bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of coadsorbed CH3Cl and D2O layers on Pd(111) studied by sum frequency generation
Authors: Fournier Frédéric , Dubost Henri , Carrez Serge , Zheng Wanquan , Bourguignon Bernard
Published: November 2005

Adsorption of methyl chloride and coadsorption of CH3Cl and D2O on Pd(111) surfaces at T=100K have been studied under ultrahigh-vacuum conditions using femtosecond sum frequency generation (SFG) spectroscopy in the spectral regions of CH and OD bands. On the bare Pd(111) substrate, the CH3Cl coverage dependence of the resonant SFG signal is consistent with a progressive molecular rearrangement starting at half saturation followed by the growth of two ordered monolayers in which the molecular axes are perpendicular to the surface. When CH3Cl is adsorbed on top of predeposited D2O on Pd(111), the SFG signals as a function of the CH3Cl exposure indicate that methyl chloride is adsorbed onto D2O through hydrogen bonding. On the contrary when the adsorption order is reversed the strong decrease of the CH3 signal as a function of the D2O exposure is explained by assuming that water molecules penetrate inside the CH3Cl layers, leading to the formation of disordered CH3Cl clusters. In all cases a nonresonant contribution due to molecular adsorption is observed and it shows a dependence upon surface structure and coverage significantly different from that of the resonant vibrational bands.
Thermodynamically complete equations of state for nickel-titanium alloy
Authors: Swift Damian C. , Niemczura Johnathan G. , Paisley Dennis L. , Johnson Randall P. , Hauer Allan , Hackenberg Robert E. , Cooley Jason , Thoma Dan , Ackland Graeme J.
Published: November 2005

A thermodynamically complete equation of state for the compression and heating of near-equiatomic Ni–Ti alloy in the CsCl (B2) structure was predicted, based on quantum-mechanical calculations of the electron ground states and a Grüneisen lattice-thermal model. The quantum-mechanical calculations used ab initio pseudopotentials and the local-density approximation; the accuracy of the calculations was investigated for elemental Ni and Ti. These calculations demonstrated that simple averaging techniques do not provide an accurate prediction of the properties of metal alloys, and rigorous treatment of the electron wave functions is needed. Predictions were also made of the behavior of NiTi under uniaxial loading. The pressure-density relation obtained from isotropic compression did not match the mean pressure calculated from uniaxial compression, demonstrating that it is not generally accurate to split the stress response of a material into a scalar equation of state and a stress deviator according to the usual prescription. Polycrystalline NiTi samples were prepared with a range of compositions, in the form of disks from 100 to 400μm thick and 5mm in diameter. Flyer impact experiments were performed using a long-pulse laser drive at the TRIDENT facility to obtain shock wave data on the response of NiTi to around 15GPa; the new data were consistent with the published results from gas gun experiments. The theoretical equation of state was consistent with the shock wave data.
Pure gravitational radiation with twisting rays in the linear approximation
Authors: Nita Bogdan G. , MacAlevey Paul , Downes Phillip T.
Published: November 2005

Solutions of types N and III with twisting rays are derived in the linear approximation by means of complex coordinate transformations. Some solutions are shown to have Riemann tensors which vanish asymptotically and are everywhere regular.
Electromechanical and electro-optical properties of nanowires
Authors: Shik A. , Ruda H. E. , Currie I. G.
Published: November 2005

In an external (static of high-frequency) electric field, image forces cause a torque moment to act on semiconducting or metallic nanowires. As a result, a system of nanowires which are suspended in a dielectric liquid acquire characteristics, typical of those of nematic liquid crystals, such as field-induced optical anisotropy. For freestanding nanowires prepared on a substrate, an applied electric field is shown to be capable of causing nanowire bending, which can potentially provide a means of nanoactuation. The bending of such nanowires in a high-frequency electric field is comprised of a superposition of static bending and induced mechanical oscillations, whose amplitude depends on the resonant mechanical vibration characteristics of the nanowires.
Si
-based magnetic tunnel transistor with single CoFe base layer
Authors: Jang S. H. , Kim Y. W. , Lee J. H. , Kim K. Y.
Published: November 2005

Magnetic tunnel transistors were prepared on Si(100) substrates by magnetron sputter deposition. By means of spin filtering through a single Co90Fe10 base layer, magnetocurrent ratios of 53%–55% and high transfer ratios of (1–2)×10−4 for emitter-base bias of 1.5–2V were obtained at 77K. The bias dependence of the collector current showed the square-law behavior. From the modified Bell-Kaiser model, attenuation lengths of majority and minority spins of hot electrons are expected as 40±5 and 16±1Å in the single Co90Fe10 layer, respectively. The decrease of transfer ratio was observed with decreasing base thickness from 80 to 30Å, which may be related to the extension of the (Co2Si and Fe) intermediate region formed at Co90Fe10∕Si interface in the thinner base layer.
Optoelectronic and structural characteristics of Er-doped amorphous AlN films
Authors: Zanatta A. R. , Ribeiro C. T. M. , Jahn U.
Published: November 2005

This work reports on the optical, electronic, and structural properties of aluminum-nitrogen (AlN) films doped with Er. The films were deposited by conventional radio-frequency sputtering at 200°C in an atmosphere of pure nitrogen. Their main characteristics have been investigated by experimental techniques such as optical transmission, photo- and cathodoluminescence, Raman scattering, and x-ray photoelectron spectroscopy. All films exhibit Er3+-related optical emissions in the visible and infrared regions, which are considerably enhanced after thermal annealing and on measurements at low temperature. Moreover, Raman spectroscopy indicates that the films remain amorphous even after thermal treatment at 900°C. Based on the composition and on the structural and luminescent properties of these Er-doped amorphous AlN films it was possible to conclude that energy excitation of Er3+ ions takes place according to different routes when electrons or photons are used. In the former case, energy is transferred from the amorphous host to the Er3+ ions by carrier-mediated processes. As a result, relatively strong Er3+-related optical transitions can be observed in the ∼400–1600nm range. Excitation with 488.0nm photons also produces visible and infrared Er3+-related luminescence, but most of the optical excitation occurs through direct excitation of the F7∕24 level of Er3+. Finally, the role played by nitrogen atoms and thermal treatments on the achievement of light emission from the present AlN films is discussed and compared with the existing literature.
Laser processed channels of easy vortex motion in YBa2Cu3O7−δ films
Authors: Jukna A. , Barboy I. , Jung G. , Banerjee S. S. , Myasoedov Y. , Plausinaitiene V. , Abrutis A. , Li X. , Wang D. , Sobolewski Roman
Published: November 2005

Vortex dynamics in laser-patterned channels for easy motion in YBa2Cu3O7−δ thin-film bridges has been investigated by electric transport and magneto-optical measurements. It has been found that the laser-writing technique, relying on selective deoxygenation of the illuminated areas of YBa2Cu3O7−δ films, enables manufacturing of channels with the decreased field of the first penetration and pinning strength. Current-induced vortices confined in such channels move coherently within a limited temperature and bias ranges. Coherence in vortex motion was confirmed by the direct observation of self-resonant, Josephson-like current steps on the bridge current-voltage characteristics.
Helical CdS nanowire ropes by simple aqueous chemical growth
Authors: Wang Wenlong , Bai Fenglian
Published: November 2005

Long and flexible crystalline CdS nanowire ropes were synthesized in bulk quantities via a simple aqueous chemical growth route, which has previously been successful for the growth of short CdS nanorods. The as-grown CdS nanoropes exhibit a unique helically twisted structural feature, as confirmed by both microscopic observation and circular dichroism spectroscopic characterization. The nucleation and growth kinetics of these related CdS one-dimensional(1D) nanocrystals was investigated by monitoring the temporal evolution of the UV-visible spectrum. It was found that cadmium and sulfide monomers were first nucleated out as “magic number” CdS nanoclusters in the initial nucleation stage, and then grew to regular sized CdS 1D nanocrystals during the subsequent Ostwald ripening process.
Field emission at 10Vcm−1 with surface emission cathodes on negative-electron-affinity insulators
Authors: Geis M. W. , Deneault S. , Krohn K. E. , Marchant M. , Lyszczarz T. M. , Cooke D. L.
Published: November 2005

Surface emission cathodes reported here consist of two electrodes separated by ∼10μm on a negative-electron-affinity glass, Cs2Si4O9. The electrodes consist of a W film suspended over the insulator by a gap of 0–70 nm. When electron emission is initiated with a bias of 0–300 V, between the electrodes, the cathodes continue to emit after the bias is removed and for anode voltages as low as 20 V, electric fields <10Vcm−1. The emission is modeled by the electrons tunneling from the electrode onto the glass surface and from there they are emitted into vacuum. Emission without bias is the result of positive charge in the insulator, which replaces the need for a bias voltage.
Electro-optic modulation using single-crystal film of an organic molecular salt in a Fabry-Perot cavity
Authors: Kutty S. P. , Thakur M.
Published: November 2005

Electro-optic modulation using single-crystal film of an organic molecular salt placed in a Fabry-Perot cavity has been measured at 633 and 750nm. Large modulation depth (80%) at a low applied field (0.5V∕μm) has been observed in the field-induced birefringence geometry (mirror reflectivity ∼70%) for a bias point which was controlled by moving one of the mirrors. A modulation of about 60% with a higher throughput was obtained when no analyzer was used and the incident polarization was parallel to the dipole-axis.
Three-dimensional optical tomographic imaging of scattering objects in tissue-simulating turbid media using independent component analysis
Authors: Alrubaiee M. , Xu M. , Gayen S. K. , Brito M. , Alfano R. R.
Published: November 2005

An information-theory-based approach for the detection and three-dimensional localization of scattering targets embedded in a turbid medium, such as a tumor in the breast, is introduced. The approach uses multisource illumination of the medium, multidetector transillumination signal acquisition, and independent component analysis of the information theory for target detection and localization. The efficacy of the approach is demonstrated by detecting and obtaining location information about scattering targets embedded in human breast tissue-simulating turbid media of thickness 50 times the transport mean-free path.
Laser-powered thermoelectric generators operating at cryogenic temperatures
Authors: Harutyunyan S. R. , Vardanyan V. H. , Kuzanyan A. S. , Nikoghosyan V. R. , Kunii S. , Winzer K. , Wood K. S. , Gulian A. M.
Published: November 2005

A thermoelectric generator, operating in a cryostat at liquid helium temperatures, is described. Energy to the generator is supplied via an external laser beam. For this prototype device the associated heat load at permanent operation is comparable with the heat load associated with power delivery via metallic wires. Estimates indicate that still better performance can be enabled with existing thermoelectric materials, thereby far exceeding efficiency of traditional cryostat wiring. We used a prototype generator to produce electric power for measuring critical currents in Nb3Sn-films at 4K.
Relation between the Widom line and the dynamic crossover in systems with a liquid–liquid phase transition
Authors: Xu Limei , Kumar Pradeep , Buldyrev S. V. , Chen S.-H. , Poole P. H. , Sciortino F. , Stanley H. E.
Published: November 2005

We investigate, for two water models displaying a liquid–liquid critical point, the relation between changes in dynamic and thermodynamic anomalies arising from the presence of the liquid–liquid critical point. We find a correlation between the dynamic crossover and the locus of specific heat maxima

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(“Widom line”) emanating from the critical point. Our findings are consistent with a possible relation between the previously hypothesized liquid–liquid phase transition and the transition in the dynamics recently observed in neutron scattering experiments on confined water. More generally, we argue that this connection between

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and dynamic crossover is not limited to the case of water, a hydrogen bond network-forming liquid, but is a more general feature of crossing the Widom line. Specifically, we also study the Jagla potential, a spherically symmetric two-scale potential known to possess a liquid–liquid critical point, in which the competition between two liquid structures is generated by repulsive and attractive ramp interactions.
Influence of ß2-adrenoceptor gene polymorphisms on diet-induced thermogenesis
Authors: Oomen J. M. , Waijers P. M. C. M. , van Rossum C. , Hoebee B. , Saris W. H. M. , van Baak M. A.
Published: November 2005

The sympathetic nervous system is involved in the control of energy metabolism and expenditure. Diet-induced thermogenesis is mediated partly by the ß-adrenergic component of this system. The aim of the present study was to investigate the role of genetic variation in the ß2-adrenoceptor in diet-induced thermogenesis. Data from twenty-four subjects (fourteen men and ten women; BMI 26·7(sem 0·8) kg/m2; age 45·2(sem1·4) years) with different polymorphisms of the ß2-adrenoceptor at codon 16 (Gly16Gly, Gly16Arg or Arg16Arg) were recruited for this study. Subjects were given a high-carbohydrate liquid meal, and the energy expenditure, respiratory exchange ratio, and plasma concentrations of NEFA, glycerol, glucose, insulin and catecholamines were measured before and over 4 h after the meal. The AUC of energy expenditure (diet-induced thermogenesis) was not significantly different between polymorphism groups, nor was the response of any of the other measured variables to the meal. In a multiple regression model, the only variable that explained a significant proportion (32 %) of the variation in diet-induced thermogenesis was the increase in plasma adrenaline in response to the meal (P<0·05). The ß2-adrenoceptor codon16 polymorphisms did not contribute significantly. In conclusion, an independent contribution of the codon 16 polymorphism of the ß2-adrenoceptor gene to the variation in thermogenic response to a high-carbohydrate meal could not be demonstrated. The interindividual variation in thermogenic response to the meal was correlated with variations in the plasma adrenaline response to the meal.
Short-chain fatty acid formation in the hindgut of rats fed oligosaccharides varying in monomeric composition, degree of polymerisation and solubility
Authors: Nilsson Ulf , Nyman Margareta
Published: November 2005

The contents of short-chain fatty acids were investigated in rats fed lactitol, lactulose and four fructo-oligosaccharides of different degree of polymerisation and solubility. Fructo-oligosaccharides with a low degree of polymerisation (2–8) generated the highest levels of butyric acid all along the hindgut, whereas fructo-oligosaccharides with a high degree of polymerisation (10–60) generated the highest levels of propionic acid. These specific differences were also generally reflected in the caecal pools and molar proportions of short-chain fatty acids. The lower solubility of the fructo-oligosaccharides was related to a lower degree of caecal fermentation. Lactulose and lactitol yielded high proportions of acetic acid and low proportions of butyric acid. It is concluded that both the degree of polymerisation and the solubility may affect short-chain fatty acid formation, whereas the fructose contentper seseem to be of less importance. This may be of interest when designing foods with specific health effects.
Rats treated with oleoyl-oestrone maintain glucidic homeostasis: comparisons with a pair-fed model
Authors: Salas Anna , Esteve Montserrat , Grasa M. Mar , Remesar Xavier
Published: November 2005

To determine whether or not the weight (and fat) loss induced by oleoyl-oestrone treatment results only as a consequence of decreased food intake, we compared treated animals with a pair-fed model. To this end, Wistar female rats received daily oral gavages of 10μmol/kg per d oleoyl-oestrone in sunflower oil, or vehicle alone for 10 or 20d. A second group of rats received the gavage of sunflower oil and the same amount of food ingested as the oleoyl-oestrone-treated animals (pair-fed group). Rats treated with oleoyl-oestrone maintained glucidic metabolism homeostasis despite a marked decrease in adipose tissue weight (P<0·001). Pair-fed rats exhibited a different pattern, comparable to short-term starvation, with greatly decreased glycogen stores (P<0·0001). The most significant effects were detected in the 10d period groups. Oleoyl-oestrone affected the activity of the ponderostat system not only by decreasing appetite but also by modifying energy partition: treated animals maintained their glucose and energy homeostasis despite decreased food intake and the massive depletion of lipid stores.
Dietary silicon intake in post-menopausal women
Authors: McNaughton S. A. , Bolton-Smith C. , Mishra G. D. , Jugdaohsingh R. , Powell J. J.
Published: November 2005

Si has been suggested as an essential element, and may be important in optimal bone, skin and cardiovascular health. However, there are few estimates of dietary Si intakes in man, especially in a UK population. Following the development of a UK food composition database for Si, the aim of the present study was to investigate dietary intakes of Si amongst healthy women aged over 60 years and to identify important food sources of Si in their diet. Healthy, post-menopausal female subjects (>60 years of age;n209) were recruited from the general population around Dundee, Scotland as part of an unrelated randomised controlled intervention study where dietary intake was assessed using a self-administered, semi-quantitative food-frequency questionnaire at five time-points over a 2-year period. Food composition data on the Si content of UK foods was used to determine the Si content of food items on the food-frequency questionnaire. Mean Si intake was 18·6 (sd 4·6) mg and did not vary significantly across the 2 years of investigation. Cereals provided the greatest amount of Si in the diet (about 30%), followed by fruit, beverages (hot, cold and alcoholic beverages combined) and vegetables; together these foods provided over 75% about Si intake. Si intakes in the UK appear consistent with those reported previously for elderly women in Western populations, but lower than those reported for younger women or for men.
A diet rich in phosphatidylethanolamine increases plasma homocysteine in mink: a comparison with a soyabean oil diet
Authors: Müller Hanne , Grande Terje , Ahlstrøm Øystein , Skrede Anders
Published: November 2005

The effects of high dietary levels of phosphatidylethanolamine (PE) on plasma concentrations of homocysteine (tHcy) have not previously been studied. Eighteen mink (Mustela vison) studied were fed one of three diets during a 25d period in a parallel-group design. The compared diets had 0, 17 and 67% extracted lipids from natural gas-utilising bacteria (LNGB), which were rich in PE. The group with 0% LNGB was fed a diet of 100% soyabean oil (SB diet). Phospholipids are the main lipid components in LNGB andMethylococcus capsulatusis the main bacteria (90%). The fasting plasma concentration of tHcy was significantly higher when the mink consumed the diet with 67% LNGB than when they consumed the SB diet (P=0·039). A significantly lower glutathione peroxidase activity was observed in mink consuming the 17% LNGB diet or the 67% LNGB diet than was observed in mink fed the SB diet. The lack of significant differences in the level of plasma PE due to the diets indicates that most of the PE from the 67% LNGB diet was converted to phosphatidylcholine (PC) in the liver. It has previously been hypothesised that phosphatidylethanolamine N-methyltransferase is an important source of tHcy. The present results indicate that plasma tHcy is at least partly regulated by phospholipid methylation from PE to PC. This methylation reaction is a regulator of physiological importance.
Intra- and interindividual variability of resting energy expenditure in healthy male subjects – biological and methodological variability of resting energy expenditure
Authors: Bader Nicolle , Bosy-Westphal Anja , Dilba Britta , Müller Manfred J.
Published: November 2005

The objective of the present study was to investigate the contribution of intra-individual variance of resting energy expenditure (REE) to interindividual variance in REE. REE was measured longitudinally in a sample of twenty-three healthy men using indirect calorimetry. Over a period of 2 months, two consecutive measurements were done in the whole group. In subgroups of seventeen and eleven subjects, three and four consecutive measurements were performed over a period of 6 months. Data analysis followed a standard protocol considering the last 15min of each measurement period and alternatively an optimised protocol with strict inclusion criteria. Intra-individual variance in REE and body composition measurements (CVintra) as well as interindividual variance (CVinter) were calculated and compared with each other as well as with REE prediction from a population-specific formula. Mean CVintra for measured REE and fat-free mass (FFM) ranged from 5·0 to 5·6% and from 1·3 to 1·6%, respectively. CVintra did not change with the number of repeated measurements or the type of protocol (standard v. optimised protocol). CVinter for REE and REE adjusted for FFM (REEadj) ranged from 12·1 to 16·1% and from 10·4 to 13·6%, respectively. We calculated total error to be 8%. Variance in body composition (CVintra FFM) explains 19% of the variability in REEadj, whereas the remaining 81% is explained by the variability of the metabolic rate (CVintra REE). We conclude that CVintra of REE measurements was neither influenced by type of protocol for data analysis nor by the number of repeated measurements. About 20% of the variance in REEadj is explained by variance in body composition.
Effect on appetite control of minor cereal and pseudocereal products
Authors: Berti Cristiana , Riso Patrizia , Brusamolino Antonella , Porrini Marisa
Published: November 2005

Recent findings suggest that Western diets based on highly palatable foods are likely to be much less satiating than more traditional diets or those typical of less developed countries. In particular, some alternative crops (for example, buckwheat, oat, barley, spelt, rye, quinoa, amaranth) seem to be of great nutritional interest and to represent important recipes for healthier and typical regional foods. The objective of the present study was to investigate the effect on subsequent food intake and feelings of satiety of alternative oat bread, oat and buckwheat pasta and of quinoa as compared with their wheat counterparts and rice, respectively. Three different experiments (one specific for each alternative crop food) were conducted, all with a within-subjects design. The preloading paradigm strategy was used. Results showed that preload energy level influenced total energy intake (preload plus ad libitum test meal intake), larger preloads inducing more eating than smaller preloads. No effect of formulation was observed on energy intake, as the consumption of alternative crop formulations did not decrease the total energy intake as compared with that of the counterparts. Satiating efficiency indices (SEI) for alternative crop foods were higher with respect to traditional cereal foods. In particular, white bread was the least satisfying food (SEI =0·2) and the different time of consumption (for lunch or as a snack) did not affect energy intake. In conclusion, oat or buckwheat formulations, and also quinoa, may be exploited for their potential impact on eating behaviour, particularly considering they are good sources of functional substances.
Does regular walnut consumption lead to weight gain?
Authors: Sabaté Joan , Cordero-MacIntyre Zaida , Siapco Gina , Torabian Setareh , Haddad Ella
Published: November 2005

Studies consistently show the beneficial effects of eating nuts, but as high-energy foods, their regular consumption may lead to weight gain. We tested if daily consumption of walnuts (approximately 12% energy intake) for 6 months would modify body weight and body composition in free-living subjects. Ninety participants in a 12-month randomized cross-over trial were instructed to eat an allotted amount of walnuts (28–56g) during the walnut-supplemented diet and not to eat them during the control diet, with no further instruction. Subjects were unaware that body weight was the main outcome. Dietary compliance was about 95% and mean daily walnut consumption was 35g during the walnut-supplemented diet. The walnut-supplemented diet resulted in greater daily energy intake (557kJ (133kcal)), which should theoretically have led to a weight gain of 3·1kg over the 6-month period. For all participants, walnut supplementation increased weight (0·4 (se 0·1) kg), BMI (0·2 (se 0·1) kg/m2), fat mass (0·2 (se 0·1) kg) and lean mass (0·2 (se 0·1) kg). But, after adjusting for energy differences between the control and walnut-supplemented diets, no significant differences were observed in body weight or body composition parameters, except for BMI (0·1 (se 0·1) kg/m2). The weight gain from incorporating walnuts into the diet (control→walnut sequence) was less than the weight loss from withdrawing walnuts from the diet (walnut→control sequence). Our findings show that regular walnut intake resulted in weight gain much lower than expected and which became non-significant after controlling for differences in energy intake.
Evidence of unmetabolised folic acid in cord blood of newborn and serum of 4-day-old infants
Authors: Sweeney Mary R. , McPartlin Joseph , Weir Donald G. , Daly Sean , Pentieva Kristina , Daly Leslie , Scott John M.
Published: November 2005

Oral folic acid above certain threshold doses results in unmetabolised folic acid in serum. This raises a number of public health safety issues, principally the potential to mask pernicious anaemia; more recently the theoretical potential for high-dose folic acid to promote cancer has been highlighted. In this paper we set out to examine the appearance of unmetabolised folic acid both in cord blood from newborn full-term and premature infants and serum from 4-d-old infants post-formula feeding. Blood was collected from the umbilical cord of eleven infants in the delivery room immediately after birth. A follow-up serum sample (n 9) was collected 4d later from infants post-formula feeding. We detected unmetabolised folic acid in cord blood from all infants at birth. In addition, unmetabolised folic acid was present in serum of seven infants post-formula feeding, six of which had increased from birth. Our results imply that infants in Ireland, which does not yet have mandatory fortification, could potentially have circulatory unmetabolised folic acid at the time of birth. We do not know if the presence of folic acid in cord blood will have any adverse consequences. However, if theoretical safety concerns are borne out by future research, the likelihood is that the longer the exposure the more likely the potential for harm. This would also be the case in infants exposed to unmetabolised folic acid as a result of formula feeding.
Production and content management implications for archival projects: a snapshot in May 2005
Authors: Inger Simon
Published: November 2005

The British Library, under the auspices of the Joint Committee on Legal Deposit's sub‐committee for e‐journals, is conducting a pilot project to lay the groundwork for possible legislation for the legal deposit of electronic journals. One component of the project has been to understand the production environment that governs the creation of the published data, the content management systems that publishers have deployed and the ways in which publishers are able to distribute content to their partners. This work is a snapshot of a cross‐section of the UK journal‐publishing industry taken in May 2005.
A Genomewide Screen for Petite-negative Yeast Strains Yields a New Subunit of the i-AAA Protease Complex
Authors: Dunn Cory D. , Lee Marina S. , Spencer Forrest A. , Jensen Robert E.
Published: November 2005

Unlike many other organisms, the yeast Saccharomyces cerevisiae can tolerate the loss of mitochondrial DNA (mtDNA). Although a few proteins have been identified that are required for yeast cell viability without mtDNA, the mechanism of mtDNA-independent growth is not completely understood. To probe the relationship between the mitochondrial genome and cell viability, we conducted a microarray-based, genomewide screen for mitochondrial DNA-dependent yeast mutants. Among the several genes that we discovered is MGR1, which encodes a novel subunit of the i-AAA protease complex located in the mitochondrial inner membrane. mgr1Δ mutants retain some i-AAA protease activity, yet mitochondria lacking Mgr1p contain a misassembled i-AAA protease and are defective for turnover of mitochondrial inner membrane proteins. Our results highlight the importance of the i-AAA complex and proteolysis at the inner membrane in cells lacking mitochondrial DNA.
Conserved Prefusion Protein Assembly in Regulated Exocytosis
Authors: Rickman Colin , Jiménez José L , Graham Margaret E. , Archer Deborah A. , Soloviev Mikhail , Burgoyne Robert D. , Davletov Bazbek
Published: November 2005

The regulated release of hormones and neurotransmitters is a fundamental process throughout the animal kingdom. The short time scale for the calcium triggering of vesicle fusion in regulated secretion suggests that the calcium sensor synaptotagmin and the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) membrane fusion machinery are well ordered before the calcium signal. To gain insight into the organization of the prefusion protein assembly in regulated exocytosis, we undertook a structural/functional study of the vesicular synaptotagmin1 and the plasma membrane SNARE proteins, which copurify from the brain in the absence of calcium. Based on an evolutionary analysis, mutagenesis screens, and a computational protein docking approach, we now provide the first testable description of the supramolecular prefusion assembly. Perturbing the determined synaptotagmin/SNARE-interacting interface in several models of regulated exocytosis altered the secretion of hormones and neurotransmitters. These mutations also disrupted the constitutive synaptotagmin/SNARE link in full agreement with our model. We conclude that the interaction of synaptotagmin with preassembled plasma membrane SNARE proteins, before the action of calcium, can provide a precisely organized “tethering” scaffold that underlies regulated secretion throughout evolution.
An Uncleavable uPAR Mutant Allows Dissection of Signaling Pathways in uPA-dependent Cell Migration
Authors: Mazzieri Roberta , D'Alessio Silvia , Kenmoe Richard Kamgang , Ossowski Liliana , Blasi Francesco
Published: November 2005

Urokinase-type plasminogen activator (uPA) binding to uPAR induces migration, adhesion, and proliferation through multiple interactions with G proteins-coupled receptor FPRL1, integrins, or the epidermal growth factor (EGF) receptor (EGFR). At least two forms of uPAR are present on the cell surface: full-length and cleaved uPAR, each specifically interacting with one or more transmembrane proteins. The connection between these interactions and the effects on the signaling pathways activation is not clear. We have exploited an uPAR mutant (hcr, human cleavage resistant) to dissect the pathways involved in uPA-induced cell migration. This mutant is not cleaved by proteases, is glycosylphosphatidylinositol anchored, and binds uPA with a normal Kd. Both wild-type (wt) and hcr-uPAR are able to mediate uPA-induced migration, are constitutively associated with the EGFR, and associate with α3β1 integrin upon uPA binding. However, they engage different pathways in response to uPA. wt-uPAR requires both integrins and FPRL1 to mediate uPA-induced migration, and association of wt-uPAR to α3β1 results in uPAR cleavage and extracellular signal-regulated kinase (ERK) activation. On the contrary, hcr-uPAR does not activate ERK and does not engage FPRL1 or any other G protein-coupled receptor, but it activates an alternative pathway initiated by the formation of a triple complex (uPAR-α3β1-EGFR) and resulting in the autotyrosine phosphorylation of EGFR.
Binding of Src to Na+/K+-ATPase Forms a Functional Signaling Complex
Authors: Tian Jiang , Cai Ting , Yuan Zhaokan , Wang Haojie , Liu Lijun , Haas Michael , Maksimova Elena , Huang Xin-Yun , Xie Zi-Jian
Published: November 2005

We have shown that ouabain activates Src, resulting in subsequent tyrosine phosphorylation of multiple effectors. Here, we tested if the Na+/K+-ATPase and Src can form a functional signaling complex. In LLC-PK1 cells the Na+/K+-ATPase and Src colocalized in the plasma membrane. Fluorescence resonance energy transfer analysis indicated that both proteins were in close proximity, suggesting a direct interaction. GST pulldown assay showed a direct, ouabain-regulated, and multifocal interaction between the α1 subunit of Na+/K+-ATPase and Src. Although the interaction between the Src kinase domain and the third cytosolic domain (CD3) of α1 is regulated by ouabain, the Src SH3SH2 domain binds to the second cytosolic domain constitutively. Functionally, binding of Src to either the Na+/K+-ATPase or GST-CD3 inhibited Src activity. Addition of ouabain, but not vanadate, to the purified Na+/K+-ATPase/Src complex freed the kinase domain and restored the Src activity. Consistently, exposure of intact cells to ouabain apparently increased the distance between the Na+/K+-ATPase and Src. Concomitantly, it also stimulated tyrosine phosphorylation of the proteins that are associated with the Na+/K+-ATPase. These new findings illustrate a novel molecular mechanism of signal transduction involving the interaction of a P-type ATPase and a nonreceptor tyrosine kinase.
Phosphoinositide 3-Kinase Activity Controls the Chemoattractant-mediated Activation and Adaptation of Adenylyl Cyclase
Authors: Comer Frank I. , Parent Carole A.
Published: November 2005

The binding of chemoattractants to cognate G protein-coupled receptors activates a variety of signaling cascades that provide spatial and temporal cues required for chemotaxis. When subjected to uniform stimulation, these responses are transient, showing an initial peak of activation followed by a period of adaptation, in which activity subsides even in the presence of stimulus. A tightly regulated balance between receptor-mediated stimulatory and inhibitory pathways controls the kinetics of activation and subsequent adaptation. In Dictyostelium, the adenylyl cyclase expressed during aggregation (ACA), which synthesizes the chemoattractant cAMP, is essential to relay the signal to neighboring cells. Here, we report that cells lacking phosphoinositide 3-kinase (PI3K) activity are deficient in signal relay. In LY294002-treated cells, this defect is because of a loss of ACA activation. In contrast, in cells lacking PI3K1 and PI3K2, the signal relay defect is because of a loss of ACA adaptation. We propose that the residual low level of 3-phosphoinositides in pi3k1-/2-cells is sufficient to generate the initial peak of ACA activity, yet is insufficient to sustain the inhibitory phase required for its adaptation. Thus, PI3K activity is poised to regulate both ACA activation and adaptation, thereby providing a link to ensure the proper balance of counteracting signals required to maintain optimal chemoresponsiveness.
Slx4 Regulates DNA Damage Checkpoint-dependent Phosphorylation of the BRCT Domain Protein Rtt107/Esc4
Authors: Roberts Tania M. , Kobor Michael S. , Bastin-Shanower Suzanne A. , Ii Miki , Horte Sonja A. , Gin Jennifer W. , Emili Andrew , Rine Jasper , Brill Steven J. , Brown Grant W.
Published: November 2005

RTT107 (ESC4, YHR154W) encodes a BRCA1 C-terminal-domain protein that is important for recovery from DNA damage during S phase. Rtt107 is a substrate of the checkpoint protein kinase Mec1, although the mechanism by which Rtt107 is targeted by Mec1 after checkpoint activation is currently unclear. Slx4, a component of the Slx1-Slx4 structure-specific nuclease, formed a complex with Rtt107. Deletion of SLX4 conferred many of the same DNA-repair defects observed in rtt107Δ, including DNA damage sensitivity, prolonged DNA damage checkpoint activation, and increased spontaneous DNA damage. These phenotypes were not shared by the Slx4 binding partner Slx1, suggesting that the functions of the Slx4 and Slx1 proteins in the DNA damage response were not identical. Of particular interest, Slx4, but not Slx1, was required for phosphorylation of Rtt107 by Mec1 in vivo, indicating that Slx4 was a mediator of DNA damage-dependent phosphorylation of the checkpoint effector Rtt107. We propose that Slx4 has roles in the DNA damage response that are distinct from the function of Slx1-Slx4 in maintaining rDNA structure and that Slx4-dependent phosphorylation of Rtt107 by Mec1 is critical for replication restart after alkylation damage.
A genotype calling algorithm for affymetrix SNP arrays
Authors: Rabbee Nusrat , Speed Terence P.
Published: November 2005

Motivation: A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the features associated with one chip and one SNP at a time. Using a large training sample where the genotype labels are known, we develop a supervised learning algorithm to obtain more accurate classification results on new data. The method we propose, RLMM, is based on a robustly fitted, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variance is reduced through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as across thousands of SNPs for accurate classification. In this paper, we apply RLMM to Affymetrix 100 K SNP array data, present classification results and compare them with genotype calls obtained from the Affymetrix procedure DM, as well as to the publicly available genotype calls from the HapMap project.

Availability: The RLMM software is implemented in R and is available from Bioconductor or from the first author at nrabbee@post.harvard.edu.

Contact:  nrabbee@stat.berkeley.edu

Supplementary information:
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation
Authors: Ji Xinglai , Xu Ying
Published: November 2005

Summary: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (μ, λ)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory.

Availability: The source code (in C) is free for academic users at

Contact:  xyn@bmb.uga.edu

Supplementary information: Detailed documentation for libSRES is available at
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
Authors: Castrignanò Tiziana , De Meo Paolo D'Onorio , Grillo Giorgio , Liuni Sabino , Mignone Flavio , Talamo Ivano Giuseppe , Pesole Graziano
Published: November 2005

Summary: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.

Availability: . GenoMiner software and documentation is available from the authors upon request.

Contact:  graziano.pesole@unimi.it
Topology and static response of interaction networks in molecular biology
Authors: Radulescu Ovidiu , Lagarrigue Sandrine , Siegel Anne , Veber Philippe , Le Borgne Michel
Published: November 2005

We introduce a mathematical framework describing static response of networks occurring in molecular biology. This formalism has many similarities with the Laplace–Kirchhoff equations for electrical networks. We introduce the concept of graph boundary and we show how the response of the biological networks to external perturbations can be related to the Dirichlet or Neumann problems for the corresponding equations on the interaction graph. Solutions to these two problems are given in terms of path moduli (measuring path rigidity with respect to the propagation of interaction along the graph). Path moduli are related to loop products in the interaction graph via generalized Mason–Coates formulae. We apply our results to two specific biological examples: the lactose operon and the genetic regulation of lipogenesis. Our applications show consistency with experimental results and in the case of lipogenesis check some hypothesis on the behaviour of hepatic fatty acids on fasting.
Numerical modelling of the laser surface processing of magnesia partially stabilized zirconia by the means of three-dimensional transient finite element analysis
Authors: Hao L , Lawrence J
Published: November 2005

A numerical technique has been employed to use the ABAQUS finite element analysis (FEA) package in order to simulate the CO2laser surface processing of a magnesia partially stabilized zirconia (MgO-PSZ) bioinert ceramic. The transient FEA takes into account the heat radiation, heat convection and phase change during the laser processing. The heat source has been modelled as a stepwise moving laser source with small steps in the scanning direction to approximate continuous movement. It further extends and validates numerical methods by comparing experimental data of surface temperature for laser surface processing of the MgO-PSZ to the solution from the FEA model. Experiments involving CO2laser surface melting of the MgO-PSZ were also carried out using various laser process parameters, and the measured melt width and depth of laser-treated tracks were used to evaluate the validity of the models. In order to prevent the crack formation in the laser processing, pre- and post-heating were proposed by using the scanning of laser beam with the lower power before and after laser processing with high power to lower the thermal gradient.
Functional and aggregative responses of harbour seals to changes in salmonid abundance
Authors: Middlemas Stuart J , Barton Tim R , Armstrong John D , Thompson Paul M
Published: November 2005

There is intense debate over the potential impact of seal predation on declining salmon stocks in both the Pacific and Atlantic oceans. However, efforts to model such interactions have been constrained by a lack of data on the functional and numerical responses of these predators. Based upon theory, and data from small-scale terrestrial and freshwater systems, a type 3 functional response is expected to best describe predation by generalist pinnipeds. Similarly, theory also predicts that seal numbers should increase with salmon density in rivers following an aggregative response of predator to prey. We tested these predictions by studying the diet and local density of harbour seals in relation to seasonal variations in the abundance of salmonid in a Scottish river system. As predicted, the abundance of seals in the river was directly related to the abundance of returning salmon, and dietary data supported the type 3 functional response to changes in salmonid abundance. These studies provide empirical support for the use of type 3 response in modelling studies.
Age-dependent genetic variance in a life-history trait in the mute swan
Authors: Charmantier Anne , Perrins Christopher , McCleery Robin H , Sheldon Ben C
Published: November 2005

Genetic variance in characters under natural selection in natural populations determines the way those populations respond to that selection. Whether populations show temporal and/or spatial constancy in patterns of genetic variance and covariance is regularly considered, as this will determine whether selection responses are constant over space and time. Much less often considered is whether characters show differing amounts of genetic variance over the life-history of individuals. Such age-specific variation, if present, has important potential consequences for the force of natural selection and for understanding the causes of variation in quantitative characters. Using data from a long-term study of the mute swanCygnus olor, we report the partitioning of phenotypic variance in timing of breeding (subject to strong natural selection) into component parts over 12 different age classes. We show that the additive genetic variance and heritability of this trait are strongly age-dependent, with higher additive genetic variance present in young and, particularly, old birds, but little evidence of any genetic variance for birds of intermediate ages. These results demonstrate that age can have a very important influence on the components of variation of characters in natural populations, and consequently that separate age classes cannot be assumed to be equivalent, either with respect to their evolutionary potential or response.