bluuebunny/crossref_metadata_2025 huggingface dataset:
Mean flows driven by weak eddies in rotating systems
Authors: Mcewan A. D. , Thompson R. O. R. Y. , Plumb R. A.
Published: April 2006

General relations are derived for the forcing of a mean zonal flow in a damped rotating barotropic system through the action of weak eddies. In particular it is found that if the eddies are forced at localized latitudes the induced motion away from these latitudes is likely to be counter to the rotation (i.e. ‘easterly’). Over the forcing latitude the mean motion is always westerly except when the forcing provides a sink of relative momentum. In the case when the background field is deformed topographically to generate eddies the divergence of the Reynolds stress is balanced at lowest order by a dynamic pressure drag, and the mean motion takes the direction of propagation of the forcing.

The relations are applied to a linearized Rossby wave field in a viscous fluid driven by a moving system of boundary sources and sinks or hills and hollows. The results are compared with laboratory experiments. All major predictions are confirmed qualitatively, but the discrepancies in detail indicate the influence of nonlinear effects other than those incorporated in the theory.
A strong interaction theory for the creeping motion of a sphere between plane parallel boundaries. Part 2. Parallel motion
Authors: Ganatos Peter , Pfeffer Robert , Weinbaum Sheldon
Published: April 2006

Exact solutions are presented for the three-dimensional creeping motion of a sphere of arbitrary size and position between two plane parallel walls for the following conditions: (a) pure translation parallel to two stationary walls, (b) pure rotation about an axis parallel to the walls, (c) Couette flow past a rigidly held sphere induced by the motion of one of the boundaries and (d) two-dimensional Poiseuille flow past a rigidly held sphere in a channel. The combined analytic and numerical solution procedure is the first application for bounded flow of the three-dimensional boundary collocation theory developed in Ganatos, Pfeffer & Weinbaum (1978). The accuracy of the solution technique is tested by detailed comparison with the exact bipolar co-ordinate solutions of Goldman, Cox & Brenner (1967a, b) for the drag and torque on a sphere translating parallel to a single plane wall, rotating adjacent to the wall or in the presence of a shear field. In all cases, the converged collocation solutions are in perfect agreement with the exact solutions for all spacings tested. The new collocation solutions have also been used to test the accuracy of existing solutions for the motion of a sphere parallel to two walls using the method of reflexions technique. The first-order reflexion theory of Ho & Leal (1974) provides reasonable agreement with the present results for the drag when the sphere is five or more radii from both walls. At closer spacings first-order reflexion theory is highly inaccurate and predicts an erroneous direction for the torque on the sphere for a wide range of sphere positions. Comparison with the classical higher-order method of reflexions solutions of Faxen (1923) reveals that the convergence of the multiple reflexion series solution is poor when the sphere centre is less than two radii from either boundary.

Solutions have also been obtained for the fluid velocity field. These solutions show that, for certain wall spacings and particle positions, a separated region of closed streamlines forms adjacent to the sphere which reverses the direction of the torque acting on a translating sphere.
Linear Rayleigh-Taylor stability of viscous fluids with mass and heat transfer
Authors: Ho S-P.
Published: April 2006

The linear Rayleigh–Taylor stability of superposed viscous fluids with interfacial transfer of mass and heat is first considered for layers of finite thickness. A dispersion relation is obtained. It is then employed to derive stability and instability criteria for the case of two semi-infinite layers as well as the case where one of the layers is finite. From these criteria one arrives at a critical dispersion relation and a new critical wavenumber. This new critical wavenumber is distinct from the classical value owing to the presence of a parameter which depends, in a very simple manner, upon the kinematic viscosity of the fluids, the surface tension and the rate of interfacial transfer of mass and energy. Also it is found that the stabilizing effect of the surface tension is neither affected by the arrangement of the system nor the direction of the temperature gradient. However, the effects of the viscosity and the gravity will depend upon the relative positions of the superposed fluids and the direction of the temperature gradient at the interface.
The steady flow due to a rotating sphere at low and moderate Reynolds numbers
Authors: Dennis S. C. R. , Singh S. N. , Ingham D. B.
Published: April 2006

The problem of determining the steady axially symmetrical motion induced by a sphere rotating with constant angular velocity about a diameter in an incompressible viscous fluid which is at rest at large distances from it is considered. The basic independent variables are the polar co-ordinates (r, θ) in a plane through the axis of rotation and with origin at the centre of the sphere. The equations of motion are reduced to three sets of nonlinear second-order ordinary differential equations in the radial variable by expanding the flow variables as series of orthogonal Gegenbauer functions with argument μ = cosθ. Numerical solutions of the finite set of equations obtained by truncating the series after a given number of terms are obtained. The calculations are carried out for Reynolds numbers in the range R = 1 to R = 100, and the results are compared with various other theoretical results and with experimental observations.

The torque exerted by the fluid on the sphere is found to be in good agreement with theory at low Reynolds numbers and appears to tend towards the results of steady boundary-layer theory for increasing Reynolds number. There is excellent agreement with experimental results over the range considered. A region of inflow to the sphere near the poles is balanced by a region of outflow near the equator and as the Reynolds number increases the inflow region increases and the region of outflow becomes narrower. The radial velocity increases with Reynolds number at the equator, indicating the formation of a radial jet over the narrowing region of outflow. There is no evidence of any separation of the flow from the surface of the sphere near the equator over the range of Reynolds numbers considered.
The evolution of slender inviscid drops in an axisymmetric straining flow
Authors: Hinch E. J.
Published: April 2006

The evolution of the shape of a slender inviscid drop in an axisymmetric straining motion is studied at low Reynolds numbers. It is found that the shape equation can be solved by polynommals with time-dependent coefficients. A global stability result can be used to show simply that only one possible equilibrium is stable. It is further shown that if the slender drop starts with a long-wavelength waist then it cannot go to this stable equilibrium and must either extend indefinitely or burst. In the class of trinomial shapes, it is shown that the drop either bursts or goes to the stable equilibrium, depending on whether or not the initial shape has a waist.
The Taiwan‐Ryukyu subduction‐collision complex: Folding of a viscoelastic slab and the double seismic zone
Authors: Chou Han‐Chiang , Kuo Ban‐Yuan , Hung Shu‐Huei , Chiao Ling‐Yun , Zhao Dapeng , Wu Yih‐Min
Published: April 2006

The termination of the Ryukyu trench against Eurasia and the oblique subduction of the Philippine Sea plate create a subduction‐collision complex offshore Taiwan, which has not previously been elucidated in detail. We combine traveltime data from the seismic networks in Taiwan and Japan to better illuminate how the subducting Ryukyu slab deforms in this subduction‐collision zone. More than 5000 events recorded by both networks were relocated with the double‐difference method using an optimal regional one‐dimensional velocity model. The offshore seismicity indicates that the double seismic zone, with a gap of 15–20 km, exists in the subducting slab in the depth range of 40–80 km. Focal mechanisms suggest that the double seismic zone is caused by east‐west compression resulting from oblique convergence. The improved hypocentral locations for the first time reveal folding of the slab into a horizontal curvature larger in magnitude than and opposite in sign to that of the Ryukyu trench in the depth range 50–100 km. The anomalous curvature, together with the focal mechanisms, suggests that the slab folds against the Eurasian lithosphere and that this deformation cannot be fully elastic. We model this deformation mode as the developing instability of a viscoelastic Maxwell layer embedded in a viscous medium. The characteristic wavelength of the instability, i.e., ∼250 km, is consistent with folding of a slab whose viscosity is 100 times higher than that of the surrounding mantle for an along‐strike elastic membrane strain as small as 0.01, or more than 3 orders of magnitude higher if 5% elastic strain is allowed.
Band-gap energy and electron effective mass of polycrystalline Zn3N2
Authors: Suda Toshikazu , Kakishita Kazuhiko
Published: April 2006

Zn 3 N 2 polycrystalline films with n+-type conductivity have been grown by metalorganic chemical vapor deposition and rf-molecular beam epitaxy with carrier concentration in the range between 1019 and ∼1020cm−3. Oxygen contamination without an intentional doping was found to be a cause of high electron concentration, leading to a larger band-gap energy due to Burstein-Moss shift. The significant blue shift of the optical band gap Eopt with increasing carrier concentration ne obeys the relation Eopt=1.06+1.30×10−14ne2∕3. This evaluation enables the conclusion that the actual band-gap energy of Zn3N2 is 1.06eV. Electron effective mass m* for Zn3N2 has been deduced from Fourier transform infrared reflectivity measurements to be (0.29±0.05)mo.
Förster and Dexter energy-transfer processes in fluorescent BAlq thin films doped with phosphorescent Ir(ppy)3 molecules
Authors: Tanaka Isao , Tabata Yuichiro , Tokito Shizuo
Published: April 2006

We studied the photoluminescence proprieties of bis(2-methyl-8-quinolinato)-4-phenylphenolate aluminum (BAlq) thin films doped with fac tris(2-phenylpyridine) iridium [Ir(ppy)3] over a wide temperature range from 8to295K. The efficient Förster and Dexter energy transfers between the fluorescent BAlq molecule and the phosphorescent Ir(ppy)3 one enabled us to observe strong yellow phosphorescence from BAlq, where Ir(ppy)3 plays an important role as a phosphorescent sensitizer for BAlq. It was found that BAlq acts not only as a donor but also as an acceptor in the energy transfer between BAlq and Ir(ppy)3. The triplet energy of BAlq was estimated to be 2.18eV from the highest energy peak of the phosphorescence spectra, and the phosphorescence lifetime was 16ms at 8K. Furthermore, it was revealed from the temperature dependence of the photoluminescence intensity that the triplet-excited states in BAlq are in thermal equilibrium with those in Ir(ppy)3 at temperatures above ∼200K in the BAlq:Ir(ppy)3 system.
Relaxor behavior of layer structured SrBi1.65La0.35Nb2O9
Authors: Huang Shiming , Sun Lin , Feng Chude , Chen Lidong
Published: April 2006

Sr Bi 1.65 La 0.35 Nb 2 O 9 ceramics were prepared by a conventional solid-state reaction method. X-ray diffraction analysis indicated that single phase layered perovskites were obtained. Dielectric response of SrBi1.65La0.35Nb2O9 was found to be characteristic of relaxor ferroelectrics. The dielectric relaxation of SrBi1.65La0.35Nb2O9 was modeled using the Vögel-Fulcher relationship [D. Viehland et al., J. Appl. Phys. 68, 2916 (1990)], and this result suggests that SrBi1.65La0.35Nb2O9 is analogous to a spin glass with thermally activated polarization fluctuations above a static freezing temperature.
Imaging of dielectric cylinders from experimental stepped-frequency data
Authors: Dubois Anthony , Geffrin Jean-Michel , Belkebir Kamal , Saillard Marc
Published: April 2006

This letter reports on the characterization of two-dimensional targets from measured transient scattered fields. The problem is formulated in the frequency domain rather than directly in the time domain, and an iterative construction of the unknown dielectric constant is derived. Improvement of the resolution is suggested by marching on in the central frequency of the incident pulse. The efficiency of this approach is emphasized through examples of reconstructions of an inhomogeneous target from experimental data.
Distinct genetic interactions between multiple Vegf receptors are required for development of different blood vessel types in zebrafish
Authors: Covassin L. D. , Villefranc J. A. , Kacergis M. C. , Weinstein B. M. , Lawson N. D.
Published: April 2006

Recent evidence indicates a specific role for vascular endothelial growth factor a (Vegfa) during artery development in both zebrafish and mouse embryos, whereas less is known about signals that govern vein formation. In zebrafish, loss of
vegfa
blocks segmental artery formation and reduces artery-specific gene expression, whereas veins are largely unaffected. Here, we describe a mutation in the zebrafish
vegf receptor-2
homolog,
kdra
, which eliminates its kinase activity and leads to specific defects in artery development. We further find that Flt4, a receptor for Vegfc, cooperates with Kdr during artery morphogenesis, but not differentiation. We also identify an additional zebrafish
vegfr
-
2
ortholog, referred to as
kdrb
, which can partially compensate for loss of
kdra
but is dispensable for vascular development in wild-type embryos. Interestingly, we find that these Vegf receptors are also required for formation of veins but in distinct genetic interactions that differ from those required for artery development. Taken together, our results indicate that formation of arteries and veins in the embryo is governed in part by different Vegf receptor combinations and suggest a genetic mechanism for generating blood vessel diversity during vertebrate development.
FZL, an FZO-like protein in plants, is a determinant of thylakoid and chloroplast morphology
Authors: Gao Hongbo , Sage Tammy L. , Osteryoung Katherine W.
Published: April 2006

FZO is a dynamin-related membrane-remodeling protein that mediates fusion between mitochondrial outer membranes in animals and fungi. We identified a single FZO-like protein in
Arabidopsis
, FZL, a new plant-specific member of the dynamin superfamily. FZL is targeted to chloroplasts and associated with thylakoid and envelope membranes as punctate structures.
fzl
knockout mutants have abnormalities in chloroplast and thylakoid morphology, including disorganized grana stacks and alterations in the relative proportions of grana and stroma thylakoids. Overexpression of FZL-GFP also conferred defects in thylakoid organization. Mutation of a conserved residue in the predicted FZL GTPase domain abolished both the punctate localization pattern and ability of FZL-GFP to complement the
fzl
mutant phenotype. FZL defines a new protein class within the dynamin superfamily of membrane-remodeling GTPases that regulates organization of the thylakoid network in plants. Notably, FZL levels do not affect mitochondrial morphology or ultrastructure, suggesting that mitochondrial morphology in plants is regulated by an FZO-independent mechanism.
Kruppel-like factor 2 (KLF2) regulates proinflammatory activation of monocytes
Authors: Das Hiranmoy , Kumar Ajay , Lin Zhiyong , Patino Willmar D. , Hwang Paul M. , Feinberg Mark W. , Majumder Pradip K. , Jain Mukesh K.
Published: April 2006

The mechanisms regulating activation of monocytes remain incompletely understood. Herein we provide evidence that Kruppel-like factor 2 (KLF2) inhibits proinflammatory activation of monocytes.
In vitro
, KLF2 expression in monocytes is reduced by cytokine activation or differentiation. Consistent with this observation, KLF2 expression in circulating monocytes is reduced in patients with chronic inflammatory conditions such as coronary artery disease. Adenoviral overexpression of KLF2 inhibits the LPS-mediated induction of proinflammatory factors, cytokines, and chemokines and reduces phagocytosis. Conversely, short interfering RNA-mediated reduction in KLF2 increased inflammatory gene expression. Reconstitution of immunodeficient mice with KLF2-overexpressing monocytes significantly reduced carrageenan-induced acute paw edema formation. Mechanistically, KLF2 inhibits the transcriptional activity of both NF-κB and activator protein 1, in part by means of recruitment of transcriptional coactivator p300/CBP-associated factor. These observations identify KLF2 as a novel negative regulator of monocytic activation.
Evidence on the chromosomal location of centromeric DNA in
Plasmodium falciparum
from etoposide-mediated topoisomerase-II cleavage
Authors: Kelly John M. , McRobert Louisa , Baker David A.
Published: April 2006

Centromeres are the chromosomal loci that facilitate segregation, and, in most eukaryotes, they encompass extensive regions of genomic DNA. Topoisomerase-II has been identified as a crucial regulator of segregation in a wide range of organisms and exhibits premitotic accumulation at centromeres. Consistent with this property, treatment of cells with the topoisomerase-II inhibitor etoposide promotes chromosomal cleavage at sites within centromeric DNA. In the case of the human malaria parasite
Plasmodium falciparum
, despite a completed genome sequence, there are no experimental data on the nature of centromeres. To address this issue, we have used etoposide-mediated topoisomerase-II cleavage as a biochemical marker to map centromeric DNA on all 14 parasite chromosomes. We find that topoisomerase-II activity is concentrated at single chromosomal loci and that cleavage sites extend over ≈10 kb. A shared feature of these topoisomerase-II cleavage sites is the presence of an extremely AT-rich (≈97%) domain with a strictly defined size limit of 2.3–2.5 kb. Repetitive arrays identified within the domains do not display interchromosomal conservation in terms of length, copy number, or sequence. These unusual properties suggest that
P. falciparum
chromosomes contain a class of “regional” centromere distinct from those described in other eukaryotes, including the human host.
ADP-ribosylating and vacuolating cytotoxin of
Mycoplasma pneumoniae
represents unique virulence determinant among bacterial pathogens
Authors: Kannan T. R. , Baseman Joel B.
Published: April 2006

Unlike many bacterial pathogens,
Mycoplasma pneumoniae
is not known to produce classical toxins, and precisely how
M. pneumoniae
injures the respiratory epithelium has remained a mystery for >50 years. Here, we report the identification of a virulence factor (MPN372) possibly responsible for airway cellular damage and other sequelae associated with
M. pneumoniae
infections in humans. We show that
M. pneumoniae
MPN372 encodes a 68-kDa protein that possesses ADP-ribosyltransferase (ART) activity. Within its N terminus, MPN372 contains key amino acids associated with NAD binding and ADP-ribosylating activity, similar to pertussis toxin (PTX) S1 subunit (PTX-S1). Interestingly, MPN372 ADP ribosylates both identical and distinct mammalian proteins when compared with PTX-S1. Remarkably, MPN372 elicits extensive vacuolization and ultimate cell death of mammalian cells, including distinct and progressive patterns of cytopathology in tracheal rings in organ culture that had been previously ascribed to infection with WT virulent
M. pneumoniae
. We observed dramatic seroconversion to MPN372 in patients diagnosed with
M. pneumoniae
-associated pneumonia, indicating that this toxin is synthesized
in vivo
and possesses highly immunogenic epitopes.
Monitoring chaperone engagement of substrates in the endoplasmic reticulum of live cells
Authors: Snapp Erik L. , Sharma Ajay , Lippincott-Schwartz Jennifer , Hegde Ramanujan S.
Published: April 2006

The folding environment in the endoplasmic reticulum (ER) depends on multiple abundant chaperones that function together to accommodate a range of substrates. The ways in which substrate engagement shapes either specific chaperone dynamics or general ER attributes
in vivo
remain unknown. In this study, we have evaluated how changes in substrate flux through the ER influence the diffusion of both the lectin chaperone calreticulin and an inert reporter of ER crowdedness. During acute changes in substrate load, the inert probe revealed no changes in ER organization, despite significant changes in calreticulin dynamics. By contrast, inhibition of the lectin chaperone system caused rapid changes in the ER environment that could be reversed over time by easing new substrate burden. Our findings provide insight into the normal organization and dynamics of an ER chaperone and characterize the capacity of the ER to maintain homeostasis during acute changes in chaperone activity and availability.
Multireplicon genome architecture of
Lactobacillus
salivarius
Authors: Claesson Marcus J. , Li Yin , Leahy Sinead , Canchaya Carlos , van Pijkeren Jan Peter , Cerdeño-Tárraga Ana M. , Parkhill Julian , Flynn Sarah , O’Sullivan Gerald C. , Collins J. Kevin , Higgins Des , Shanahan Fergus , Fitzgerald Gerald F. , van Sinderen Douwe , O’Toole Paul W.
Published: April 2006

Lactobacillus salivarius
subsp.
salivarius
strain UCC118 is a bacteriocin-producing strain with probiotic characteristics. The 2.13-Mb genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously have not been characterized in lactic acid bacteria or intestinal lactobacilli. Annotation of the genome sequence indicated an intermediate level of auxotrophy compared with other sequenced lactobacilli. No single-copy essential genes were located on the megaplasmid. However, contingency amino acid metabolism genes and carbohydrate utilization genes, including two genes for completion of the pentose phosphate pathway, were megaplasmid encoded. The megaplasmid also harbored genes for the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation locus, and other genes potentially relevant for probiotic properties. Two subspecies of
L. salivarius
are recognized,
salivarius
and
salicinius
, and we detected megaplasmids in both subspecies by pulsed-field gel electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of megaplasmids of widely varying size in
L. salivarius
suggests a possible mechanism for genome expansion or contraction to adapt to different environments.
Disparate thermodynamics governing T cell receptor–MHC-I interactions implicate extrinsic factors in guiding MHC restriction
Authors: Ely Lauren K. , Beddoe Travis , Clements Craig S. , Matthews Jacqueline M. , Purcell Anthony W. , Kjer-Nielsen Lars , McCluskey James , Rossjohn Jamie
Published: April 2006

The underlying basis of major histocompatibility complex (MHC) restriction is unclear. Nevertheless, current data suggest that a common thermodynamic signature dictates αβ T cell receptor (TcR) ligation. To evaluate whether this thermodynamic signature defines MHC restriction, we have examined the thermodynamic basis of a highly characterized immunodominant TcR interacting with its cognate peptide–MHC-I ligand. Surprisingly, we observed this interaction to be governed by favorable enthalpic and entropic forces, which is in contrast to the prevailing generality, namely, enthalpically driven interactions combined with markedly unfavorable entropic forces. We conclude that extrinsic molecular factors, such as coreceptor ligation, conformational adjustments involved in TcR signaling, or constraints dictated by higher-order arrangement of ligated TcRs, might play a greater role in guiding MHC restriction than appreciated previously.
Posttranslational myristoylation of caspase-activated p21-activated protein kinase 2 (PAK2) potentiates late apoptotic events
Authors: Vilas Gonzalo L. , Corvi Maria M. , Plummer Greg J. , Seime Andrea M. , Lambkin Gareth R. , Berthiaume Luc G.
Published: April 2006

p21-activated protein kinase (PAK) 2 is a small GTPase-activated serine/threonine kinase regulating various cytoskeletal functions and is cleaved by caspase-3 during apoptosis. We demonstrate that the caspase-cleaved PAK2 C-terminal kinase fragment (C-t-PAK2) is posttranslationally myristoylated, although myristoylation is typically a cotranslational process. Myristoylation and an adjacent polybasic domain of C-t-PAK2 are sufficient to redirect EGFP from the cytosol to membrane ruffles and internal membranes. Membrane localization and the ability of C-t-PAK2 to induce cell death are significantly reduced when myristoylation is abolished. In addition, the proper myristoylation-dependent membrane localization of C-t-PAK2 significantly increased signaling through the stress-activated c-Jun N-terminal kinase signaling pathway, which often regulates apoptosis. Interestingly, C-t-PAK2 promoted cell death without compromising mitochondrial integrity. Posttranslational myristoylation of caspase-cleaved proteins involved in cytoskeletal dynamics (e.g., PAK2, actin, and gelsolin) might be part of a unique series of mechanisms involved in the regulation of the later events of apoptosis.
Phospholipase DZ2 plays an important role in extraplastidic galactolipid biosynthesis and phosphate recycling in
Arabidopsis
roots
Authors: Cruz-Ramírez Alfredo , Oropeza-Aburto Araceli , Razo-Hernández Francisco , Ramírez-Chávez Enrique , Herrera-Estrella Luis
Published: April 2006

Low phosphate (Pi) availability is one of the major constraints for plant productivity in natural and agricultural ecosystems. Plants have evolved a myriad of developmental and biochemical mechanisms to increase internal Pi uptake and utilization efficiency. One important biochemical pathway leading to an increase in internal Pi availability is the hydrolysis of phospholipids. Hydrolyzed phospholipids are replaced by nonphosphorus lipids such as galactolipids and sulfolipids, which help to maintain the functionality and structure of membrane systems. Here we report that a member of the
Arabidopsis
phospholipase D gene family (
PLDZ2
) is gradually induced upon Pi starvation in both shoots and roots. From lipid content analysis we show that an
Arabidopsis pldz2
mutant is defective in the hydrolysis of phospholipids and has a reduced capacity to accumulate galactolipids under limiting Pi conditions. Morphological analysis of the
pldz2
root system shows a premature change in root architecture in response to Pi starvation. These results show that PLDZ2 is involved in the eukaryotic galactolipid biosynthesis pathway, specifically in hydrolyzing phosphatidylcholine and phosphatidylethanolamine to produce diacylglycerol for digalactosyldiacylglycerol synthesis and free Pi to sustain other Pi-requiring processes.
EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure
Authors: Robinson Philip J. J. , Fairall Louise , Huynh Van A. T. , Rhodes Daniela
Published: April 2006

Chromatin structure plays a fundamental role in the regulation of nuclear processes such as DNA transcription, replication, recombination, and repair. Despite considerable efforts during three decades, the structure of the 30-nm chromatin fiber remains controversial. To define fiber dimensions accurately, we have produced very long and regularly folded 30-nm fibers from
in vitro
reconstituted nucleosome arrays containing the linker histone and with increasing nucleosome repeat lengths (10 to 70 bp of linker DNA). EM measurements show that the dimensions of these fully folded fibers do not increase linearly with increasing linker length, a finding that is inconsistent with two-start helix models. Instead, we find that there are two distinct classes of fiber structure, both with unexpectedly high nucleosome density: arrays with 10 to 40 bp of linker DNA all produce fibers with a diameter of 33 nm and 11 nucleosomes per 11 nm, whereas arrays with 50 to 70 bp of linker DNA all produce 44-nm-wide fibers with 15 nucleosomes per 11 nm. Using the physical constraints imposed by these measurements, we have built a model in which tight nucleosome packing is achieved through the interdigitation of nucleosomes from adjacent helical gyres. Importantly, the model closely matches raw image projections of folded chromatin arrays recorded in the solution state by using electron cryo-microscopy.
Assessing the fidelity of the fossil record by using marine bivalves
Authors: Valentine James W. , Jablonski David , Kidwell Susan , Roy Kaustuv
Published: April 2006

Taxa that fail to become incorporated into the fossil record can reveal much about the biases of this record and provide the information needed to correct such biases in empirical analyses of the history of life. Yet little is known about the characteristics of taxa missing from the fossil record. For the marine Bivalvia, which have become a model system for macroevolutionary and macroecological analysis in the fossil record, 308 of the 1,292 living genera and subgenera (herein termed “taxa”) are not recorded as fossils. These missing taxa are not a random sample of the clade, but instead tend to have small body size, reactive shell structures, commensal or parasitic habit, deep-sea distribution, narrow geographic range, restriction to regions exposing few Neogene marine sediments, or recent date of formal taxonomic description in the neontological literature. Most missing taxa show two or more of these features and tend to be concentrated in particular families. When we exclude the smallest taxa (<1 cm) and deep-sea endemics, date of published description and geographic range become the strongest predictors of the missing taxa; other factors are statistically insignificant or have relatively small effects. These biases might influence a variety of analyses including the use of fossil data in support of phylogenetic analyses, molecular clock calibrations, and analyses of spatial and temporal dynamics of clades and biotas. Clade inventories such as these can be used to develop protocols that minimize the biases imposed by sampling and preservation.
Antagonism of the prostaglandin D
2
receptor 1 suppresses nicotinic acid-induced vasodilation in mice and humans
Authors: Cheng Kang , Wu Tsuei-Ju , Wu Kenneth K. , Sturino Claudio , Metters Kathleen , Gottesdiener Keith , Wright Samuel D. , Wang Zhaoyin , O’Neill Gary , Lai Eseng , Waters M. Gerard
Published: April 2006

Nicotinic acid (NA) is commonly used to treat dyslipidemia, but it elicits an adverse effect, termed flushing, which consists of cutaneous vasodilation with associated discomfort. An animal model of NA-induced flushing has been established in mice. As in humans, NA stimulated vasodilation in a dose-dependent manner, was associated with an increase of the vasodilatory prostaglandin (PG) D
2
in plasma and could be blocked by pretreatment with aspirin. Two PGD
2
receptors have been identified: PGD
2
receptor 1 (DP1, also called DP) and PGD
2
receptor 2 (DP2, sometimes termed CRTH2). DP2 does not mediate NA-induced vasodilation; the DP2-specific agonist DK-PGD
2
(13,14-dihydro-15-keto-PGD
2
) did not induce cutaneous vasodilation, and DP2
−/−
mice had a normal vasodilatory response to NA. By contrast, BW245C, a DP1-selective agonist, induced vasodilation in mice, and MK-0524, a DP1-selective antagonist, blocked both PGD
2
- and NA-induced vasodilation. NA-induced vasodilation was also studied in DP1
+/+
, DP1
+/−
, and DP1
−/−
mice; although NA-induced vasodilation depended almost completely on DP1 in female mice, it depended only partially on DP1 in male mice. The residual NA-induced vasodilation in male DP
−/−
mice was aspirin-sensitive. Thus, in the mouse, DP1 appears to be an important component involved in NA-induced vasodilation, but other cyclooxygenase-dependent mechanisms also may be involved. A clinical study in healthy men and women demonstrated that treatment with MK-0524 reduced the symptoms of flushing and the increase in skin perfusion after the administration of NA. These studies suggest that DP1 receptor antagonism may be an effective means to suppress NA-induced flushing in humans.
Characterization of Su48, a centrosome protein essential for cell division
Authors: Wang Qiang , Du Xiulian , Meinkoth Judy , Hirohashi Yoshihiko , Zhang Hongtao , Liu Qingdu , Richter Mark , Greene Mark I.
Published: April 2006

The centrosome functions as the major microtubule-organizing center and plays a vital role in guiding chromosome segregation during mitosis. Centrosome abnormalities are frequently seen in a variety of cancers, suggesting that dysfunction of this organelle may contribute to malignant transformation. In our efforts to identify the protein components of the centrosome and to understand the structure features involved in the assembly and functions of this organelle, we cloned and characterized a centrosome-associated protein called Su48. We found that a coiled coil-containing subdomain of Su48 was both sufficient and required for its centrosome localization. In addition, this structure also modulates Su48 dimerization. Moreover, ectopic expression of Su48 causes abnormal mitosis, and a mutant form of Su48 disrupts the localization of γ-tubulin to the centrosome. Finally, by microinjection of an anti-Su48 antibody, we found that disruption of normal Su48 functions leads to mitotic failure, possibly due to centrosome defects or incomplete cytokinesis. Thus, Su48 represents a previously unrecognized centrosome protein that is essential for cell division. We speculate that Su48 abnormalities may cause aberrant chromosome segregation and may contribute to aneuploidy and malignant transformation.
Evidence for a role of developmental genes in the origin of obesity and body fat distribution
Authors: Gesta Stephane , Blüher Matthias , Yamamoto Yuji , Norris Andrew W. , Berndt Janin , Kralisch Susan , Boucher Jeremie , Lewis Choy , Kahn C. Ronald
Published: April 2006

Obesity, especially central obesity, is a hereditable trait associated with a high risk for development of diabetes and metabolic disorders. Combined gene expression analysis of adipocyte- and preadipocyte-containing fractions from intraabdominal and subcutaneous adipose tissue of mice revealed coordinated depot-specific differences in expression of multiple genes involved in embryonic development and pattern specification. These differences were intrinsic and persisted during
in vitro
culture and differentiation. Similar depot-specific differences in expression of developmental genes were observed in human subcutaneous versus visceral adipose tissue. Furthermore, in humans, several genes exhibited changes in expression that correlated closely with body mass index and/or waist/hip ratio. Together, these data suggest that genetically programmed developmental differences in adipocytes and their precursors in different regions of the body play an important role in obesity, body fat distribution, and potential functional differences between internal and subcutaneous adipose tissue.
Dual roles for the trimeric G protein Go in asymmetric cell division in
Drosophila
Authors: Katanaev Vladimir L. , Tomlinson Andrew
Published: April 2006

During asymmetric division, a cell polarizes and differentially distributes components to its opposite ends. The subsequent division differentially segregates the two component pools to the daughters, which thereby inherit different developmental directives. In
Drosophila
sensory organ precursor cells, the localization of Numb protein to the cell's anterior cortex is a key patterning event and is achieved by the combined action of many proteins, including Pins, which itself is localized anteriorly. Here, a role is described for the trimeric G protein Go in the anterior localization of Numb and daughter cell fate specification. Go is shown to interact with Pins. In addition to a role in recruiting Numb to an asymmetric location in the cell's cortex, Go transduces a signal from the Frizzled receptor that directs the position in which the complex forms. Thus, Go likely integrates the signaling that directs the formation of the complex with the signaling that directs where the complex forms.
A live, attenuated recombinant West Nile virus vaccine
Authors: Monath Thomas P. , Liu Jian , Kanesa-Thasan Niranjan , Myers Gwendolyn A. , Nichols Richard , Deary Alison , McCarthy Karen , Johnson Casey , Ermak Thomas , Shin Sunheang , Arroyo Juan , Guirakhoo Farshad , Kennedy Jeffrey S. , Ennis Francis A. , Green Sharone , Bedford Philip
Published: April 2006

West Nile (WN) virus is an important cause of febrile exanthem and encephalitis. Since it invaded the U.S. in 1999, >19,000 human cases have been reported. The threat of continued epidemics has spurred efforts to develop vaccines. ChimeriVax-WN02 is a live, attenuated recombinant vaccine constructed from an infectious clone of yellow fever (YF) 17D virus in which the premembrane and envelope genes of 17D have been replaced by the corresponding genes of WN virus. Preclinical tests in monkeys defined sites of vaccine virus replication
in vivo
. ChimeriVax-WN02 and YF 17D had similar biodistribution but different multiplication kinetics. Prominent sites of replication were skin and lymphoid tissues, generally sparing vital organs. Viruses were cleared from blood by day 7 and from tissues around day 14. In a clinical study, healthy adults were inoculated with 5.0 log
10
plaque-forming units (PFU) (
n
= 30) or 3.0 log
10
PFU (
n
= 15) of ChimeriVax-WN02, commercial YF vaccine (YF-VAX,
n
= 5), or placebo (
n
= 30). The incidence of adverse events in subjects receiving the vaccine was similar to that in the placebo group. Transient viremia was detected in 42 of 45 (93%) of ChimeriVax-WN02 subjects, and four of five (80%) of YF-VAX subjects. All subjects developed neutralizing antibodies to WN or YF, respectively, and the majority developed specific T cell responses. ChimeriVax-WN02 rapidly elicits strong immune responses after a single dose, and is a promising candidate warranting further evaluation for prevention of WN disease.
MTA1, a transcriptional activator of breast cancer amplified sequence 3
Authors: Gururaj Anupama E. , Singh Rajesh R. , Rayala Suresh K. , Holm Caroline , den Hollander Petra , Zhang Hao , Balasenthil Seetharaman , Talukder Amjad H. , Landberg Goran , Kumar Rakesh
Published: April 2006

Here we define a function of metastasis-associated protein 1 (MTA1), a presumed corepressor of estrogen receptor α (ERα), as a transcriptional activator of Breast Cancer Amplified Sequence 3 (BCAS3), a gene amplified and overexpressed in breast cancers. We identified BCAS3 as a MTA1 chromatin target in a functional genomic screen. MTA1 stimulation of BCAS3 transcription required ERα and involved a functional ERE half-site in
BCAS3
. Furthermore, we discovered that MTA1 is acetylated on lysine 626, and that this acetylation is necessary for a productive transcriptional recruitment of RNA polymerase II complex to the BCAS3 enhancer sequence. BCAS3 expression was elevated in mammary tumors from MTA1 transgenic mice and 60% of the human breast tumors, and correlated with the coexpression of MTA1 as well as with tumor grade and proliferation of primary breast tumor samples. These findings reveal a previously unrecognized function of MTA1 in stimulating
BCAS3
expression and suggest an important role for MTA1-BCAS3 pathway in promoting cancerous phenotypes in breast tumor cells.
Mutations in the MicroRNA Complementarity Site of the INCURVATA4 Gene Perturb Meristem Function and Adaxialize Lateral Organs in Arabidopsis
Authors: Ochando Isabel , Jover-Gil Sara , Ripoll Juan José , Candela Héctor , Vera Antonio , Ponce María Rosa , Martínez-Laborda Antonio , Micol José Luis
Published: April 2006

Here, we describe how the semidominant, gain-of-function icu4-1 and icu4-2 alleles of the INCURVATA4 (ICU4) gene alter leaf phyllotaxis and cell organization in the root apical meristem, reduce root length, and cause xylem overgrowth in the stem. The ICU4 gene was positionally cloned and found to encode the ATHB15 transcription factor, a class III homeodomain/leucine zipper family member, recently named CORONA. The icu4-1 and icu4-2 alleles bear the same point mutation that affects the microRNA complementarity site of ICU4 and is identical to those of several semidominant alleles of the class III homeodomain/leucine zipper family members PHABULOSA and PHAVOLUTA. The icu4-1 and icu4-2 mutations significantly increase leaf transcript levels of the ICU4 gene. The null hst-1 allele of the HASTY gene, which encodes a nucleocytoplasmic transporter, synergistically interacts with icu4-1, the double mutant displaying partial adaxialization of rosette leaves and carpels. Our results suggest that the ICU4 gene has an adaxializing function and that it is down-regulated by microRNAs that require the HASTY protein for their biogenesis.
Systematic Analysis of Arabidopsis Organelles and a Protein Localization Database for Facilitating Fluorescent Tagging of Full-Length Arabidopsis Proteins
Authors: Li Shijun , Ehrhardt David W. , Rhee Seung Y.
Published: April 2006

Cells are organized into a complex network of subcellular compartments that are specialized for various biological functions. Subcellular location is an important attribute of protein function. To facilitate systematic elucidation of protein subcellular location, we analyzed experimentally verified protein localization data of 1,300 Arabidopsis (Arabidopsis thaliana) proteins. The 1,300 experimentally verified proteins are distributed among 40 different compartments, with most of the proteins localized to four compartments: mitochondria (36%), nucleus (28%), plastid (17%), and cytosol (13.3%). About 19% of the proteins are found in multiple compartments, in which a high proportion (36.4%) is localized to both cytosol and nucleus. Characterization of the overrepresented Gene Ontology molecular functions and biological processes suggests that the Golgi apparatus and peroxisome may play more diverse functions but are involved in more specialized processes than other compartments. To support systematic empirical determination of protein subcellular localization using a technology called fluorescent tagging of full-length proteins, we developed a database and Web application to provide preselected green fluorescent protein insertion position and primer sequences for all Arabidopsis proteins to study their subcellular localization and to store experimentally verified protein localization images, videos, and their annotations of proteins generated using the fluorescent tagging of full-length proteins technology. The database can be searched, browsed, and downloaded using a Web browser at http://aztec.stanford.edu/gfp/. The software can also be downloaded from the same Web site for local installation.
Subcellular Localization and Membrane Topology of the Melon Ethylene Receptor CmERS1
Authors: Ma Biao , Cui Min-Long , Sun Hyeon-Jin , Takada Keita , Mori Hitoshi , Kamada Hiroshi , Ezura Hiroshi
Published: April 2006

Ethylene receptors are multispanning membrane proteins that negatively regulate ethylene responses via the formation of a signaling complex with downstream elements. To better understand their biochemical functions, we investigated the membrane topology and subcellular localization of CmERS1, a melon (Cucumis melo) ethylene receptor that has three putative transmembrane domains at the N terminus. Analyses using membrane fractionation and green fluorescent protein imaging approaches indicate that CmERS1 is predominantly associated with the endoplasmic reticulum (ER) membrane. Detergent treatments of melon microsomes showed that the receptor protein is integrally bound to the ER membrane. A protease protection assay and N-glycosylation analysis were used to determine membrane topology. The results indicate that CmERS1 spans the membrane three times, with its N terminus facing the luminal space and the large C-terminal portion lying on the cytosolic side of the ER membrane. This orientation provides a platform for interaction with the cytosolic signaling elements. The three N-terminal transmembrane segments were found to function as topogenic sequences to determine the final topology. High conservation of these topogenic sequences in all ethylene receptor homologs identified thus far suggests that these proteins may share the same membrane topology.
Functional Analysis of anArabidopsisTranscription Factor, DREB2A, Involved in Drought-Responsive Gene Expression
Authors: Sakuma Yoh , Maruyama Kyonoshin , Osakabe Yuriko , Qin Feng , Seki Motoaki , Shinozaki Kazuo , Yamaguchi-Shinozaki Kazuko
Published: April 2006

Transcription factors DREB1A/CBF3 and DREB2A specifically interact with cis-acting dehydration-responsive element/C-repeat (DRE/CRT) involved in cold and drought stress–responsive gene expression in Arabidopsis  thaliana. Intact DREB2A expression does not activate downstream genes under normal growth conditions, suggesting that DREB2A requires posttranslational modification for activation, but the activation mechanism has not been clarified. DREB2A domain analysis using Arabidopsis protoplasts identified a transcriptional activation domain between residues 254 and 335, and deletion of a region between residues 136 and 165 transforms DREB2A to a constitutive active form. Overexpression of constitutive active DREB2A resulted in significant drought stress tolerance but only slight freezing tolerance in transgenic Arabidopsis plants. Microarray and RNA gel blot analyses revealed that DREB2A regulates expression of many water stress–inducible genes. However, some genes downstream of DREB2A are not downstream of DREB1A, which also recognizes DRE/CRT but functions in cold stress–responsive gene expression. Synthetic green fluorescent protein gave a strong signal in the nucleus under unstressed control conditions when fused to constitutive active DREB2A but only a weak signal when fused to full-length DREB2A. The region between DREB2A residues 136 and 165 plays a role in the stability of this protein in the nucleus, which is important for protein activation.
The Molecular Basis of Temperature Compensation in the Arabidopsis Circadian Clock
Authors: Gould Peter D. , Locke James C.W. , Larue Camille , Southern Megan M. , Davis Seth J. , Hanano Shigeru , Moyle Richard , Milich Raechel , Putterill Joanna , Millar Andrew J. , Hall Anthony
Published: April 2006

Circadian clocks maintain robust and accurate timing over a broad range of physiological temperatures, a characteristic termed temperature compensation. In Arabidopsis thaliana, ambient temperature affects the rhythmic accumulation of transcripts encoding the clock components TIMING OF CAB EXPRESSION1 (TOC1), GIGANTEA (GI), and the partially redundant genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The amplitude and peak levels increase for TOC1 and GI RNA rhythms as the temperature increases (from 17 to 27°C), whereas they decrease for LHY. However, as temperatures decrease (from 17 to 12°C), CCA1 and LHY RNA rhythms increase in amplitude and peak expression level. At 27°C, a dynamic balance between GI and LHY allows temperature compensation in wild-type plants, but circadian function is impaired in lhy and gi mutant plants. However, at 12°C, CCA1 has more effect on the buffering mechanism than LHY, as the cca1 and gi mutations impair circadian rhythms more than lhy at the lower temperature. At 17°C, GI is apparently dispensable for free-running circadian rhythms, although partial GI function can affect circadian period. Numerical simulations using the interlocking-loop model show that balancing LHY/CCA1 function against GI and other evening-expressed genes can largely account for temperature compensation in wild-type plants and the temperature-specific phenotypes of gi mutants.