bluuebunny/crossref_metadata_2025 huggingface dataset:
Particle flux in the northeast Atlantic Ocean during the POMME experiment (2001): Results from mass, carbon, nitrogen, and lipid biomarkers from the drifting sediment traps
Authors: Goutx Madeleine , Guigue Catherine , Leblond Nathalie , Desnues Anne , Dufour Aurélie , Aritio Diego , Guieu Cécile
Published: July 2005

During 48 hour stations during the three Programme Océan Multidisciplinaire Méso Echelle (POMME) cruises in 2001 (late winter, spring, and late summer) at different locations within the region studied (38°–45°N, 15°–21°W), drifting sediment traps were deployed at 200 m and 400 m. Fluxes increased from late winter (POMME 1) to spring (POMME 2), with highest values in the North Atlantic gyre (109.1, 20.1, and 3.5 mg m−2 d−1 for mass, C, and N, respectively) and decreased during POMME 3 to reach threshold values (19.1 ± 6.0, 4.4 ± 1.1, and 0.7 ± 0.2 mg m−2 d−1, respectively). Lipid class tracers and their fatty acid composition analyzed by gaseous chromatography were used to assess the quality and quantity of organic matter fluxes. Wide seasonal variability was observed in biogenic lipid fluxes (0.42 ± 0.19 and 0.39 ± 0.13 mg m−2 d−1, 1.78 ± 1.08 and 0.69 ± 0.56 mg m−2 d−1, and 0.71 ± 0.14 and 0.45 mg m−2 d−1 on average at 200 m and 400 m during late winter, spring, and late summer, respectively) in relation with the development of the spring phytoplankton bloom. In a northern persistent anticyclonic eddy a major export of algal matter occurred through zooplankton activity. In contrast with this pattern, the southernmost anticyclonic eddy exhibited the lowest particle fluxes in relation to the low productivity and the high bacterial carbon demand prevailing in the surface waters. In the main cyclonic structure (C4) and the saddle zone (during POMME 2) the pattern of lipid biotracers reflected the permanence of a zooplankton community and likely advective transfer of matter between 43.5°N and 42°N through subsurface water circulation.
Modeling the middle Pliocene climate with a global atmospheric general circulation model
Authors: Jiang Dabang , Wang Huijun , Ding Zhongli , Lang Xianmei , Drange Helge
Published: July 2005

A new climate simulation for the middle Pliocene (ca. 3 Ma BP) is performed by a global grid‐point atmospheric general circulation model developed at the Institute of Atmospheric Physics (IAP AGCM) with boundary conditions provided by the U. S. Geological Survey's Pliocene Research, Interpretations, and Synoptic Mapping (PRISM) group. It follows that warmer and slightly wetter conditions dominated at the middle Pliocene with a globally annual mean surface temperature increase of 2.60°C, and an increase in precipitation of 4.0% relative to today. At the middle Pliocene, globally annual terrestrial warming was 1.86°C, with stronger warming toward high latitudes. Annual precipitation enhanced notably at high latitudes, with the augment reaching 33.5% (32.5%) of the present value at 60–90°N (60–90°S). On the contrary, drier conditions were registered over most parts at 0–30°N, especially in much of East Asia and the northern tropical Pacific. In addition, both boreal summer and winter monsoon significantly decreased in East Asia at the middle Pliocene. It is indicated that the IAP AGCM simulation is generally consistent with the results from other atmospheric models and agrees well with available paleoclimatic reconstructions in East Asia. Additionally, it is further revealed that the PRISM warmer sea surface temperature and reduced sea ice extent are main factors determining the middle Pliocene climate. The simulated climatic responses arising from the PRISM reconstructed vegetation and continental ice sheet cannot be neglected on a regional scale at mid to high latitudes (like over Greenland and the Qinghai‐Tibetan Plateau, and around the circum‐Antarctic) but have little influence on global climate.
Convection‐induced gravity waves observed by the Equatorial Atmosphere Radar (0.20°S, 100.32°E) in Indonesia
Authors: Dhaka S. K. , Yamamoto M. K. , Shibagaki Y. , Hashiguchi H. , Yamamoto M. , Fukao S.
Published: July 2005

Two days of continuous data acquired using the Equatorial Atmosphere Radar (EAR), Boundary Layer Radar (BLR), X‐band radar, radiosonde and other collocated facilities were analyzed to demonstrate the relationship between the evolution of strong convection and its role in forcing gravity waves that penetrate from the troposphere into the lower stratosphere. Vertical winds in the troposphere and lower stratosphere were strongly modulated for about 6–8 hours by each convection event during the period 10–11 April 2004. Temporal and spatial structure of momentum flux anomalies showed development from sources located near the middle troposphere. These anomalies developed due to convection‐induced gravity waves, and were marginally biased in the meridional direction. Radiosonde observations showed that atmospheric stability and gradual increase in vertical wind shear above convection played a key role in filtering the waves and modifying their vertical wavelength (∼2 km).
Seasonal transition of predominant precipitation type and lightning activity over tropical monsoon areas derived from TRMM observations
Authors: Kodama Yasu‐Masa , Ohta Akihiro , Katsumata Masaki , Mori Shuichi , Satoh Shinsuke , Ueda Hiroaki
Published: July 2005

Monthly statistics from TRMM‐PR and LIS observations for the three years 1998 to 2000 describe large‐scale features in rainfall and lightning activity during pre‐monsoon and monsoon periods of the Asian and South American summer monsoons. Heavy (∼5–10 mm/day) pre‐monsoon rainfall in the one or two months before onset was widespread mainly over land. Pre‐monsoon rainfall was highly convective and characterized by active lightning, a high ratio of convective rain, and high echo tops. After onset, in contrast, intense rains also occurred over the ocean and land, however, convective intensity over land was diminished. Lightning activity was suppressed over the Amazon basin and Bangladesh during the latter half of the summer monsoon.
Arctic Oscillation–induced variability in satellite‐derived tropospheric ozone
Authors: Creilson John K. , Fishman Jack , Wozniak Amy E.
Published: July 2005

The Arctic Oscillation (AO) has been identified as the dominant mode of near‐surface climate variability in the Northern Hemisphere. In this study, we examine the interaction between the AO and the distribution of tropospheric ozone derived from satellite observations. Our analysis shows that there is a statistically significant correlation between the AO and the springtime tropospheric ozone distribution over the northeastern Atlantic, but not over the Pacific. This finding is consistent with our understanding of the differing effect that the AO has on the Atlantic versus Pacific basins and the strong influence that the El Niño phenomenon has in the Pacific. The insight gained from this study will contribute to the growing use of teleconnections as a forecast tool, providing insight into the interaction between prevailing meteorological conditions and the formation of significant pollution events.
Localization of seismic coda at Merapi volcano (Indonesia)
Authors: Friedrich C. , Wegler U.
Published: July 2005

The energy of the seismic coda generated by multiple scattering at small scale heterogeneities in the Earth is generally uniformly distributed in space at some late lapse time. 3‐component seismogram envelopes of volcano tectonic B‐type earthquakes recorded at Merapi volcano, on the contrary, show a systematic decrease of the coda amplitude with distance from the summit of the volcano. We present two different models to explain this observation. In the first model seismic energy transport is described as a diffusion process and the observed coda localization is explained by an inhomogeneous distribution of the diffusion coefficient (D = D(r)). As a simple analytical model we use a strongly scattering cylinder (representing the volcano) embedded in a homogeneous half‐space (representing the surrounding crust). In the second model we assume the disorder within the strato volcano to be so large that diffusion theory breaks down and a transition to the so called ‘Anderson localization regime’ occurs. This model predicts a concentration of seismic energy near the source region and can thus also explain the observed coda localization.
Responses of the Kuroshio and the Kuroshio Extension to global warming in a high‐resolution climate model
Authors: Sakamoto Takashi T. , Hasumi Hiroyasu , Ishii Masayoshi , Emori Seita , Suzuki Tatsuo , Nishimura Teruyuki , Sumi Akimasa
Published: July 2005

Using a high‐resolution atmosphere–ocean coupled climate model, responses of the Kuroshio and the Kuroshio Extension (KE) to global warming are investigated. In a climate change experiment with atmospheric CO2 concentration ideally increased by 1% year−1, the current velocity of the Kuroshio and KE increases, while the latitude of the Kuroshio separation to the east of Japan does not change significantly. The increase of the current velocity is up to 0.3 m s−1 at 150°E. This acceleration of the Kuroshio and KE is due to changes in wind stress over the North Pacific and consequent spin‐up of the Kuroshio recirculation gyre. The acceleration of the currents may affect sea level along the southern coast of Japan and northward heat transport under global warming.
Differences in the spectra of anomalous cosmic ray helium nuclei in two solar magnetic polarity cycles
Authors: Webber W. R. , Cummings A. C. , Stone E. C. , McDonald F. B. , Lal N. , Heikkila B.
Published: July 2005

We compare the spectra of anomalous He nuclei measured in the heliosphere by the IMP, Voyager, and Pioneer spacecraft at heliospheric distances ranging from 1 to over 80 AU in the time period from 1977 to 2003. Striking differences in the energy spectra of these nuclei are found between positive and negative solar magnetic polarity cycles. These differences are such that the spectra observed in negative polarity cycles appear to be greatly deficient in particles with energies of less than ∼15 MeV but have an excess intensity above >25 MeV, relative to the spectra observed in positive cycles. These spectral differences are complex and may be related to both solar modulation effects inside of the heliospheric termination shock as well as differences occurring at or near the termination shock itself. At the modulation minimum in 1998 when V2 was at a distance of 56 AU and V1 at 71 AU, a high intensity of low‐energy anomalous He particles was observed with a peak in the spectrum at ∼5 MeV/nuc. In late 2001 after the solar magnetic polarity had changed from positive to negative and the 11‐year solar modulation had increased, the previous high intensities of the anomalous He nuclei seen in 1998 were greatly reduced at both V1 and V2, and the energy of the peak intensity had moved up to ∼20–25 MeV/nuc. However, in both polarity periods the highest‐energy part of this spectrum above ∼30 MeV/nuc is similar with a slope of −2.8 ± 0.2. The details of these complex spectral changes are described in this paper.
Electronic structure and magnetic properties of small manganese oxide clusters
Authors: Han Myung Joon , Ozaki Taisuke , Yu Jaejun
Published: July 2005

To investigate the electronic structure and magnetic properties of manganese oxide clusters, we carried out first-principles electronic structure calculations for small MnO clusters. Among various structural and magnetic configurations of the clusters, the bulklike [111]-antiferromagnetic ordering is found to be favored energetically, while the surface atoms of the clusters exhibit interesting electronic and magnetic characteristics which are different from their bulk ones. The distinct features of the surface atoms are mainly attributed to the reduction of Mn coordination numbers and the bond-length contractions in the clusters, which may serve as a key factor for the understanding of physical and chemical properties of magnetic oxide nanoparticles.
Gas-phase electronic spectra of C18 and C22 rings
Authors: Boguslavskiy A. E. , Ding H. , Maier J. P.
Published: July 2005

The electronic spectra of C18 and C22 in the 15150–36900cm−1 range have been detected in the gas phase by a mass-selective resonant two-color two-photon ionization technique coupled to a laser ablation source. The spectra were assigned to several electronic systems of monocyclic cumulenic isomers with a D9h symmetry for C18 and D11h for C22, based on time-dependent-density-functional calculations and reactivity with respect to H2. The best cooling conditions were achieved with Kr as the buffer gas, and the origin of the Ã1A2″←X̃1A1′ transition of C18 at 592.89nm shows a pair of 1cm−1 broadbands spaced by 1.5cm−1. The next electronic transitions exhibited much broader, ∼30 (in the visible) to 200cm−1 (in ultraviolet range), features. The spectrum of C22 exhibits an absorption pattern similar to C18, except that the narrow features to the red are missing; the oscillator strength of the Ã←X̃ transition is predicted to be low.
Molecular modeling of water diffusion in amorphous SiC
Authors: He Haiying , Deshpande Mrinalini , Brown Richard E. , Pandey Ravindra , Pernisz Udo C.
Published: July 2005

The diffusion of water in amorphous SiC (a-SiC) was investigated by molecular modeling methods based on density functional theory. It was assumed that the structure of a-SiC at the molecular level can be described by a model that takes into account a distribution of cage structures which consist of SiC units forming n-member rings from a suitable precursor in a chemical vapor deposition process. Electronic structure calculations are then performed to determine the energy barrier that the water molecule encounters when it penetrates through SiC rings of various sizes. It has been found that along its diffusion path through the SiC network the water molecule neither breaks up nor attaches itself to the SiC network and the energy barrier for diffusion depends mainly on the local SiC ring topology.
Existence theorems for two-fluid magnetohydrodynamics
Authors: Núñez Manuel
Published: July 2005

The description of a plasma as composed by two types of fluids, formed by ions and electrons, is more complete than the classical one-fluid magnetohydrodynamics (MHD) model and it has proved necessary to explain the phenomena of fast magnetic reconnection. We prove a finite-time theorem of existence and uniqueness of solutions for this system for either Dirichlet or periodic boundary conditions in dimension three. It turns out that the regularity estimates for the magnetic field are finer than the MHD ones.
Existence and regularity for an energy maximization problem in two dimensions
Authors: Kamvissis Spyridon , Rakhmanov Evguenii A.
Published: July 2005

We consider the variational problem of maximizing the weighted equilibrium Green’s energy of a distribution of charges free to move in a subset of the upper half-plane, under a particular external field. We show that this problem admits a solution and that, under some conditions, this solution is an S-curve (in the sense of Gonchar-Rakhmanov). The above problem appears in the theory of the semiclassical limit of the integrable focusing nonlinear Schrödinger equation. In particular, its solution provides a justification of a crucial step in the asymptotic theory of nonlinear steepest descent for the inverse scattering problem of the associated linear non-self-adjoint Zakharov-Shabat operator and the equivalent Riemann-Hilbert factorization problem.
Terahertz gain on intersubband transitions in multilayer delta-doped p-Ge structures
Authors: Dolguikh M. V. , Muravjov A. V. , Peale R. E. , Klimov M. , Kuznetsov O. A. , Uskova E. A.
Published: July 2005

A far-infrared laser concept based on intersubband transitions of holes in p-type periodically delta-doped semiconductor films is studied using numerical Monte Carlo simulation of hot-hole dynamics. The considered device consists of monocrystalline pure Ge layers periodically interleaved with delta-doped layers and operates with vertical hole transport in the presence of an in-plane magnetic field. Population inversion on intersubband transitions arises due to light-hole accumulation in E⊥B fields, as in the bulk p-Ge laser. However, the considered structure achieves spatial separation of hole accumulation regions from the doped layers, which reduces ionized-impurity and carrier-carrier scattering for the majority of light holes. This allows a remarkable increase of the gain in comparison with bulk p-Ge lasers. Population inversion and gain sufficient for laser operation are expected up to 77K. Test structures grown by chemical-vapor deposition demonstrate feasibility of producing the device with sufficient active thickness to allow quasioptical electrodynamic cavity solutions.
Energy levels of a nonlocal functional
Authors: Bellettini G. , De Masi A. , Presutti E.
Published: July 2005

We study the critical points of a nonlocal free energy functional. The functional has two minimizers (ground states) m(±) with zero energy. We prove that there is a first excited state identified as the instanton m̂L, and that above the energy of the instanton there is a gap. We also characterize parts of the basin of attraction of m(±) and m̂L under a dynamics associated to the free energy functional. The result completes the analysis of tunneling from m(−) to m(+).
Finite-time stochastic reduction models
Authors: Brody Dorje C. , Hughston Lane P.
Published: July 2005

A new energy-based stochastic extension of the Schrödinger equation for which the wave function collapses after the passage of a finite amount of time is proposed. An exact closed-form solution to the dynamical equation, valid for all finite-dimensional quantum systems, is presented and used to verify explicitly that reduction of the state vector to an energy eigenstate occurs. A time-change technique is introduced to construct a “clock” variable that relates the asymptotic and the finite-time collapse models by means of a nonlinear transformation.
Nonlinear fractional diffusion equation: Exact results
Authors: Lenzi E. K. , Mendes R. S. , Fa Kwok Sau , Moraes L. S. , da Silva L. R. , Lucena L. S.
Published: July 2005

The nonlinear fractional diffusion equation ∂tρ=r1−d∂rμ′{rd−1D(r,t;ρ)∂rμρν}−r1−d∂r{rd−1F(r,t)ρ}+α¯(t)ρ is studied by considering the diffusion coefficient D(r,t;ρ)=D(t)r−θργ and the external force F(r,t)=−k1(t)r+kαrα. In addition, a rich class of diffusive processes, including normal and anomalous ones, is obtained from the study present in this work.
Endothelial nitric oxide synthase is critical for ischemic remodeling, mural cell recruitment, and blood flow reserve
Authors: Yu Jun , deMuinck Ebo D. , Zhuang Zhenwu , Drinane Mary , Kauser Katalin , Rubanyi Gabor M. , Qian Hu Sheng , Murata Takahisa , Escalante Bruno , Sessa William C.
Published: July 2005

The genetic loss of endothelial-derived nitric oxide synthase (eNOS) in mice impairs vascular endothelial growth factor (VEGF) and ischemia-initiated blood flow recovery resulting in critical limb ischemia. This result may occur through impaired arteriogenesis, angiogenesis, or mobilization of stem and progenitor cells. Here, we show that after ischemic challenge, eNOS knockout mice [eNOS (-/-)] have defects in arteriogenesis and functional blood flow reserve after muscle stimulation and pericyte recruitment, but no impairment in endothelial progenitor cell recruitment. More importantly, the defects in blood flow recovery, clinical manifestations of ischemia, ischemic reserve capacity, and pericyte recruitment into the growing neovasculature can be rescued by local intramuscular delivery of an adenovirus encoding a constitutively active allele of eNOS, eNOS S1179D, but not a control virus. Collectively, our data suggest that endogenous eNOS-derived NO exerts direct effects in preserving blood flow, thereby promoting arteriogenesis, angiogenesis, and mural cell recruitment to immature angiogenic sprouts.
Drier summers cancel out the CO
2
uptake enhancement induced by warmer springs
Authors: Angert A. , Biraud S. , Bonfils C. , Henning C. C. , Buermann W. , Pinzon J. , Tucker C. J. , Fung I.
Published: July 2005

An increase in photosynthetic activity of the northern hemisphere terrestrial vegetation, as derived from satellite observations, has been reported in previous studies. The amplitude of the seasonal cycle of the annually detrended atmospheric CO
2
in the northern hemisphere (an indicator of biospheric activity) also increased during that period. We found, by analyzing the annually detrended CO
2
record by season, that early summer (June) CO
2
concentrations indeed decreased from 1985 to 1991, and they have continued to decrease from 1994 up to 2002. This decrease indicates accelerating springtime net CO
2
uptake. However, the CO
2
minimum concentration in late summer (an indicator of net growing-season uptake) showed no positive trend since 1994, indicating that lower net CO
2
uptake during summer cancelled out the enhanced uptake during spring. Using a recent satellite normalized difference vegetation index data set and climate data, we show that this lower summer uptake is probably the result of hotter and drier summers in both mid and high latitudes, demonstrating that a warming climate does not necessarily lead to higher CO
2
growing-season uptake, even in high-latitude ecosystems that are considered to be temperature limited.
The voltage-gated potassium channel Kv1.3 is highly expressed on inflammatory infiltrates in multiple sclerosis brain
Authors: Rus Horea , Pardo Carlos A. , Hu Lina , Darrah Erika , Cudrici Cornelia , Niculescu Teodora , Niculescu Florin , Mullen Katharine M. , Allie Rameeza , Guo Liping , Wulff Heike , Beeton Christine , Judge Susan I. V. , Kerr Douglas A. , Knaus Hans-Gunther , Chandy K. George , Calabresi Peter A.
Published: July 2005

Multiple Sclerosis (MS) is characterized by central nervous system perivenular and parenchymal mononuclear cell infiltrates consisting of activated T cells and macrophages. We recently demonstrated that elevated expression of the voltage-gated potassium channel, Kv1.3, is a functional marker of activated effector memory T (TEM) cells in experimental allergic encephalomyelitis and in myelin-specific T cells derived from the peripheral blood of patients with MS. Herein, we show that Kv1.3 is highly expressed in postmortem MS brain inflammatory infiltrates. The expression pattern revealed not only Kv1.3+T cells in the perivenular infiltrate but also high expression in the parenchyma of demyelinated MS lesions and both normal appearing gray and white matter. These cells were uniformly chemokine receptor 7 negative (CCR7-), consistent with an effector memory phenotype. Using double-labeling immunohistochemistry and confocal microscopy, we demonstrated colocalization of Kv1.3 with CD3, CD4, CD8, and some CD68 cells. The expression patterns mirroredin vitroexperiments showing polarization of Kv1.3 to the immunological synapse. Kv1.3 was expressed in low to moderate levels on CCR7+central memory T cells from cerebrospinal fluid, but, when these cells were stimulatedin vitro, they rapidly became Kv1.3high/CCR7-TEM, suggesting that a subset of cerebrospinal fluid cells existed in a primed state ready to become TEM. These studies provide further rationale for the use of specific Kv1.3 antagonists in MS.
Repression of phase-variable
cup
gene expression by H-NS-like proteins in
Pseudomonas aeruginosa
Authors: Vallet-Gely Isabelle , Donovan Katherine E. , Fang Rui , Joung J. Keith , Dove Simon L.
Published: July 2005

The
cupA
gene cluster of
Pseudomonas aeruginosa
encodes components of a putative fimbrial structure that enable this opportunistic human pathogen to form biofilms on abiotic surfaces. In
P. aeruginosa
,
cupA
gene expression is repressed by MvaT, a putative transcription regulator thought to belong to the H-NS family of nucleoid-associated proteins that typically function by repressing transcription. Here, we present evidence that MvaT controls phase-variable (ON/OFF) expression of the
cupA
fimbrial gene cluster. Using a directed proteomic approach, we show that MvaT associates with a related protein in
P. aeruginosa
called MvaU. Analysis with a bacterial two-hybrid system designed to facilitate the study of protein dimerization indicates that MvaT and MvaU can form both heteromeric and homomeric complexes, and that formation of these complexes is mediated through the N-terminal regions of MvaT and MvaU, both of which are predicted to adopt a coiled-coil conformation. We show further that, like MvaT, MvaU can repress phase-variable expression of the
cupA
gene cluster. Our findings suggest that fimbrial genes important for biofilm formation can be expressed in a phase-variable manner in
P. aeruginosa
, provide insight into the molecular mechanism of MvaT-dependent gene control, and lend further weight to the postulate that MvaT proteins are H-NS-like in nature.
Structure, function, and evolution of transient and obligate protein–protein interactions
Authors: Mintseris Julian , Weng Zhiping
Published: July 2005

Recent analyses of high-throughput protein interaction data coupled with large-scale investigations of evolutionary properties of interaction networks have left some unanswered questions. To what extent do protein interactions act as constraints during evolution of the protein sequence? How does the type of interaction, specifically transient or obligate, play into these constraints? Are the mutations in the binding site of an interacting protein correlated with mutations in the binding site of its partner? We address these and other questions by relying on a carefully curated dataset of protein complex structures. Results point to the importance of distinguishing between transient and obligate interactions. We conclude that residues in the interfaces of obligate complexes tend to evolve at a relatively slower rate, allowing them to coevolve with their interacting partners. In contrast, the plasticity inherent in transient interactions leads to an increased rate of substitution for the interface residues and leaves little or no evidence of correlated mutations across the interface.
Facilitated replacement of Kupffer cells expressing a paraoxonase-1 transgene is essential for ameliorating atherosclerosis in mice
Authors: Bradshaw Gary , Gutierrez Alejandra , Miyake Jon H. , Davis Kimberly R. , Li Andrew C. , Glass Christopher K. , Curtiss Linda K. , Davis Roger A.
Published: July 2005

Resident macrophages (i.e., Kupffer cells) are derived from hematopoietic stem cells (HSCs) and are primarily responsible for the removal from plasma of oxidized forms of low-density lipoprotein (LDL). The therapeutic potential of Kupffer cell expression of a transgene encoding paraoxonase-1 (PON1), whose plasma activity correlates with the protection from atherosclerosis, was examined in mice rendered atherosclerosis-susceptible through genetic deletion of the LDL receptor. Mice having their bone marrow engrafted with HSCs expressing the PON1 transgene (PON1-Tg) driven by a macrophage-specific promoter were injected i.v. with saline (vehicle only) or with gadolinium chloride (GdCl
3
), an agent that rapidly causes Kupffer cell apoptosis. One month later, GdCl
3
-facilitated Kupffer cell apoptosis increased the hepatic expression of transgenic PON1 mRNA by 9-fold. After 12 weeks of being fed a cholesterol-enriched atherogenic diet, mice injected with GdCl
3
exhibited 50% reductions in both aortic sinus atherosclerotic lesions (
P
< 0.0097) and surface lesions of the abdominal aorta (
P
< 0.006). In contrast, mice receiving HSCs expressing the PON1-Tg but not treated with GdCl
3
showed no protection from atherosclerosis. In addition, mice engrafted with HSCs not expressing the PON1-Tg but injected with GdCl
3
also showed no protection from atherosclerosis. These findings, showing that GdCl
3
-enhanced hepatic expression of the PON1-Tg is essential for reducing atherosclerosis, indicate that Kupffer cells play an important role in atherogenesis. GdCl
3
-facilated replacement of Kupffer cells may enhance the efficacy of other HSC-based gene therapies.
Permeation-driven flow in poly(dimethylsiloxane) microfluidic devices
Authors: Randall Greg C. , Doyle Patrick S.
Published: July 2005

Poly(dimethylsiloxane) is currently the material of choice for rapidly fabricating microfluidic devices. As the size of these devices decreases, a significant hydrodynamic flow is generated due to permeation of fluid through the channel walls. We develop a theoretical model verified by single bead tracking experiments, which demonstrates that large flow rates (>10 μm/s) can be passively generated in a straight microchannel filled with water. Realizing that this flow may be unwanted in some applications, we present a method to eliminate it by inhibiting mass transfer of water into the poly(dimethylsiloxane) walls. Furthermore, we explore applications to harness this passively generated flow inside a microfluidic device such as bead stacking, chemical concentration, and passive pumping.
Electrically monitoring DNA repair by photolyase
Authors: DeRosa Maria C. , Sancar Aziz , Barton Jacqueline K.
Published: July 2005

Cyclobutane pyrimidine dimers are the major DNA photoproducts produced upon exposure to UV radiation. If left unrepaired, these lesions can lead to replication errors, mutation, and cell death. Photolyase is a light-activated flavoenzyme that binds to pyrimidine dimers in DNA and repairs them in a reaction triggered by electron transfer from the photoexcited flavin cofactor to the dimer. Using gold electrodes modified with DNA duplexes containing a cyclobutane thymine dimer (T<>T), here we probe the electrochemistry of the flavin cofactor in
Escherichia coli
photolyase. Cyclic and square-wave voltammograms of photolyase deposited on these electrodes show a redox signal at 40 mV versus normal hydrogen electrode, consistent with electron transfer to and from the flavin in the DNA-bound protein. This signal is dramatically attenuated on surfaces where the π-stacking of the DNA bases is perturbed by the presence of an abasic site below the T<>T, an indication that the redox pathway is DNA-mediated. DNA repair can, moreover, be monitored electrically. Exposure of photolyase on T<>T-damaged DNA films to near-UV/blue light leads to changes in the flavin signal consistent with repair, as confirmed by parallel HPLC experiments. These results demonstrate the exquisite sensitivity of DNA electrochemistry to perturbations in base pair stacking and the applicability of this chemistry to probe reactions of proteins with DNA.
Agrin promotes synaptic differentiation by counteracting an inhibitory effect of neurotransmitter
Authors: Misgeld Thomas , Kummer Terrance T. , Lichtman Jeff W. , Sanes Joshua R.
Published: July 2005

Synaptic organizing molecules and neurotransmission regulate synapse development. Here, we use the skeletal neuromuscular junction to assess the interdependence of effects evoked by an essential synaptic organizing protein, agrin, and the neuromuscular transmitter, acetylcholine (ACh). Mice lacking agrin fail to maintain neuromuscular junctions, whereas neuromuscular synapses differentiate extensively in the absence of ACh. We now demonstrate that agrin's action
in vivo
depends critically on cholinergic neurotransmission. Using double-mutant mice, we show that synapses do form in the absence of agrin provided that ACh is also absent. We provide evidence that ACh destabilizes nascent postsynaptic sites, and that one major physiological role of agrin is to counteract this “antisynaptogenic” influence. Similar interactions between neurotransmitters and synaptic organizing molecules may operate at synapses in the central nervous system.
HIV-1 Nef down-regulates the hemochromatosis protein HFE, manipulating cellular iron homeostasis
Authors: Drakesmith Hal , Chen Nan , Ledermann Hannah , Screaton Gavin , Townsend Alain , Xu Xiao-Ning
Published: July 2005

The multifunctional Nef protein of HIV-1 is important for the progression to AIDS. One action of Nef is to down-regulate surface MHC I molecules, helping infected cells to evade immunity. We found that Nef also down-regulates the macrophage-expressed MHC 1b protein HFE, which regulates iron homeostasis and is mutated in the iron-overloading disorder hemochromatosis. In model cell lines, Nef reroutes HFE to a perinuclear structure that overlaps the trans-Golgi network, causing a 90% reduction of surface HFE. This activity requires a Src-kinase-binding proline-rich domain of Nef and a conserved tyrosine-based motif in the cytoplasmic tail of HFE. HIV-1 infection of
ex vivo
macrophages similarly down-regulates naturally expressed surface HFE in a Nef-dependent manner. The effect of Nef expression on cellular iron was explored; iron and ferritin accumulation were increased in HIV-1-infected
ex vivo
macrophages expressing wild-type HFE, but this effect was lost with Nef-deleted HIV-1 or when infecting macrophages from hemochromatosis patients expressing mutated HFE. The iron accumulation in HIV-1-infected HFE-expressing macrophages was paralleled by an increase in cellular HIV-1-gag expression. We conclude that, through Nef and HFE, HIV-1 directly regulates cellular iron metabolism, possibly benefiting viral growth.
Comparison of the complete genome sequences of
Pseudomonas syringae
pv.
syringae
B728a and pv.
tomato
DC3000
Authors: Feil Helene , Feil William S. , Chain Patrick , Larimer Frank , DiBartolo Genevieve , Copeland Alex , Lykidis Athanasios , Trong Stephen , Nolan Matt , Goltsman Eugene , Thiel James , Malfatti Stephanie , Loper Joyce E. , Lapidus Alla , Detter John C. , Land Miriam , Richardson Paul M. , Kyrpides Nikos C. , Ivanova Natalia , Lindow Steven E.
Published: July 2005

The complete genomic sequence of
Pseudomonas syringae
pv.
syringae
B728a (
Pss
B728a) has been determined and is compared with that of
P. syringae
pv.
tomato
DC3000 (
Pst
DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with
Pss
having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and
Pst
DC3000 having a more pronounced apoplastic growth habitat. The
Pss
B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the
Pst
DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to
Pss
B728a when compared with
Pst
DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences unique to
Pss
B728a when compared with
Pst
DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of
Pseudomonas aeruginosa
PAO1. Among the 976 genes of
Pss
B728a with no counterpart in
Pst
DC3000 are those encoding for syringopeptin, syringomycin, indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for
Pss
B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism.
Mid- to late-Holocene El Niño-Southern Oscillation dynamics reflected in the subtropical terrestrial realm
Authors: Donders Timme H. , Wagner Friederike , Dilcher David L. , Visscher Henk
Published: July 2005

High resolution pollen analysis of mid- to late-Holocene peat deposits from southwest Florida reveals a stepwise increase in wetland vegetation that points to an increased precipitation-driven fresh water flow during the past 5,000 years. The tight coupling between winter precipitation patterns in Florida and the strength of the El Niño-Southern Oscillation (ENSO) strongly suggests that the paleo-hydrology record reflects changes in ENSO intensity. A terrestrial subtropical record outside the Indo Pacific Warm Pool both documents ecosystem response to the known onset of modern-day ENSO periodicities, between ≈7,000 and 5,000 years B.P., and subsequent ENSO intensification after 3,500 years B.P. The observed increases in “wetness” are sustained by a gradual rise in relative sea level that prevents a return to drier vegetation through natural succession.
The molecular structure of the Toll-like receptor 3 ligand-binding domain
Authors: Bell Jessica K. , Botos Istvan , Hall Pamela R. , Askins Janine , Shiloach Joseph , Segal David M. , Davies David R.
Published: July 2005

Innate immunity is the first line of defense against invading pathogens. Toll-like receptors (TLRs) act as sentinels of the innate immune system, sensing a variety of ligands from lipopolysaccharide to flagellin to dsRNA through their ligand-binding domain that is composed of leucine-rich repeats (LRRs). Ligand binding initiates a signaling cascade that leads to the up-regulation of inflammation mediators. In this study, we have expressed and crystallized the ectodomain (ECD) of human TLR3, which recognizes dsRNA, a molecular signature of viruses, and have determined the molecular structure to 2.4-Å resolution. The overall horseshoe-shaped structure of the TLR3-ECD is formed by 23 repeating LRRs that are capped at each end by specialized non-LRR domains. The extensive β-sheet on the molecule's concave surface forms a platform for several modifications, including insertions in the LRRs and 11
N
-linked glycans. The TLR3-ECD structure indicates how LRR loops can establish distinct pathogen recognition receptors.
Nuclear DNA content of the whitefly Bemisia tabaci (Aleyrodidae: Hemiptera) estimated by flow cytometry
Authors: Brown J.K. , Lambert G.M. , Ghanim M. , Czosnek H. , Galbraith D.W.
Published: July 2005

The nuclear DNA content of the whitefly Bemisia tabaci (Gennnadius) was estimated using flow cytometry. Male and female nuclei were stained with propidium iodide and their DNA content was estimated using chicken red blood cells and Arabidopsis thaliana L. (Brassicaceae) as external standards. The estimated nuclear DNA content of male and female B. tabaci was 1.04 and 2.06 pg, respectively. These results corroborated previous reports based on chromosome counting, which showed that B. tabaci males are haploid and females are diploid. Conversion between DNA content and genome size (1 pg DNA = 980 Mbp) indicate that the haploid genome size of B. tabaci is 1020 Mbp, which is approximately five times the size of the genome of the fruitfly Drosophila melanogaster Meigen. These results provide an important baseline that will facilitate genomics-based research for the B. tabaci complex.
Development, survivorship and reproduction of Eretmocerus sp. nr furuhashii (Hymenoptera: Aphelinidae) parasitizing Bemisia tabaci (Hemiptera: Aleyrodidae) on glabrous and non-glabrous host plants
Authors: Qiu B.-L. , De Barro P.J. , Ren S.X.
Published: July 2005

The developmental, survivorship and reproductive biology of Eretmocerus sp. nr furuhashii Rose & Zolnerowich parasitizing Bemisia tabaci (Gennadius) biotype B on tomato, cucumber, eggplant and collard at 26±0.5°C was studied. The mean longevity ranged from 6.5 days on tomato to 8.1 days on collard. The mean lifetime fecundities on tomato, cucumber, eggplant and collard were 35.4, 37.3, 41.4 and 46.4 eggs, whereas the mean lifetime fertility was 20.2, 22.7, 28.3 and 33.6 offspring, respectively. Developmental time was longest on cucumber (17.1 days) and shortest on collard (15.9 days). Survival rates varied significantly across host plants. Sex ratio (♀:♂) varied from 1.71 to 1.93 across the four hosts. The intrinsic rate of increase (rm) was highest (0.157) on collard and lowest on tomato (0.133). Mean generation time (R0) ranged from 14.7 to 20.9 days. All the data demonstrated that the reproductive success and overall performance of E. sp. nr furuhashii increased as the density of leaf hairs declined. As leaf hairs play a key role in determining efficacy, it is unlikely that effective biological control of B. tabaci using E. sp. nr furuhashii will be achieved on non-glabrous crop varieties.
Anopheles (Cellia) epiroticus (Diptera: Culicidae), a new malaria vector species in the Southeast Asian Sundaicus Complex
Authors: Linton Y.-M. , Dusfour I. , Howard T.M. , L. F. Ruiz , Manh Nguyen Duc , Dinh Trung Ho , Sochanta T. , Coosemans M. , Harbach R.E.
Published: July 2005

Anopheles sundaicus species A of the Southeast Asian A. sundaicus complex is formally named Anopheles epiroticus Linton & Harbach based on DNA sequence differentiation of the whole nuclear ITS2 region and a portion of both the cytochrome b and cytochrome c oxidase I mitochondrial genes. Detailed comparative morphological studies of the adult, larval and pupal stages did not reveal any differential or diagnostic differences that reliably distinguish A. epiroticus from A. sundaicus s.s. Information is provided on the bionomics and systematics of the new species.
Restriction fragment length polymorphisms of different DNA regions as genetic markers in the hoverfly Episyrphus balteatus (Diptera: Syrphidae)
Authors: Hondelmann P. , Borgemeister C. , Poehling H.-M.
Published: July 2005

A polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis using mitochondrial (A + T-rich region; mtDNA) and genomic (zen-region; nDNA) DNA was performed on 182 female individuals of Episyrphus balteatus (DeGeer), a widespread aphidophagous hoverfly with supposed migratory behaviour. Specimens originated from 13 sampling sites in six European countries. The analyses revealed 12 and 18 haplotypes, respectively, for the two DNA types, several of them with a wide distribution, although seven and eight haplotypes, respectively, occurred only in one location. In contrast to other studies on mobile insects, the genetic diversity was relatively high. However, lack of population subdivision, low genetic distances between populations, the very high gene flow rates, and the complete lack of isolation by distance suggest that E. balteatus populations are largely connected and that there is an absence of large-scale geographic structuring. These results support the hypothesis that E. balteatus is a migratory hoverfly species, capable of moving over large distances. These findings related to the seasonal migrations of this species are discussed.
Gene-flow between populations of cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is highly variable between years
Authors: Scott K.D. , Wilkinson K.S. , Lawrence N. , Lange C.L. , Scott L.J. , Merritt M.A. , Lowe A.J. , Graham G.C
Published: July 2005

Both large and small scale migrations of Helicoverpa armigera Hübner in Australia were investigated using AMOVA analysis and genetic assignment tests. Five microsatellite loci were screened across 3142 individuals from 16 localities in eight major cotton and grain growing regions within Australia, over a 38-month period (November 1999 to January 2003). From November 1999 to March 2001 relatively low levels of migration were characterized between growing regions. Substantially higher than average gene-flow rates and limited differentiation between cropping regions characterized the period from April 2001 to March 2002. A reduced migration rate in the year from April 2002 to March 2003 resulted in significant genetic structuring between cropping regions. This differentiation was established within two or three generations. Genetic drift alone is unlikely to drive genetic differentiation over such a small number of generations, unless it is accompanied by extreme bottlenecks and/or selection. Helicoverpa armigera in Australia demonstrated isolation by distance, so immigration into cropping regions is more likely to come from nearby regions than from afar. This effect was most pronounced in years with limited migration. However, there is evidence of long distance dispersal events in periods of high migration (April 2001–March 2002). The implications of highly variable migration patterns for resistance management are considered.
Hospital mealtimes: action research for change?
Authors: Dickinson Angela , Welch Carol , Ager Laurie , Costar Aileen
Published: July 2005

Poor nutritional care within the hospital setting continues despite decades of work chronicling and measuring the problems. To address the problem changes in practice have been attempted to improve the patients’ experience of mealtimes. In order to implement patient-centred mealtimes for older patients by changing the focus from institutional convenience to one that focuses on the requirements of the patients, an action research approach has been used that focuses on action and change, and thus appears to have much to offer those who seek to change practice. The present paper focuses on the first two phases in a three-phase approach. In phase one the nature of everyday mealtime care and the wider context are explored using focus groups, interviews and observations. The data fall into three main themes that all impact on patients’ experiences of mealtimes: institutional and organisational constraints; mealtime care and nursing priorities; eating environment. Following feedback of phase 1 findings to staff and identification of areas of concern a model of practice development was selected to guide the change process of the second phase. Changes to mealtime nursing practice and the ward environment have been made, indicating that action research has the potential to improve the mealtime care of patients.
Biochemical homeostasis and body growth are reliable end points in clinical nutrition trials
Authors: Heird William C.
Published: July 2005

Studies of biochemical homeostasis and/or body growth have been included as outcome variables in most nutrition trials in paediatric patients. Moreover, these outcome variables have provided important insights into the nutrient requirements of infants and children, and continue to do so. Examples of the value of such studies in improving parenteral nutrition, in defining essential fatty acid metabolism and requirements of infants and in defining the protein and energy needs of low-birth-weight infants are discussed. Data from such studies have helped to define the mechanism of metabolic acidosis and hyperammonaemia associated with the use of early crystalline amino acid mixture and, hence, how to prevent these disorders. Such studies have allowed the development of parenteral amino acid mixtures that circumvent grossly abnormal plasma concentrations of most amino acids and appear to be utilized more efficiently. These studies have also helped define micronutrient requirements, including requirements for several such nutrients that had not been previously recognized as essential (e.g. Cr, Se, Mo, α-linolenic acid). Studies of body growth have been particularly valuable in defining the nutritional requirements of low-birth-weight infants. Finally, studies of metabolic homeostasis coupled with more sophisticated metabolic studies have provided considerable insight into the metabolism of the essential fatty acids, linoleic acid (18:2n-6) and α-linolenic acid (18:3n-3). Although such studies have not defined the amount of the longer-chain PUFA synthesized from each of these essential fatty acids, i.e. arachidonic acid (20:4n-6) and DHA (22:6n-3), they have shown that the rates of conversion are extremely variable from infant to infant, suggesting a possible explanation of why some studies show developmental advantages from intake of these fatty acids while others do not.