bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation and relaxation of excited states in solution: A new time dependent polarizable continuum model based on time dependent density functional theory
Authors: Caricato Marco , Mennucci Benedetta , Tomasi Jacopo , Ingrosso Francesca , Cammi Roberto , Corni Stefano , Scalmani Giovanni
Published: March 2006

In this paper a novel approach to study the formation and relaxation of excited states in solution is presented within the integral equation formalism version of the polarizable continuum model. Such an approach uses the excited state relaxed density matrix to correct the time dependent density functional theory excitation energies and it introduces a state-specific solvent response, which can be further generalized within a time dependent formalism. This generalization is based on the use of a complex dielectric permittivity as a function of the frequency, ε̂(ω). The approach is here presented in its theoretical formulation and applied to the various steps involved in the formation and relaxation of electronic excited states in solvated molecules. In particular, vertical excitations (and emissions), as well as time dependent Stokes shift and complete relaxation from vertical excited states back to ground state, can be obtained as different applications of the same theory. Numerical results on two molecular systems are reported to better illustrate the features of the model.
Calculation of solid-liquid interfacial free energy: A classical nucleation theory based approach
Authors: Bai Xian-Ming , Li Mo
Published: March 2006

We present a simple approach to calculate the solid-liquid interfacial free energy. This new method is based on the classical nucleation theory. Using the molecular dynamics simulation, we employ spherical crystal nuclei embedded in the supercooled liquids to create an ideal model of a homogeneous nucleation. The interfacial free energy is extracted by fitting the relation between the critical nucleus size and the reciprocal of the critical undercooling temperature. The orientationally averaged interfacial free energy is found to be 0.302±0.002 (in standard LJ unit). The temperature dependence of the interfacial free energy is also obtained in this work. We find that the interfacial free energy increases slightly with increasing temperature. The positive temperature coefficient of the interfacial free energy is in qualitative agreement with Spaepen’s analysis [Solid State Phys. 47, FS181 (1994)] and Turnbull’s empirical estimation [J. Appl. Phys. 21, 1022 (1950)].
Multichannel time-of-flight technique for plasma potential profile measurements by heavy ion beam diagnostic on the tokamak ISTTOK
Authors: Nedzelskiy I. S. , Malaquias A. J. , Tashchev Yu. I. , Silva C. , Figueiredo H. , Fernandes H. , Varandas C. A. F.
Published: March 2006

This article summarizes the current implementation of the time-of-flight (TOF) energy analysis for plasma potential measurements by the heavy ion beam diagnostic of the tokamak ISTTOK. The technique [beam modulation, TOF energy analyzer (TOFEA), and data acquisition system], the calibration procedures, the method used to obtain the plasma potential, and the resolution of the measurements are described in detail. The main TOFEA advantage is the possibility to realize simultaneous multichannel detection with a multiple cell array detector. The first measurements of the plasma potential profile obtained with a four-channel TOFEA are presented.
Novel passive spectroscopy system for absolutely referenced plasma rotation measurements in clean plasmas
Authors: Rapisarda D. , Zurro B. , Baciero A. , Tribaldos V.
Published: March 2006

A novel method for measuring absolutely calibrated rotation velocities in fusion plasmas by means of passive spectroscopy, using a single plasma view, is presented. The method consists of simultaneously recording the emission lines from the plasma and from a calibration lamp by means of a double fiber-fiber guide. A software simultaneously analyzes the plasma and calibration lines, which are obtained with a high-resolution spectrometer equipped with an intensified linear detector array, and provides absolute rotation measurements. Experimental results of carbon impurity ion rotation measured in the TJ-II stellarator are reported, demonstrating an accuracy of better than 0.3km∕s.
Subpicosecond high-power mode locking using flared waveguide monolithic quantum-dot lasers
Authors: Thompson M. G. , Rae A. , Sellin R. L. , Marinelli C. , Penty R. V. , White I. H. , Kovsh A. R. , Mikhrin S. S. , Livshits D. A. , Krestnikov I. L.
Published: March 2006

Ultrashort pulse, high-power mode locking is demonstrated in InGaAs quantum dot lasers using a flared waveguide laser incorporating a narrow waveguide sections acting as both a mode filter and saturable absorber. 24GHz mode locking with 780fs pulses and 500mW peak powers are demonstrated at an emissions wavelength of 1.3μm.
Photoemission investigation on copper phthalocyanine:fullerene blend film
Authors: Lozzi L. , Santucci S. , La Rosa S.
Published: March 2006

The electronic structure of thin blend films composed by copper phthalocyanine (CuPc) and fullerene (C60) have been studied by soft x-ray photoemission spectroscopy. Several samples with different C60∕CuPc concentration ratios were prepared by thermal evaporation in ultrahigh vacuum conditions. As the C60 concentration increases, strong shifts of the CuPc highest occupied molecular orbital (HOMO) level towards the Fermi level and of the C60 HOMO level to higher binding energies have been observed. This experimental result suggests that there is a sizeable interaction between CuPc and C60 molecules that can be interpreted in terms of a charge transfer from C60 to CuPc. These shifts play an important role in the application of the CuPc:C60 blend films for instance in the construction of solar cells on flexible substrates.
Tapered-amplified antireflection-coated laser diodes for potassium and rubidium atomic-physics experiments
Authors: Nyman R. A. , Varoquaux G. , Villier B. , Sacchet D. , Moron F. , Le Coq Y. , Aspect A. , Bouyer P.
Published: March 2006

We present a system of room-temperature extended-cavity grating-diode lasers for production of light in the range of 760–790nm. The extension of the tuning range towards the blue is permitted by the weak feedback in the cavity: the diodes are antireflection coated, and the grating has just 10% reflectance. The light is then amplified using semiconductor tapered amplifiers to give more than 400mW of power. The outputs are shown to be suitable for atomic-physics experiments with potassium (767nm), rubidium (780nm), or both, of particular relevance to doubly degenerate boson-fermion mixtures.
A near-field scanned microwave probe for spatially localized electrical metrology
Authors: Talanov Vladimir V. , Scherz André , Moreland Robert L. , Schwartz Andrew R.
Published: March 2006

We have developed a near-field scanned microwave probe with a sampling volume of approximately 10μm in diameter, which is the smallest one achieved in near-field microwave microscopy. This volume is defined to confine >99% of the probe’s net sampling reactive energy, thus making the response virtually independent of the sample properties outside of this region. The probe is formed by a 4GHz balanced stripline resonator tapered down to a few-micrometer tip size and provides noncontact, noninvasive measurement capability. It is uniquely suited for spatially localized electrical metrology applications, such as evaluation of Cu/low-k interconnects on semiconductor production wafers.
Frequency-controlled interaction between magnetic microspheres
Authors: Zhang Xu , Liu Liyu , Qi Yabing , Liu Zhengyou , Shi Jing , Wen Weijia
Published: March 2006

We show that the interaction between magnetic microspheres, fabricated by coating glass microspheres with a layer of nickel, can be controlled by varying the frequency of the applied magnetic field. By floating two such microspheres on the meniscus of glycerin and applying an ac magnetic field, it is shown that the spheres achieve an equilibrium separation owing to the balance between the repulsive dipole-dipole interaction and the “attractive” force due to the weight of the particles. A monotonic decrease of the magnetorheological effect with frequency increasing is observed. Good agreement between theory and experiment is observed.
Electrically small isotropic three-dimensional magnetic resonators for metamaterial design
Authors: Baena J. D. , Jelinek L. , Marqués R. , Zehentner J.
Published: March 2006

The problem of the design of artificial magnetic resonators for isotropic metamaterials is addressed. The internal symmetries that ensure an isotropic behavior of such resonators are analyzed and some specific designs based on the proper arrangement of modified split ring resonators are proposed. These proposals are validated by electromagnetic simulations and experiments. The reported results are likely to have applications in the design of devices such as negative refractive index materials, superlenses, and metasurfaces with isotropic response.
Ambipolar organic field-effect transistors with air stability, high mobility, and balanced transport
Authors: Wang Haibo , Wang Jun , Yan Xuanjun , Shi Jianwu , Tian Hongkun , Geng Yanhou , Yan Donghang
Published: March 2006

Ambipolar organic field-effect transistors (OFETs) based on the organic heterojunction of copper-hexadecafluoro-phthalocyanine (F16CuPc) and 2,5-bis(4-biphenylyl) bithiophene (BP2T) were fabricated. The ambipolar OFETs eliminated the injection barrier for the electrons and holes though symmetrical Au source and drain electrodes were used, and exhibited air stability and balanced ambipolar transport behavior. High field-effect mobilities of 0.04cm2∕Vs for the holes and 0.036cm2∕Vs for the electrons were obtained. The capacitance-voltage characteristic of metal-oxide-semiconductor (MOS) diode confirmed that electrons and holes are transported at F16CuPc and BP2T layers, respectively. On this ground, complementary MOS-like inverters comprising two identical ambipolar OFETs were constructed.
Electrically addressing a single self-assembled quantum dot
Authors: Ellis D. J. P. , Bennett A. J. , Shields A. J. , Atkinson P. , Ritchie D. A.
Published: March 2006

We report on the use of an aperture in an aluminum oxide layer to restrict current injection into a single self-assembled InAs quantum dot from an ensemble of such dots within a large mesa. The insulating aperture is formed through the wet oxidation of a layer of AlAs. Under photoluminescence we observe that only one quantum dot in the ensemble exhibits a Stark shift, and that the same single dot is visible under electroluminescence. Autocorrelation measurements performed on the electroluminescence confirm that we are observing emission from a single quantum dot.
Wide range pressure sensor based on a piezoelectric bimorph microcantilever
Authors: Mortet V. , Petersen R. , Haenen K. , D’Olieslaeger M.
Published: March 2006

Since the development of the atomic force microscope, interest in microfabricated cantilevers has grown. Cantilevers are excellent micromechanical sensors. In this work, we use a commercially available piezoelectric bimorph cantilever as pressure and temperature sensor. The piezoelectric layer acts as both sensor and actuator. The sensor detects the change in the resonance frequencies due to the drag force of the surrounding gas. The frequency shift of the resonant modes is measured as a function of the pressure and the temperature. The results show that both pressure and temperature can be measured simultaneously using the piezoelectric bimorph cantilever’s resonant frequencies.
Oxidation of Si(001) with a hyperthermal O-atom beam at room temperature: Suboxide distribution and residual order structure
Authors: Tagawa Masahito , Sogo Chie , Yokota Kumiko , Yoshigoe Akitaka , Teraoka Yuden , Shimura Takayoshi
Published: March 2006

Synchrotron radiation photoelectron spectroscopy (SR-PES) and crystal truncation rod (CTR) scattering profiles were used to investigate an ultrathin SiO2 overlayer on a Si(001) surface formed by a 5eV O-atom beam at room temperature. The SR-PES spectra indicated that the suboxides in the O-atom-beam oxidized film were concentrated on the SiO2 surface rather than at the Si∕SiO2 interface. The CTR scattering data of the O-atom-beam oxidation film had a lower intensity near (11L) (0.3<L<0.8), suggesting a lower content of the SiO2 ordered structure in the oxide film. An inverse diffusion of the interstitial Si atoms in the oxidation kinetics can explain the data.
Optical waveguides via viscosity-mismatched microfluidic flows
Authors: Brown Matt , Vestad Tor , Oakey John , Marr David W. M.
Published: March 2006

This letter describes all-liquid optical waveguiding within microfluidic channels that employs viscosity-mismatched core and cladding fluids. Efficient optical coupling is achieved through superior control of fluid flow profiles obtained via hydrodynamic focusing and models describing the control of the viscosity-mismatched, graded index fluid waveguides are presented. As a demonstration of this approach, a fluorescence quantification assay is performed using dyed colloidal particles.
Observation of deep level defects within the waveguide of red-emitting high-power diode lasers
Authors: Ropers Claus , Tien Tran Quoc , Lienau Christoph , Tomm Jens W. , Brick Peter , Linder Norbert , Mayer Bernd , Müller Martin , Tautz Sönke , Schmid Wolfgang
Published: March 2006

The waveguides of 650nm emitting high-power laser diodes are analyzed regarding the presence of deep level defects by photoelectrical techniques, namely, photocurrent spectroscopy, laser beam induced current, and near-field optical beam induced current (NOBIC). Deep level configurations in pristine devices and the kinetics of defect creation during device operation are monitored and discussed. The localization of the defects within the epitaxial layer sequence is done by NOBIC. We show that light, which is confined within the laser waveguide, interacts with the deep level defects detected. This demonstrates that the presence of deep level defects directly affects the device properties.
Future Directions in Astronomy Visualization
Authors: Fluke Christopher J. , Bourke Paul D. , O'Donovan David
Published: March 2006

Despite the large budgets spent annually on astronomical research equipment such as telescopes, instruments, and supercomputers, the general trend is to analyze and view the resulting datasets using small, two-dimensional displays. We report here on alternative advanced image displays, with an emphasis on displays that we have constructed, including stereoscopic projection, multiple projector tiled displays, and a digital dome. These displays can provide astronomers with new ways of exploring the terabyte and petabyte datasets that are now regularly being produced from all-sky surveys, high-resolution computer simulations, and Virtual Observatory projects. We also present a summary of the Advanced Image Displays for Astronomy (AIDA) survey which we conducted from 2005 March–May, in order to raise some issues pertinent to the current and future level of use of advanced image displays.
Radio Detection of Colliding Wind Binaries
Authors: Benaglia Paula , Koribalski Bärbel , Colombo Juan F. Albacete
Published: March 2006

Four massive, early-type stars, three of which are confirmed binaries, have been observed with the Australia Telescope Compact Array at 1.4, 2.4, 4.8, and 8.6 GHz. The earliest star cataloged so far, HD 93129A, was also observed at 17.8 and 24.5 GHz. Here we present an analysis of the spectra as well as the structure of the stellar systems. All four spectra show clear evidence of non-thermal emission, indicative of a binary system with a colliding wind region. We discuss the magnetic field of the emitting region of HD 93129A and make predictions on the radiation at high energies. Archive X-ray observations towards the target sources are also investigated and interpreted in the light of the non-thermal emission detected.
A physical model of axonal damage due to oxidative stress
Authors: Counterman Anne E. , D'Onofrio Terrence G. , Andrews Anne Milasincic , Weiss Paul S.
Published: March 2006

Oxidative damage is implicated in the pathogenesis of neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's diseases, and in normal aging. Here, we model oxidative stress in neurons using photogenerated radicals in a simplified membrane-encapsulated microtubule system. Using fluorescence and differential interference contrast microscopies, we monitor photochemically induced microtubule breakdown on the supported region of membrane in encapsulating synthetic liposomes as a function of lipid composition and environment. Degradation of vesicle-encapsulated microtubules is caused by attack from free radicals formed upon UV excitation of the lipid-soluble fluorescent probe, 6-(9-anthroyloxy)stearic acid. Probe concentration was typically limited to a regime in which microtubule degradation was slow, and microtubule degradation was monitored by changes in the observed protrusion of the membrane surface. The kinetics of microtubule degradation are influenced by lipid saturation level, fluorescent probe concentration, and the presence of free-radical scavengers. This system is sufficient to reproduce some degenerative morphologies found
in vivo
.
The zebrafish homologue of mammalian chimerin Rac-GAPs is implicated in epiboly progression during development
Authors: Leskow Federico Coluccio , Holloway Beth A. , Wang HongBin , Mullins Mary C. , Kazanietz Marcelo G.
Published: March 2006

In this paper, we report an
in vivo
model for the chimerins, a family of Rac GTPase-activating proteins (Rac-GAPs) that are uniquely regulated by the lipid second messenger diacylglycerol and have been implicated in the control of actin dynamics, migration, and proliferation. We cloned the zebrafish homologue of mammalian α2-chimerin (
chn1
) and determined that it possesses Rac-GAP activity and a C1 domain with phorbol ester/diacylglycerol-binding capability.
chn1
morpholino knockdown embryos exhibit severe abnormalities, including the development of round somites, lack of yolk extension, and a kinked posterior notochord. These zebrafish morphants show Rac hyperactivation and progress faster through epiboly, leading to tailbud-stage embryos that have a narrow axis and an enlarged tailbud with expanded
bmp4
and
shh
expression. Phenotypic rescue was achieved by mRNA microinjection of
chn1
or an active chimerin Rac-GAP domain into the yolk syncytial layer but not by a chn1 mutant deficient in Rac-GAP activity, suggesting that the lack of
chn1
Rac-GAP activity in the yolk syncytial layer was causative of the misbalance in morphogenetic movements. Our results reveal a crucial role for
chn1
in early development and implicate Rac as a key regulator of morphogenetic movements during zebrafish epiboly.
Virulence of
Leishmania major
in macrophages and mice requires the gluconeogenic enzyme fructose-1,6-bisphosphatase
Authors: Naderer Thomas , Ellis Miriam A. , Sernee M. Fleur , De Souza David P. , Curtis Joan , Handman Emanuela , McConville Malcolm J.
Published: March 2006

Leishmania
are protozoan parasites that replicate within mature phagolysosomes of mammalian macrophages. To define the biochemical composition of the phagosome and carbon source requirements of intracellular stages of
L. major
, we investigated the role and requirement for the gluconeogenic enzyme fructose-1,6-bisphosphatase (FBP).
L. major
FBP was constitutively expressed in both extracellular and intracellular stages and was primarily targeted to glycosomes, modified peroxisomes that also contain glycolytic enzymes. A
L. major FBP
-null mutant was unable to grow in the absence of hexose, and suspension in glycerol-containing medium resulted in rapid depletion of internal carbohydrate reserves.
L. major
Δ
fbp
promastigotes were internalized by macrophages and differentiated into amastigotes but were unable to replicate in the macrophage phagolysosome. Similarly, the mutant persisted in mice but failed to generate normal lesions. The data suggest that
Leishmania
amastigotes reside in a glucose-poor phagosome and depend heavily on nonglucose carbon sources. Feeding experiments with [
13
C]fatty acids showed that fatty acids are poor gluconeogenic substrates, indicating that amino acids are the major carbon source
in vivo
. The need for amino acids may have forced
Leishmania
spp. to adapt to life in the mature phagolysosome.
Messages diffuse faster than messengers
Authors: Pando Bernardo , Dawson Silvina Ponce , Mak Don-On Daniel , Pearson John E.
Published: March 2006

In many cell-signaling pathways, information is transmitted by the diffusion of messenger molecules. Diffusion coefficients characterize the messenger's spatial range and the characteristic times of signal propagation. Inside cells, particles usually diffuse in the presence of immobile binding sites (or traps). It is well known that binding to traps results in an effective diffusion coefficient that is smaller than the free coefficient in media free of traps. To measure effective diffusion coefficients in cells, “tagged” particles are often used. Radioactive calcium was used in a giant squid axon and in cytosolic extracts of
Xenopus laevis
oocytes. Fluorescence recovery after photobleaching yields diffusion coefficients from observations of the distribution of fluorescently labeled proteins. In the absence of traps, free diffusion coefficients give both the rate at which single-particle mean square displacements increase and the rate at which information in the form of inhomogeneities in particle concentration spread out with time. We show here that, in the presence of traps, information diffuses faster than single particles. Thus, messages diffuse faster than messengers. Tagged-particle experiments give the single-particle diffusion coefficients and, thus, can underestimate the rate of diffusive signal propagation.
Wnt 5a signaling is critical for macrophage-induced invasion of breast cancer cell lines
Authors: Pukrop T. , Klemm F. , Hagemann Th. , Gradl D. , Schulz M. , Siemes S. , Trümper L. , Binder C.
Published: March 2006

Interactions between neoplastic and stromal cells contribute to tumor progression. Wnt genes, involved in cell migration and often deregulated in cancers, are attractive candidates to regulate these effects. We have recently shown that coculture of breast cancer cells with macrophages enhances invasiveness via matrix metalloproteases and TNF-α. Here we demonstrate that coculture of MCF-7 cells and macrophages leads to up-regulation of Wnt 5a in the latter. This was accompanied by activation ofAP-1/c-Junin MCF-7. Recombinant Wnt 5a mimicked the coculture effect. Wnt 5a was also detectable in tumor-associated macrophages in primary breast cancers. Experiments with agonists and antagonists of Wnt signaling revealed that a functional canonical pathway in the tumor cells was a necessary prerequisite; however, noncanonical signaling via Wnt 5a and the Jun-N-terminal kinase pathway was critical for invasiveness. It was also responsible for induction of matrix metalloprotease-7, known to release TNF-α. All these effects could be antagonized by dickkopf-1. Our results indicate that Wnt 5a is essential for macrophage-induced invasiveness, because it regulates tumor cell migration as well as proteolytic activity of the macrophages. The function of Wnt 5a as either a suppressor or promoter of malignant progression seems to be modulated by intercellular interactions. Wnt 5a detection in tumor-associated macrophages in breast cancer biopsies supports the assumption that similar events play a rolein vivo.
Neural mechanisms of genetic risk for impulsivity and violence in humans
Authors: Meyer-Lindenberg Andreas , Buckholtz Joshua W. , Kolachana Bhaskar , R. Hariri Ahmad , Pezawas Lukas , Blasi Giuseppe , Wabnitz Ashley , Honea Robyn , Verchinski Beth , Callicott Joseph H. , Egan Michael , Mattay Venkata , Weinberger Daniel R.
Published: March 2006

Neurobiological factors contributing to violence in humans remain poorly understood. One approach to this question is examining allelic variation in the X-linked monoamine oxidase A (
MAOA
) gene, previously associated with impulsive aggression in animals and humans. Here, we have studied the impact of a common functional polymorphism in
MAOA
on brain structure and function assessed with MRI in a large sample of healthy human volunteers. We show that the low expression variant, associated with increased risk of violent behavior, predicted pronounced limbic volume reductions and hyperresponsive amygdala during emotional arousal, with diminished reactivity of regulatory prefrontal regions, compared with the high expression allele. In men, the low expression allele is also associated with changes in orbitofrontal volume, amygdala and hippocampus hyperreactivity during aversive recall, and impaired cingulate activation during cognitive inhibition. Our data identify differences in limbic circuitry for emotion regulation and cognitive control that may be involved in the association of
MAOA
with impulsive aggression, suggest neural systems-level effects of X-inactivation in human brain, and point toward potential targets for a biological approach toward violence.
Chlorella
virus MT325 encodes water and potassium channels that interact synergistically
Authors: Gazzarrini Sabrina , Kang Ming , Epimashko Svetlana , Van Etten James L. , Dainty Jack , Thiel Gerhard , Moroni Anna
Published: March 2006

Fast and selective transport of water through cell membranes is facilitated by water channels. Water channels belonging to the major intrinsic proteins (MIPs) family have been found in all three domains of life, Archaea, Bacteria, and Eukarya. Here we show that
Chlorella
virus MT325 has a water channel gene,
aqpv1
, that forms a functional aquaglyceroporin in oocytes.
aqpv1
is transcribed during infection together with MT325
kcv
, a gene encoding a previously undescribed type of viral potassium channel. Coexpression of AQPV1 and MT325-Kcv in
Xenopus
oocytes synergistically increases water transport, suggesting a possible concerted action of the two channels in the infection cycle. The two channels operate by a thermodynamically coupled mechanism that simultaneously alters water conductance and driving force for water movement. Considering the universal role of osmosis, this mechanism is relevant to any cell coexpressing water and potassium channels and could have pathological as well as basic physiological relevance.
The evolutionary diversification of cyanobacteria: Molecular–phylogenetic and paleontological perspectives
Authors: Tomitani Akiko , Knoll Andrew H. , Cavanaugh Colleen M. , Ohno Terufumi
Published: March 2006

Cyanobacteria have played a significant role in Earth history as primary producers and the ultimate source of atmospheric oxygen. To date, however, how and when the group diversified has remained unclear. Here, we combine molecular phylogenetic and paleontological studies to elucidate the pattern and timing of early cyanobacterial diversification. 16S rRNA,
rbcL
, and
hetR
genes were sequenced from 20 cyanobacterial strains distributed among 16 genera, with particular care taken to represent the known diversity of filamentous taxa. Unlike most other bacteria, some filamentous cyanobacteria evolved a degree of cell differentiation, producing both specialized cells for nitrogen fixation (heterocysts) and resting cells able to endure environmental stress (akinetes). Phylogenetic analyses support the hypothesis that cyanobacteria capable of cell differentiation are monophyletic, and the geological record provides both upper and lower bounds on the origin of this clade. Fossil akinetes have been identified in 1,650- to 1,400-mega-annum (Ma) cherts from Siberia, China, and Australia, and what may be the earliest known akinetes are preserved in ≈2,100-Ma chert from West Africa. Geochemical evidence suggests that oxygen first reached levels that would compromise nitrogen fixation (and hence select for heterocyst differentiation) 2,450–2,320 Ma. Integrating phylogenetic analyses and geological data, we suggest that the clade of cyanobacteria marked by cell differentiation diverged once between 2,450 and 2,100 Ma, providing an internal bacterial calibration point for studies of molecular evolution in early organisms.
Molecular evidence for two-stage learning and partial laterality in eyeblink conditioning of mice
Authors: Park Jin-Sung , Onodera Takashi , Nishimura Shin-ichi , Thompson Richard F. , Itohara Shigeyoshi
Published: March 2006

The anterior interpositus nucleus (AIN) is the proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remain unknown. To elucidate the molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delay eyeblink conditioning using microarray, quantitative real-time RT-PCR, and
in situ
hybridization techniques. Microarray analyses suggested that transcriptionally up-regulated gene sets were largely different between early (3-d training) and late (7-d) stages. Quantitative real-time RT-PCR aided by laser microdissection indicated that the expression of representative EARLY genes (
Sgk
,
IkBa
, and
Plekhf1
) peaked at 1-d training in both the paired and unpaired conditioning groups, and was maintained at a higher level in the paired group than in the unpaired group after 3-d training.
In situ
hybridization revealed increased expression of these genes in broad cerebellar areas, including the AIN, with no hemispheric preferences. In contrast, the expression of representative LATE genes (
Vamp1
,
Camk2d
, and
Prkcd
) was selectively increased in the AIN of the 7-d paired group, with dominance in the ipsilateral AIN. Increased
Vamp1
mRNA expression was restricted to the ipsilateral dorsolateral hump, a subregion of the AIN. These expression patterns of two distinct subsets of genes fit well with the two-stage learning theory, which proposes emotional and motor learning phases, and support the notion that AIN has a crucial role in memory formation of eyeblink conditioning.
Phylogenetic fate mapping
Authors: Salipante Stephen J. , Horwitz Marshall S.
Published: March 2006

Cell fate maps describe how the sequence of cell division, migration, and apoptosis transform a zygote into an adult. Yet, it is only in
Caenorhabditis elegans
where microscopic observation of each cell division has allowed for construction of a complete fate map. More complex, and opaque, animals prove less yielding. DNA replication, however, generates somatic mutations. Consequently, multicellular organisms comprise mosaics where most cells acquire unique genomes that are potentially capable of delineating their ancestry. Here we take a phylogenetic approach to passively retrace embryonic relationships by deducing the order in which mutations have arisen during development. We show that polyguanine repeat DNA sequences are particularly useful genetic markers, because they frequently change length during mitosis. To demonstrate feasibility, we phylogenetically reconstruct the lineage of cultured mouse NIH 3T3 cells based on mutations affecting the length of polyguanine markers. We then employ whole genome amplification to genotype polyguanine markers in single cells taken from a mouse and use phylogenetics to infer the developmental relationships of the sampled tissues. The result is consistent with the present understanding of embryogenesis and demonstrates the large scale potential of this method for producing a complete mammalian cell fate at the resolution of a single cell.
Effects of conjugated linoleic acid on linoleic and linolenic acid metabolism in man
Authors: Turpeinen Anu M. , Bärlund Sonja , Freese Riitta , Lawrence Peter , Brenna Thomas
Published: March 2006

Evidence from animal studies suggests that conjugated linoleic acid (CLA) modulates plasma and tissue appearance of newly synthesized PUFA. The effects of a 1·2g (0·5% energy) daily intake of thecis-9,trans-11 (c9,t11) isomer of CLA,trans-10,cis-12 (t10,c12) isomer of CLA or olive oil (placebo) on linoleic acid (LA) and linolenic acid (LNA) metabolism in healthy human volunteers was investigated. Fifteen subjects were fed an experimental diet and supplemented withc9,t11-CLA,t10,c12-CLA or placebo for 7d before consuming a tracer dose of U-[13C]La (50%Mg) And U-[13C]Lna (50Mg). Blood Samples Were Taken At 0, 2, 4, 6, 8, 24, 48, 72 and 168%h and analysed using high-precision MS. No differences between the groups in peak plasma [13C]LA (10·3–11·6% of dose), [13C]LNA (2·5–2·9% of dose), [13C]arachidonic acid (0·09–0·12% of dose), [13C]EPA (0·04–0·06% of dose) or [13C]Dha (0c·06–0·10% of dose) were detected. ConcentrationV. time curves (area under the curve) also showed no significant differences between groups. This suggests that, in healthy human subjects consuming a diet with adequate intake of essential fatty acids, CLA does not affect metabolism of LA or LNA
Effects of ingestion of tomatoes, tomato juice and tomato purée on contents of lycopene isomers, tocopherols and ascorbic acid in human plasma as well as on lycopene isomer pattern
Authors: Fröhlich Kati , Kaufmann Karin , Bitsch Roland , Böhm Volker
Published: March 2006

Tomatoes are an important part of the diet. Lycopene, the predominant carotenoid in tomatoes, is hypothesised to mainly mediate the health benefits of tomato products. Anticancer activity of tomato products and lycopene has been suggested by numerous studies. The aim of the present study was to investigate the effect of ingestion of three different tomato-based foodstuffs on plasma contents of lycopene, tocopherols and ascorbic acid. Because isomers of lycopene may have different biological activities, a special interest was to look how the lycopene isomer pattern is changed depending on the matrix of tomato products. Following a 2-week depletion phase volunteers ingested 12·5mg lycopene/d for 4 weeks comprising tomatoes, tomato juice or tomato purée. The basal levels of lycopene in plasma were comparable for all groups and decreased significantly during the 2 weeks of depletion to approximately half of the basal values. Following intervention, plasma lycopene concentration increased significantly. Conversely, supplementation did not significantly affect levels of tocopherols and ascorbic acid in plasma. Regarding isomers of lycopene, the (Z)-lycopene:(all-E)-lycopene plasma isomer ratio was significantly changed during the study for all groups. A remarkable enrichment of the relative contents of (5Z)-lycopene was observed during the depletion period, which supports the hypothesis that lycopene (Z)-isomers are formed within the human body after ingestion of (all-E)-lycopene. After dietary intervention with lycopene-rich products the isomer ratios returned to those observed at the start of the study. Further investigations will clarify the process of isomerisation in more detail.
Intake of high levels of vitamin A and polyunsaturated fatty acids during different developmental periods modifies the expression of morphogenesis genes in European sea bass (Dicentrarchus labrax)
Authors: Villeneuve Laure A. N. , Gisbert Enric , Moriceau Jacques , Cahu Chantal L. , Infante José L. Zambonino
Published: March 2006

The effect of the feeding period on larval development was investigated in European sea bass larvae by considering the expression level of some genes involved in morphogenesis. Larvae were fed a control diet except during three different periods (period A: from 8 to 13d post-hatching (dph); period B: from 13 to 18dph; period C: from 18 to 23dph) with two compound diets containing high levels of vitamin A or PUFA. European sea bass morphogenesis was affected by these two dietary nutrients during the early stages of development. The genes involved in morphogenesis could be modulated between 8 and 13dph, and our results indicated that retinoids and fatty acids influenced two different molecular pathways that in turn implicated two different gene cascades, resulting in two different kinds of malformation. Hypervitaminosis A delayed development, reducing the number of vertebral segments and disturbing bone formation in the cephalic region. These malformations were correlated to an upregulation of retinoic acid receptor γ, retinoid X receptor (RXR) α and bone morphogenetic protein (BMP)4. An excess of PUFA accelerated the osteoblast differentiation process through the upregulation of RXRα and BMP4, leading to a supernumerary vertebra. These results suggest that the composition of diets devoted to marine fish larvae has a particularly determining effect before 13dph on the subsequent development of larvae and juvenile fish.
Validity and reproducibility of a semi-quantitative food-frequency questionnaire for estimating calcium intake in Belgian preschool children
Authors: Huybrechts Inge , Bacquer Dirk De , Matthys Christophe , Backer Guy De , Henauw Stefaan De
Published: March 2006

Relative validity and reproducibility of a semi-quantitative food-frequency questionnaire (FFQ) for measuring preschool children's usual Ca intake were assessed using parents or guardians as a proxy. Estimated diet records (EDR; 3d) were used as the reference method and reproducibility was measured by repeated FFQ administrations 5 weeks apart. From 2095 preschool children (2·5–6·5 years) randomly selected in Flanders (Flemish region of Belgium), 1052 returned a FFQ and EDR. Stringent exclusion procedures reduced the sample for validity analyses to 509 children. From a separate sample of 244 preschool children, 124 returned two FFQ, of whom sixty were included in the reproducibility analysis. Mean Ca intakes were 838 (sd 305) and 777 (sd 296) mg/d for EDR and FFQ respectively, indicating a mean difference of 60·9 (sd 294·4) mg/d (p<0·001). Pearson's correlation was 0·52. Cross-classification analysis of the FFQ and EDR classified 83%of the subjects in the same or adjacent category and 2·4% in extreme quartiles. Actual values for surrogate FFQ quartiles showed a progressive increase in Ca intake (p<0·001). The FFQ correctly identified 77% of the children consuming less Ca than the age-specific RDA (800mg/d). Correlation between repeated administrations was 0·79. No significant difference between mean Ca intakes was established by two administrations (23·8 (sd 161·2) mg/d). Cross-classification of repeated administrations classified 93·4% of the subjects in the same or adjacent category and no subjects in extreme categories. This FFQ tended to underestimate preschool children's Ca intake when administered by a proxy. However, it demonstrated good repeatability and fairly good ability to classify subjects into extremes of Ca intake.
Daily consumption of a high-phenol extra-virgin olive oil reduces oxidative DNA damage in postmenopausal women
Authors: Salvini Simonetta , Sera Francesco , Caruso Donatella , Giovannelli Lisa , Visioli Francesco , Saieva Calogero , Masala Giovanna , Ceroti Marco , Giovacchini Valentina , Pitozzi Vanessa , Galli Claudio , Romani Annalisa , Mulinacci Nadia , Bortolomeazzi Renzo , Dolara Piero , Palli Domenico
Published: March 2006

Extra-virgin olive oils (EVOO), high in phenolic compounds with antioxidant properties, could be partly responsible for the lower mortality and incidence of cancer and CVD in the Mediterranean region. The present study aims to measure oxidative DNA damage in healthy human subjects consuming olive oils with different concentrations of natural phenols. A randomised cross-over trial of high-phenol EVOO (high-EVOO; 592mg total phenols/kg)Vlow-phenol EVOO (low-EVOO; 147mg/kg) was conducted in ten postmenopausal women in Florence. Subjects were asked to substitute all types of fat and oils habitually consumed with the study oil (50g/d) for 8 weeks in each period. Oxidative DNA damage was measured by the comet assay in peripheral blood lymphocytes, collected at each visit during the study period. Urine samples over 24h were collected to measure the excretion of the olive oil phenols. The average of the four measurements of oxidative DNA damage during treatment with high-EVOO was 30% lower than the average during the low-EVOO treatment (p=0·02). Urinary excretion of hydroxytyrosol and its metabolite homovanillyl alcohol were significantly increased in subjects consuming high-EVOO. Despite the small sample size, the present study showed a reduction of DNA damage by consumption of an EVOO rich in phenols, particularly hydroxytyrosol.
Differential effects of konbu and nori seaweed dietary supplementation on liver glutathione status in normo- and hypercholesterolaemic growing rats
Authors: Bocanegra Aránzazu , Beneduí Juana , Sé nchez-Muniz Francisco J.
Published: March 2006

The effects of six balanced diets for 3 weeks on dietary intake, growth, liver weight and fat, plasma cholesterol, total antioxidant capacity, liver glutathione status and antioxidant enzymes in growing male Wistar rats were studied. Ten rats per group were fed casein- and soyabean-based diets with or without 2·4% cholesterol-raising agent. Seven percent of the diet consisted of a cellulose–wheat starch mix (35:65; control diets), freeze-dried nori (nori diets) or konbu (konbu diets). The 7% dietary supplement of seaweeds was well accepted and induced normal growth rates in rats. Except for food intake, total and reduced glutathione and total antioxidant capacity, dietary cholesterol addition significantly affected (at leastP<0·05) all parameters studied. Alga consumption affected total and reduced glutathione, glutathione reductase activity, plasma cholesterol, and total and cholesterol-adjusted total antioxidant capacity (at leastP<0·05). A significant cholesterol–alga interaction was found for liver weight, total glutathione peroxidase (GSH-Px) and the Se-dependent GSH-Px:total GSH-Px ratio (at leastP<0·05). GSH-Px activity increased in cholesterol-fed nori rats mainly as Se-dependent GSH-Px, while in konbu and control groups the GSH-Px activity was related to increases in both non-Se-dependent and Se-dependent GSH-Px activities. The decrease in the antioxidant status of konbu rats was related to the high As content of this alga, which led to a compensatory increase in glutathione reductase activity in these animals. In conclusion, although some antioxidant compounds are present in algae, other dietary compounds, such as As, induced poor antioxidant status in rats.
The effect of multi-vitamin/mineral supplementation on mortality during treatment of pulmonary tuberculosis: a randomised two-by-two factorial trial in Mwanza, Tanzania
Authors: Range Nyagosya , Changalucha John , Krarup Henrik , Magnussen Pascal , Andersen Âse B. , Friis Henrik
Published: March 2006

Malnutrition is common in pulmonary tuberculosis (TB), and may impair survival. The objective of this study was to assess effects of multi-vitamin/mineral (MVM) and zinc (Zn) supplementation during TB treatment on mortality. Patients diagnosed with sputum-positive pulmonary TB in Mwanza, Tanzania, were randomised, using a two-by-two factorial design, to Zn (45mg) or placebo, and MVM (vitamins A, B, C, D, E, and selenium and copper) or placebo. Survival status was ascertained at the end of the 8-month TB treatment and supplementation period. Of 499 TB patients, 213 (43%) had HIV. The mean weight gain at 7 months was 6·88kg (95% CI 6·36, 7·41). Zn and MVM combined, but neither alone (interaction, p=0·03), increased weight gain by 2·37kg (95% CI 0·91, 3·83), irrespective of HIV status. Survival status at 8 months was determined for 422 patients (84·6%), of which fifty-two (12·3%) had died. Among fifty-two deaths, there were no effects of MVM (relative risk (RR) 0·73; 95% CI 0·43, 1·23) and Zn (RR 0·76; 95% CI 0·46, 1·28). However, among HIV co-infected patients, marginally significant effects of both MVM (RR 0·60; 95% CI 0·34, 1·05) and Zn (RR 0·63, 95% CI 0·37, 1·08) were seen, and MVM and Zn combined reduced mortality (RR 0·29; 95% CI 0·10, 0·80; interaction ratio 0·52). In conclusion, supplementation with MVM, including Zn, during treatment of pulmonary TB may reduce mortality in those co-infected with HIV. A randomised trial of the effect of the combined intervention used in this study should be conducted in a different setting to confirm the finding.
n−3 PUFA fail to affectin vivo, antigen-driven CD8+T-cell proliferation in the spleen of naïve mice
Authors: Irons Robert , Fritsche Kevin L.
Published: March 2006

One of the most frequently reported immunomodulatory actions ofn−3 PUFA is their ability to diminishin vivolymphocyte proliferation. The purpose of this study was to determine ifn−3 PUFA intake affects the kinetics or magnitude of the antigen-driven expansion of CD8+T-lymphocytesin vivo. In this study we utilized a well-characterized model of T-cell immunity (i.e. infection with the intracellular bacterium,Listeria monocytogenes). Weanling BALB/c mice were fed one of two experimental diets that differed solely in fat source. Our control diet contained lard (180g/kg) and was devoid of long-chainn−3 PUFA. The experimental diet contained 150g/kg menhaden fish oil and 30g/kg corn oil, thus providing approximately 8% of energy from long-chainn−3 PUFA. After 4 weeks, mice were infected intravenously with 106colony-forming units of actA-deficientL. monocytogenes. Clonal expansion of antigen-specific CD8+T-cells in the spleen was measured at 5, 7, 9 and 14d post-challenge using a class I MHC tetramer loaded with the immunodominant peptide from this pathogen (i.e. Kd:LLO91–99). We report that feeding mice a diet rich inn−3 fatty acids did not significantly impact either the kinetics or magnitude ofin vivo, antigen-driven expansion of CD8+T-cells. Furthermore, contraction of this T-cell population was not affected byn−3 PUFA treatment. To our knowledge this is the first time MHC tetramers have been used to investigate the influence ofn−3 PUFA onin vivoCD8+T-cell proliferation.
Intake of fish and long-chainn−3 fatty acids and the risk of coronary heart mortality in men and women
Authors: Järvinen Ritva , Knekt Paul , Rissanen Harri , Reunanen Antti
Published: March 2006

This prospective study investigated the relationship between the consumption of fish and intake of long-chainn−3 fatty acids and the risk of coronary heart mortality in 2775 men and 2445 women aged from 30 to 79 years who were free of CHD and had participated in a health examination survey from 1967 to 1972. In total, 335 men and 163 women died of CHD during a follow-up until the end of 1992. A dietary history interview method provided data on habitual consumption of fish and other foods over the preceding year at baseline. The intakes of long-chainn−3 fatty acids were calculated on the basis of food composition values of Finnish foods. Higher consumption of fish was associated with a decreased risk of CHD among women, whereas no significant association was seen among men. The relative risk between the highest and the lowest quintile for fish consumption was 1·00 (95% CI 0·70, 1·43;pfor trend 0·83) for men and 0·59 (95% CI 0·36, 0·99;pfor trend 0·02) for women in analysis adjusting for age, energy intake, geographical area, BMI, serum cholesterol, blood pressure, smoking, occupation and diabetes; however, after adjustment for dietary confounders this association was no longer significant. The intake ofn−3 fatty acids was not significantly associated with the risk of CHD in either men or women. In conclusion, our results for women are in line with the suggested protective effect of fish consumption against CHD but a similar association was not, however, found in men.