specific, imbalanced monocyte signaling profile, with inhibition of STAT and enhancement of MAPK signaling, associated with HIV-1 infection. This understanding of altered monocyte signaling responses that contribute to defective antigen presentation during HIV-1 infection could lead to immunotherapeutic approaches that compensate for the deficiency.