bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of chronic activation of peroxisome proliferator-activated receptor-α or high-fat feeding in a rat infarct model of heart failure
Authors: Morgan Eric E. , Rennison Julie H. , Young Martin E. , McElfresh Tracy A. , Kung Theodore A. , Tserng Kou-Yi , Hoit Brian D. , Stanley William C. , Chandler Margaret P.
Published: December 2005

Intracardiac accumulation of lipid and related intermediates (e.g., ceramide) is associated with cardiac dysfunction and may contribute to the progression of heart failure (HF). Overexpression of nuclear receptor peroxisome proliferator-activated receptor-α (PPARα) increases intramyocellular ceramide and left ventricular (LV) dysfunction. We tested the hypothesis that activation of fatty acid metabolism with fat feeding or a PPARα agonist increases myocardial triglyceride and/or ceramide and exacerbates LV dysfunction in HF. Rats with infarct-induced HF ( n = 38) or sham-operated rats ( n = 10) were either untreated (INF, n = 10), fed a high-fat diet (45% kcal fat, INF + Fat, n = 15), or fed the PPARα agonist fenofibrate (150 mg·kg−1·day−1, INF + Feno, n = 13) for 12 wk. LV ejection fraction was significantly reduced with HF (49 ± 6%) compared with sham operated (86 ± 2%) with no significant differences in ejection fraction (or other functional or hemodynamic measures) among the three infarcted groups. Treatment with the PPARα agonist resulted in LV hypertrophy (24% increase in LV/body mass ratio) and induced mRNAs encoding for PPARα-regulated genes, as well as protein expression and activity of medium chain acyl-CoA dehydrogenase (compared with INF and INF + Fat groups). Myocardial ceramide content was elevated in the INF group compared with sham-operated rats, with no further change in the INF + Fat or INF + Feno groups. Myocardial triglyceride was unaffected by infarction but increased in the INF + Fat group. In conclusion, LV dysfunction and dilation are not worsened despite upregulation of the fatty acid metabolic pathway and LV hypertrophy or accumulation of myocardial triglyceride in the rat infarct model of HF.
Energy Fluxes due to the Surface and Internal Tides in Knight Inlet, British Columbia
Authors: Stacey Michael W. , Pond S.
Published: December 2005

A laterally integrated (two dimensional) nonlinear numerical model is used to examine the flux of M2 tidal energy in Knight Inlet. The simulated flux of tidal energy into the inlet is somewhat smaller than that estimated using the change in phase of the M2 tidal height along the inlet, a method that does not account for the effect of the internal tide on the surface elevation. The simulated energy flux into the inlet is close to the energy flux of the internal tide away from the sill determined from observations using an acoustic Doppler current profiler (ADCP). The net flux due to the internal tide is significantly less than (<1/2 of) the rate at which energy is removed from the surface tide. Earlier linear models of the internal tide produced energy fluxes that agreed with those estimated from the phase change of the tidal height but were larger than the fluxes that could be found in the observations. The reason for this discrepancy is not that these simple models neglected nonlinear effects, but rather that they did not take reflections of the internal tide into account. Also, the simulated flux of energy into the inlet less the net flux of internal tidal energy away from the sill is about equal to the simulated dissipation within 2 km on either side of the sill. The simulated net flux of internal tidal energy away from the sill is in agreement with the flux determined from the ADCP observations on the downinlet side of the sill, but not on the upinlet side of the sill. A possible explanation is that only the first internal mode (which is surface intensified) was important on the downinlet side but the first three internal modes were important on the upinlet side. The flux calculation using the ADCP observations took variations in the inlet width into account but did not take depth variations into account; thus, the reflection coefficients of the second and third modes may have been underestimated.
Experiments and Simulations on Coastal Flows in the Presence of a Topographic Slope
Authors: Sansón L. Zavala , Serravall R. , Carnevale G. F. , van Heijst G. J. F.
Published: December 2005

The evolution of a barotropic coastal current in the presence of a bottom ramp-shaped topography is studied by means of laboratory experiments and numerical simulations. The experiments are performed in a rectangular rotating tank filled with freshwater. The fluid depth is shallow at one side of the domain and deeper at the other side, and both regions are divided by a narrow slope, whose depth contours are perpendicular to the long sides of the tank. A current approaching the slope is produced along one of the vertical walls, having the boundary at its right. Two configurations are analyzed: when the current flows from shallow to deep water and when flowing in the opposite direction. In the first scenario, the current is divided in two parts, one of them following the coastline. The other part of the current pairs with a cell of negative relative vorticity generated at the slope due to squeezing effects, forming a dipolar structure moving offshore, back toward the shallow side. In addition, a weak current moving inshore along the slope is clearly formed. In the second configuration, when the flow goes from deep to shallow water, a part of or even the whole current might be forced to move along the contours of the topography, away from the coast. In this case there is no dipole formation. The experiments are well reproduced by means of quasigeostrophic numerical simulations, which allow a more detailed systematic study of the influence of flow parameters such as the topography height and the width of the slope.
Bispectral Analysis of Energy Transfer within the Two-Dimensional Oceanic Internal Wave Field
Authors: Furuichi Naoki , Hibiya Toshiyuki , Niwa Yoshihiro
Published: December 2005

Bispectral analysis of the numerically reproduced spectral responses of the two-dimensional oceanic internal wave field to the incidence of the low-mode semidiurnal internal tide is performed. At latitudes just equatorward of 30°, the low-mode semidiurnal internal tide dominantly interacts with two high-vertical-wavenumber diurnal (near inertial) internal waves, forming resonant triads of parametric subharmonic instability (PSI) type. As the high-vertical-wavenumber near-inertial energy level is raised by this interaction, the energy cascade to small horizontal and vertical scales is enhanced. Bispectral analysis thus indicates that energy in the low-mode semidiurnal internal tide is not directly transferred to small scales but via the development of high-vertical-wavenumber near-inertial current shear. In contrast, no noticeable energy cascade to high vertical wavenumbers is recognized in the bispectra poleward of ∼30° as well as equatorward of ∼25°. A new finding is that, although PSI is possible equatorward of ∼30°, the efficiency drops sharply as the latitude falls below ∼25°. At all latitudes, another resonant interaction suggestive of induced diffusion is found to occur between the low-mode semidiurnal internal tide and two high-frequency internal waves, although bispectral analysis shows that this interaction plays only a minor role in cascading the low-mode semidiurnal internal tide energy.
The PPAR-α activator fenofibrate fails to provide myocardial protection in ischemia and reperfusion in pigs
Authors: Xu Ya , Lu Li , Greyson Clifford , Rizeq Mona , Nunley Karin , Wyatt Beata , Bristow Michael R. , Long Carlin S. , Schwartz Gregory G.
Published: December 2005

Rodent studies suggest that peroxisome proliferator-activated receptor-α (PPAR-α) activation reduces myocardial ischemia-reperfusion (I/R) injury and infarct size; however, effects of PPAR-α activation in large animal models of myocardial I/R are unknown. We determined whether chronic treatment with the PPAR-α activator fenofibrate affects myocardial I/R injury in pigs. Domestic farm pigs were assigned to treatment with fenofibrate 50 mg·kg−1·day−1 orally or no drug treatment, and either a low-fat (4% by weight) or a high-fat (20% by weight) diet. After 4 wk, 66 pigs underwent 90 min low-flow regional myocardial ischemia and 120 min reperfusion under anesthetized open-chest conditions, resulting in myocardial stunning. The high-fat group received an infusion of triglyceride emulsion and heparin during this terminal experiment to maintain elevated arterial free fatty acid (FFA) levels. An additional 21 pigs underwent 60 min no-flow ischemia and 180 min reperfusion, resulting in myocardial infarction. Plasma concentration of fenofibric acid was similar to the EC50 for activation of PPAR-α in vitro and to maximal concentrations achieved in clinical use. Myocardial expression of PPAR-α mRNA was prominent but unaffected by fenofibrate treatment. Fenofibrate increased expression of carnitine palmitoyltransferase (CPT)-I mRNA in liver and decreased arterial FFA and lactate concentrations (each P < 0.01). However, fenofibrate did not affect myocardial CPT-I expression, substrate uptake, lipid accumulation, or contractile function during low-flow I/R in either the low- or high-fat group, nor did it affect myocardial infarct size. Despite expression of PPAR-α in porcine myocardium and effects of fenofibrate on systemic metabolism, treatment with this PPAR-α activator does not alter myocardial metabolic or contractile responses to I/R in pigs.
Nicotinamide adenine dinucleotide is released from sympathetic nerve terminals via a botulinum neurotoxin A-mediated mechanism in canine mesenteric artery
Authors: Smyth Lisa M. , Breen Leanne T. , Mutafova-Yambolieva Violeta N.
Published: December 2005

Using high-performance liquid chromatography techniques with fluorescence and electrochemical detection, we found that β-nicotinamide adenine dinucleotide (β-NAD) is released in response to electrical field stimulation (4–16 Hz, 0.3 ms, 15 V, 120 s) along with ATP and norepinephrine (NE) in the canine isolated mesenteric arteries. The release of β-NAD increases with number of pulses/stimulation frequencies. Immunohistochemistry analysis showed dense distribution of tyrosine hydroxylase-like immunoreactivity (TH-LI) and sparse distribution of TH-LI-negative nerve processes, suggesting that these blood vessels are primarily under sympathetic nervous system control with some contribution of other (e.g., sensory) neurons. Exogenous NE (3 μmol/l), α,β-methylene ATP (1 μmol/l), neuropeptide Y (NPY, 0.1 μmol/l), CGRP (0.1 μmol/l), vasoactive intestinal peptide (VIP, 0.1 μmol/l), and substance P (SP, 0.1 μmol/l) had no effect on the basal release of β-NAD, suggesting that the overflow of β-NAD is evoked by neither the sympathetic neurotransmitters NE, ATP, and NPY, nor the neuropeptides CGRP, VIP, and SP. Botulinum neurotoxin A (BoNTA, 0.1 μmol/l) abolished the evoked release of NE, ATP, and β-NAD at 4 Hz, suggesting that at low levels of neural activity, release of these neurotransmitters results from N-ethylmaleimide-sensitive factor attachment protein receptor/synaptosomal-associated protein of 25 kDa-mediated exocytosis. At 16 Hz, however, the evoked release of NE, ATP, and β-NAD was reduced by BoNTA by ∼90, 60, and 80%, respectively, suggesting that at higher levels of neural activity, β-NAD is likely to be released from different populations of synaptic vesicles or different populations of nerve terminals (i.e., sympathetic and sensory terminals).
The "Relative Universality" of Human Rights: An Assessment
Authors: On Steve
Published: December 2005

This essay makes an assessment of Jack Donnelly's model of overlapping consensus on the Universal Declaration of Human Rights. It raises key questions, such as: How to adjudicate competing rights; what is to become of "unreasonable" views; whence come reasonable views; and, beyond the obvious cases of slavery and genocide, how is the overlapping consensus obtained? While an alternative theory is not developed, a critical perspective is provided that might facilitate further inquiries.
The United Nations and International Security in the New Millennium
Authors: Knight W. Andy
Published: December 2005

The end of the Cold War opened a window of opportunity for the United Nations to play a greater role in international security than it was allowed to play in the midst of the ideological conflict between the United States and the former Soviet Union. However, the expected "peace dividend" never materialized in the post-Cold War period. Instead, a number of civil conflicts erupted and new threats to security, particularly to human security, emerged. This chapter critically examines the evolution of the UN's role in addressing international security problems since 1945, including global terrorism. It also outlines recent attempts by the world body, through extension of its reach beyond the territorial constraints of sovereignty, to build sustained peace through preventive measures and protect human security globally.
Permits to Search Shipwrecks: Recent Amendment to the Act Concerning the Maritime Areas of the Polish Republic and the Marine Administration of 21st March 1991
Authors: Blazkiewicz Bernard
Published: December 2005

The purpose of these short comments is to shed some light on Polish new regulations concerning permits to search shipwrecks. Comments first provide brief description of the regulations and their enabling act, and second argue that the regulations lack the precision in determining their scope of application. As a result, this lack of precision leads to the inconsistency of the new regulations with the international law of the sea. Regulations provide jurisdiction to issue permits to search shipwreck, over all persons in Polish Maritime Areas, including exclusive economic zone, which is contrary to the United Nations Convention on the Law of the Sea, ratified by Poland. In that case, and in accordance with Polish law, international obligations prevail over national rule, and in consequence, the maritime administration cannot issue permits for search of shipwreck for aliens within Polish EEZ.
Withdrawing Life Support from Patients in a Persistent Vegetative State: the Law in The Netherlands
Authors: Gevers Sjef
Published: December 2005

This article sets out how a case like that of ms. Schiavo is likely to be decided in a Dutch court and compares that with the law in the United States. In the Netherlands there is one case with striking similarities: the decision of the Arnhem Court of Appeal of 1989. After describing that case (which to a large extent still reflects the legal state of the art), comments are given on several aspects of the issue, such as the labelling of artifical feeding as a medical intervention, the role of the physician, the position of the proxy or surrogate, the ways to resolve dispute in case of conflict, and the significance of advance directives. The analysis will show that, although there is more consensus on the issue now than there was 16 years ago, there are still several questions that need to be addressed in the future.
Terri Schiavo: the Assessment of the Persistent Vegetative State in Accordance with German Law
Authors: Becker-Schwarze Kathrin
Published: December 2005

The case of Terri Schiavo in the USA served to intensify the debate in Germany which itself had in part already been characterised by fundamentalism. Now that some time has elapsed and the political debate has quietened, this case is to be taken up again in discussing the permissibility and the prerequisites of passive euthanasia for patients in a persistent vegetative state. A short reconstruction of the facts of the case (II) is to be followed by a survey of the case law of the Criminal Panels(III) which is essential to understand the present legal policy debate to be discussed at a later stage (IV).
Wave-Forced Barotropic Currents
Authors: Broström Göran
Published: December 2005

Waves rolling in to shallow seas will start to dissipate as a result of the bottom friction. The wave momentum will decrease from the dissipation process, and there is a transfer of momentum that accelerates an Eulerian bottom current. Water piles up toward the coast, thereby generating a return flow. When rotation is included, the return flows accelerate an alongshore current that moves to the left of the direction of the incoming wave field (Northern Hemisphere). With the assumption that the turbulent exchange can be mimicked by a constant exchange coefficient, there is a fairly simple analytical solution that relates the strength of the barotropic current to the incoming wave field. For deep water, that is, H ≫ 2υt/f, where f is the Coriolis force and νt is the turbulent exchange coefficient, the strength of the alongshore barotropic current becomes 3/2 of the Stokes drift near the bottom or 3ωka2/4 sinh(kH), where ω and k are the wave angular frequency and wavenumber, and a is the amplitude of the wave. Notably, the above expression is equal to the strength of the Eulerian streaming generated under a progressive wave by the wave-induced Reynold stresses in the viscous wave bottom boundary layer.
Energy Transmission by Barotropic Rossby Waves Revisited
Authors: Matano R. P. , Palma E. D.
Published: December 2005

This article presents a semianalytic method to investigate the properties of energy transmission across bottom topography by barotropic Rossby waves. The method is first used to revisit the analytical estimates derived from wave-matching techniques and Wentzel–Kramers–Brillouin (WKB) approximations. The comparison between the semianalytic method and WKB indicates that the results of the latter are valid for waves with periods longer than a month and ridges taller than ∼1000 m and wider than ∼500 km. For these parameter values both methods predict the passage of low-frequency waves and the reflection of high-frequency waves. The semianalytic method is then used to discuss the energy transmission properties of a cross section of the Mid-Atlantic Ridge. It is shown that the filtering characteristics of realistic bottom topographies depend not only on the spatial scale set by the cross-section envelope, but also on the scales of the individual peaks. This dependence is related to the fact that topographies narrower than ∼400 km (e.g., peaks) are high-pass filters of incoming waves, while topographies wider than that (e.g., cross-section envelopes) are low-pass filters. In the particular case of the Mid-Atlantic Ridge the neglect of the contribution of individual peaks leads to an erroneous estimate of the filtering properties of the massif.
Embryonic Stem–Derived Versus Somatic Neural Stem Cells: A Comparative Analysis of Their Developmental Potential and Molecular Phenotype
Authors: Colombo Elena , Giannelli Serena G. , Galli Rossella , Tagliafico Enrico , Foroni Chiara , Tenedini Elena , Ferrari Sergio , Ferrari Stefano , Corte Giorgio , Vescovi Angelo , Cossu Giulio , Broccoli Vania
Published: December 2005

Reliable procedures to induce neural commitment of totipotent undifferentiated embryonic stem (ES) cells have provided new tools for investigating the molecular mechanisms underlying cell fate choices. We extensively characterized the developmental potential of ES-induced neural cells obtained using an adaptation of the multistep induction protocol. We provided evidence that ES-derived neural proliferating cells are endowed with stem cell properties such as extensive self-renewal capacity and single-cell multipotency. In differentiating conditions, cells matured exclusively into neurons, astrocytes, and oligodendrocytes. All these features have been previously described in only somatic neural stem cells (NSCs). Therefore, we consider it more appropriate to rename our cells ES-derived NSCs. These similarities between the two NSC populations induced us to carefully compare their proliferation ability and differentiation potential. Although they were very similar in overall behavior, we scored specific differences. For instance, ES-derived NSCs proliferated at higher rate and consistently generated a higher number of neurons compared with somatic NSCs. To further investigate their relationships, we carried out a molecular analysis comparing their transcriptional profiles during proliferation. We observed a large fraction of shared expressed transcripts, including genes previously described to be critical in defining somatic NSC traits. Among the genes differently expressed, candidate genes possibly responsible for divergences between the two cell types were selected and further investigated. In particular, we showed that an enhanced MAPK (mitogen-activated protein kinase) signaling is acting in ES-induced NSCs, probably triggered by insulin-like growth factor–II. This may contribute to the high proliferation rate exhibited by these cells in culture.
Novel phosphate glass/polyamide 6 hybrids: Miscibility, crystallization kinetics, and mechanical properties
Authors: Urman Kevin , Otaigbe Joshua
Published: December 2005

The miscibility, crystallization kinetics, and mechanical properties of a novel low Tg phosphate glass (Pglass)/polyamide 6 hybrid material were investigated. Here, we report the first evidence for miscibility of inorganic phosphate glass and organic polymer prepared by blending both components in the liquid phase using conventional polymer processing methods. From classical melting point depression measurements, we obtained a chi interaction parameter (χ) of −0.067 for the Pglass/polyamide 6 hybrid, indicating that the inorganic glass and polyamide 6 are miscible. The crystallization kinetic parameters for the hybrids were determined using the Avrami approach and found to depend on the volume fraction of Pglass present in the system. In addition, we studied both the dynamic and static mechanical behavior of the hybrids. The results showed a single Tg that decreased by up to 10 °C with increasing phosphate glass volume percent for the hybrids, giving further evidence for the hybrid component miscibility and plasticizing action of the phosphate glass in the pure polyamide 6, respectively. The tensile (static) mechanical properties of the hybrids were found to be remarkably similar to those obtained from typical polymers plasticized with relatively low molecular weight compounds. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 441–450, 2006
Effects of microscale calcium carbonate and nanoscale calcium carbonate on the fusion, thermal, and mechanical characterizations of rigid poly(vinyl chloride)/calcium carbonate composites
Authors: Chen Cheng‐Ho , Teng Chih‐Chun , Su Shun‐Fua , Wu Wen‐Chang , Yang Chien‐Hsin
Published: December 2005

A Haake torque rheometer equipped with an internal mixer has been used to study the influence of microscale calcium carbonate (micro‐CaCO3) and nanoscale calcium carbonate (nano‐CaCO3) on the fusion, thermal, and mechanical characteristics of rigid poly(vinyl chloride) (PVC)/micro‐CaCO3 and PVC/nano‐CaCO3 composites, respectively. The fusion characteristics discussed in this article include the fusion time, fusion temperature, fusion torque, and fusion percolation threshold (FPT). The fusion time, fusion temperature, and FPT of rigid PVC/calcium carbonate (CaCO3) composites increase with an increase in the addition of micro‐CaCO3 or nano‐CaCO3. In contrast, the fusion torque of rigid PVC/CaCO3 composites decreases with an increase in the addition of micro‐CaCO3 or nano‐CaCO3. The results of thermal analysis show that the first thermal degradation onset temperature (Tonset) of rigid PVC/micro‐CaCO3 is 7.5 °C lower than that of PVC. Meanwhile, the glass‐transition temperature (Tg) of rigid PVC/micro‐CaCO3 is similar to that of PVC. However, Tonset and Tg of PVC/nano‐CaCO3 composites can be increased by up to 30 and 4.4%, respectively, via blending with 10 phr nano‐CaCO3. Mechanical testing results for PVC/micro‐CaCO3 composites with the addition of 5–15 phr micro‐CaCO3 and PVC/nano‐CaCO3 composites with the addition of 5–20 phr nano‐CaCO3 are better than those of PVC. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 451–460, 2006
On the relation between sensory deafferentation, pain and thalamic activity in Wallenberg's syndrome: A PET‐scan study before and after motor cortex stimulation
Authors: Garcia‐Larrea Luis , Maarrawi Joseph , Peyron Roland , Costes Nicolas , Mertens Patrick , Magnin Michel , Laurent Bernard
Published: December 2005

Decrease of thalamic blood flow contralateral to neuropathic pain has been described by several groups, but its relation with sensory deafferentation remains unclear. Here we report one instance where the thalamic effects of sensory deafferentation could be dissociated from those of neuropathic pain. A 50‐year‐old patient underwent a left medullary infarct leading to right‐sided thermal and pain hypaesthesia up to the third right trigeminal division, as well as in the left face. During the following months the patient developed neuropathic pain limited to the left side of the face. Although the territory with sensory loss was much wider in the right (non painful) than in the left (painful) side of the body, PET‐scan demonstrated significant reduction of blood flow in the right thalamus (contralateral to the small painful area) relative to its homologous region. After 3 months of right motor cortex stimulation the patient reported 60% relief of his left facial pain, and a new PET‐scan showed correction of the thalamic asymmetry. We conclude that thalamic PET‐scan hypoactivity contralateral to neuropathic pain does not merely reflect deafferentation, but appears related to the pain pathophysiology, and may be normalized in parallel with pain relief. The possible mechanisms linking thalamic hypoactivity and pain are discussed in relation with findings in epileptic patients, possible compensation phenomena and bursting thalamic discharges described in animals and humans. Restoration of thalamic activity in neuropathic pain might represent one important condition to obtain successful relief by analgesic procedures, including cortical neurostimulation.
Identification of otubain 1 as a novel substrate for the Yersinia protein kinase using chemical genetics and mass spectrometry
Authors: Juris Stephen J. , Shah Kavita , Shokat Kevan , Dixon Jack E. , Vacratsis Panayiotis O.
Published: December 2005

Yersinia encodes a protein kinase, YpkA, which disrupts the actin cytoskeleton. Using an approach termed chemical genetics, we identified a 36‐kDa substrate for YpkA in both J774 lysates and bovine brain cytosol. Mass spectrometry analysis identified this substrate as FLJ20113, an open reading frame that corresponds to otubain 1, a deubiquitinating enzyme implicated in immune cell clonal anergy. We demonstrate that otubain 1 is phosphorylated by YpkA in vitro and interacts with YpkA and actin in vivo. Identification of otubain 1 as a YpkA substrate suggests that regulation of immune cell anergy may be a survival mechanism for Yersinia.
Transformation‐associated gene regulation by ATF6α during hepatocarcinogenesis
Authors: Arai Masaaki , Kondoh Nobuo , Imazeki Nobuo , Hada Akiyuki , Hatsuse Kazuo , Kimura Fumihiro , Matsubara Osamu , Mori Kazutoshi , Wakatsuki Toru , Yamamoto Mikio
Published: December 2005

We have previously reported that the endoplasmic reticulum (ER) stress‐regulated transmembrane transcription factor 6 α (ATF6α) is implicated in the pathogenesis of hepatocellular carcinomas (HCCs). In order to further identify genes that are regulated by ATF6α, the global gene expression profiles of the ATF6α‐transfected and untransfected HCC cell line, HLF, were analyzed. These results were then compared with the differential gene expression patterns of poorly differentiated HCC and control non‐tumorous liver tissue. Our findings demonstrate that at least 18 genes are specifically upregulated by ATF6α, while another UPR mediator, XBP1 or ER‐stress inducer, thapsigargin could partially stimulate or even repress some of them in HCC cells. Moreover, six of these identified genes contain potential ER stress‐responsive elements and/or unfolded protein response elements in their 5′ regulatory regions.
Shoot circumnutation and winding movements require gravisensing cells
Authors: Kitazawa Daisuke , Hatakeda Yasuko , Kamada Motoshi , Fujii Nobuharu , Miyazawa Yutaka , Hoshino Atsushi , Iida Shigeru , Fukaki Hidehiro , Morita Miyo Terao , Tasaka Masao , Suge Hiroshi , Takahashi Hideyuki
Published: December 2005

Circumnutation and winding in plants are universal growth movements that allow plants to survive despite their sessile nature. However, the detailed molecular mechanisms controlling these phenomena remain unclear. We previously found that a gravitropic mutant of Japanese morning glory (
Pharbitis nil
or
Ipomoea nil
), Shidare-asagao (
weeping
), is defective not only in circumnutation but also in the winding response. This phenotype is similar to that of the
Arabidopsis SCARECROW
(
SCR
) mutant. We therefore investigated whether morning glory
SCR
(
PnSCR
) is involved in the
weeping
phenotype. We found that one amino acid was inserted into the highly conserved VHIID motif in
weeping
-type PnSCR; this mutation caused abnormal endodermal differentiation. We introduced either the mutant or WT
PnSCR
into
Arabidopsis scr
mutants for complementation tests.
PnSCR
of the WT, but not of
weeping
, rescued the shoot gravitropism and circumnutation of
scr
. These results show that both the abnormal gravitropism and the circumnutation defect in
weeping
are attributable to a loss of PnSCR function. Thus, our data show that gravisensing endodermal cells are indispensable for shoot circumnutation and the winding response and that PnSCR is responsible for the abnormal phenotypes of
weeping
.
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
Authors: Frost Simon D. W. , Wrin Terri , Smith Davey M. , Pond Sergei L. Kosakovsky , Liu Yang , Paxinos Ellen , Chappey Colombe , Galovich Justin , Beauchaine Jeff , Petropoulos Christos J. , Little Susan J. , Richman Douglas D.
Published: December 2005

HIV type 1 (HIV-1) can rapidly escape from neutralizing antibody responses. The genetic basis of this escapein vivois poorly understood. We compared the pattern of evolution of the HIV-1envgene between individuals with recent HIV infection whose virus exhibited either a low or a high rate of escape from neutralizing antibody responses. We demonstrate that the rate of viral escape at a phenotypic level is highly variable among individuals, and is strongly correlated with the rate of amino acid substitutions. We show that dramatic escape from neutralizing antibodies can occur in the relative absence of changes in glycosylation or insertions and deletions (“indels”) in the envelope; conversely, changes in glycosylation and indels occur even in the absence of neutralizing antibody responses. Comparison of our data with the predictions of a mathematical model support a mechanism in which escape from neutralizing antibodies occurs via many amino acid substitutions, with low cross-neutralization between closely related viral strains. Our results suggest that autologous neutralizing antibody responses may play a pivotal role in the diversification of HIV-1 envelope during the early stages of infection.
The tethered motor domain of a kinesin-microtubule complex catalyzes reversible synthesis of bound ATP
Authors: Hackney David D.
Published: December 2005

Although the steps for the forward reaction of ATP hydrolysis by the motor protein kinesin have been studied extensively, the rates for the reverse reactions and thus the energy changes at each step are not as well defined. Oxygen isotopic exchange between water and P
i
was used to evaluate the reverse rates. The fraction of the kinesin·ADP·P
i
complex that reverts to ATP before release of P
i
during net hydrolysis was ≈0 and ≈2.6% in the absence and presence of microtubules (MTs), respectively. The rate of synthesis of bound ATP from free P
i
and the MT·kinesin·ADP complex was ≈1.7 M
–1
·s
–1
(
K
0.5
ADP = 70 μM) with monomeric kinesin in the absence of net hydrolysis. Synthesis of bound ATP from the ADP of the tethered head of a dimer–MT complex was 20-fold faster than for the monomer–MT complex. This MT-activated ATP synthesis at the tethered head is in marked contrast to the lack of MT stimulation of ADP release from the same site. The more rapid ATP synthesis with dimers suggests that the tethered head binds behind the strongly attached head, because this positions the neck linker of the tethered head toward the plus end of the MT and would thus facilitate its docking on synthesis of ATP. The observed rate of ATP synthesis also puts limits on the overall energetics that suggest that a significant fraction of the free energy of ATP hydrolysis is available to drive the docking of the neck linker on binding of ATP.
Mapping Dmef2-binding regulatory modules by using a ChIP-enriched
in silico
targets approach
Authors: Junion Guillaume , Jagla Teresa , Duplant Sebastien , Tapin Romain , Da Ponte Jean-Philippe , Jagla Krzysztof
Published: December 2005

Mapping the regulatory modules to which transcription factors bind
in vivo
is a key step toward understanding of global gene expression programs. We have developed a chromatin immunoprecipitation (ChIP)-chip strategy for identifying factor-specific regulatory regions acting
in vivo
. This method, called the ChIP-enriched
in silico
targets (ChEST) approach, combines immunoprecipitation of cross-linked protein-DNA complexes (X-ChIP) with
in silico
prediction of targets and generation of computed DNA microarrays. We report the use of ChEST in
Drosophila
to identify several previously unknown targets of myocyte enhancer factor 2 (MEF2), a key regulator of myogenic differentiation. Our approach was validated by demonstrating that the identified sequences act as enhancers
in vivo
and are able to drive reporter gene expression specifically in MEF2-positive muscle cells. Presented here, the ChEST strategy was originally designed to identify regulatory modules in
Drosophila
, but it can be adapted for any sequenced and annotated genome.
An antiviral role for the RNA interference machinery in
Caenorhabditis elegans
Authors: Schott Daniel H. , Cureton David K. , Whelan Sean P. , Hunter Craig P.
Published: December 2005

RNA interference (RNAi) is a sequence-specific gene-silencing mechanism triggered by exogenous dsRNA. In plants an RNAi-like mechanism defends against viruses, but the hypothesis that animals possess a similar natural antiviral mechanism related to RNAi remains relatively untested. To test whether genes needed for RNAi defend animal cells against virus infection, we infected wild-type and RNAi-defective cells of the nematode
C. elegans
with vesicular stomatitis virus engineered to encode a GFP fusion protein. We show that upon infection, cells lacking components of the RNAi apparatus produce more GFP and infective particles than wild-type cells. Furthermore, we show that mutant cells with enhanced RNAi produce less GFP. Our observation that multiple genes required for RNAi are also required for resistance to vesicular stomatitis virus suggests that the RNAi machinery functions in resistance to viruses in nature.
Autoreactive CD8 T cells associated with β cell destruction in type 1 diabetes
Authors: Pinkse Gabrielle G. M. , Tysma Odette H. M. , Bergen Cees A. M. , Kester Michel G. D. , Ossendorp Ferry , van Veelen Peter A. , Keymeulen Bart , Pipeleers Danny , Drijfhout Jan W. , Roep Bart O.
Published: December 2005

Type 1 diabetes is a T cell-mediated autoimmune disease, and insulin is an important target of the autoimmune response associated with β cell destruction. The mechanism of destruction is still unknown. Here, we provide evidence for CD8 T cell autoreactivity associated with recurrent autoimmunity and loss of β cell function in type 1 diabetic islet transplant recipients. We first identified an insulin B chain peptide (insB10-18) with extraordinary binding affinity to HLA-A2(*0201) that is expressed by the majority of type 1 diabetes patients. We next demonstrated that this peptide is naturally processed by both constitutive and immuno proteasomes and translocated to the endoplasmic reticulum by the peptide transporter TAP1 to allow binding to HLA-A2 in the endoplasmic reticulum and cell surface presentation. Peripheral blood mononuclear cells from a healthy donor were primedin vitrowith this peptide, and CD8 T cells were isolated that specifically recognize target cells expressing the insulin B chain peptide. HLA-A2insB10-18tetramer staining revealed a strong association between detection of autoreactive CD8 T cells and recurrent autoimmunity after islet transplantation and graft failure in type 1 diabetic patients. We demonstrate that CD8 T cell autoreactivity is associated with β cell destruction in type 1 diabetes in humans.
Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein
Authors: Hu Jin-Shan , Feng Hanqiao , Zeng Wangyong , Lin Guang-xin , Xi Xu Guang
Published: December 2005

Werner syndrome (WS) is an autosomal recessive disease that results in premature aging. Mutations in the WS gene (
WRN
) result in a loss of expression of the WRN protein and predispose WS patients to accelerated aging. As a helicase and a nuclease, WRN is unique among the five human RecQ helicase family members and is capable of multiple functions involved in DNA replication, repair, recombination, and telomere maintenance. A 144-residue fragment of WRN was previously determined to be a multifunctional DNA- and protein-binding domain (DPBD) that interacts with structure-specific DNA and a variety of DNA-processing proteins. In addition, DPBD functions as a nucleolar targeting sequence of WRN. The solution structure of the DPBD, the first of a WRN fragment, has been solved by NMR. DPBD consists of a winged helix-like motif and an unstructured C-terminal region of ≈20 aa. The putative DNA-binding surface of DPBD has been identified by using known structural and biochemical data. Based on the structural data and on the biochemical data, we suggest a surface on the DPBD for interacting with other proteins. In this structural model, a single winged helix domain binds to both DNA and other proteins. Furthermore, we propose that DPBD functions as a regulatory domain to regulate the enzymatic activity of WRN and to direct cellular localization of WRN through protein–protein interaction.
Structure and Architecture of the Maize Genome
Authors: Haberer Georg , Young Sarah , Bharti Arvind K. , Gundlach Heidrun , Raymond Christina , Fuks Galina , Butler Ed , Wing Rod A. , Rounsley Steve , Birren Bruce , Nusbaum Chad , Mayer Klaus F.X. , Messing Joachim
Published: December 2005

Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%–63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.
The Photorespiratory Arabidopsis shm1 Mutant Is Deficient in SHM1
Authors: Voll Lars M. , Jamai Aziz , Renné Petra , Voll Hildegard , McClung C. Robertson , Weber Andreas P.M.
Published: December 2005

Mitochondrial serine hydroxymethyltransferase (SHMT), combined with glycine decarboxylase, catalyzes an essential sequence of the photorespiratory C2 cycle, namely, the conversion of two molecules of glycine into one molecule each of CO2, NH4+, and serine. The Arabidopsis (Arabidopsis thaliana) mutant shm (now designated shm1-1) is defective in mitochondrial SHMT activity and displays a lethal photorespiratory phenotype when grown at ambient CO2, but is virtually unaffected at elevated CO2. The Arabidopsis genome harbors seven putative SHM genes, two of which (SHM1 and SHM2) feature predicted mitochondrial targeting signals. We have mapped shm1-1 to the position of the SHM1 gene (At4g37930). The mutation is due to a G → A transition at the 5′ splice site of intron 6 of SHM1, causing aberrant splicing and a premature termination of translation. A T-DNA insertion allele of SHM1, shm1-2, and the F1 progeny of a genetic cross between shm1-1 and shm1-2 displayed the same conditional lethal phenotype as shm1-1. Expression of wild-type SHM1 under the control of either the cauliflower mosaic virus 35S or the SHM1 promoter in shm1-1 abrogated the photorespiratory phenotype of the shm mutant, whereas overexpression of SHM2 or expression of SHM1 under the control of the SHM2 promoter did not rescue the mutant phenotype. Promoter-β-glucuronidase analyses revealed that SHM1 is predominantly expressed in leaves, whereas SHM2 is mainly transcribed in the shoot apical meristem and roots. Our findings establish SHM1 as the defective gene in the Arabidopsis shm1-1 mutant.
The Serine/Arginine-Rich Protein Family in Rice Plays Important Roles in Constitutive and Alternative Splicing of Pre-mRNA
Authors: Isshiki Masayuki , Tsumoto Ayako , Shimamoto Ko
Published: December 2005

Ser/Arg-rich (SR) proteins play important roles in the constitutive and alternative splicing of pre-mRNA. We isolated 20 rice (Oryza sativa) genes encoding SR proteins, of which six contain plant-specific characteristics. To determine whether SR proteins modulate splicing efficiency and alternative splicing of pre-mRNA in rice, we used transient assays in rice protoplasts by cotransformation of SR protein genes with the rice Waxyb (Wxb)-β-glucuronidase fusion gene. The results showed that plant-specific RSp29 and RSZp23, an SR protein homologous to human 9G8, enhanced splicing and altered the alternative 5′ splice sites of Wxb intron 1. The resulting splicing pattern was unique to each SR protein; RSp29 stimulated splicing at the distal site, and RSZp23 enhanced splicing at the proximal site. Results of domain-swapping experiments between plant-specific RSp29 and SCL26, which is a homolog of human SC35, showed the importance of RNA recognition motif 1 and the Arg/Ser-rich (RS) domain for the enhancement of splicing efficiencies. Overexpression of plant-specific RSZ36 and SRp33b, a homolog of human ASF/SF2, in transgenic rice changed the alternative splicing patterns of their own pre-mRNAs and those of other SR proteins. These results show that SR proteins play important roles in constitutive and alternative splicing of rice pre-mRNA.
Activation of Nrf2/ARE pathway protects endothelial cells from oxidant injury and inhibits inflammatory gene expression
Authors: Chen Xi-Lin , Dodd Geraldine , Thomas Suzanne , Zhang Xiaolan , Wasserman Martin A. , Rovin Brad H. , Kunsch Charles
Published: December 2005

The antioxidant response element (ARE) is a transcriptional control element that mediates expression of a set of antioxidant proteins. NF-E2-related factor 2 (Nrf2) is a transcription factor that activates ARE-containing genes. In endothelial cells, the ARE-mediated genes are upregulated by atheroprotective laminar flow through a Nrf2-dependent mechanism. We tested the hypothesis that activation of ARE-regulated genes via adenovirus-mediated expression of Nrf2 may suppress redox-sensitive inflammatory gene expression. Expression of Nrf2 in human aortic endothelial cells (HAECs) resulted in a marked increase in ARE-driven transcriptional activity and protected HAECs from H2O2-mediated cytotoxicity. Nrf2 suppressed TNF-α-induced monocyte chemoattractant protein (MCP)-1 and VCAM-1 mRNA and protein expression in a dose-dependent manner and inhibited TNF-α-induced monocytic U937 cell adhesion to HAECs. Nrf2 also inhibited IL-1β-induced MCP-1 gene expression in human mesangial cells. Expression of Nrf2 inhibited TNF-α-induced activation of p38 MAP kinase. Furthermore, expression of a constitutively active form of MKK6 (an upstream kinase for p38 MAP kinase) partially reversed Nrf2-mediated inhibition of VCAM-1 expression, suggesting that p38 MAP kinase, at least in part, mediates Nrf2's anti-inflammatory action. In contrast, Nrf2 did not inhibit TNF-α-induced NF-κB activation. These data identify the Nrf2/ARE pathway as an endogenous atheroprotective system for antioxidant protection and suppression of redox-sensitive inflammatory genes, suggesting that targeting the Nrf2/ARE pathway may represent a novel therapeutic approach for the treatment of inflammatory diseases such as atherosclerosis.
Cardiac vagal modulation of heart rate during prolonged submaximal exercise in animals with healed myocardial infarctions: effects of training
Authors: Kukielka Monica , Seals Douglas R. , Billman George E.
Published: December 2005

The present study investigated the effects of long-duration exercise on heart rate variability [as a marker of cardiac vagal tone (VT)]. Heart rate variability (time series analysis) was measured in mongrel dogs ( n = 24) with healed myocardial infarctions during 1 h of submaximal exercise (treadmill running at 6.4 km/h at 10% grade). Long-duration exercise provoked a significant (ANOVA, all P < 0.01, means ± SD) increase in heart rate (1st min, 165.3 ± 15.6 vs. last min, 197.5 ± 21.5 beats/min) and significant reductions in high frequency (0.24 to 1.04 Hz) power (VT: 1st min, 3.7 ± 1.5 vs. last min, 1.0 ± 0.9 ln ms2), R-R interval range (1st min, 107.9 ± 38.3 vs. last min, 28.8 ± 13.2 ms), and R-R interval SD (1st min, 24.3 ± 7.7 vs. last min 6.3 ± 1.7 ms). Because endurance exercise training can increase cardiac vagal regulation, the studies were repeated after either a 10-wk exercise training ( n = 9) or a 10-wk sedentary period ( n = 7). After training was completed, long-duration exercise elicited smaller increases in heart rate (pretraining: 1st min, 156.0 ± 13.8 vs. last min, 189.6 ± 21.9 beats/min; and posttraining: 1st min, 149.8 ± 14.6 vs. last min, 172.7 ± 8.8 beats/min) and smaller reductions in heart rate variability (e.g., VT, pretraining: 1st min, 4.2 ± 1.7 vs. last min, 0.9 ± 1.1 ln ms2; and posttraining: 1st min, 4.8 ± 1.1 vs. last min, 2.0 ± 0.6 ln ms2). The response to long-duration exercise did not change in the sedentary animals. Thus the heart rate increase that accompanies long-duration exercise results, at least in part, from reductions in cardiac vagal regulation. Furthermore, exercise training attenuated these exercise-induced reductions in heart rate variability, suggesting maintenance of a higher cardiac vagal activity during exercise in the trained state.