bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass spectrometric studies on brain metabolism, using stable isotopes
Authors: Ando Susumu , Tanaka Yasukazu
Published: July 2005

In fields related to biomedicine, mass spectrometry has been applied to metabolism research and chemical structural analysis. The introduction of stable isotopes has advanced research related to in vivo metabolism. Stable‐isotope labeling combined with mass spectrometry appears to be a superior method for the metabolism studies, because it compensates for the shortcomings of conventional techniques that use radioisotopes. Biomolecules labeled with stable isotopes have provided solid evidence of their metabolic pathways. Labeled large molecules, however, cannot homogeneously mix in vivo with the corresponding endogenous pools. To overcome that problem, small tracers labeled with stable isotopes have been applied to in vivo studies because they can diffuse and attain a homogeneous distribution throughout the inter‐ and intracellular spaces. In particular, D2O‐labeling methods have been used for studies of the metabolism in different organs, including the brain, which is isolated from other extraneural organs by the blood–brain barrier (BBB). Cellular components, such as lipids, carbohydrates, proteins, and DNA, can be endogenously and concurrently labeled with deuterium, and their metabolic fluxes examined by mass spectrometry. Application of the D2O‐labeling method to the measurements of lipid metabolism and membrane turnover in the brain is described, and the potential advantages of this method are discussed in this review. This methodology also appears to have the potential to be applied to dynamic and functional metabolomics. © 2005 Wiley Periodicals, Inc., Mass Spec Rev 24:865–886, 2005
Enhancement of the positive secondary ion yield during low‐energy, dual‐beam depth profiling of polytetrafluoroethylene with 1‐keV Cs+
Authors: Francis J. T. , McIntyre N. S.
Published: July 2005

This work documents the behaviour of the positive secondary ion yield of bulk polytetrafluoroethylene (PTFE) under dual‐beam depth profiling conditions employing 1 keV Ar+, Cs+ and SF5+. A unique chemical interaction is observed in the form of a dramatic enhancement of the positive secondary ion yield when PTFE is dual‐beam profiled with 1 keV Cs+. The distinct absence of such an enhancement is noted for comparison on two non‐fluorinated polymers, polyethylene terephthalate (PET) and polydimethylsiloxane (PDMS). The bulk PTFE was probed using 15‐keV, 69Ga+ primary ions in dual beam mode under static conditions; 1‐keV Ar+ (a non‐reactive, light, noble element), Cs+ (a heavier metallic ion known to form clusters) and SF5+ (a polyatomic species) served as the sputter ion species. The total accumulated primary ion dose was of the order of 1015 ions/cm2, which is well beyond the static limit. The enhancement of the positive secondary yield obtained when profiling with 1‐keV Cs+ far exceeds that obtained when SF5+ is employed. An explanation of this apparent reactive ion effect in PTFE is offered in terms of polarisation of CF bonds by Cs+ in the vicinity of the implantation site thereby predisposing them to facile scission. The formation of peculiar, periodic CsxFy+ (where y = x − 1) and CsxCyFz+ clusters that can extend to masses approaching 2000 amu are also observed. Such species may serve as useful fingerprints for fluorocarbons that can be initiated via pre‐dosing a sample with low‐energy Cs+ prior to static 15‐keV Ga+ analysis. Copyright © 2005 John Wiley & Sons, Ltd.
Fidelity of Gaussian Channels
Authors: Caves Carlton M. , Wódkiewicz Krzysztof
Published: July 2005

A noisy Gaussian channel is defined as a channel in which an input field mode is subjected to random Gaussian displacements in phase space. We introduce the quantum fidelity of a Gaussian channel for pure and mixed input states, and we derive a universal scaling law of the fidelity for pure initial states. We also find the maximum fidelity of a Gaussian channel over all input states. Quantum cloning and continuous-variable teleportation are presented as physical examples of Gaussian channels to which the fidelity results can be applied.
Some Remarks on the Role of Minimal Length of Positive Maps in Constructing Entanglement Witnesses
Authors: Jamiołkowski A.
Published: July 2005

The main objective of this paper is to discuss correspondence between the concept of entanglement witnesses (self-adjoint operators on a composite Hilbert space [Formula: see text] that are, in general, not positive, but are positive on separable states) and positive maps [Formula: see text] which are not completely positive. The notion of minimal length of linear positive map is introduced and the role of this quantity in the constructing of entanglement witnesses is explained.
Phonon Dephasing of the Exciton in InAs/GaAs Quantum Dots
Authors: Janutka A. , Jacak L. , Krasnyj J. , Machnikowski P.
Published: July 2005

The interaction of a exciton confined in a semiconductor quantum dot (QD) with bulk phonons (acoustical and optical) responsible for the exciton dephasing is studied. The decoherence of the exciton due to the creation of a polaron with long-living or decaying phonons is described. Characteristic dephasing times for an InAs / GaAs QD are estimated using Green function methods in order to determine fundamental time limitations for use of the QD exciton in quantum information processing.
Wildfire effects on microbial biomass and diversity in pine forests at three topographic positions
Authors: Mabuhay J. A. , Isagi Y. , Nakagoshi N.
Published: July 2005

The aim of this study was to determine microbial biomass carbon and diversity at three topographic positions (ridge, middle slope and valley bottom) at varying periods after the occurrence of wildfire. The purpose of this study was to enhance knowledge on the microbiological status of post‐fire sites for a better estimate of the success of their restoration. Results showed that the biomass carbon and microbial diversity were affected by fire: the averages of the burnt plots were <50% of those of the unburnt plots. In addition, the biomass carbon at the sites studied 3 years after and 25 years after fire, and 5 months after and 9 years after fire, were not significantly different from each other. On the other hand, the site studied 5 months after fire showed the highest microbial diversity, followed by the ones studied 3, 25, 9 and 6 years after fire. In terms of topographic position, the ridge was shown to be the most affected by fire. These results show that fire can adversely affect the microbial biomass carbon and microbial diversity of the soil, the recovery of which may take a long time.
Pain among women: Associations with socio‐economic and work conditions
Authors: Jablonska Beata , Soares Joaquim J.F. , Sundin Örjan
Published: July 2005

We examined pain prevalence (general/body sites) and its characteristics/consequences among a randomised sample of women from the general population between 18 and 64 years (n= 3616). We also scrutinised associations between pain and various factors (e.g. socio‐economic) by means of multivariate logistic/linear regression analyses. The women completed a questionnaire assessing various areas (e.g. pain). The design was cross‐sectional and data were collected during 8 consecutive weeks. Sixty‐three per cent of women reported pain during the last 3 months, of which 65% during more than 3 months. The multivariate analyses revealed associations between various socio‐economic factors (e.g. financial strain) and pain in general/all studied body sites. In addition, psychosocial work conditions (i.e. work strain and social support) were significantly related to pain. Moreover, the multivariate analyses conducted among women with pain indicated relationships between socio‐economic/psychosocial work conditions, and pain characteristics (e.g. intensity) and consequences (i.e. disability). A large number of women from the general population suffer from pain, in particularly prolonged pain. Women in a deprived socio‐economic situation not only run a higher pain risk, but also experience their pain as more severe/disabling than their more privileged counterparts. Improvements of, for example, the socio‐economic status among women living in deprived social and material circumstances, along with improved working environment may be crucial to reduce women's pain problems.
Cell and tissue responses to electric shocks
Authors: Ashihara Takashi , Trayanova Natalia A.
Published: July 2005

Aim

Existing models of myocardial membrane kinetics have not been able to reproduce the experimentally-observed negative bias in the asymmetry of transmembrane potential changes (ΔVm) induced by strong electric shocks. The goals of this study are (1) to demonstrate that this negative bias could be reproduced by the addition, to the membrane model, of electroporation and an outward current, Ia, part of the K+ flow through the L-type Ca2+-channel, and (2) to determine how such modifications in the membrane model affect shock-induced break excitation in a 2D preparation.

Methods and results

We conducted simulations of shocks in bidomain fibres and sheets with membrane dynamics represented by the Luo–Rudy dynamic model (LRd'2000), to which electroporation (LRd+EP model) and the outward current, Ia, activated upon strong shock-induced depolarization (aLRd model) was added. Assuming Ia is a part of K+ flow through the L-type Ca2+-channel enabled us to reproduce both the experimentally observed rectangularly-shaped positive ΔVm and the value of near 2 of the negative-to-positive ΔVm ratio. In the sheet, Ia not only contributed to the negative bias in ΔVm asymmetry at sites polarized by physical and virtual electrodes, but also restricted positive ΔVm. Electroporation, in its turn, was responsible for the decrease in cathode-break excitation threshold in the aLRd sheet, compared with the other two cases, as well as for the occurrence of the excitation after the shock-end rather than during the shock.

Conclusions

The incorporation of electroporation and Ia in a membrane model ensures match between simulation results and experimental data. The use of the aLRd model results in a lower threshold for shock-induced break excitation.
Fluorescence resonance energy transfer (FRET) microscopy in living cells as a novel tool for the study of cytokine action
Authors: Gertler Arieh , Biener Eva , Ramanujan Krishnan V. , Djiane Jean , Herman Brian
Published: July 2005

Fluorescence resonance energy transfer (FRET) microscopy was used to study interactions between proteins in intact cells. We showed that growth hormone (GH) causes transient homodimerization of GH receptors tagged with yellow or cyan fluorescent proteins. The peak of FRET signaling occurred 2 to 4 min after hormonal stimulation and was followed by a decrease in FRET signal. Repeating those experiments in cells pretreated with the inhibitor of internalization methyl-β-cyclodextrin, or in potassium-depleted cells showed no difference in the kinetics of FRET signaling as compared with the non-treated cells, indicating that the decrease in FRET signal does not result from receptor internalization by the pathways inhibited by methyl-β-cyclodextrin or potassium depleted but might occur by other pathways of internalization. Using a similar methodology, we also demonstrated that ovine placental lactogen (oPL) causes transient heterodimerization of GH and prolactin (PRL) receptors 2·5 to 3 min after oPL application. On the other hand, oGH or oPRL had no effect at all, further substantiating the finding the oPL, which lacks a specific receptor, acts in homologous systems by heterodimerization of GH and PRL receptors. We also demonstrated that both PRL and leptin (LEP) are capable of transactivation of the oncogenic receptors erbB2 and erbB3. Upon PRL or LEP stimulation of HEK-293T cells transfected with LEP or PRL receptors and erbB2 or erbB3, erbB proteins are first phosphorylated and then activate MAPK (erk1/erk2). However, the FRET experiments failed to document any evidence of a direct interaction between erbB2 and the PRL or LEP receptors, suggesting that erbB activation probably occurs via activated JAK2, translocated from the respective receptors to erbB2.
Indirect estimation of the solar wind conditions in 29–31 October 2003
Authors: Dmitriev A. V. , Chao J.‐K. , Suvorova A. V. , Ackerson K. , Ishisaka K. , Kasaba Y. , Kojima H. , Matsumoto H.
Published: July 2005

A comparative analysis of the solar wind conditions was performed for extremely disturbed event on 29–31 October 2003. It was found that the ACE and Geotail upstream monitors provided very similar data on the IMF but that plasma measurements in the SOHO CELIAS/MTOF, ACE SWEPAM, IMP 8 MIT, and Geotail CPI experiments are very different. The solar wind velocity was indirectly estimated using the time lag for propagation of such solar wind structures as interplanetary shock, Alfven waves, rotational, and tangential discontinuities from point L1 to the Earth. We found the best correspondence of the estimated velocity was with the ACE SWEPAM data, which displayed very fast (up to 2000 km/s) solar wind, while the IMP 8, Geotail, and SOHO plasma instruments are unable to measure such a fast solar wind stream. Application of the magnetopause models to a data set of numerous geosynchronous magnetopause crossings observed by GOES and LANL satellites enabled estimation of the solar wind dynamic pressure. In general the estimated pressure and density are in agreement with the solar wind plasma parameters provided by the ACE SWEPAM experiment. An estimation of the solar wind density corresponds very well to the electron density restored from the Geotail PWI data. However, during 1600–1800 UT on 29 October, 1700–1800 UT on 30 October, and 0000–0400 UT on 31 October, the estimated solar wind pressure and density are several times larger than provided by the Geotail PWI and ACE SWEPAM. A large helium abundance is considered as a possible reason for the solar wind pressure underestimation in the first case. The understated solar wind density on 30–31 October might be explained by errors in the method for restoring of the plasma data in fast solar wind (>900 km/s) accompanied with intensive fluxes (few tens of particles per cm2 s sr) of high‐energy (>30 MeV) solar energetic protons.
CORONAS‐F/SPIRIT EUV observations of October–November 2003 solar eruptive events in combination with SOHO/EIT data
Authors: Grechnev V. V. , Chertok I. M. , Slemzin V. A. , Kuzin S. V. , Ignat'ev A. P. , Pertsov A. A. , Zhitnik I. A. , Delaboudinière J.‐P. , Auchère F.
Published: July 2005

The extraordinary solar activity of October–November 2003 manifested itself in many powerful eruptive events, including large coronal mass ejections (CMEs) and extremely powerful flares. A number of major events were accompanied by practically all known phenomena of the solar activity, both local and large‐scale, and caused severe space weather disturbances. We study large‐scale posteruptive activity manifestations on the Sun associated with CMEs, i.e., dimmings and coronal waves, observed with extreme‐ultraviolet telescopes, the SPIRIT on the CORONAS‐F spacecraft and the EIT on the SOHO. During that period, observations with a cadence of 15 to 45 min were carried out by the SPIRIT in the 175 Å and 304 Å bands simultaneously. The EIT observed with 12‐min cadence in the 195 Å band as well as with 6‐hour cadence in the 171, 284, and 304 Å bands. These data complement each other both in the temporal and spectral coverage. Our analysis reveals that largest‐scale dimmings covered almost the whole southern part of the Sun's visible side and exhibited homology, with one homological structure being changed to another configuration on 28 October. These structures show connections between large superactive and smaller regions that constituted a huge activity complex responsible for the extraordinary solar activity of that period. Coronal waves were observed at 175 Å as well as at 195 Å in some events, in areas where there were no active regions, but in the 175 Å images they look fainter. They were not accompanied by deep, long‐living dimmings. By contrast, such dimmings were observed in active regions, in their vicinity, and between them. These facts rule out the direct relation of the phenomena of long‐term dimmings and coronal waves. On 18 November, a motion of an ejecta was observed at the solar disk as a propagation of a dark feature only in the 304 Å band, which can be interpreted as an absorption in a “cloud” formed from material of the eruptive filament, which probably failed to become a CME core.
Planetary foreshock radio emissions
Authors: Kuncic Zdenka , Cairns Iver H.
Published: July 2005

The electron foreshock regions upstream of Earth's bow shock and upstream of traveling interplanetary shocks are known to be propitious sites for a variety of energetic particle and plasma wave phenomena, including radio emissions. A quantitative theoretical model has been developed for radio emissions associated with the terrestrial foreshock and for type II radio bursts associated with interplanetary shocks. Here, we generalize this model and apply it to other planetary foreshocks. We present predictions for the levels of planetary foreshock radio emissions and compare these with observations by past and present space missions. One key result is that Mercury can be a strong source of foreshock radio emissions, and this prediction may be testable with the anticipated BepiColombo space mission. Although the terrestrial foreshock radio emissions are the most detectable with existing instruments, our results predict that they are the second strongest in absolute terms, following the Jovian foreshock emissions. Indeed, we predict that the radio instrument on board Ulysses should have detected Jovian foreshock radio emissions, and we suggest that there is some evidence in the data to support this. We also suggest that Cassini was potentially capable of detecting foreshock emissions from Venus during its gravity‐assist flybys and may possibly be capable of detecting foreshock emissions from Saturn under favorable solar wind conditions.
Determining shock velocities for inputs to Sun‐to‐Earth models from radio and coronagraph data
Authors: Smith Z. , Dryer M. , Fry C. D.
Published: July 2005

The speed of a shock that precedes ejecta from a solar energetic eruption is one of the key parameters used for input by many numerical models that predict the arrival of interplanetary shocks at Earth. These shocks are likely to be followed by significant geomagnetic activity. Near‐real‐time “fearless forecasts” of shock arrival times at the L1 libration point have been made for more than 6 years with several models. Initially, these models used, for input speeds near the Sun, speeds obtained from observations of metric type II radio bursts that are signatures of shocks propagating out through the solar corona. More recently, speeds of halo/partial halo coronal mass ejections (CMEs) were also considered in these models as another measure of shock speeds close to the Sun. During the period of high solar activity in October–November 2003, the data required for input into the models were often available in near real time from a number of observing stations. Therefore the fearless forecasts were issued in some cases with alternative inputs. These forecasts provided a basis on which to compare the success of the predictions (in terms of how close each prediction of the shock arrival time was to the observed time). The results of the analysis of this data set provide guidelines for selecting the input speed for shock propagation models. Both CME and metric type II radio burst measurements are shown to be useful and complementary. In general, the highest speed gave the best predictions. This demonstrates the desirability of having coronagraph data available for operational use.
What are the limits to statistical error correction in land surface schemes when projecting the future?
Authors: Pitman A. J. , Abramowitz G.
Published: July 2005

An artificial neural net is used to correct a land surface model (LSM) using present‐day observational data. These data are split into a training and a testing set for the correction with the mean air temperature of each differing by a fixed amount. We investigate the success of the correction as this difference increases from 1°C to 20°C. We show that errors associated with the LSM's simulation of latent heat, sensible heat and net ecosystem exchange is substantially smaller if the model is corrected. The reduction in error remains large even as the temperature difference between the training and testing data sets reaches 10°C. We conclude that an artificial neural net can error‐correct an off‐line LSM under current and warmer climates, at least up to a warming of 10°C. The statistical correction of LSMs using present day data may therefore retain value in future climate applications.
Additive neuroprotective effects of creatine and cyclooxygenase 2 inhibitors in a transgenic mouse model of amyotrophic lateral sclerosis
Authors: Klivenyi Peter , Kiaei Mahmoud , Gardian Gabrielle , Calingasan Noel Y. , Beal M. Flint
Published: July 2005

There is substantial evidence implicating both inflammation and mitochondrial dysfunction in amyotrophic lateral sclerosis (ALS) pathogenesis. We investigated the therapeutic effects of cyclooxygenase 2 (COX‐2) inhibitors both alone and in combination with creatine in the G93A transgenic mouse model of ALS. Oral administration of either celecoxib or rofecoxib significantly improved motor performance, attenuated weight loss and extended survival. The administration of COX‐2 inhibitors significantly reduced prostaglandin E2 levels at 110 days of age. The combination of creatine with COX‐2 inhibitors produced additive neuroprotective effects and extended survival by approximately 30%. The COX‐2 inhibitors significantly protected against depletion of anterior horn motor neurons and creatine with COX‐2 inhibitors showed greater protection than COX‐2 inhibitors alone. These results suggest that combinations of therapies targeting different disease mechanisms may be a useful strategy in the treatment of ALS.
An ab initio study of tunneling splittings in the water trimer
Authors: Takahashi Mariko , Watanabe Yumiko , Taketsugu Tetsuya , Wales David J.
Published: July 2005

Tunneling splittings in the water trimer have been determined by the semiclassical WKB method, based on pathways characterized at the computational level of second-order Møller-Plesset theory with basis sets of aug-cc-pVTZ quality. This calculation takes into account the single-flip and bifurcation tunneling rearrangements of the water trimer. The predicted splittings are 37.93cm−1 for the flip and 6.50×10−3cm−1 for bifurcation, which agree quite well with the corresponding experimental values of 43.52cm−1 and 9.63×10−3cm−1.
X-ray absorption and photoelectron spectroscopy studies on graphite and single-walled carbon nanotubes: Oxygen effect
Authors: Abbas M. , Wu Z. Y. , Zhong J. , Ibrahim K. , Fiori A. , Orlanducci S. , Sessa V. , Terranova M. L. , Davoli Ivan
Published: July 2005

We have investigated the electronic states of highly oriented pyrolitic graphite and single-walled carbon nanotubes using x-ray absorption spectroscopy (XAS) before and after annealing treatment in ultrahigh vacuum, and observed that the small peak between π* and σ* features, which has been previously assigned to free-electron-like interlayer states, disappears after in situ annealing treatment, suggesting that the signal may be assigned to a surface contamination, especially oxygen contamination introduced by chemical processing or gas adsorption. Additional experiments by photoelectron spectroscopy as well as XAS methods, performed after aging in air, fully support this interpretation.
Human serotonin transporter variants display altered sensitivity to protein kinase G and p38 mitogen-activated protein kinase
Authors: Prasad Harish C. , Zhu Chong-Bin , McCauley Jacob L. , Samuvel Devadoss J. , Ramamoorthy Sammanda , Shelton Richard C. , Hewlett William A. , Sutcliffe James S. , Blakely Randy D.
Published: July 2005

Human serotonin [5-hydroxytryptamine (5-HT)] transporters (hSERT, 5HTT, and
SLC6A4
) inactivate 5-HT after release and are prominent targets for therapeutic intervention in mood, anxiety, and obsessive-compulsive disorders. Multiple hSERT coding variants have been identified, although to date no comprehensive functional analysis of these variants has been reported. We transfected hSERT or 10 hSERT coding variants and examined total and surface protein expression, antagonist recognition, and transporter modulation by posttranslational, regulatory pathways. Two variants, Pro339Leu and Ile425Val, demonstrated significant changes in surface expression supporting alterations in 5-HT transport capacity (
V
max
). Regardless of basal transport activity, all SERT variants displayed a capacity for rapid, phorbol ester-triggered down-regulation. Remarkably, five variants (Thr4Ala, Gly56Ala, Glu215Lys, Lys605Asn, and Pro612Ser) demonstrated no capacity for 5-HT uptake stimulation after acute protein kinase G (PKG)/p38 mitogen-activated protein kinase (MAPK) activation. Epstein–Barr virus (EBV)-transformed lymphocytes natively expressing the most common of these variants (Gly56Ala) exhibited a similar loss of 5-HT uptake stimulation by PKG/p38 MAPK activators. HeLa cells transfected with the Gly56Ala variant demonstrated elevated basal phosphorylation and, unlike hSERT, could not be further phosphorylated after 8-bromo cGMP (8BrcGMP) treatments. These studies reveal cellular phenotypes associated with naturally occurring human SERT coding variants and suggest that altered transporter regulation by means of PKG/p38 MAPK-linked pathways may influence risk for disorders attributed to compromised 5-HT signaling.
Cationic liposome–microtubule complexes: Pathways to the formation of two-state lipid–protein nanotubes with open or closed ends
Authors: Raviv Uri , Needleman Daniel J. , Li Youli , Miller Herbert P. , Wilson Leslie , Safinya Cyrus R.
Published: July 2005

Intermolecular interactions between charged membranes and biological polyelectrolytes, tuned by physical parameters, which include the membrane charge density and bending rigidity, the membrane spontaneous curvature, the biopolymer curvature, and the overall charge of the complex, lead to distinct structures and morphologies. The self-assembly of cationic liposome–microtubule (MT) complexes was studied, using synchrotron x-ray scattering and electron microscopy. Vesicles were found to either adsorb onto MTs, forming a “beads on a rod” structure, or undergo a wetting transition and coating the MT. Tubulin oligomers then coat the external lipid layer, forming a tunable lipid–protein nanotube. The beads on a rod structure is a kinetically trapped state. The energy barrier between the states depends on the membrane bending rigidity and charge density. By controlling the cationic lipid/tubulin stoichiometry it is possible to switch between two states of nanotubes with either open ends or closed ends with lipid caps, a process that forms the basis for controlled chemical and drug encapsulation and release.
In vivoengineering of organs: The bone bioreactor
Authors: Stevens Molly M. , Marini Robert P. , Schaefer Dirk , Aronson Joshua , Langer Robert , Shastri V. Prasad
Published: July 2005

Treatment of large defects requires the harvest of fresh living bone from the iliac crest. Harvest of this limited supply of bone is accompanied by extreme pain and morbidity. This has prompted the exploration of other alternatives to generate new bone using traditional principles of tissue engineering, wherein harvested cells are combined with porous scaffolds and stimulated with exogenous mitogens and morphogensin vitroand/orin vivo. We now show that large volumes of bone can be engineered in a predictable manner, without the need for cell transplantation and growth factor administration. The crux of the approach lies in the deliberate creation and manipulation of an artificial space (bioreactor) between the tibia and the periosteum, a mesenchymal layer rich in pluripotent cells, in such a way that the body's healing mechanism is leveraged in the engineering of neotissue. Using the “in vivobioreactor” in New Zealand White rabbits, we have engineered bone that is biomechanically identical to native bone. The neobone formation followed predominantly an intramembraneous path, with woven bone matrix subsequently maturing into fully mineralized compact bone exhibiting all of the histological markers and mechanical properties of native bone. We harvested the bone after 6 weeks and transplanted it into contralateral tibial defects, resulting in complete integration after 6 weeks with no apparent morbidity at the donor site. Furthermore, in a proof-of-principle study, we have shown that by inhibiting angiogenesis and promoting a more hypoxic environment within the “in vivobioreactor space,” cartilage formation can be exclusively promoted.
Adult mice cloned from migrating primordial germ cells
Authors: Yamazaki Yukiko , Low Eleanor W. , Marikawa Yusuke , Iwahashi Kazuhiro , Bartolomei Marisa S. , McCarrey John R. , Yanagimachi Ryuzo
Published: July 2005

We previously reported that the genomes of gonadal germ cells at 11.5–19.5 days postcoitum (dpc) are incompetent to support full-term development of cloned mouse embryos. In this study, we performed nuclear transfer using primordial germ cells (PGCs) from earlier stages at 8.5–10.5 dpc. When PGC nuclei at 8.5, 9.5, and 10.5 dpc were transferred into enucleated oocytes, seven cloned embryos developed into full-term offspring. Of these, five, all derived from 8.5- or 9.5-dpc PGCs, developed into healthy adults with normal fertility. Of the remaining two offspring derived from 10.5-dpc PGCs, one died shortly after birth, and the other showed slight growth retardation but subsequently developed into a fertile adult. We examined allele-specific methylation at the imprinted
H19
and
Snrpn
loci in 9.5- to 11.5-dpc PGCs. Although the beginning of methylation erasure was evident on the
H19
paternal allele at 9.5 dpc, most PGCs did not demonstrate significant erasure of paternal allele-specific methylation until 10.5 dpc. Maternal allele-specific methylation was largely erased from
Snrpn
by 10.5 dpc. By 11.5 dpc, the majority of PGCs showed nearly complete or complete erasure of allele-specific methylation in both
H19
and
Snrpn
. These results demonstrate that at least some genomic imprints remain largely intact in 8.5- to 9.5-dpc PGCs and then undergo erasure at ≈10.5 dpc as the PGCs enter the genital ridges. Thus, migrating PGCs at 8.5–9.5 dpc can be successfully used as donors for nuclear transfer, whereas gonadal PGCs at 11.5 dpc and later are incompetent to support full-term development.
Generating chromosome instability through the simultaneous deletion of
Mad2
and
p53
Authors: Burds Aurora A. , Lutum Annegret Schulze , Sorger Peter K.
Published: July 2005

Cancer cells exhibit high levels of chromosome instability (CIN), and considerable interest surrounds the possibility that inactivation of the spindle checkpoint is involved. However, homozygous disruption of
Mad
and
Bub
checkpoint genes in metazoans causes cell death rather than CIN. We now report the isolation and characterization of blastocysts and two independent mouse embryonic fibroblast lines carrying deletions in
Mad2
and
p53
. These cells lack a functional spindle checkpoint, undergo anaphase prematurely, and exhibit an extraordinarily high level of CIN. We conclude that the mitotic checkpoint is not essential for viability
per se
and that a CIN phenotype can be established in culture through the inactivation of both the
Mad2
- and
p53
-dependent checkpoint pathways.
A note concerning the Lighthill “sandwich model” of tropical cyclones
Authors: Barenblatt G. I. , Chorin A. J. , Prostokishin V. M.
Published: July 2005

The basic element of Lighthill's “sandwich model” of tropical cyclones is the existence of “ocean spray,” a layer intermediate between air and sea made up of a cloud of droplets that can be viewed as a “third fluid.” We propose a mathematical model of the flow in the ocean spray based on a semiempirical turbulence theory and demonstrate that the availability of the ocean spray over the waves in the ocean can explain the tremendous acceleration of the wind as a consequence of the reduction of the turbulence intensity by droplets. This explanation complements the thermodynamic arguments proposed by Lighthill.
The Kinesinlike Protein Subito Contributes to Central Spindle Assembly and Organization of the Meiotic Spindle inDrosophilaOocytes
Authors: Jang J. K. , Rahman T. , McKim K. S.
Published: July 2005

In the oocytes of many species, bipolar spindles form in the absence of centrosomes. Drosophila melanogaster oocyte chromosomes have a major role in nucleating microtubules, which precedes the bundling and assembly of these microtubules into a bipolar spindle. Here we present evidence that a region similar to the anaphase central spindle functions to organize acentrosomal spindles. Subito mutants are characterized by the formation of tripolar or monopolar spindles and nondisjunction of homologous chromosomes at meiosis I. Subito encodes a kinesinlike protein and associates with the meiotic central spindle, consistent with its classification in the Kinesin 6/MKLP1 family. This class of proteins is known to be required for cytokinesis, but our results suggest a new function in spindle formation. The meiotic central spindle appears during prometaphase and includes passenger complex proteins such as AurB and Incenp. Unlike mitotic cells, the passenger proteins do not associate with centromeres before anaphase. In the absence of Subito, central spindle formation is defective and AurB and Incenp fail to properly localize. We propose that Subito is required for establishing and/or maintaining the central spindle in Drosophila oocytes, and this substitutes for the role of centrosomes in organizing the bipolar spindle.
Mechanism of IFN-γ-induced Endocytosis of Tight Junction Proteins: Myosin II-dependent Vacuolarization of the Apical Plasma Membrane
Authors: Utech Markus , Ivanov Andrei I. , Samarin Stanislav N. , Bruewer Matthias , Turner Jerrold R. , Mrsny Randall J. , Parkos Charles A. , Nusrat Asma
Published: July 2005

Disruption of epithelial barrier by proinflammatory cytokines such as IFN-γ represents a major pathophysiological consequence of intestinal inflammation. We have previously shown that IFN-γ increases paracellular permeability in model T84 epithelial cells by inducing endocytosis of tight junction (TJ) proteins occludin, JAM-A, and claudin-1. The present study was designed to dissect mechanisms of IFN-γ-induced endocytosis of epithelial TJ proteins. IFN-γ treatment of T84 cells resulted in internalization of TJ proteins into large actin-coated vacuoles that originated from the apical plasma membrane and resembled the vacuolar apical compartment (VAC) previously observed in epithelial cells that lose cell polarity. The IFN-γ dependent formation of VACs required ATPase activity of a myosin II motor but was not dependent on rapid turnover of F-actin. In addition, activated myosin II was observed to colocalize with VACs after IFN-γ exposure. Pharmacological analyses revealed that formation of VACs and endocytosis of TJ proteins was mediated by Rho-associated kinase (ROCK) but not myosin light chain kinase (MLCK). Furthermore, IFN-γ treatment resulted in activation of Rho GTPase and induced expressional up-regulation of ROCK. These results, for the first time, suggest that IFN-γ induces endocytosis of epithelial TJ proteins via RhoA/ROCK-mediated, myosin II-dependent formation of VACs.
TheCaenorhabditis elegans aristalessOrthologue,alr-1, Is Required for Maintaining the Functional and Structural Integrity of the Amphid Sensory Organs
Authors: Tucker Morgan , Sieber Matt , Morphew Mary , Han Min
Published: July 2005

The homeobox-containing aristaless-related protein ARX has been directly linked to the development of a number of human disorders involving mental retardation and epilepsy and clearly plays a critical role in development of the vertebrate central nervous system. In this work, we investigate the role of ALR-1, the Caenorhabditis elegans aristaless orthologue, in amphid sensory function. Our studies indicate that ALR-1 is required for maintenance of the amphid organ structure throughout larval development. Mutant analysis indicates a progressive loss in the amphid neurons' ability to fill with lipophilic dyes as well as a declining chemotactic response. The degeneration in amphid function corresponds with a failure of the glial-like amphid socket cell to maintain its specific cell shape and cell–cell contacts. Consistent with ALR-1 expression within the amphid socket cell, our results indicate a cell autonomous role for ALR-1 in maintaining cell shape. Furthermore, we demonstrate a role for ALR-1 in the proper morphogenesis of the anterior hypodermis. Genetic interaction tests also suggest that ALR-1 may function cooperatively with the cell adhesion processes in maintaining the amphid sensory organs.
The Retrotranslocation Protein Derlin-1 Binds Peptide:N-Glycanase to the Endoplasmic Reticulum
Authors: Katiyar Samiksha , Joshi Shivanjali , Lennarz William J.
Published: July 2005

The deglycosylating enzyme, peptide:N-glycanase, acts on misfolded N-linked glycoproteins dislocated from the endoplasmic reticulum (ER) to the cytosol. Deglycosylation has been demonstrated to occur at the ER membrane and in the cytosol. However, the mechanism of PNGase association with the ER membrane was unclear, because PNGase lacked the necessary signal to facilitate its incorporation in the ER membrane, nor was it known to bind to an integral ER protein. Using HeLa cells, we have identified a membrane protein that associates with PNGase, thereby bringing it in close proximity to the ER and providing accessibility to dislocating glycoproteins. This protein, Derlin-1, has recently been shown to mediate retrotranslocation of misfolded glycoproteins. In this study we demonstrate that Derlin-1 interacts with the N-terminal domain of PNGase via its cytosolic C-terminus. Moreover, we find PNGase distributed in two populations; ER-associated and free in the cytosol, which suggests the deglycosylation process can proceed at either site depending on the glycoprotein substrate.
Helicobacter pyloriVacA Cytotoxin: A Probe for a Clathrin-independent and Cdc42-dependent Pinocytic Pathway Routed to Late Endosomes
Authors: Gauthier Nils C. , Monzo Pascale , Kaddai Vincent , Doye Anne , Ricci Vittorio , Boquet Patrice
Published: July 2005

The vacuolating cytotoxin VacA is a major virulence factor of Helicobacter pylori, a bacterium responsible for gastroduodenal ulcers and cancer. VacA associates with lipid rafts, is endocytosed, and reaches the late endocytic compartment where it induces vacuolation. We have investigated the endocytic and intracellular trafficking pathways used by VacA, in HeLa and gastric AGS cells. We report here that VacA was first bound to plasma-membrane domains localized above F-actin structures that were controlled by the Rac1 GTPase. VacA was subsequently pinocytosed by a clathrin-independent mechanism into cell peripheral early endocytic compartments lacking caveolin 1, the Rab5 effector early endosomes antigen-1 (EEA1) and transferrin. These compartments took up fluid-phase (as evidenced by the accumulation of fluorescent dextran) and glycosylphosphatidylinositol-anchored proteins (GPI-APs). VacA pinocytosis was controlled by Cdc42 and did not require cellular tyrosine kinases, dynamin 2, ADP-ribosylating factor 6, or RhoA GTPase activities. VacA was subsequently routed to EEA1-sorting endosomes and then sorted to late endosomes. During all these different endocytic steps, VacA was continuously associated with detergent resistant membrane domains. From these results we propose that VacA might be a valuable probe to study raft-associated molecules, pinocytosed by a clathrin-independent mechanism, and routed to the degradative compartment.
Celiac Disease with Mild to Moderate Histologic Changes is a Common Cause of Chronic Diarrhea in Indian Children
Authors: Bhatnagar Shinjini , Gupta Sidhartha Datta , Mathur Meera , Phillips Alan D , Kumar Ramesh , Knutton Stuart , Unsworth Joe , Lock Bob , Natchu Uma C. M , Mukhopadhyaya Sanjay , Saini Savita , Bhan Maharaj K
Published: July 2005

Objectives:

In developed countries, small bowel histology in coeliac disease is a spectrum, ranging from normal with increased intraepithelial lymphocytes to the classic flat mucosa. In developing countries, mild to moderate enteropathies in children with chronic diarrhea and growth failure are assumed to be caused by tropical sprue, persistent infections, or malnutrition with bacterial overgrowth. We report the prevalence and histology of coeliac disease in children with chronic diarrhea at a tertiary referral hospital in North India.

Methods:

Two hundred fifty‐nine children with symptoms indicating coeliac disease attended the All India Institute of Medical Sciences. Histology was graded after a modified Marsh classification. Serum immunoglobulin A anti‐endomysial antibodies (AEA) were assayed using indirect immunofluorescence. Subjects with abnormal histology and positive AEA were put on a gluten free diet (GFD). Coeliac disease was diagnosed on small intestinal biopsy changes and a clinical response to a GFD.

Results:

Severe enteropathies were present in 63 (24%) subjects, and 58 (92%) responded to a GFD. Sixty‐six (25%) had moderate histologic changes, 61 responding to a GFD. AEA was positive in 56 of 63 patients with severe and 65 of 66 with moderate enteropathies. Fifty‐seven children had mild enteropathies, and 19 of 20 with positive AEA responded clinically to a GFD.

Conclusions:

Coeliac disease is more common than previously believed. It presents a variable histology, and diagnoses may be missed or delayed if based only on severe enteropathies. Serology is a useful adjunct to diagnosis, and diagnostic criteria need to be developed appropriately for coeliac disease in developing countries despite limited facilities.
The determination of best values of the fundamental physical constants
Authors: Taylor Barry N
Published: July 2005

The purpose of this paper is to provide an overview of how a self-consistent set of ‘best values’ of the fundamental physical constants for use worldwide by all of science and technology is obtained from all of the relevant data available at a given point in time. The basis of the discussion is the 2002 Committee on Data for Science and Technology (CODATA) least-squares adjustment of the values of the constants, the most recent such study available, which was carried out under the auspices of the CODATA Task group on fundamental constants. A detailed description of the 2002 CODATA adjustment, which took into account all relevant data available by 31 December 2002, plus selected data that became available by Fall of 2003, may be found in the January 2005 issue of the
Reviews of Modern Physics
. Although the latter publication includes the full set of CODATA recommended values of the fundamental constants resulting from the 2002 adjustment, the set is also available electronically at
http://physics.nist.gov/constants
.
Pharmacogenetics in drug development
Authors: McCarthy Alun D , Kennedy James L , Middleton Lefkos T
Published: July 2005

Over the last two decades, identification of polymorphisms that influence human diseases has begun to have an impact on the provision of medical care. The promise of genetics lies in its ability to provide insights into an individual's susceptibility to disease, the likely nature of the disease and the most appropriate therapy. For much of its history, pharmacogenetics (PGx—the use of genetic information to impact drug choice) has been limited to comparatively simple phenotypes such as plasma drug levels. Progress in genetics technologies has broadened the scope of PGx efficacy and safety studies that can be implemented, impacting on a broad spectrum of drug discovery and development activities. Recent PGx data show the ability of this approach to generate information that can be applied to dose selection, efficacy determination and safety issues. This in turn will lead to significant opportunities to affect both the approach to clinical development and the probability of success—the latter being an important aspect for pharmaceutical companies and for the patients who will benefit from these new medicines.
Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila
Authors: Baeg Gyeong-Hun , Zhou Rui , Perrimon Norbert
Published: July 2005

The cytokine-activated Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway plays an important role in the control of a wide variety of biological processes. When misregulated, JAK/STAT signaling is associated with various human diseases, such as immune disorders and tumorigenesis. To gain insights into the mechanisms by which JAK/STAT signaling participates in these diverse biological responses, we carried out a genome-wide RNA interference (RNAi) screen in cultured Drosophila cells. We identified 121 genes whose double-stranded RNA (dsRNA)-mediated knockdowns affected STAT92E activity. Of the 29 positive regulators, 13 are required for the tyrosine phosphorylation of STAT92E. Furthermore, we found that the Drosophila homologs of RanBP3 and RanBP10 are negative regulators of JAK/STAT signaling through their control of nucleocytoplasmic transport of STAT92E. In addition, we identified a key negative regulator of Drosophila JAK/STAT signaling, protein tyrosine phosphatase PTP61F, and showed that it is a transcriptional target of JAK/STAT signaling, thus revealing a novel negative feedback loop. Our study has uncovered many uncharacterized genes required for different steps of the JAK/STAT signaling pathway.
Green Sperm. Identification of Male Gamete Promoters in Arabidopsis
Authors: Engel Michele L. , Holmes-Davis Rachel , McCormick Sheila
Published: July 2005

Previously, in an effort to better understand the male contribution to fertilization, we completed a maize (Zea mays) sperm expressed sequence tag project. Here, we used this resource to identify promoters that would direct gene expression in sperm cells. We used reverse transcription-polymerase chain reaction to identify probable sperm-specific transcripts in maize and then identified their best sequence matches in the Arabidopsis (Arabidopsis thaliana) genome. We tested five different Arabidopsis promoters for cell specificity, using an enhanced green fluorescent protein reporter gene. In pollen, the AtGEX1 (At5g55490) promoter is active in the sperm cells and not in the progenitor generative cell or in the vegetative cell, but it is also active in ovules, roots, and guard cells. The AtGEX2 (At5g49150) promoter is active only in the sperm cells and in the progenitor generative cell, but not in the vegetative cell or in other tissues. A third promoter, AtVEX1 (At5g62580), was active in the vegetative cell during the later stages of pollen development; the other promoters tested (At1g66770 and At1g73350) did not function in pollen. Comparisons among GEX1 and GEX2 homologs from maize, rice (Oryza sativa), Arabidopsis, and poplar (Populus trichocarpa) revealed a core binding site for Dof transcription factors. The AtGEX1 and AtGEX2 promoters will be useful for manipulating gene expression in sperm cells, for localization and functional analyses of sperm proteins, and for imaging of sperm dynamics as they are transported in the pollen tube to the embryo sac.