bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening Extremophiles for Bioconversion Potentials
Authors: Kim Jin‐Woo , Peeples Tonya L.
Published: November 2006

A screening protocol was developed and implemented to evaluate extremophiles, in particular hyperthermophiles and thermoacidophiles, for their capacity to transform starch‐based feedstocks to high‐value organic acids and solvents. Screening results of 14 extremophiles showed promising growth and biotransformation potentials. In particular, Hyperthermus butylicus, Thermococcus litoralis, and Sulfolobus acidocaldarius were identified as producers of both organic acids and solvents under the screening protocol. The screening effort presented here represents an important step toward realization of biotransformation potentials of extremophiles, potentially improving upon biomass‐based processes.
Characteristics of high‐latitude vertical plasma flow from the Defense Meteorological Satellite Program
Authors: Coley W. R. , Heelis R. A. , Hairston M. R.
Published: November 2006

We have examined characteristics of the vertical O+ flux in the topside high‐latitude ionosphere from measurements of the vertical ion drift and ion number density made by the Defense Meteorological Satellite Program (DMSP) F13 spacecraft from June 1996 to January 1997, June 1998 to January 1999, and June 2001 to January 2002. In the polar cap the vertical ion flux is, on average, downward at all locations. However, in the auroral zone the ion flux is highly structured, and a net upward flux is produced primarily by spatially and temporally confined events containing upward fluxes in excess of 109 cm−2s−1. These dominant high‐flux events tend to be produced more commonly by high densities rather than by high velocities. The range of vertical velocity and number density changes with season and solar cycle with greater variability in the vertical velocity occurring during winter and at lower levels of solar activity. There is also evidence that the vertical fluxes are a function of the interplanetary magnetic field, with upward fluxes in the auroral zones for negative Bz and upward fluxes in the polar cap for positive Bz.
Stable carbon isotope records of carbonates tracing fossil seep activity off Indonesia
Authors: Wiedicke M. , Weiss W.
Published: November 2006

Stable isotope records of carbonates from up to 20 m long sediment cores from the forearc basin of the Sunda arc display significant 13C depletion, deviating from expected normal marine levels by 5 to 40‰ (Peedee belemnite (PDB)). This depletion is interpreted to be caused by methane seepage and associated authigenic carbonate precipitation in sediments near the seafloor. About 2‐μm‐sized globular carbonate particles found in isotopically depleted samples support this interpretation. Their shape suggests microbial mediation of the precipitation process. Investigation of benthic foraminiferal assemblages in cores which record seep influence indicate times of high abundance with an up to twentyfold increase of the population and a dominance of opportunistic infaunal taxa. We relate these “events” to the seepage of methane, thus providing an understanding of the duration and age of this postdepositional process: postulated seep activity is most intense between 3–7 kyr B.P. and 27–33 kyr B.P. As cores with 13C isotope depletion were taken atop active fault zones in the forearc, we suggest a tectonic control of the seepage. Records of seep activity thus may have the potential to archive imprints of tectonic activity.
Low‐temperature magnetic properties of magnetite using first‐order reversal curve analysis: Implications for the pseudo‐single‐domain state
Authors: Smirnov A. V.
Published: November 2006

Low‐temperature magnetic hysteresis properties of nearly stoichiometric magnetite were studied using the first‐order reversal curve (FORC) technique. FORC distributions were measured at 20 K after cooling in zero magnetic field or cooling in the presence of a strong (1.5 T) magnetic field. Five polycrystalline samples ranged in mean grain size and shape, representing mostly single‐domain (SD), pseudo‐single‐domain (PSD), and multidomain (MD) magnetic hysteresis behavior. The FORC distributions measured from PSD magnetite after zero field cooling (ZFC) manifest an unusual behavior, characterized by two distinct maxima located almost symmetrically with respect to the zero interaction field (Hu = 0) axis on a FORC diagram. In contrast, the low‐temperature FORC distributions for SD and MD samples have a single maximum located at the Hu = 0 axis. The appearance of two maxima on low‐temperature FORC distributions is interpreted as a manifestation of a perminvar‐like behavior due to stabilization of the magnetic domain structure by irregularities of crystalline lattice induced by twinning in monoclinic magnetite. The experimental data suggest that the effect of monoclinic twinning on remagnetization is only pronounced within a certain grain size range. The double‐maxima ZFC FORC distribution appears to be a distinctive property of PSD hysteresis behavior, which cannot be reproduced by mixing SD and MD magnetites.
Sensitivity of surface climate to land surface parameters: A case study using the simple biosphere model SiB2
Authors: Bounoua Lahouari , Masek Jeffrey , Tourre Yves M.
Published: November 2006

Significant uncertainties may result from numerical models if fed with inappropriate input data. Biosphere‐atmosphere transfer models are sensitive to input vegetation parameters, and the degree to which parameter estimates rely on the definition of the land cover type varies with models. In this study we use the simple biosphere model (SiB2) to evaluate uncertainties associated with misclassification of the land cover type and how they propagate to surface climate variables. We estimate that in regions with heterogeneous landscapes, the aggregation of land cover types from 1 × 1 km to 100 × 100 km horizontal resolution overestimates the area of the dominant type by up to 70%. The largest uncertainties associated with land cover misclassification are found in leaf area index and roughness length both of which have significant impact on the fluxes of carbon, water and energy at the earth surface. Other important uncertainties occur when the misclassification confuses plants with different carbon pathways. An assessment of the uncertainties is obtained comparing outcomes resulting from a choice of a dominant type in a 100 × 100 km area to those obtained using a mosaic of land cover composition weighted by its fractional cover. The difference shows the choice of the dominant type to be cooler by 0.6°C than the average of the mosaic at local noon, while at night it is warmer by 1.7°C. Our results indicate that the diurnal temperature range (dtr) varies from 13°C for the dominant type to 15°C for the weighted average. The difference in the dtr is due to higher minimum temperature simulated with the dominant type. The choice of a dominant type also results in a daily carbon assimilation loss of 28,000 gC compared to the average.
A critical β6–β7 loop in the pleckstrin homology domain of ceramide kinase
Authors: Rovina Philipp , Jaritz Markus , Höfinger Siegfried , Graf Christine , Dévay Piroska , Billich Andreas , Baumruker Thomas , Bornancin Frédéric
Published: November 2006

CerK (ceramide kinase) produces ceramide 1-phosphate, a sphingophospholipid with recognized signalling properties. It localizes to the Golgi complex and fractionates essentially between detergent-soluble and -insoluble fractions; however, the determinants are unknown. Here, we made a detailed mutagenesis study of the N-terminal PH domain (pleckstrin homology domain) of CerK, based on modelling, and identified key positively charged amino acid residues within an unusual motif in the loop interconnecting β-strands 6 and 7. These residues are critical for CerK membrane association and polyphosphoinositide binding and activity. Their mutagenesis results in increased thermolability, sensitivity to proteolysis, reduced apparent molecular mass as well as propensity of the recombinant mutant protein to aggregate, indicating that this loop impacts the overall conformation of the CerK protein. This is in contrast with most PH domains whose function strongly relies on charges located in the β1–β2 loop.
Molecular and functional characterization of microsomal UDP-glucuronic acid uptake by members of the nucleotide sugar transporter (NST) family
Authors: Kobayashi Tsutomu , Sleeman Judith E. , Coughtrie Michael W. H. , Burchell Brian
Published: November 2006

Transport of the co-substrate UDPGA (UDP-glucuronic acid) into the lumen of the endoplasmic reticulum is an essential step in glucuronidation reactions due to the intraluminal location of the catalytic site of the enzyme UGT (UDP-glucuronosyltransferase). In the present study, we have characterized the function of several NSTs (nucleotide sugar transporters) and UGTs as potential carriers of UDPGA for glucuronidation reactions. UDPGlcNAc (UDP-N-acetylglucosamine)-dependent UDPGA uptake was found both in rat liver microsomes and in microsomes prepared from the rat hepatoma cell line H4IIE. The latency of UGT activity in microsomes derived from rat liver and V79 cells expressing UGT1A6 correlated well with mannose-6-phosphatase latency, confirming the UGT in the recombinant cells retained a physiology similar to rat liver microsomes. In the present study, four cDNAs coding for NSTs were obtained; two were previously reported (UGTrel1 and UGTrel7) and two newly identified (huYEA4 and huYEA4S). Localization of NSTs within the human genome sequence revealed that huYEA4S is an alternatively spliced form of huYEA4. All the cloned NSTs were stably expressed in V79 (Chinese hamster fibroblast) cells, and were able to transport UDPGA after preloading of isolated microsomal vesicles with UDPGlcNAc. The highest uptake was seen with UGTrel7, which displayed a Vmax approx. 1% of rat liver microsomes. Treatment of H4IIE cells with β-naphthoflavone induced UGT protein expression but did not affect the rate of UDPGA uptake. Furthermore, microsomes from UGT1-deficient Gunn rat liver showed UDPGA uptake similar to those from control rats. These data show that NSTs can act as UDPGA transporters for glucuronidation reactions, and indicate that UGTs of the 1A family do not function as UDPGA carriers in microsomes. The cell line H4IIE is a useful model for the study of UDPGA transporters for glucuronidation reactions.
The translation initiation factor eIF2β is an interactor of protein phosphatase-1
Authors: Wakula Paulina , Beullens Monique , van Eynde Aleyde , Ceulemans Hugo , Stalmans Willy , Bollen Mathieu
Published: November 2006

It is reasonably well understood how the initiation of translation is controlled by reversible phosphorylation of the eukaryotic translation initiation factors eIF2α, eIF2Bϵ and eIF4E. Other initiation factors, including eIF2β, are also established phosphoproteins but the physiological impact of their phosphorylation is not known. Using a sequence homology search we found that the central region of eIF2β contains a putative PP1-(protein phosphatase-1) binding RVxF-motif. The predicted eIF2β-PP1 interaction was confirmed by PP1 binding and co-immunoprecipitation assays on cell lysates as well as with the purified components. Site-directed mutagenesis showed that eIF2β contains, in addition to an RVxF-motif, at least one other PP1-binding site in its C-terminal half. eIF2β functioned as an inhibitor for the dephosphorylation of glycogen phosphorylase and Ser51of eIF2α by PP1, but did not affect the dephosphorylation of Ser464 of eIF2Bϵ by this phosphatase. Strikingly, eIF2β emerged as an activator of its own dephosphorylation (Ser2, Ser67, Ser218) by associated PP1, since the substrate quality of eIF2β was decreased by the mere mutation of its RVxF-motif. These results make eIF2β an attractive candidate substrate for associated PP1 in vivo. The overexpression of wild-type eIF2β or eIF2β with a mutated RVxF-motif did not differentially affect the rate of translation, indicating that the binding of PP1 is not rate-limiting for translation under basal conditions.
Dihydrodipicolinate synthase from Thermotoga maritima
Authors: Pearce F. Grant , Perugini Matthew A. , Mckerchar Hannah J. , Gerrard Juliet A.
Published: November 2006

DHDPS (dihydrodipicolinate synthase) catalyses the branch point in lysine biosynthesis in bacteria and plants and is feedback inhibited by lysine. DHDPS from the thermophilic bacterium Thermotoga maritima shows a high level of heat and chemical stability. When incubated at 90 °C or in 8 M urea, the enzyme showed little or no loss of activity, unlike the Escherichia coli enzyme. The active site is very similar to that of the E. coli enzyme, and at mesophilic temperatures the two enzymes have similar kinetic constants. Like other forms of the enzyme, T. maritima DHDPS is a tetramer in solution, with a sedimentation coefficient of 7.2 S and molar mass of 133 kDa. However, the residues involved in the interface between different subunits in the tetramer differ from those of E. coli and include two cysteine residues poised to form a disulfide bond. Thus the increased heat and chemical stability of the T. maritima DHDPS enzyme is, at least in part, explained by an increased number of inter-subunit contacts. Unlike the plant or E. coli enzyme, the thermophilic DHDPS enzyme is not inhibited by (S)-lysine, suggesting that feedback control of the lysine biosynthetic pathway evolved later in the bacterial lineage.
Pyrrolidine dithiocarbamate protects the small bowel from warm ischaemia/reperfusion injury of the intestine: the role of haem oxygenase
Authors: Mallick Ismail H. , Winslet Marc C. , Seifalian Alexander M.
Published: November 2006

IR (ischaemia/reperfusion) injury of the intestine occurs commonly during abdominal surgery. We have previously shown that PDTC (pyrrolidine dithiocarbamate), an HO-1 (haem oxygenase-1) donor, improves intestinal microvascular perfusion. In the present study, we have investigated the effects of PDTC on the intestinal microcirculation following IR (ischaemia/reperfusion) injury of the intestine. Male Sprague–Dawley rats (n=72) were randomly assigned to four groups (n=18/group): (i) sham-operated group, who underwent laparotomy without induction of IR of the intestine; (ii) IR group, who were subjected to 30 min of superior mesenteric artery occlusion and 2 h of reperfusion; (iii) PDTC+IR group, who received PDTC prior to IR; and (iv) ZnPP group, who received the HO-1 inhibitor ZnPP (zinc protoporphyrin) followed by procedures as in group (iii). The ileum was evaluated for changes in tissue cytochrome c oxidase redox status, RBC (red blood cell) dynamics and leucocyte–endothelial interactions. The expression of HO-1 in the ileal tissue was examined at the end of the reperfusion. PDTC significantly improved the intestinal tissue oxygenation, mucosal perfusion index and RBC velocity compared with the IR and ZnPP groups. PDTC also decreased the leucocyte–endothelial interactions (P<0.05 compared with the IR and ZnPP groups). PDTC induced the expression of HO-1, whereas ZnPP abolished this effect.
Effects of adrenomedullin on acute ischaemia-induced collateral development and mobilization of bone-marrow-derived cells
Authors: Abe Minami , Sata Masataka , Suzuki Etsu , Takeda Ryo , Takahashi Masao , Nishimatsu Hiroaki , Nagata Daisuke , Kangawa Kenji , Matsuo Hisayuki , Nagai Ryozo , Hirata Yasunobu
Published: November 2006

Adrenomedullin exerts not only vasodilatory effects, but also angiogenic effects. In the present study, we investigated the effects of adrenomedullin on collateral formation and circulating bone-marrow-derived cells after acute tissue ischaemia. Bone marrow of 8–10-week-old female C57BL/6J mice was replaced with that from GFP (green fluorescent protein) transgenic mice (GFP mice). At 8 weeks after transplantation, hindlimb ischaemia was induced by resecting the right femoral artery and a plasmid expressing human adrenomedullin (50 μg) was injected into the ischaemic muscle, followed by in vivo electroporation on a weekly basis. Overexpression of adrenomedullin significantly enhanced the blood flow recovery compared with controls (blood flow ratio, 1.0±0.2 compared with 0.6±0.3 respectively, at week 4; P<0.05) and increased capillary density in the ischaemic leg as determined by anti-CD31 immunostaining of the ischaemic muscle (567±40 compared with 338±65 capillaries/mm2 respectively, at week 5; P<0.05). There were more GFP-positive cells in the thigh muscle of the mice injected with adrenomedullin than in that of the control mice (29.6±4.5 compared with 16.5±3.3 capillaries/mm2 respectively, at week 5; P<0.05). We repeated the same experiments using LacZ-knock-in mice instead of GFP mice, and obtained similar results. These findings suggest that adrenomedullin may augment ischaemia-induced collateral formation with some effects on circulating bone-marrow-derived cells.
IncreasedL-arginine transport via system b0,+ in human proximal tubular cells exposed to albumin
Authors: Ashman Neil , Brunini Tatiana M. , Mann Giovanni E. , Mendes Ribeiro A. Claudio , Yaqoob Muhammad M.
Published: November 2006

Albumin has complex effects on PTECs (proximal tubular epithelial cells) and is able to stimulate growth or injury depending on its bound moieties. Albumin itself is a mitogen, inducing proliferation through a number of pathways. In PTEC exposed to purified albumin, polyamines are required for entry into the cell cycle and are critical for proliferation. Polyamines are synthesized from L-ornithine (itself derived by the action of arginase on L-arginine), and the transport and availability of L-arginine may thus be important for subsequent polyamine-dependent proliferation. In the present study we investigated radiolabelled cationic amino-acid transport in cultured PTEC exposed to 20 mg/ml ultrapure recombinant human albumin, describing the specific kinetic characteristics of transport and the expression of transporters. L-[3H]Arginine transport capacity in human PTEC is increased after exposure for 24 h to human albumin, mediated by the broad-scope high-affinity system b0,+ and, to a lesser extent, system y+L (but not system y+) transport. Increased transport is associated with increased b0,+-associated transporter expression. Inhibition of phosphoinositide 3-kinase, a key regulator of albumin endocytosis and signalling, inhibited proliferation, but had no effect on the observed increase in transport. PTEC proliferated in response to albumin. L-Lysine, a competitive inhibitor of L-arginine transport, had no effect on albumin-induced proliferation; however, arginine deprivation effectively reversed the albumin-induced proliferation observed. In conclusion, in PTEC exposed to albumin, increased L-arginine transport is mediated by increased transcription and activity of the apical b0,+ transport system. This may make L-arginine available as a substrate for the downstream synthesis of polyamines, but is not critical for cell proliferation.
ACE gene insertion/deletion polymorphism modulates capillary permeability in hypertension
Authors: Dell'omo Giulia , Penno Giuseppe , Pucci Laura , Lucchesi Daniela , Fotino Carmen , Del Prato Stefano , Pedrinelli Roberto
Published: November 2006

A D/D (deletion/deletion) polymorphism within the ACE (angiotensin 1-converting enzyme) gene increases the risk of microalbuminuria, a predictor of atherosclerotic vascular disease, in essential hypertension. It is unknown, however, whether this genetic profile is accompanied by disturbed macromolecular permeability of systemic capillary endothelium, possibly in the context of generalized endothelial dysfunction. In the present study, the ACE gene polymorphism was determined by PCR in 79 never-treated uncomplicated hypertensive men and 16 normotensive men as controls. Evaluation variables were TERalb (transcapillary escape rate of albumin; the 1-h decline rate of intravenous 125I-albumin, a measure of integrity of systemic capillary endothelium), albuminuria and forearm vasodilation to intra-arterial acetylcholine, an index of NO (nitric oxide)-mediated vasomotion, in addition to a series of sensitive parameters of albumin permeation (blood pressure, metabolic status and smoking habits). Analyses were done by comparing D/D homozygotes with grouped I/D (insertion/deletion) and I/I (insertion/insertion) subjects. TERalb was higher in D/D hypertensives, who had higher albuminuria, more frequent microalbuminuria and comparable forearm responsiveness to intra-arterial acetylcholine. Fasting glucose and insulin, insulin sensitivity, 24-h blood pressure, smoking habits and metabolic parameters did not differ between the two groups. TERalb and urine albumin values were positively associated in the hypertensive subjects. In conclusion, ACE D/D homozygosis, independently of several confounding factors, associates with higher TERalb in men with essential hypertension. This may reflect noxious genetic influences on systemic vascular permeability, a critical control mechanism for atherogenesis in the absence of grossly impaired NO-mediated arteriolar responsiveness. The parallel behaviour of TERalb and albuminuria suggests some shared genetically mediated determinant of renal and systemic microvascular abnormalities in hypertension.
High sensitivity absorption measurement of small metal clusters embedded in an argon matrix
Authors: Conus F. , Lau J. T. , Rodrigues V. , Félix C.
Published: November 2006

We describe a new UV-Vis absorption setup designed to measure with improved sensitivity the absorption spectra of size-selected small metal clusters embedded in rare gas matrices. We aim at studying the electronic structure of clusters of different materials and their interaction with the matrix. The design, construction, and performance of the setup are discussed and demonstrated on the absorption spectrum of Ag1 in argon. The absorption spectra for the two least abundant silver cluster ions produced by our cluster source in the size range of 1–39 atoms/cluster, namely, Ag6 and Ag10, are reported. A sensitivity increase of about 20 is demonstrated.
Radiation damping effects on the ultrashort x-ray pulses generated by nonlinear Thomson backscattering
Authors: Cang Yu , Wu Hui-Chun , Zheng Jun , Xu Han , Tian You-Wei , Yu Wei
Published: November 2006

Nonlinear Thomson backscattering of an intense Gaussian laser pulse by a counterpropagating energetic electron is investigated by numerically solving the electron equation of motion taking into account the radiative damping force. The backscattered radiation characteristics are different for linearly and circularly polarized lasers because of a difference in their ponderomotive forces acting on the electron. The radiative electron energy loss weakens the backscattered power, breaks the symmetry of the backscattered-pulse profile, and prolongs the duration of the backscattered radiation. With the circularly polarized laser, an adjustable double-peaked backscattered pulse can be obtained. Such a profile has potential applications as a subfemtosecond x-ray pump and probe with adjustable time delay and power ratio.
Chemistry, photophysics, and ultrafast kinetics of two structurally related Schiff bases containing the naphthalene or quinoline ring
Authors: Fita P. , Luzina E. , Dziembowska T. , Radzewicz Cz. , Grabowska A.
Published: November 2006

The two structurally related Schiff bases, 2-hydroxynaphthylidene-(8-aminoquinoline) (HNAQ) and 2-hydroxynaphthylidene-1′-naphthylamine (HNAN), were studied by means of steady-state and time resolved optical spectroscopies as well as time-dependent density functional theory (TDDFT) calculations. The first one, HNAQ, is stable as a keto tautomer in the ground state and in the excited state in solutions, therefore it was used as a model of a keto tautomer of HNAN which exists mainly in its enol form in the ground state at room temperature. Excited state intramolecular proton transfer in the HNAN molecule leads to a very weak (quantum yield of the order of 10−4) strongly Stokes-shifted fluorescence. The characteristic time of the proton transfer (about 30fs) was estimated from femtosecond transient absorption data supported by global analysis and deconvolution techniques. Approximately 35% of excited molecules create a photochromic form whose lifetime was beyond the time window of the experiment (2ns). The remaining ones reach the relaxed S1 state (of a lifetime of approximately 4ps), whose emission is present in the decay associated difference spectra. Some evidence for the back proton transfer from the ground state of the keto form with the characteristic time of approximately 13ps was also found. The energies and orbital characteristics of main electronic transitions in both molecules calculated by TDDFT method are also discussed.
Programmable fabrication of spatial structures in a gas jet by laser machining with a spatial light modulator
Authors: Lin M.-W. , Chen Y.-M. , Pai C.-H. , Kuo C.-C. , Lee K.-H. , Wang J. , Chen S.-Y. , Lin J.-Y.
Published: November 2006

Programmable fabrication of longitudinal spatial structures in a gas jet was achieved by using laser machining with a liquid-crystal spatial light modulator as the pattern mask. By this technique single-shot fabrication of arbitrary gas and/or plasma structures is demonstrated, which establishes the crucial step toward raising the designs and applications of high-field plasma devices to the level of adaptive feedback optimization.
Minimal model of relaxation in an associating fluid: Viscoelastic and dielectric relaxations in equilibrium polymer solutions
Authors: Stukalin Evgeny B. , Freed Karl F.
Published: November 2006

Cluster formation and disintegration greatly complicate the description of relaxation processes in complex fluids. We systematically contrast the viscoelastic and dielectric properties for models of equilibrium polymers whose thermodynamic properties have previously been established. In particular, the monomer-mediated model allows chain growth to proceed only by monomer addition, while the scission-recombination model enables all particles to associate democratically, so that chain scission and fusion occur at the interior segments as well as at chain ends. The minimal models neglect hydrodynamic and entanglement interactions and are designed to explore systematically the competition between chemical reaction and internal chain relaxation and how this coupling modifies the dynamics from that of a polydisperse solution of Rouse chains with fixed lengths (i.e., “frozen” chains). As expected, the stress relaxation is nearly single exponential when the assembly-disassembly reaction is fast on the time scale of structural chain rearrangements, while multiexponential or nearly stretched exponential relaxation is obtained when this reaction rate is slow compared to the broad relaxation spectrum of almost unperturbed, nearly “dead” chains of intrinsically polydisperse equilibrium polymer solutions. More generally, a complicated intermediate behavior emerges from the interplay between the chemical kinetic events and internal chain motions.
The nature of the hydrogen bond: A synthesis from the interacting quantum atoms picture
Authors: Martín Pendás A. , Blanco M. A. , Francisco E.
Published: November 2006

The interacting quantum atoms approach [IQA, as presented by Blanco et al., J. Chem. Theory Comput. 1, 1096 (2005)] is applied to standard hydrogen bonded dimers. IQA is an interpretation tool based on a real space energy decomposition scheme fully consistent with the quantum theory of atoms in molecules. It provides a partition of every physical term present in the Hamiltonian into atomic and interatomic contributions. The procedure is orbital-free and self-contained, needing neither external references nor artificial intermediate states. Binding is the result of a competition between the destabilizing deformations suffered by the interacting fragments upon interaction and the stabilizing interaction energy itself. According to IQA, there is no incompatibility between the prevalent electrostatic image of hydrogen bonded systems and that favoring important covalent contributions. Depending on how we gather the different energetic terms, we may recover electrostatic or covalent pictures from the same underlying quantum mechanical description. Our results show that the nonclassical contributions to hydrogen bonding are spatially localized, involving only the H atom and its two nearest neighbors. IQA is well suited as a comparative tool. Its thin energetic decomposition allows us to recover exactly (or to a very good approximation) the quantities of the most widely used energy decomposition schemes. Such a comparison sheds light on the virtues and faults of the different methods and on the origin of the 50years old debate regarding the covalent/electrostatic nature of the hydrogen bond.
An accurate and simple quantum model for liquid water
Authors: Paesani Francesco , Zhang Wei , Case David A. , Cheatham Thomas E. , Voth Gregory A.
Published: November 2006

The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics simulations. The present results suggest that the inclusion of nuclear quantum effects into an empirical model for water enhances the ability of such model to faithfully represent experimental data, presumably through an increased ability of the model itself to capture realistic physical effects.
Magnetic field dependence of valley splitting in realistic Si∕SiGe quantum wells
Authors: Friesen Mark , Eriksson M. A. , Coppersmith S. N.
Published: November 2006

The authors investigate the magnetic field dependence of the energy splitting between low-lying valley states for electrons in a Si∕SiGe quantum well tilted with respect to the crystallographic axis. The presence of atomic steps at the quantum well interface may explain the unexpected, strong suppression of the valley splitting observed in recent experiments. The authors find that the suppression is caused by an interference effect associated with multiple steps, and that the magnetic field dependence arises from the lateral confinement of the electronic wave function. Using numerical simulations, the authors clarify the role of step disorder, obtaining quantitative agreement with the experiments.
p
-type Zn1−xMgxO films with Sb doping by radio-frequency magnetron sputtering
Authors: Wang Peng , Chen Nuofu , Yin Zhigang , Dai Ruixuan , Bai Yiming
Published: November 2006

Sb-doped Zn1−xMgxO films were grown on c-plane sapphire substrates by radio-frequency magnetron sputtering. The p-type conduction of the films (0.05⩽x⩽0.13) was confirmed by Hall measurements, revealing a hole concentration of 1015–1016cm−3 and a mobility of 0.6–4.5cm2∕Vs. A p-n homojunction comprising an undoped ZnO layer and an Sb-doped Zn0.95Mg0.05O layer shows a typical rectifying characteristic. Sb-doped p-type Zn1−xMgxO films also exhibit a changeable wider band gap as a function of x, implying that they can probably be used for fabrication of ZnO-based quantum wells and ultraviolet optoelectronic devices.
CARMA3/Bcl10/MALT1-dependent NF-κB activation mediates angiotensin II-responsive inflammatory signaling in nonimmune cells
Authors: McAllister-Lucas Linda M. , Ruland Jürgen , Siu Katy , Jin Xiaohong , Gu Shufang , Kim David S. L. , Kuffa Peter , Kohrt Dawn , Mak Tak W. , Nuñez Gabriel , Lucas Peter C.
Published: November 2006

Angiotensin II (Ang II) is a peptide hormone that, like many cytokines, acts as a proinflammatory agent and growth factor. After injury to the liver, the hormone assists in tissue repair by stimulating hepatocytes and hepatic stellate cells to synthesize extracellular matrix proteins and secrete secondary cytokines and by stimulating myofibroblasts to proliferate. However, under conditions of chronic liver injury, all of these effects conspire to promote pathologic liver fibrosis. Much of this effect of Ang II results from activation of the proinflammatory NF-κB transcription factor in response to stimulation of the type 1 Ang II receptor, a G protein-coupled receptor. Here, we characterize a previously undescribed signaling pathway mediating Ang II-dependent activation of NF-κB, which is composed of three principal proteins, CARMA3, Bcl10, and MALT1. Blocking the function of any of these proteins, through the use of either dominant-negative mutants, RNAi, or gene targeting, effectively abolishes Ang II-dependent NF-κB activation in hepatocytes. In addition, Bcl10
−/−
mice show defective hepatic cytokine production after Ang II treatment. Evidence also is presented that this pathway activates NF-κB through ubiquitination of IKKγ, the regulatory subunit of the IκB kinase complex. These results elucidate a concrete series of molecular events that link ligand activation of the type 1 Ang II receptor to stimulation of the NF-κB transcription factor. These findings also uncover a function of the CARMA, Bcl10, and MALT1 proteins in cells outside the immune system.
Short-chain ubiquitination mediates the regulated endocytosis of the aquaporin-2 water channel
Authors: Kamsteeg Erik-Jan , Hendriks Giel , Boone Michelle , Konings Irene B. M. , Oorschot Viola , van der Sluijs Peter , Klumperman Judith , Deen Peter M. T.
Published: November 2006

To regulate mammalian water homeostasis, arginine-vasopressin (AVP) induces phosphorylation and thereby redistribution of renal aquaporin-2 (AQP2) water channels from vesicles to the apical membrane. Vice versa, AVP (or forskolin) removal and hormones activating PKC cause AQP2 internalization, but the mechanism is unknown. Here, we show that a fraction of AQP2 is modified with two to three ubiquitin moieties
in vitro
and
in vivo
. Mutagenesis revealed that AQP2 is ubiquitinated with one K63-linked chain at K270 only. In Madin–Darby canine kidney cells, AQP2 ubiquitination occurs preferentially when present in the apical membrane, is transiently increased with forskolin removal or PKC activation, and precedes its internalization. Internalization kinetics assays with wild type (wt) and ubiquitination-deficient (K270R) AQP2 revealed that ubiquitination enhances AQP2 endocytosis. Electron microscopy showed that a translational fusion of AQP2 with ubiquitin (AQP2-Ub) localized particularly to internal vesicles of multivesicular bodies (MVBs), whereas AQP2-K270R largely localized to the apical membrane, early endosomes, and the limiting membrane of MVBs. Consistent with this distribution pattern, lysosomal degradation was extensive for AQP2-Ub, low for AQP2-K270R, and intermediate for wt-AQP2. Our data show that short-chain ubiquitination is involved in the regulated endocytosis, MVB sorting, and degradation of AQP2 and may be the mechanism used by AVP removal and PKC-activating hormones to reduce renal water reabsorption. Moreover, because several other channels are also (short-chain) ubiquitinated, our data suggest that ubiquitination may be a general mediator for the regulated endocytosis and degradation of channels in higher eukaryotes.
Suppression of
Arabidopsis
vesicle-SNARE expression inhibited fusion of H
2
O
2
-containing vesicles with tonoplast and increased salt tolerance
Authors: Leshem Yehoram , Melamed-Book Naomi , Cagnac Olivier , Ronen Gil , Nishri Yossi , Solomon Mazal , Cohen Gil , Levine Alex
Published: November 2006

Intracellular vesicle trafficking performs essential functions in eukaryotic cells, such as membrane trafficking and delivery of molecules to their destinations. A major endocytotic route in plants is vesicle trafficking to the vacuole that plays an important role in plant salt tolerance. The final step in this pathway is mediated by the AtVAMP7C family of vesicle soluble
N
-ethylmaleimide-sensitive factor attachment protein receptors (v-SNAREs) that carry out the vesicle fusion with the tonoplast. Exposure to high-salt conditions causes immediate ionic and osmotic stresses, followed by production of reactive oxygen species. Here, we show that the reactive oxygen species are produced intracellularly, in endosomes that were targeted to the central vacuole. Suppression of the
AtVAMP7C
genes expression by antisense
AtVAMP711
gene or in mutants of this family inhibited fusion of H
2
O
2
-containing vesicles with the tonoplast, which resulted in formation of H
2
O
2
-containing megavesicles that remained in the cytoplasm. The antisense and mutant plants exhibited improved vacuolar functions, such as maintenance of ΔpH, reduced release of calcium from the vacuole, and greatly improved plant salt tolerance. The antisense plants exhibited increased calcium-dependent protein kinase activity upon salt stress. Improved vacuolar ATPase activity during oxidative stress also was observed in a yeast system, in a Δ
Vamp7
knockout strain. Interestingly, a microarray-based analysis of the
AtVAMP7C
genes showed a strong down-regulation of most genes in wild-type roots during salt stress, suggesting an evolutionary molecular adaptation of the vacuolar trafficking.
Genetically modified pigs produced with a nonviral episomal vector
Authors: Manzini Stefano , Vargiolu Alessia , Stehle Isa M , Bacci Maria Laura , Cerrito Maria Grazia , Giovannoni Roberto , Zannoni Augusta , Bianco Maria Rosaria , Forni Monica , Donini Pierluigi , Papa Michele , Lipps Hans J , Lavitrano Marialuisa
Published: November 2006

Genetic modification of cells and animals is an invaluable tool for biotechnology and biomedicine. Currently, integrating vectors are used for this purpose. These vectors, however, may lead to insertional mutagenesis and variable transgene expression and can undergo silencing. Scaffold/matrix attachment region-based vectors are nonviral expression systems that replicate autonomously in mammalian cells, thereby making possible safe and reliable genetic modification of higher eukaryotic cells and organisms. In this study, genetically modified pig fetuses were produced with the scaffold/matrix attachment region-based vector pEPI, delivered to embryos by the sperm-mediated gene transfer method. The pEPI vector was detected in 12 of 18 fetuses in the different tissues analyzed and was shown to be retained as an episome. The reporter gene encoded by the pEPI vector was expressed in 9 of 12 genetically modified fetuses. In positive animals, all tissues analyzed expressed the reporter gene; moreover in these tissues, the positive cells were on the average 79%. The high percentage of EGFP-expressing cells and the absence of mosaicism have important implications for biotechnological and biomedical applications. These results are an important step forward in animal transgenesis and can provide the basis for the future development of germ-line gene therapy.
Dramatic amplification of a rice transposable element during recent domestication
Authors: Naito Ken , Cho Eunyoung , Yang Guojun , Campbell Matthew A , Yano Kentaro , Okumoto Yutaka , Tanisaka Takatoshi , Wessler Susan R.
Published: November 2006

Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature inverted-repeat transposable element (
mPing
) has amplified from ≈50 to ≈1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of
mPing
to attain high copy numbers is because of three factors: (
i
) the rapid selection against detrimental insertions, (
ii
) the neutral or minimal effect of the remaining insertions on gene transcription, and (
iii
) the continued mobility of
mPing
elements in strains that already have >1,000 copies. The rapid increase in
mPing
copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice.
Structural changes in troponin in response to Ca
2+
and myosin binding to thin filaments during activation of skeletal muscle
Authors: Sun Yin-Biao , Brandmeier Birgit , Irving Malcolm
Published: November 2006

Contraction of skeletal and cardiac muscle is regulated by Ca
2+
-dependent structural changes in troponin that control the interaction between myosin and actin. We measured the orientations of troponin domains in skeletal muscle fibers using polarized fluorescence from bifunctional rhodamine probes on the C and E helices of troponin C. The C helix, in the regulatory head domain, tilts by ≈30° when muscle is activated in physiological conditions, with a Ca
2+
-sensitivity similar to that of active force. Complete inhibition of active force did not affect C-helix orientation, and binding of rigor myosin heads did not affect its orientation at saturating [Ca
2+
]. The E helix, in the IT arm of troponin, tilted by ≈10° on activation, and this was reduced to only 3° when active force was inhibited. Binding of rigor myosin heads produced a larger tilt of the E helix. Thus,
in situ
, the regulatory head acts as a pure Ca
2+
-sensor, whereas the IT arm is primarily sensitive to myosin head binding. The polarized fluorescence data from active muscle are consistent with an
in vitro
structure of the troponin core complex in which the D and E helices of troponin C are collinear. The present data were used to orient this structure in the fiber and suggest that the IT arm is at ≈30° to the filament axis in active muscle. In relaxed muscle, the IT arm tilts to ≈40° but the D/E helix linker melts, allowing the regulatory head to tilt through a larger angle.
LRRTM3
promotes processing of amyloid-precursor protein by BACE1 and is a positional candidate gene for late-onset Alzheimer's disease
Authors: Majercak John , Ray William J. , Espeseth Amy , Simon Adam , Shi Xiao-Ping , Wolffe Carrie , Getty Krista , Marine Shane , Stec Erica , Ferrer Marc , Strulovici Berta , Bartz Steven , Gates Adam , Xu Min , Huang Qian , Ma Lei , Shughrue Paul , Burchard Julja , Colussi Dennis , Pietrak Beth , Kahana Jason , Beher Dirk , Rosahl Thomas , Shearman Mark , Hazuda Daria , Sachs Alan B. , Koblan Kenneth S. , Seabrook Guy R. , Stone David J.
Published: November 2006

Rare familial forms of Alzheimer's disease (AD) are thought to be caused by elevated proteolytic production of the Aβ42 peptide from the β-amyloid-precursor protein (APP). Although the pathogenesis of the more common late-onset AD (LOAD) is not understood, BACE1, the protease that cleaves APP to generate the N terminus of Aβ42, is more active in patients with LOAD, suggesting that increased amyloid production processing might also contribute to the sporadic disease. Using high-throughput siRNA screening technology, we assessed 15,200 genes for their role in Aβ42 secretion and identified leucine-rich repeat transmembrane 3 (
LRRTM3
) as a neuronal gene that promotes APP processing by BACE1. siRNAs targeting
LRRTM3
inhibit the secretion of Aβ40, Aβ42, and sAPPβ, the N-terminal APP fragment produced by BACE1 cleavage, from cultured cells and primary neurons by up to 60%, whereas overexpression increases Aβ secretion. LRRTM3 is expressed nearly exclusively in the nervous system, including regions affected during AD, such as the dentate gyrus. Furthermore,
LRRTM3
maps to a region of chromosome 10 linked to both LOAD and elevated plasma Aβ42, and is structurally similar to a family of neuronal receptors that includes the NOGO receptor, an inhibitor of neuronal regeneration and APP processing. Thus,
LRRTM3
is a functional and positional candidate gene for AD, and, given its receptor-like structure and restricted expression, a potential therapeutic target.
Human Opiorphin, a natural antinociceptive modulator of opioid-dependent pathways
Authors: Wisner Anne , Dufour Evelyne , Messaoudi Michaël , Nejdi Amine , Marcel Audrey , Ungeheuer Marie-Noelle , Rougeot Catherine
Published: November 2006

Mammalian zinc ectopeptidases play important roles in turning off neural and hormonal peptide signals at the cell surface, notably those processing sensory information. We report here the discovery of a previously uncharacterized physiological inhibitor of enkephalin-inactivating zinc ectopeptidases in humans, which we have named Opiorphin. It is a QRFSR peptide that inhibits two enkephalin-catabolizing ectoenzymes, human neutral ecto-endopeptidase, hNEP (EC 3.4.24.11), and human ecto-aminopeptidase, hAP-N (EC 3.4.11.2). Opiorphin displays potent analgesic activity in chemical and mechanical pain models by activating endogenous opioid-dependent transmission. Its function is closely related to the rat sialorphin peptide, which is an inhibitor of pain perception and acts by potentiating endogenous μ- and δ-opioid receptor-dependent enkephalinergic pathways. Here we demonstrate the functional specificity
in vivo
of human Opiorphin. The pain-suppressive potency of Opiorphin is as effective as morphine in the behavioral rat model of acute mechanical pain, the pin-pain test. Thus, our discovery of Opiorphin is extremely exciting from a physiological point of view in the context of endogenous opioidergic pathways, notably in modulating mood-related states and pain sensation. Furthermore, because of its
in vivo
properties, Opiorphin may have therapeutic implications.