bluuebunny/crossref_metadata_2025 huggingface dataset:
MODELING AND ANALYSIS OF GENE EXPRESSION TIME-SERIES BASED ON CO-EXPRESSION
Authors: MÖLLER-LEVET CARLA S. , YIN HUJUN
Published: September 2005

In this paper a novel approach is introduced for modeling and clustering gene expression time-series. The radial basis function neural networks have been used to produce a generalized and smooth characterization of the expression time-series. A co-expression coefficient is defined to evaluate the similarities of the models based on their temporal shapes and the distribution of the time points. The profiles are grouped using a fuzzy clustering algorithm incorporated with the proposed co-expression coefficient metric. The results on artificial and real data are presented to illustrate the advantages of the metric and method in grouping temporal profiles. The proposed metric has also been compared with the commonly used correlation coefficient under the same procedures and the results show that the proposed method produces better biologicaly relevant clusters.
FRANKSUM: NEW FEATURE SELECTION METHOD FOR PROTEIN FUNCTION PREDICTION
Authors: AL-SHAHIB ALI , BREITLING RAINER , GILBERT DAVID
Published: September 2005

In the study of in silico functional genomics, improving the performance of protein function prediction is the ultimate goal for identifying proteins associated with defined cellular functions. The classical prediction approach is to employ pairwise sequence alignments. However this method often faces difficulties when no statistically significant homologous sequences are identified. An alternative way is to predict protein function from sequence-derived features using machine learning. In this case the choice of possible features which can be derived from the sequence is of vital importance to ensure adequate discrimination to predict function. In this paper we have successfully selected biologically significant features for protein function prediction. This was performed using a new feature selection method (FrankSum) that avoids data distribution assumptions, uses a data independent measurement (p-value) within the feature, identifies redundancy between features and uses an appropiate ranking criterion for feature selection. We have shown that classifiers generated from features selected by FrankSum outperforms classifiers generated from full feature sets, randomly selected features and features selected from the Wrapper method. We have also shown the features are concordant across all species and top ranking features are biologically informative. We conclude that feature selection is vital for successful protein function prediction and FrankSum is one of the feature selection methods that can be applied successfully to such a domain.
FONT CLASSIFICATION USING NMF WITH HIERARCHICAL CLUSTERING
Authors: LEE CHANG WOO , KANG HYUN , KIM HANG JOON , JUNG KEECHUL
Published: September 2005

The current paper proposes a font classification method for document images that uses non-negative matrix factorization (NMF), that is able to learn part-based representations of objects. The basic idea of the proposed method is based on the fact that the characteristics of each font are derived from parts of individual characters in each font rather than holistic textures. Spatial localities, parts composing of font images, are automatically extracted using NMF and, then, used as features representing each font. Using hierarchical clustering algorithm, these feature sets are generalized for font classification, resulting in the prototype templates construction. In both the prototype construction and font classification, earth mover's distance (EMD) is used as the distance metric, which is more suitable for the NMF feature space than Cosine or Euclidean distance. In the experimental results, the distribution of features and the appropriateness of the features specifying each font are investigated, and the results are compared with a related algorithm: principal component analysis (PCA). The proposed method is expected to improve the performance of optical character recognition (OCR), document indexing and retrieval systems, when such systems adopt a font classifier as a preprocessor.
IMPROVEMENT OF POWER SUPPLY ELECTROMAGNETIC COMPATIBILITY BY EXTENSION OF CHAOS ANTICONTROL
Authors: MOREL CRISTINA , BOURCERIE MARC , CHAPEAU-BLONDEAU FRANÇOIS
Published: September 2005

Switch-mode power supplies usually emit electromagnetic interferences at the switching frequency and its harmonics. Inducing chaos in these systems has recently been suggested as a means of reducing these spectral emissions, yet at the expense of aggravating the overall magnitude of the ripple in the output voltage. We propose here a new nonlinear feedback control method, which induces chaos, and which is able at the same time to achieve low spectral emission and to maintain a small ripple in the output. The feasibility and usefulness of this new and simple method is shown here with a numerical example, which includes a comparison with the previous control method.
A ZERO PHASE-LAG HOMODYNE DEMODULATION TECHNIQUE FOR SYNCHRONOUS MEASUREMENT APPLICATIONS AND ITS FPGA IMPLEMENTATION
Authors: DAM B. , BANERJEE K. , MAJUMDAR K. , BANERJEE R. , PATRANABIS D.
Published: September 2005

A simple homodyne direct digital demodulation technique that is insensitive to sensor induced phase-error and its innovative FPGA implementation are presented here. This novel demodulation scheme does not need a low pass filter; thereby the inherent filter time lag is eliminated. A direct digital read-out of the demodulated signal, i.e., the measurand value, is obtained through analog-to-digital conversion of the modulated signal at an instant that coincides with its peak. This peak sampling eliminates the processor time required in quadrature demodulators to obtain the measurand from the in-phase and quadrature components. For this purpose a quadrature square wave is first generated from the reference carrier. Digital measures of carrier time period and sensor induced time lag/lead are used to ensure that the rising edges of this quadrature square wave coincide with the peak instants of the modulated signal. The required sampling instants for digitization of the modulated signal are generated in synchronism with its rising edges. The digital read-out of the measurand is directly obtained without taking recourse to the standard sequence of multiplication, low-pass filtering and the subsequent processing common in existing synchronous phase-sensitive demodulators. With an a priori knowledge of the sensor-type used, this innovative FPGA-based implementation accommodates sensors introducing lagging or leading phase-shift in the modulated carrier.
AN EFFICIENT MEMORY ADDRESS CONVERTER FOR SoC-BASED 3D GRAPHICS SYSTEM
Authors: KIM JOUNG-YOUN , KIM LEE-SUP
Published: September 2005

In this paper, we propose an architecture level analysis of the frame buffer access pattern of the recent 3D graphics accelerators that utilize multiple pipelined rendering engines. Based on this analysis, we propose an energy efficient memory address converter for an SoC-based 3D graphics system with an SDRAM frame buffer. About 30% of energy reduction and 20% of runtime reduction is obtained with the address converter. With dynamic power management feature of SDRAM, the energy gains increase to about 50%. The energy and runtime gains are generated by an access pattern analysis based division and assignment of frame buffer onto multiple memory modules. With this proposed access pattern analysis, a frame buffer system optimization of an IP-based 3D graphics accelerator can be performed at early architecture design level.
SHELF-SPACE ALLOCATION AND ADVERTISING DECISIONS IN THE MARKETING CHANNEL: A DIFFERENTIAL GAME APPROACH
Authors: MARTÍN-HERRÁN GUIOMAR , TABOUBI SIHEM
Published: September 2005

This paper deals with the issue of shelf-space allocation and advertising decisions in marketing channels. We consider a network composed of a unique retailer offering the products of two competing manufacturers. The retailer controls the amount of shelf-space to allocate to both brands, while the manufacturers make advertising decisions in order to build their brand image (i.e. the goodwill stock). The demand for each brand is affected by its own goodwill level and the shelf-space allocated to the brand at retailer's store. The problem is formulated as a Stackelberg differential game played over an infinite horizon, with the manufacturers as leaders and the retailer as the follower. Stationary feedback equilibria are computed. Our main results indicate that the shelf-space allocated to each brand, manufacturers' advertising strategies at the equilibrium and channel members' value functions are affected by the goodwill levels of both products.
MODELING CANCER AS AN EVOLUTIONARY GAME
Authors: VINCENT THOMAS L. , GATENBY ROBERT A.
Published: September 2005

We present two different mathematical models that examine the role of cellular evolution in the development and treatment of cancer. The first is a Lotka-Volterra model of an invasive cancer subjected to chemotherapy that demonstrates rapid evolution of drug-resistant phenotypes. The second model represents a major refinement of the first one with the objective of producing a simple, but realistic model of carcinogenesis. It is a consumer-resource model (consumers = normal + mutuant cells, resource = glucose). We conclude that if mutant cells are not allowed to evolve, they will not ordinarily progress to cancer. However, if accumulating mutations allow cellular evolution and successful adaptation to proliferation constraints, normal cells will develop into invasive cancer. We find this progression is possible because normal cellular populations are not at an evolutionarily stable state and so are subject to invasion by more fit phenotypes.
COARSE-GRAINED PARALLELIZATION OF THE ADVANCED NEUROSIMULATOR FAUN 1.0 WITH PVM AND THE ENHANCED CORNERED RAT GAME REVISITED
Authors: VON METTENHEIM HANS-JÖRG , BREITNER MICHAEL H.
Published: September 2005

Today artificial neural networks are very useful to solve complex dynamic games of various types, i.e., to approximate optimal strategies with sufficient accuracy. Exemplarily four synthesis approaches for the solution of zero-sum, noncooperative dynamic games are outlined and discussed. Either value function, adjoint vector components or optimal strategies can be synthesized as functions of the state variables. In principle all approaches enable the solution of dynamic games. Nevertheless every approach has advantages and disadvantages which are discussed. The neural network training usually is very difficult and computationally very expensive. The coarse-grained parallelization FAUN 1.0-HPC-PVM of the advanced neurosimulator FAUN uses PVM subroutines and runs on heterogeneous and decentralized networks interconnecting general-purpose workstations, PCs and also high-performance computers. Computing times of days, weeks or months can be cut down to hours. An enhanced cornered rat game — formulated and analyzed in 1993 — serves as an example. Optimal strategies for cat and rat are synthesized. For this purpose open-loop representations of optimal strategies on an equidistant grid in the state space are used. An important end game modification is presented.
Vesicular transport and apotransferrin in intestinal iron absorption, as shown in the Caco-2 cell model
Authors: Moriya Mizue , Linder Maria C.
Published: September 2005

The potential roles of vesicular transport and apotransferrin (entering from the blood) in intestinal Fe absorption were investigated using Caco-2 cell monolayers with tight junctions in bicameral chambers as a model. As shown previously, addition of 39 μM apotransferrin (apoTf) to the basolateral fluid during absorption studies markedly stimulated overall transport of 1 μM59Fe from the apical to the basal chamber and stimulated its basolateral release from prelabeled cells, implicating endo- and exocytosis. Rates of transport more than doubled. Uptake was also stimulated, but only 20%. Specific inhibitors of aspects of vesicular trafficking were applied to determine their potential effects on uptake, retention, and basolateral (overall) transport of59Fe. Nocodazole and 5′-(4-fluorosulfonylbenzoyl)-adenosine each reduced uptake and basolateral transport up to 50%. Brefeldin A inhibited about 10%. Tyrphostin A8 (AG10) reduced uptake 35% but markedly stimulated basolateral efflux, particularly that dependent on apoTf. Cooling of cells to 4°C (which causes depolymerization of microtubules and lowers energy availability) profoundly inhibited uptake and basolateral transfer of Fe (7- to 12-fold). Apical efflux (which was substantial) was not temperature affected. Our results support the involvement of apoTf cycling in intestinal Fe absorption and indicate that as much as half of the iron uses apoTf and non-apoTf-dependent vesicular pathways to cross the basolateral membrane and brush border of enterocytes.
Role of intestinal sterol transporters Abcg5, Abcg8, and Npc1l1 in cholesterol absorption in mice: gender and age effects
Authors: Duan Li-Ping , Wang Helen H. , Ohashi Akira , Wang David Q.-H.
Published: September 2005

Recent studies have indicated that intestinal cholesterol absorption is a multistep process, which is regulated by multiple genes at the enterocyte level. However, the molecular mechanisms whereby there are gender differences in intestinal cholesterol absorption efficiency and the efficiency of cholesterol absorption increases with age have not yet been fully understood. To explore whether aging increases cholesterol absorption via intestinal sterol transporters, we studied the higher cholesterol-absorbing C57L/J vs. the lower cholesterol-absorbing AKR/J mice at 8 (young adult), 36 (older adult), and 50 (aged) wk of age. To test the hypothesis that estrogen receptor (ER )α plays an important regulatory role in cholesterol absorption, we investigated the gonadectomized mice of both genders treated with 17β-estradiol-releasing pellets at 0, 3, or 6 μg/day and antiestrogenic ICI 182,780 at 125 μg/day. We found that hepatic outputs of biliary cholesterol were significantly increased with age and in response to high levels of estrogen. Aging significantly enhances cholesterol absorption by suppressing expression of the jejunal and ileal sterol efflux transporters [ATP-binding cassette ( Abc) g5 and Abcg8] and upregulating expression of the putative duodenal and jejunal sterol influx transporter Npc1l1. Estrogen significantly augmented cholesterol absorption mostly due to an upregulated expression of intestinal Npc1l1, Abcg5, and Abcg8 via the intestinal ERα pathway, which can be fully abolished by the antagonist. We conclude that ERα activated by estrogen and aging enhances cholesterol absorption by increasing biliary lipid output and mediating intestinal sterol transporters favoring influx of intraluminal cholesterol molecules across the apical membrane of the enterocyte.
RhoA- and PKC-α-mediated phosphorylation of MYPT and its association with HSP27 in colonic smooth muscle cells.
Authors: Patil Suresh B. , Bitar Khalil N.
Published: September 2005

Agonist-induced activation of the RhoA/Rho kinase (ROCK) pathway results in inhibition of myosin phosphatase and maintenance of myosin light chain (MLC20) phosphorylation. We have shown that RhoA/ROCKII translocates and associates with heat shock protein (HSP)27 in the particulate fraction. We hypothesize that inhibition of the 130-kDa regulatory myosin-binding subunit (MYPT) requires its association with HSP27 in the particulate fraction. Furthermore, it is not certain whether regulation of MYPT by CPI-17 or by ROCKII is due to cross talk between RhoA and PKC-α. Presently, we examined the cross talk between RhoA and PKC-α in the regulation of MYPT phosphorylation in rabbit colon smooth muscle cells. Acetylcholine induced 1) sustained phosphorylation of PKC-α, CPI-17, and MYPT; 2) an increase in the association of phospho-MYPT with HSP27 in the particulate fraction; 3) a decrease in myosin phosphatase activity (66.21 ± 3.52 and 42.19 ± 3.85%nM/ml lysate at 30 s and 4 min); and 4) an increase in PKC activity (298.12 ± 46.60% and 290.59 ± 22.07% at 30 s and 4 min). Inhibition of RhoA/ROCKII by Y-27632 inhibited phosphorylation of MYPT and its association with HSP27. Both Y27632 and a negative dominant construct of RhoA inhibited phosphorylation of MYPT and CPI-17. Inhibition of PKCs or calphostin C or selective inhibition of PKC-α by negative dominant constructs inhibited phosphorylation of MYPT and CPI-17. The results suggest that 1) acetylcholine induces activation of both RhoA and/or PKC-α pathways, suggesting cross talk between RhoA and PKC-α resulting in phosphorylation of MYPT, inhibition of myosin phosphatase activity, and maintenance of MLC phosphorylation; and 2) phosphorylated MYPT is associated with HSP27 and translocated to the particulate fraction, suggesting a scaffolding role for HSP27 in mediating the association of the complex MYPT/RhoA-ROCKII. Thus both pathways (PKC and RhoA) converge on the regulation of myosin phosphatase activities and modulate sustained phosphorylation of MLC20.
Reduction of infarct size with d-myo-inositol trisphosphate: role of PI3-kinase and mitochondrial KATP channels
Authors: Przyklenk Karin , Maynard Michelle , Whittaker Peter
Published: September 2005

Prophylactic treatment with d- myo-inositol 1,4,5-trisphosphate hexasodium [d- myo-Ins(1,4,5)P3], the sodium salt of the endogenous second messenger Ins(1,4,5)P3, triggers a reduction of infarct size comparable in magnitude to that seen with ischemic preconditioning (PC). However, the mechanisms underlying d- myo-Ins(1,4,5)P3-induced protection are unknown. Accordingly, our aim was to investigate the role of four archetypal mediators implicated in PC and other cardioprotective strategies (i.e., PKC, PI3-kinase/Akt, and mitochondrial and/or sarcolemmal KATP channels) in the infarct-sparing effect of d- myo-Ins(1,4,5)P3. Fifteen groups of isolated buffer-perfused rabbit hearts [5 treated with d- myo-Ins(1,4,5)P3, 5 treated with PC, and 5 control cohorts] underwent 30 min of coronary artery occlusion and 2 h of reflow. One set of control, d- myo-Ins(1,4,5)P3, and PC groups received no additional treatment, whereas the remaining sets were infused with chelerythrine, LY-294002, 5-hydroxydecanoate (5-HD), or HMR-1098 [inhibitors of PKC, PI3-kinase, and mitochondrial and sarcolemmal ATP-sensitive K+ (KATP) channels, respectively]. Infarct size (delineated by tetrazolium staining) was, as expected, significantly reduced in both d- myo-Ins(1,4,5)P3- and PC-treated hearts versus controls. d- myo-Ins(1,4,5)P3-induced cardioprotection was blocked by 5-HD but not HMR-1098, thereby implicating the involvement of mitochondrial, but not sarcolemmal, KATP channels. Moreover, the benefits of d- myo-Ins(1,4,5)P3 were abrogated by LY-294002, whereas, in contrast, chelerythrine had no effect. These latter pharmacological data were corroborated by immunoblotting: d- myo-Ins(1,4,5)P3 evoked a significant increase in expression of phospho-Akt but had no effect on the activation/translocation of the cardioprotective ε-isoform of PKC. Thus PI3-kinase/Akt signaling and mitochondrial KATP channels participate in the reduction of infarct size afforded by prophylactic administration of d- myo-Ins(1,4,5)P3.
Differential effects of repetitive activity on sarcoplasmic reticulum responses in rat muscles of different oxidative potential
Authors: Holloway G. P. , Green H. J. , Tupling A. R.
Published: September 2005

We investigated the hypothesis that muscles of different oxidative potential would display differences in sarcoplasmic reticulum (SR) Ca2+handling responses to repetitive contractile activity and recovery. Repetitive activity was induced in two muscles of high oxidative potential, namely, soleus (SOL) and red gastrocnemius (RG), and in white gastrocnemius (WG), a muscle of low oxidative potential, by stimulation in adult male rats. Measurements of SR properties, performed in crude homogenates, were made on control and stimulated muscles at the start of recovery (R0) and at 25 min of recovery (R25). Maximal Ca2+-ATPase activity ( Vmax, μmol·g protein−1·min−1) at R0 was lower in stimulated SOL (105 ± 9 vs. 135 ± 7) and RG (269 ± 22 vs. 317 ± 26) and higher ( P < 0.05) in WG (795 ± 32 vs. 708 ± 34). At R25, Vmaxremained lower ( P < 0.05) in SOL and RG but recovered in WG. Ca2+uptake, measured at 2,000 nM, was depressed ( P < 0.05) in SOL and RG by 34 and 13%, respectively, in stimulated muscles at R0 and remained depressed ( P < 0.05) at R25. In contrast, Ca2+uptake was elevated ( P < 0.05) in stimulated WG at R0 by 9% and remained elevated ( P < 0.05) at R25. Ca2+release, unaltered in SOL and RG at both R0 and R25, was increased ( P < 0.05) in stimulated WG at both R0 and R25. We conclude that SR Ca2+-handling responses to repetitive contractile activity and recovery are related to the oxidative potential of muscle.
Tesaglitazar, a dual PPARα/γ agonist, ameliorates glucose and lipid intolerance in obese Zucker rats
Authors: Oakes Nicholas D. , Thalén Pia , Hultstrand Therese , Jacinto Severina , Camejo Germán , Wallin Boel , Ljung Bengt
Published: September 2005

Insulin resistance, impaired glucose tolerance, high circulating levels of free fatty acids (FFA), and postprandial hyperlipidemia are associated with the metabolic syndrome, which has been linked to increased risk of cardiovascular disease. We studied the metabolic responses to an oral glucose/triglyceride (TG) (1.7/2.0 g/kg lean body mass) load in three groups of conscious 7-h fasted Zucker rats: lean healthy controls, obese insulin-resistant/dyslipidemic controls, and obese rats treated with the dual peroxisome proliferator-activated receptor α/γ agonist, tesaglitazar, 3 μmol·kg−1·day−1for 4 wk. Untreated obese Zucker rats displayed marked insulin resistance, as well as glucose and lipid intolerance in response to the glucose/TG load. The 2-h postload area under the curve values were greater for glucose (+19%), insulin (+849%), FFA (+53%), and TG (+413%) compared with untreated lean controls. Treatment with tesaglitazar lowered fasting plasma glucose, improved glucose tolerance, substantially reduced fasting and postload insulin levels, and markedly lowered fasting TG and improved lipid tolerance. Fasting FFA were not affected, but postprandial FFA suppression was restored to levels seen in lean controls. Mechanisms of tesaglitazar-induced lowering of plasma TG were studied separately using the Triton WR1339 method. In anesthetized, 5-h fasted, obese Zucker rats, tesaglitazar reduced hepatic TG secretion by 47%, increased plasma TG clearance by 490%, and reduced very low-density lipoprotein (VLDL) apolipoprotein CIII content by 86%, compared with obese controls. In conclusion, the glucose/lipid tolerance test in obese Zucker rats appears to be a useful model of the metabolic syndrome that can be used to evaluate therapeutic effects on impaired postprandial glucose and lipid metabolism. The present work demonstrates that tesaglitazar ameliorates these abnormalities and enhances insulin sensitivity in this animal model.
Inducing late phase of infarct protection in skeletal muscle by remote preconditioning: efficacy and mechanism
Authors: Moses Michael A. , Addison Patrick D. , Neligan Peter C. , Ashrafpour Homa , Huang Ning , McAllister Sandra E. , Lipa Joan E. , Forrest Christopher R. , Pang Cho Y.
Published: September 2005

We have previously demonstrated that remote ischemic preconditioning (IPC) by instigation of three cycles of 10-min occlusion/reperfusion in a hindlimb of the pig elicits an early phase of infarct protection in local and distant skeletal muscles subjected to 4 h of ischemia immediately after remote IPC. The aim of this project was to test our hypothesis that hindlimb remote IPC also induces a late phase of infarct protection in skeletal muscle and that KATP channels play a pivotal role in the trigger and mediator mechanisms. We observed that pig bilateral latissimus dorsi (LD) muscle flaps sustained 46 ± 2% infarction when subjected to 4 h of ischemia/48 h of reperfusion. The late phase of infarct protection appeared at 24 h and lasted up to 72 h after hindlimb remote IPC. The LD muscle infarction was reduced to 28 ± 3, 26 ± 1, 23 ± 2, 24 ± 2 and 24 ± 4% at 24, 28, 36, 48 and 72 h after remote IPC, respectively ( P < 0.05; n = 8). In subsequent studies, hindlimb remote IPC or intravenous injection of the sarcolemmal KATP (sKATP) channel opener P-1075 (2 μg/kg) at 24 h before 4 h of sustained ischemia (i.e., late preconditioning) reduced muscle infarction from 43 ± 4% (ischemic control) to 24 ± 2 and 19 ± 3%, respectively ( P < 0.05, n = 8). Intravenous injection of the sKATP channel inhibitor HMR 1098 (6 mg/kg) or the nonspecific KATP channel inhibitor glibenclamide (Glib; 1 mg/kg) at 10 min before remote IPC completely blocked the infarct- protective effect of remote IPC in LD muscle flaps subjected to 4 h of sustained ischemia at 24 h after remote IPC. Intravenous bolus injection of the mitochondrial KATP (mKATP) channel inhibitor 5-hydroxydecanoate (5-HD; 5 mg/kg) immediately before remote IPC and 30-min intravenous infusion of 5-HD (5 mg/kg) during remote IPC did not affect the infarct-protective effect of remote IPC in LD muscle flaps. However, intravenous Glib or 5-HD, but not HMR 1098, given 24 h after remote IPC completely blocked the late infarct-protective effect of remote IPC in LD muscle flaps. None of these drug treatments affected the infarct size of control LD muscle flaps. The late phase of infarct protection was associated with a higher ( P < 0.05) muscle content of ATP at the end of 4 h of ischemia and 1.5 h of reperfusion and a lower ( P < 0.05) neutrophilic activity at the end of 1.5 h of reperfusion compared with the time-matched control. In conclusion, these findings support our hypothesis that hindlimb remote IPC induces an uninterrupted long (48 h) late phase of infarct protection, and sKATP and mKATP channels play a central role in the trigger and mediator mechanism, respectively.
Temperature and Ca2+dependence of [3H]ryanodine binding in the burbot (Lota lotaL.) heart
Authors: Vornanen Matti
Published: September 2005

Opening and closing of the cardiac ryanodine (Ry) receptor (RyR) are coordinated by the free intracellular Ca2+concentration, thus making the Ca2+binding properties of the RyR important for excitation-contraction coupling. Unlike mammalian cardiac RyRs, which lose their normal function at low temperatures, RyRs of ectothermic vertebrates remain operative at 2–4°C, as indicated by Ry sensitivity of contractile force. To investigate the mechanisms of low temperature adaptation of ectothermic RyRs, we compared Ca2+-dependent kinetics of [3H]ryanodine binding in cardiac preparations of a fish (burbot, Lota lota) and a mammal (rat). The number of ventricular [3H]ryanodine binding sites determined at 20°C was 1.54 times higher in rat than burbot heart (0.401 ± 0.039 and 0.264 ± 0.019 pmol/mg protein, respectively) ( P < 0.02), while the binding affinity ( Kd) for [3H]ryanodine was similar (3.38 ± 0.63 and 4.38 ± 1.14 nM for rat and burbot, respectively) ( P = 0.47). The high-affinity [3H]ryanodine binding to burbot and rat cardiac preparations was tightly coordinated by the free Ca2+concentration at both 20°C and 2°C and did not differ between the two species. Half-maximal [3H]ryanodine binding occurred at 0.191 ± 0.027 μM and 0.164 ± 0.034 μM Ca2+for rat and at 0.212 ± 0.035 μM and 0.188 ± 0.039 μM Ca2+for burbot ( P = 0.65), at 2°C and 20°C, respectively. In two other fish species, rainbow trout ( Oncorhynchus mykiss) and crucian carp ( Carassius carassius), the Ca2+-binding affinity at 20°C was 4.4 and 5.9 times lower, respectively, than in the burbot. At 20°C, the rate of [3H]ryanodine binding to the high-affinity binding site was similar in rat and burbot but was drastically slowed in rat at 2°C. At 2°C, [3H]ryanodine failed to dissociate from rat cardiac RyRs, and at 10°C and 20°C, the rate of dissociation was two to three times slower in rat than burbot preparations. The latter finding is compatible with a channel gating mechanism, where the closing of the Ca2+release channel is impaired or severely retarded by low temperature in rat but less so in burbot preparations. The stronger effect of low temperature on association and dissociation rate of [3H]ryanodine binding in rat compared with burbot suggests that RyRs of the ectothermic fish, unlike those of endothermic rat, are better able to open and close at low temperatures.
Acute antihypertensive action of nitroxides in the spontaneously hypertensive rat
Authors: Patel Kinjal , Chen Yifan , Dennehy Kathryn , Blau Jonathan , Connors Stephanie , Mendonca Margarida , Tarpey Margaret , Krishna Murali , Mitchell James B. , Welch William J. , Wilcox Christopher S.
Published: September 2005

Tempol is an amphipathic radical nitroxide (N) that acutely reduces blood pressure (BP) and heart rate (HR) in the spontaneously hypertensive rat (SHR). We investigated the hypothesis that the response to nitroxides is determined by SOD mimetic activity or lipophilicity. Groups ( n = 6–10) of anesthetized SHRs received graded intravenous doses of Ns: tempol (T), 4-amino-tempo (AT), 4-oxo-tempo (OT), 4-trimethylammonium-2,2,6,6-tetramethylpiperidine-1-oxyl iodide (CAT-1), 3-carbamoyl-proxyl (3-CP), or 3-carboxy-proxyl (3-CTPY). Others received native or liposomal (L) Cu/Zn SOD. T and OT are uncharged, AT is positively charged and cell-permeable, and CAT-1 is positively charged and cell-impermeable. 3-CP and 3-CTPY have five-member pyrrolidine rings, whereas T, AT, OT, and CAT-1 have six-member piperidine rings. T and AT reduced mean arterial pressure (MAP) similarly (−48 ± 2 mmHg and −55 ± 8 mmHg) but more ( P < 0.05) than OT and CAT-1. 3-CP and 3-CTPY were ineffective. The group mean change in MAP with piperidine Ns correlated with SOD activity ( r = −0.94), whereas their ED50correlated with lipophilicity ( r = 0.89). SOD and L-SOD did not lower BP acutely but reduced it after 90 min (−32 ± 5 and −31 ± 6 mmHg; P < 0.05 vs. vehicle). Pyrrolidine nitroxides are ineffective antihypertensive agents. The antihypertensive response to piperidine Ns is predicted by SOD mimetic action, and the sensitivity of response is by hydrophilicity. SOD exerts a delayed hypotensive action that is not enhanced by liposome encapsulation, suggesting it must diffuse to an extravascular site.
Ultrastructural localization of UT-A and UT-B in rat kidneys with different hydration status
Authors: Lim Sun-Woo , Han Ki-Hwan , Jung Ju-Young , Kim Wan-Young , Yang Chul-Woo , Sands Jeff M. , Knepper Mark A. , Madsen Kirsten M. , Kim Jin
Published: September 2005

Urea transport in the kidney is mediated by a family of transporter proteins, including renal urea transporters (UT-A) and erythrocyte urea transporters (UT-B). We aimed to determine whether hydration status affects the subcellular distribution of urea transporters. Male Sprague-Dawley rats were divided into three groups: dehydrated rats (WD) given minimum water, hydrated rats (WL) given 3% sucrose in water for 3 days before death, and control rats given free access to water. We labeled kidney sections with antibodies against UT-A1and UT-A2(L194), UT-A3(Q2), and UT-B using preembedding immunoperoxidase and immunogold methods. In control animals, UT-A1and UT-A3immunoreactivities were observed throughout the cytoplasm in inner medullary collecting duct (IMCD) cells, and weak labeling was observed on the basolateral plasma membrane. UT-A2immunoreactivity in the descending thin limbs (DTL) was observed mainly on the apical and basolateral membranes of type I epithelium, and very faint labeling was observed in the long-loop DTL at the border between the outer and inner medulla. UT-A1immunoreactivity intensity was markedly lower, and UT-A3immunoreactivity was higher in IMCD of WD vs. controls. UT-A2immunoreactivity intensities in the plasma membrane and cytoplasm of type I, II, and III epithelia of DTL were greater in WD vs. controls. In contrast, UT-A1expression was greater and UT-A2and UT-A3expressions were lower in WL vs. controls. The subcellular distribution of UT-A in DTL or IMCD did not differ between control and experimental animals. UT-B was expressed in the plasma membrane of the descending vasa recta of both control and experimental animals. UT-B intensity was higher in WD and lower in WL vs. controls. These data indicate that changes in hydration status over 3 days affected urea transporter protein expression without changing its subcellular distribution.
Parallel and divergent adaptations of rat soleus and plantaris to chronic exercise and hypergravity
Authors: Fuller Patrick M. , Baldwin Kenneth M. , Fuller Charles A.
Published: September 2005

It has been demonstrated that endurance exercise and chronic acceleration, i.e., hypergravity, produce comparable adaptations in a variety of physiological systems, including decreased adiposity, increased energy metabolism, and altered intermediary metabolism. Similar adaptations have not been demonstrated for skeletal muscle per se. To further differentiate between these general responses with respect to gravity and exercise, this study tested the hypothesis that chronic exercise (voluntary wheel running) and chronic acceleration (2 G via centrifugation) will induce similar changes in muscle myosin heavy chain (MHC) isoform expression in rat plantaris, a fast extensor, and in rat soleus, a slow “antigravity” extensor. The experimental design involved four groups of mature male rats ( n = 8/group): 1 G and 2 G with running wheels, and 1 G and 2 G controls without running wheels. The primary observations from the study were as follows: 1) 8 wk of 2 G are an adequate stimulus for MHC compositional changes in rat plantaris and soleus muscle; 2) both exercise and +G caused an increase in the slow MHC1 isoform in soleus muscle, suggesting that loading is a primary stimulus for this shift; and 3) 2 G and exercise appeared to have differential effects on the plantaris muscle MHC isoforms, with 2 G causing an increase in MHC2b, and exercise causing a decrease in MHC2b with a concomitant increase in MHC1, suggesting that factors other than enhanced loading, possibly locomotor activity levels, are the primary stimulus for this shift.
Dietary NaCl supplementation prevents muscle necrosis in a mouse model of Duchenne muscular dystrophy
Authors: Yoshida Mizuko , Yonetani Akira , Shirasaki Toshihiro , Wada Keiji
Published: September 2005

The mdx mouse is an animal model for Duchenne muscular dystrophy. Mdx mice fed a 12% NaCl diet from birth up to 20 days of age (mdx-Na mice) had an ∼50% reduction in serum creatine kinase (CK) activity compared with mdx mice fed a standard diet. Most notably, necrotic fibers in tibialis anterior (TA) muscle of mdx-Na mice were reduced by 99% and were similar in control mice. These mdx mice displayed significantly elevated blood Ca2+ and Na+ levels, while the total calcium content of their TA muscle was reduced to the level of control mice. In addition, mdx-Na mice had elevated zinc and magnesium contents in their TA muscle. These results suggest that elevated serum Na+ leads to Ca2+ extrusion from muscle via the Na+/Ca2+ exchanger causing a decrease in intracellular Ca2+ levels and an increase in blood Ca2+ levels. Extracellular Ca2+ and, in addition, Zn2+ and Mg2+ might also contribute to the stabilization of the cell membrane. Other possibilities explaining the surprisingly efficacious beneficial effect of dietary sodium exist and are discussed.
Age-dependent modulation of endothelium-dependent vasodilatation by chronic hypoxia in ovine cranial arteries
Authors: Williams James M. , Pearce William J.
Published: September 2005

Although abundant evidence indicates that chronic hypoxia can induce pulmonary vascular remodeling, very little is known of the effects of chronic hypoxia on cerebrovascular structure and function, particularly in the fetus. Thus the present study explored the hypothesis that chronic hypoxemia also influences the size and shape of cerebrovascular smooth muscle and endothelial cells, with parallel changes in the reactivity of these cells to endothelium-dependent vasodilator stimuli. To test this hypothesis, measurements of endothelial and vascular smooth muscle cell size and density were made in silver-stained common carotid and middle cerebral arteries from term fetal and nonpregnant adult sheep maintained at an altitude of 3,820 m for 110 days. Chronic hypoxia induced an age-dependent remodeling that led to smooth muscle cells that were larger in fetal arteries but smaller in adult arteries. Chronic hypoxia also increased endothelial cell density in fetal arteries but reduced it in adult arteries. These combined effects resulted in an increased (adult carotid), decreased (adult middle cerebral), or unchanged (fetal arteries) per cell serosal volume of distribution for endothelial factors. Despite this heterogeneity, the magnitude of endothelium-dependent vasodilatation to A23187 , measured in vitro, was largely preserved, although sensitivity to this relaxant was uniformly depressed. NG-nitro-l-arginine methyl ester, 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, and endothelium denudation each independently blocked A23187 -induced vasodilation without unmasking any residual vasoconstrictor effect. Indomethacin did not significantly attenuate A23187 -induced relaxation except in the hypoxic adult middle cerebral, where a small contribution of prostanoids was evident. Vascular sensitivity to exogenous nitric oxide (NO) was uniformly increased by chronic hypoxia. From these results, we conclude that chronic hypoxia reduced endothelial NO release while also upregulating some component of the NO-cGMP-PKG vasodilator pathway. These offsetting effects appear to preserve endothelium-dependent vasodilation after adaptation to chronic hypoxia.
Inhibition of stretch-activated channels during eccentric muscle contraction attenuates p70S6K activation
Authors: Spangenburg Espen E. , McBride Todd A.
Published: September 2005

Eccentric contractions (EC) are known to result in muscle hypertrophy, potentially through activation of the Akt-mammalian target of rapamycin-p70 S6 kinase (p70S6K) signaling pathway. Previous work has also demonstrated that EC result in the opening of stretch-activated channels (SAC), and inhibition of these channels resulted in an attenuation of EC-induced muscle hypertrophy. The purpose of this study was to test the hypothesis that a known intracellular pathway directly associated with muscle hypertrophy is coupled to the opening of SAC. Specifically, we measured the activation of the Akt, GSK-3β, p70S6K, and ribosomal protein S6 following a single bout of EC in the rat tibialis anterior (TA) muscle. The TA muscles performed four sets of six repetitions of EC. In vivo blockade of SAC was performed by a continuous oral treatment with streptomycin in the drinking water (4 g/l) or by intravenous infusion of 80 μmol/kg gadolinium (Gd3+). EC increased the degree of Akt and p70S6K phosphorylation in the TA muscle, whereas in animals in which SAC had been inhibited, there was a reduced capacity for EC to induce Akt or p70S6K phosphorylation. Accompanying this reduced activation of Akt and p70S6K was a failure to phosphorylate GSK-3β or S6 when SAC were inhibited. The results from these data indicate the necessity of functional SAC for the complete activation of Akt and p70S6K pathway in response to EC.
Neuromechanical adaptation to hopping with an elastic ankle-foot orthosis
Authors: Ferris Daniel P. , Bohra Zaineb A. , Lukos Jamie R. , Kinnaird Catherine R.
Published: September 2005

When humans hop or run on different surfaces, they adjust their effective leg stiffness to offset changes in surface stiffness. As a result, the overall stiffness of the leg-surface series combination remains independent of surface stiffness. The purpose of this study was to determine whether humans make a similar adjustment when springs are placed in parallel with the leg via a lower limb orthosis. We studied seven human subjects hopping in place on one leg while wearing an ankle-foot orthosis. We used an ankle-foot orthosis because the ankle joint is primarily responsible for leg stiffness during hopping. A spring was added to the ankle-foot orthosis so that it increased orthosis stiffness by providing plantar flexor torque during ankle dorsiflexion. We hypothesized that subjects would decrease their biological ankle stiffness when the spring was added to the orthosis, keeping total ankle stiffness constant. We collected kinematic, kinetic, and electromyographic data during hopping with and without the spring on the orthosis. We found that total ankle stiffness and leg stiffness did not change across the two orthosis conditions (ANOVA, P > 0.05). This was possible because subjects decreased their biological ankle stiffness to offset the orthosis spring stiffness ( P < 0.0001). The reduction in biological ankle stiffness was accompanied by decreases in soleus, medial gastrocnemius, and lateral gastrocnemius muscle activation ( P < 0.0002). These results suggest that an elastic exoskeleton might improve human running performance by reducing muscle recruitment.
Mammalian G Proteins and Their Cell Type Specific Functions
Authors: Wettschureck Nina , Offermanns Stefan
Published: September 2005

Heterotrimeric G proteins are key players in transmembrane signaling by coupling a huge variety of receptors to channel proteins, enzymes, and other effector molecules. Multiple subforms of G proteins together with receptors, effectors, and various regulatory proteins represent the components of a highly versatile signal transduction system. G protein-mediated signaling is employed by virtually all cells in the mammalian organism and is centrally involved in diverse physiological functions such as perception of sensory information, modulation of synaptic transmission, hormone release and actions, regulation of cell contraction and migration, or cell growth and differentiation. In this review, some of the functions of heterotrimeric G proteins in defined cells and tissues are described.
Sodium Channel Inactivation: Molecular Determinants and Modulation
Authors: Ulbricht Werner
Published: September 2005

Voltage-gated sodium channels open (activate) when the membrane is depolarized and close on repolarization (deactivate) but also on continuing depolarization by a process termed inactivation, which leaves the channel refractory, i.e., unable to open again for a period of time. In the “classical” fast inactivation, this time is of the millisecond range, but it can last much longer (up to seconds) in a different slow type of inactivation. These two types of inactivation have different mechanisms located in different parts of the channel molecule: the fast inactivation at the cytoplasmic pore opening which can be closed by a hinged lid, the slow inactivation in other parts involving conformational changes of the pore. Fast inactivation is highly vulnerable and affected by many chemical agents, toxins, and proteolytic enzymes but also by the presence of β-subunits of the channel molecule. Systematic studies of these modulating factors and of the effects of point mutations (experimental and in hereditary diseases) in the channel molecule have yielded a fairly consistent picture of the molecular background of fast inactivation, which for the slow inactivation is still lacking.
Minicircle DNA Immobilized in Bacterial Ghosts: In vivo Production of Safe Non-Viral DNA Delivery Vehicles
Authors: Jechlinger Wolfgang , Azimpour Tabrizi Chakameh , Lubitz Werner , Mayrhofer Peter
Published: September 2005

DNA as an active agent is among the most promising technologies for vaccination and therapy. However, plasmid backbone sequences needed for the production of pDNA in bacteria are dispensable, reduce the efficiency of the DNA agent and, most importantly, represent a biological safety risk. In this report we describe a novel technique where a site-specific recombination system based on the ParA resolvase was applied to a self-immobilizing plasmid system (SIP). In addition, this system was combined with the protein E-specific lysis technology to produce non-living bacterial carrier vehicles loaded with minicircle DNA. The in vivo recombination process completely divided an origin plasmid into a minicircle and a miniplasmid. The replicative miniplasmid containing the origin of replication and the antibiotic resistance gene was lost during the subsequently induced PhiX174 gene E-mediated lysis process, which results in bacterial ghosts. The minicircle DNA was retained in these empty bacterial cell envelopes during the lysis process via the specific interaction of a membrane anchored protein with the minicircle DNA. Using this novel platform technology, a DNA delivery vehicle – consisting of a safe bacterial carrier with known adjuvant properties and minicircle DNA with an optimized safety profile – can be produced in vivo in a continuous process. Furthermore, this study provides the basis for the development of an efficient in vitro minicircle purification process.
Characterizing the Dynamics of the Quorum-Sensing System in Staphylococcus aureus
Authors: Gustafsson Erik , Nilsson Patric , Karlsson Stefan , Arvidson Staffan
Published: September 2005

The virulence determinants of Staphylococcus aureus are expressed in a growth phase-dependent manner governed by the autoinducible quorum-sensing system agr. Activation of the agr system results in a rapid increase in the regulator RNAIII and occurs in response to accumulation of AIP. In order to activate the agr system, a basal transcription of agr components must be assumed. This basal transcription of agr components seems to be stimulated by sarA. To better understand how SarA would affect activation of the agr system by modulating the basal agr activity, a mathematical model for autoactivation of the agr system was set up. The model predicted that the agr system is hysteretic, meaning that the agr system is activated at a specific concentration of autoinducing peptide (AIP), whereas it is inactivated at a specific lower concentration of AIP. According to the model, changing the basal agr activity only had a marginal effect on steady-state levels of RNAIII but changed the sensitivity of the cells to AIP. This was supported by Northern blot analysis of RNAIII in S. aureus mutants with different levels of SarA expression. Since natural antagonistic AIPs have been demonstrated, the effect of adding inhibitors to the system was analyzed.
Metabolic Engineering of Corynebacterium glutamicum for Fuel Ethanol Production under Oxygen-Deprivation Conditions
Authors: Inui Masayuki , Kawaguchi Hideo , Murakami Shikiko , Vertès Alain A. , Yukawa Hideaki
Published: September 2005

The central metabolic pathway of Corynebacterium glutamicum was engineered to produce ethanol. A recombinant strain which expressed the Zymomonas mobilis genes coding for pyruvate decarboxylase (pdc) and alcohol dehydrogenase (adhB) was constructed. Both genes placed under the control of the C. glutamicum ldhA promoter were expressed at high levels in C. glutamicum, resulting, under oxygen-deprivation conditions, in a significant yield ofethanol from glucose in a process characterized by the absence of cellular growth. Addition of pyruvate in trace amounts to the reaction mixture induced a 2-fold increase in the ethanol production rate. A similar effect was observed when acetaldehyde was added. Disruption of the lactate dehydrogenase (ldhA) gene led to a 3-fold higher ethanol yield than wild type, with no lactate production. Moreover, inactivation of the phosphoenolpyruvate carboxylase (ppc) and ldhA genes revealed a significant amount of ethanol production and a dramatic decrease in succinate without any lactate production, when pyruvate was added. Since the reaction occurred in the absence of cell growth, the ethanol volumetric productivity increased in proportion to cell density of ethanologenic C. glutamicum in a process under oxygen-deprivation conditions. These observations corroborate the view that intracellular NADH concentrations in C. glutamicum are correlated to oxygen-deprived metabolic flows.