bluuebunny/crossref_metadata_2025 huggingface dataset:
A volumetrically heated jet: large-eddy structure and entrainment characteristics
Authors: Bhat G. S. , Narasimha R.
Published: April 2006

We report here an experimental study of a round vertical liquid jet that, after achieving a self-preserving state, is subjected to volumetric heating between two diametral stations. The heat injection is achieved by applying a voltage across the stations, the jet fluid having been rendered electrically conducting by the addition of acid. Using laser-induced fluorescence, digital image processing and laser-Doppler anemometry, the flow properties of the jet have been studied in detail. It is found that, with sufficient heating, the jet no longer grows linearly with height, and the decay of both centreline velocity and turbulence intensity is arrested, and may even be reversed just beyond the zone of heat addition; nevertheless the entrainment decreases, which is at variance with the hypotheses often made for modelling it. This behaviour is here attributed to the disruptive influence that, as the present experiments show, the volumetric heating has on the large-scale vortical structures in the jet, which are known to be largely responsible for the engulfment of ambient fluid that is the first step in the entrainment process. It is shown that a new non-dimensional heat release number correlates the observed data on changes in jet width. An integral model that would describe the effect of local heating is proposed, and implications for cloud development in the atmosphere are discussed.
Eulerian and Lagrangian scaling properties of randomly advected vortex tubes
Authors: Malik N. A. , Vassilicos J. C.
Published: April 2006

We investigate the Eulerian and Lagrangian spectral scaling properties of vortex tubes, and the consistency of these properties with Tennekes’ (1975) statistical advection analysis and universal equilibrium arguments. We consider three different vortex tubes with power-law wavenumber spectra: a Burgers vortex tube, an inviscid Lundgren single spiral vortex sheet, and a vortex tube solution of the Euler equation. While the Burgers vortex is a steady solution of the Navier–Stokes equation, the other two are unsteady solutions of, respectively, the Navier–Stokes and the Euler equations. In our numerical experiments we study the vortex tubes by subjecting each of them to external ‘large-scale’ sinusoidal advection of characteristic frequency f and length scale ρ.

Not only do we find that the Eulerian frequency spectrum ϕE(ω) can be derived from the wavenumber spectrum E(k) using the simple Tennekes advection relation ω ∼ k for all finite advection frequencies f when the vortex is steady, but also when the vortex is unsteady, and in the Lundgren case even when f = 0 owing to the self-advection of the Lundgren vortex by its own differential rotation.

An analytical calculation using the method of stationary phases for f = 0 shows that for large enough Reynolds numbers the combination of strain with differential rotation implies that ϕL(ω) ∼ ω−2+Const for large values of ω. We verify numerically that ϕL(ω) does not change when f ≠ 0. With the Burgers vortex tube we are in a position to investigate the spectral broadening of the Eulerian frequency spectrum with respect to the Lagrangian frequency spectrum. A spectral broadening does exist but is different from the spectral broadening predicted by Tennekes (1975).
The development of asymmetry and period doubling for oscillatory flow in baffled channels
Authors: Roberts E. P. L. , Mackley M. R.
Published: April 2006

We report experimental and numerical observations on the way initially symmetric and time-periodic fluid oscillations in baffled channels develop in complexity. Experiments are carried out in a spatially periodic baffled channel with a sinusoidal oscillatory flow. At modest Reynolds number the observed vortex structure is symmetric and time periodic. At higher values the flow progressively becomes three-dimensional, asymmetric and aperiodic. A two-dimensional simulation of incompressible Newtonian flow is able to follow the flow pattern at modest oscillatory Reynolds number. At higher values we report the development of both asymmetry and a period-doubling cascade leading to a chaotic flow regime. A bifurcation diagram is constructed that can describe the progressive increase in complexity of the flow.
Emendation of the Brown & Michael equation, with application to sound generation by vortex motion near a half-plane
Authors: Howe M. S.
Published: April 2006

A reappraisal is made of the Brown & Michael (1954, 1955) equation that is widely used to model high-Reynolds-number vortex shedding in two dimensions by rectilinear vortices of time-dependent circulations. It is concluded that the equation introduces an unbalanced and unacceptable surface force that can significantly influence predicted flow characteristics. A corrected equation is derived which removes this force, and is applied to determine the sound generated at low Mach numbers when a line vortex translates around the edge of a rigid half-plane. The solution of this problem in the absence of vortex shedding (Crighton 1972) is extended by permitting shedding to occur at the edge in accordance with the unsteady Kutta condition. The shed vorticity is assumed to roll-up into a concentrated core whose motion is calculated by both the emended and original Brown & Michael equations. The two models exhibit large qualitative differences in the predicted wake flow near the edge; both predict significant reductions in the radiated sound, but the reduction is smaller by about 4 dB for the emended Brown & Michael equation.
On general transformations and variational principles for the magnetohydrodynamics of ideal fluids. Part 2. Stability criteria for two-dimensional flows
Authors: Vladimirov V. A. , Moffatt H. K. , Ilin K. I.
Published: April 2006

The techniques developed in Part 1 of the present series are here applied to two-dimensional solutions of the equations governing the magnetohydrodynamics of ideal incompressible fluids. We first demonstrate an isomorphism between such flows and the flow of a stratified fluid subjected to a field of force that we describe as ‘pseudo-gravitational’. We then construct a general Casimir as an integral of an arbitrary function of two conserved fields, namely the vector potential of the magnetic field, and the analogous potential of the ‘modified vorticity field’, the additional frozen field introduced in Part 1. Using this Casimir, a linear stability criterion is obtained by standard techniques. In §4, the (Arnold) techniques of nonlinear stability are developed, and bounds are placed on the second variation of the sum of the energy and the Casimir of the problem. This leads to criteria for nonlinear (Lyapunov) stability of the MHD flows considered. The appropriate norm is a sum of the magnetic and kinetic energies and the mean-square vector potential of the magnetic field.
Intense turbulence observed above a mesospheric temperature inversion at equatorial latitude
Authors: Lehmacher G. A. , Croskey C. L. , Mitchell J. D. , Friedrich M. , Lübken F.‐J. , Rapp M. , Kudeki E. , Fritts D. C.
Published: April 2006

Results from a sounding rocket experiment launched on September 19, 2004 from Kwajalein Atoll, Marshall Islands are reported. A large modulation of the temperature profile in the upper mesosphere was observed with a local maximum at 92 km, 40 K warmer than 2 km below. The temperature gradient between 92 and 102 km was near‐adiabatic, suggesting strong mixing. Turbulence was observed in the lower part of the mixed layer, as evidenced by neutral and plasma density fluctuations on both the upleg and downleg portions of the flight. The plasma density gradient was less steep in the mixed region. The turbulent energy dissipation rate was found to be 170 mW/kg. The thermal structure can be described as an upper mesospheric inversion layer, possibly caused by enhanced wave breaking or turbulent heat transport.
Nocturnal cold air drainage and pooling in a tropical forest
Authors: Goulden Michael L. , Miller Scott D. , da Rocha Humberto R.
Published: April 2006

The usefulness of eddy covariance for understanding terrestrial carbon exchange has been hampered by uncertainty over the magnitude and causes of a systematic underestimation of CO2 efflux on calm nights. We combined in situ measurements of the temperature, wind and CO2 profile with nocturnal Land Surface Temperature (LST) imagery from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) to infer the patterns of cold air drainage in an Amazonian tropical forest. The meteorological tower was located on a flat plateau that sloped gently to the southwest. The vertical profile from 0 to 64 m above ground level was divisible into two air parcels at night: a warm, low CO2, upper parcel and a cool, high CO2, lower parcel that was stable with respect to the upper parcel. The nocturnal wind direction of the upper parcel was from the east, a pattern that is consistent with the general circulation, whereas the wind direction of the lower parcel was from the northeast, a pattern that implies drainage down the local topographic gradient. The nocturnal patterns of LST were closely related to local topography and land use. In general, a nearby river was warm, gullies were cold, plateau centers were cold, stream drainages were cold, pastures were particularly cold, and upper slopes and plateau edges were warm. The in situ temperature and wind observations, combined with the observed relationship between elevation and nocturnal LST and the occurrence of warm thermal belts extending inward from the edges of plateaus, imply that cold air drainage occurs on clear nights. The slope of the relationship between LST and elevation varied between nights, indicating that the degree of thermal stratification, and possibly the extent of cold air drainage, also varied. The night‐to‐night variation in stratification across the landscape was correlated with the vertical temperature gradient at the tower but not the above‐canopy friction velocity (u*). Criteria associated with vertical temperature gradients may prove better than u* for screening nocturnal eddy covariance observations to eliminate periods that underestimate CO2 flux.
Role of tropospheric ozone increases in 20th‐century climate change
Authors: Shindell Drew , Faluvegi Greg , Lacis Andrew , Hansen James , Ruedy Reto , Aguilar Elliot
Published: April 2006

Human activities have increased tropospheric ozone, contributing to 20th‐century warming. Using the spatial and temporal distribution of precursor emissions, we simulated tropospheric ozone from 1890 to 1990 using the NASA Goddard Institute for Space Studies (GISS) chemistry model. Archived three‐dimensional ozone fields were then used in transient GISS climate model simulations. This enables more realistic evaluation of the impact of tropospheric ozone increases than prior simulations using an interpolation between preindustrial and present‐day ozone. We find that tropospheric ozone contributed to the greater 20th‐century warming in the Northern Hemisphere extratropics compared with the tropics and in the tropics compared with the Southern Hemisphere extratropics. Additionally, ozone increased more rapidly during the latter half of the century than the former, causing more rapid warming during that time. This is especially apparent in the tropics and is consistent with observations, which do not show similar behavior in the extratropics. Other climate forcings do not substantially accelerate warming rates in the tropics relative to other regions. This suggests that accelerated tropospheric ozone increases related to industrialization in the developing world have contributed to the accelerated tropical warming. During boreal summer, tropospheric ozone causes enhanced warming (>0.5°C) over polluted northern continental regions. Finally, the Arctic climate response to tropospheric ozone increases is large during fall, winter, and spring when ozone's lifetime is comparatively long and pollution transported from midlatitudes is abundant. The model indicates that tropospheric ozone could have contributed about 0.3°C annual average and about 0.4°C–0.5°C during winter and spring to the 20th‐century Arctic warming. Pollution controls could thus substantially reduce the rapid rate of Arctic warming.
Aerosol deposited in East Antarctica over the last glacial cycle: Detailed apportionment of continental and sea‐salt contributions
Authors: Bigler Matthias , Röthlisberger Regine , Lambert Fabrice , Stocker Thomas F. , Wagenbach Dietmar
Published: April 2006

The major ions, sodium (Na+), calcium (Ca2+), and chloride (Cl−), deposited in central Antarctica and preserved in ice cores originate from both marine and continental sources. They provide important proxy records, helping to reconstruct past climatic processes. However, it is difficult to clearly separate the individual contributions from the two sources, particularly the continental one during glacial periods. On the basis of Na+ and Ca2+ records at an unprecedented resolution from the European Project for Ice Coring in Antarctica (EPICA) Dome C ice core back to the penultimate glacial period, mean ion mass ratios were deduced for the continental and the sea‐salt aerosol body over East Antarctica. The sea‐salt ion mass ratios are in the range predicted for both wind‐induced bubble bursting of breaking waves on the open ocean and sea ice brine‐derived aerosols, respectively, thus allowing no clear decision on the contribution of sea ice to the central Antarctic sea‐salt aerosol. The continental ion mass ratios point to a substantial contribution by halide aerosols, which is in agreement with the source properties in southern South America, although these ratios do not rule out the continental shelf exposed during glacial stages as an additional source. While during cold glacial periods continental sources accounted for more than 90% of the total Ca2+ input, this contribution was highly variable during the remaining glacial periods covarying with the Antarctic warm events. During the Holocene it was less than 50%, but it was significantly higher during the last interglacial period. The sea‐salt aerosol contribution to the total Na+ input, which was mostly dominant and higher than 90%, was reduced to only two thirds during the last two glacial maxima and the period around 60 ka. Thus the glacial continental Na+ contribution appears to be more important than previously assumed, implying that Na+ records not corrected for continental Na+ do not represent a pure marine signal at the East Antarctic plateau during glacial times.
Tropopause‐level thin cirrus coverage revealed by ICESat/Geoscience Laser Altimeter System
Authors: Dessler A. E. , Palm S. P. , Hart W. D. , Spinhirne J. D.
Published: April 2006

We analyze the distribution of thin (optical depth < 0.40) cirrus in the tropics at potential temperatures of 360, 370, 377.5, and 400 K, which are levels that bracket the tropical tropopause. The observations were obtained between 29 September and 17 November 2003 by the Geoscience Laser Altimeter System (GLAS), carried on board the Ice, Cloud, and land Elevation Satellite (ICESat). The GLAS data show that these thin, near‐tropopause cirrus (TNTC) occur over broad regions of the latitude range 20°S to 30°N, with distinct maxima collocated with regions of intense convection, and that TNTC occurrence frequency decreases strongly with increasing altitude. At 377.5 K, approximately the level of the tropical tropopause, TNTC frequency over convection is two to six times larger than in the so‐called “cold pool,” the climatological temperature minimum located over the equatorial western Pacific where it has been suggested that dehydration of air entering the stratosphere is occurring. Comparisons between assimilated temperatures, outgoing longwave radiation (a proxy for deep convection), and TNTC frequency show that TNTC can be found where assimilated temperatures are low and deep convection is occurring. We find that assimilated temperatures, by themselves, are incomplete predictors of TNTC locations.
Dynamics of the sulphate aerosol size distribution on a global scale
Authors: Ma Xiaoyan , von Salzen Knut
Published: April 2006

Parameterizations for size‐dependent aerosols have been implemented in the Canadian Centre for Climate Modelling and Analysis (CCCma) atmospheric general circulation model (AGCM). This new model version considers comprehensive physical and chemical processes that are associated with the sulphate aerosol size distribution, including nucleation, condensation, hygroscopic growth, aqueous‐phase chemistry, and dry and wet deposition. Results from in situ surface and airborne observations and remote sensing were used to validate the model. The comparisons give evidence for realistic sulphate size distributions over the regions where sulphate is the dominant aerosol type. In agreement with earlier published studies, it is found in sensitivity tests that the global sulphate burden is predominantly affected by wet deposition. However, the mass size distribution is mainly affected by coagulation, condensation, and below‐cloud scavenging on the global scale. There is only weak sensitivity of the simulated mass size distribution to changes in in‐cloud oxidation and the efficiency of nucleation. It is shown that the low sensitivities are caused by a compensating effect of coagulation in the former and low sensitivity of the mass size distribution to changes in nucleation rate and condensation efficiency for the latter case.
Midlatitude westerlies, atmospheric CO2, and climate change during the ice ages
Authors: Toggweiler J. R. , Russell Joellen L. , Carson S. R.
Published: April 2006

An idealized general circulation model is constructed of the ocean's deep circulation and CO2 system that explains some of the more puzzling features of glacial‐interglacial CO2 cycles, including the tight correlation between atmospheric CO2 and Antarctic temperatures, the lead of Antarctic temperatures over CO2 at terminations, and the shift of the ocean's δ13C minimum from the North Pacific to the Atlantic sector of the Southern Ocean. These changes occur in the model during transitions between on and off states of the southern overturning circulation. We hypothesize that these transitions occur in nature through a positive feedback that involves the midlatitude westerly winds, the mean temperature of the atmosphere, and the overturning of southern deep water. Cold glacial climates seem to have equatorward shifted westerlies, which allow more respired CO2 to accumulate in the deep ocean. Warm climates like the present have poleward shifted westerlies that flush respired CO2 out of the deep ocean.
Upwelling backscatter plumes in growth phase of equatorial spread F observed with the Equatorial Atmosphere Radar
Authors: Yokoyama Tatsuhiro , Fukao Shoichiro
Published: April 2006

Upwelling radar backscatter plumes around sunset time associated with equatorial spread F (ESF) are investigated with rapid beam‐scanning capability of the Equatorial Atmosphere Radar (EAR). Nonlinear evolution of plumes which could not be understood by single fixed‐beam radar observations was observationally studied with the EAR for the first time. The rise velocity of the observed plumes ranging from a few tens to a few hundreds of meters per second is similar to nonlinear evolution of plasma bubbles simulated by the previous numerical studies. Importance of sunset terminator transition should be considered because of its comparable rise velocity. Since the rise velocity of the plumes is highly variable, many factors should contribute to growth of plasma bubbles.
Spacebased observations of oceanic influence on the annual variation of South American water balance
Authors: Liu W. Timothy , Xie Xiaosu , Tang Wenqing , Zlotnicki Victor
Published: April 2006

The mass change of South America (SA) continent measured by the Gravity Recovery and Climate Experiment (GRACE) imposes a constraint on the uncertainties in estimating the annual variation of rainfall measured by Tropical Rain Measuring Mission (TRMM) and ocean moisture influx derived from QuikSCAT data. The approximate balance of the mass change rate with the moisture influx less climatological river discharge, in agreement with the conservation principle, bolsters not only the credibility of the spacebased measurements, but supports the characterization of ocean's influence on the annual variation of continental water balance. The annual variation of rainfall is found to be in phase with the mass change rate in the Amazon and the La Plata basins, and the moisture advection across relevant segments of the Pacific and Atlantic coasts agrees with the annual cycle of rainfall in the two basins and the Andes mountains.
On the occurrence of magnetic enhancements caused by solar wind interaction with lunar crustal fields
Authors: Halekas J. S. , Brain D. A. , Mitchell D. L. , Lin R. P. , Harrison L.
Published: April 2006

We use Lunar Prospector data to identify 990 magnetic enhancements, previously termed “limb shocks” or “limb compressions”, external to the lunar wake. We find that they are clearly associated with lunar crustal sources, and sometimes occur far upstream from the limb at altitudes of ∼100 km. This is inconsistent with compressional disturbances convecting downstream with the solar wind, and implies that crustal fields are sometimes strong and coherent enough to produce a fluid‐like interaction where compressional waves steepen to form a shock extending upstream from their source. The likelihood of observing enhancements partly depends on upstream solar wind conditions, with low proton gyroradius and low β particularly favored. Low Mach numbers, implying a larger shock standoff distance, are also favored for observations which suggest shock‐like behavior.
A proteomic approach reveals transient association of reticulocalbin-3, a novel member of the CREC family, with the precursor of subtilisin-like proprotein convertase, PACE4
Authors: Tsuji Akihiko , Kikuchi Yayoi , Sato Yukimi , Koide Shizuyo , Yuasa Keizo , Nagahama Masami , Matsuda Yoshiko
Published: April 2006

SPCs (subtilisin-like proprotein convertases) are a family of seven structurally related serine endoproteases that are involved in the proteolytic activation of proproteins. In an effort to examine the substrate protein for PACE4 (paired basic amino-acid-cleaving enzyme-4), an SPC, a potent protein inhibitor of PACE4, an α1-antitrypsin RVRR (Arg-Val-Arg-Arg) variant, was expressed in GH4C1 cells. Ectopic expression of the RVRR variant caused accumulation of the 48 kDa protein in cells. Sequence analysis indicates that the 48 kDa protein is a putative Ca2+-binding protein, RCN-3 (reticulocalbin-3), which had previously been predicted by bioinformatic analysis of cDNA from the human hypothalamus. RCN-3 is a member of the CREC (Cab45/reticulocalbin/ERC45/calumenin) family of multiple EF-hand Ca2+-binding proteins localized to the secretory pathway. The most interesting feature of the RCN-3 sequence is the presence of five Arg-Xaa-Xaa-Arg motifs, which represents the target sequence of SPCs. Biosynthetic studies showed that RCN-3 is transiently associated with proPACE4, but not with mature PACE4. Inhibition of PACE4 maturation by a Ca2+ ionophore resulted in accumulation of the proPACE4–RCN-3 complex in cells. Furthermore, autoactivation and secretion of PACE4 was increased upon co-expression with RCN-3. Our findings suggest that selective and transient association of RCN-3 with the precursor of PACE4 plays an important role in the biosynthesis of PACE4.
RanBPM associates with CD39 and modulates ecto-nucleotidase activity
Authors: Wu Yan , Sun Xiaofeng , Kaczmarek Elzbieta , Dwyer Karen M. , Bianchi Elisabetta , Usheva Anny , Robson Simon C.
Published: April 2006

CD39/ecto-NTPDase 1 (nucleoside triphosphate diphosphohydrolase 1) is an ecto-nucleotidase that influences P2 receptor activation to regulate vascular and immune cell adhesion and signalling events pivotal in inflammation. Whether CD39 interacts with other membrane or cytoplasmic proteins has not been established to date. Using the yeast two-hybrid system, we note that the N-terminus of CD39 binds to RanBPM (Ran binding protein M; also known as RanBP9), a multi-adaptor scaffolding membrane protein originally characterized as a binding protein for the small GTPase Ran. We confirm formation of complexes between CD39 and RanBPM in transfected mammalian cells by co-immunoprecipitation studies. Endogenous CD39 and RanBPM are also found to be co-expressed and abundant in cell membranes of B-lymphocytes. NTPDase activity of recombinant CD39, but not of N-terminus-deleted-CD39 mutant, is substantially diminished by RanBPM co-expression in COS-7 cells. The conserved SPRY [repeats in splA and RyR (ryanodine receptor)] moiety of RanBPM is insufficient alone for complete physical and functional interactions with CD39. We conclude that CD39 associations with RanBPM have the potential to regulate NTPDase catalytic activity. This intermolecular interaction may have important implications for the regulation of extracellular nucleotide-mediated signalling.
IκB is a sensitive target for oxidation by cell-permeable chloramines: inhibition of NF-κB activity by glycine chloramine through methionine oxidation
Authors: Midwinter Robyn G. , Cheah Fook-Choe , Moskovitz Jackob , Vissers Margret C. , Winterbourn Christine C.
Published: April 2006

Hypochlorous acid (HOCl) is produced by the neutrophil enzyme, myeloperoxidase, and reacts with amines to generate chloramines. These oxidants react readily with thiols and methionine and can affect cell-regulatory pathways. In the present study, we have investigated the ability of HOCl, glycine chloramine (Gly-Cl) and taurine chloramine (Tau-Cl) to oxidize IκBα, the inhibitor of NF-κB (nuclear factor κB), and to prevent activation of the NF-κB pathway in Jurkat cells. Glycine chloramine (Gly-Cl) and HOCl were permeable to the cells as determined by oxidation of intracellular GSH and inactivation of glyceraldehyde-3-phosphate dehydrogenase, whereas Tau-Cl showed no detectable cell permeability. Both Gly-Cl (20–200 μM) and HOCl (50 μM) caused oxidation of IκBα methionine, measured by a shift in electrophoretic mobility, when added to the cells in Hanks buffer. In contrast, a high concentration of Tau-Cl (1 mM) in Hanks buffer had no effect. However, Tau-Cl in full medium did modify IκBα. This we attribute to chlorine exchange with other amines in the medium to form more permeable chloramines. Oxidation by Gly-Cl prevented IκBα degradation in cells treated with TNFα (tumour necrosis factor α) and inhibited nuclear translocation of NF-κB. IκBα modification was reversed by methionine sulphoxide reductase, with both A and B forms required for complete reduction. Oxidized IκBα persisted intracellularly for up to 6 h. Reversion occurred in the presence of cycloheximide, but was prevented if thioredoxin reductase was inhibited, suggesting that it was due to endogenous methionine sulphoxide reductase activity. These results show that cell-permeable chloramines, either directly or when formed in medium, could regulate NF-κB activation via reversible IκBα oxidation.
Mitochondria maintain maturation and secretion of lipoprotein lipase in the endoplasmic reticulum
Authors: Osibow Karin , Frank Sasa , Malli Roland , Zechner Rudolf , Graier Wolfgang F.
Published: April 2006

Considering the physiological Ca2+ dynamics within the ER (endoplasmic reticulum), it remains unclear how efficient protein folding is maintained in living cells. Thus, utilizing the strictly folding-dependent activity and secretion of LPL (lipoprotein lipase), we evaluated the impact of ER Ca2+ content and mitochondrial contribution to Ca2+-dependent protein folding. Exhaustive ER Ca2+ depletion by inhibition of sarcoplasmic/endoplasmic reticulum Ca2+-ATPases caused strong, but reversible, reduction of cell-associated and released activity of constitutive and adenovirus-encoded human LPL in CHO-K1 (Chinese-hamster ovary K1) and endothelial cells respectively, which was not due to decline of mRNA or intracellular protein levels. In contrast, stimulation with the IP3 (inositol 1,4,5-trisphosphate)-generating agonist histamine only moderately and transiently affected LPL maturation in endothelial cells that paralleled a basically preserved ER Ca2+ content. However, in the absence of extracellular Ca2+ or upon prevention of transmitochondrial Ca2+ flux, LPL maturation discontinued upon histamine stimulation. Collectively, these data indicate that Ca2+-dependent protein folding in the ER is predominantly controlled by intraluminal Ca2+ and is largely maintained during physiological cell stimulation owing to efficient ER Ca2+ refilling. Since Ca2+ entry and mitochondrial Ca2+ homoeostasis are crucial for continuous Ca2+-dependent protein maturation in the ER, their pathological alterations may result in dysfunctional protein folding.
The increase in mitochondrial association with actin precedes Bax translocation in apoptosis
Authors: Tang Ho Lam , Le Anh-Huy Phan , Lung Hong Lok
Published: April 2006

Accumulating evidence indicates the potential role of actin cytoskeleton in facilitating the mitochondrial recruitment of various pro-apoptotic proteins from the cytosol to initiate apoptosis. In the present paper, we report the observation of the increase in mitochondrial association of actin in early apoptosis. Using cell fractionation and Western blot analysis, we found that mitochondrial accumulation of β-actin occurred before the mitochondrial insertion of Bax and release of cytochrome c in apoptosis. The mitochondrial accumulation of β-actin was observed with various apoptotic stimuli in various cell lines, suggesting that this is a general apoptotic phenomenon in mammalian systems. Using fluorescence microscopy, we have shown that an apoptotic induction triggered the reorganization of the F-actin (filamentous actin) network with an increase in the association with mitochondria, which was observed before mitochondrial fission and nuclear condensation. Perhaps actin could contribute to the initiation of apoptosis by enabling cytosolic pro-apoptotic proteins to be carried to mitochondria by the cytoskeleton-driven trafficking system.
A theoretical study of the chiroptical properties of molecules with isotopically engendered chirality
Authors: Dierksen Marc , Grimme Stefan
Published: April 2006

There has been a considerable interest in the chiroptical properties of molecules whose chirality is exclusively due to an isotopic substitution and numerous examples for the electronic circular dichroism (CD) spectra of isotopically chiral systems have been reported in literature. Four different explanations have been proposed for the mechanism as to how the isotopic substitution induces a chiral perturbation of the otherwise achiral electronic wave function; however, up to now no conclusive answer has been given about the dominating effect responsible for the experimental observations. In this study we will present, for the first time, fully quantum-mechanical calculations of the CD spectra of three different molecular systems with isotopically engendered chirality. As examples, we consider the spectra of organic molecules with ketone and α-diketone carbonyl and diene chromophores. The effect of vibronic couplings for the reorientation of the electric and magnetic transition dipole moments is taken into account within the Herzberg-Teller approximation. The ground and excited state geometries and vibrational normal modes are obtained with (time-dependent) density functional theory [(TD)DFT], while the vibronic coupling effects are calculated at the TDDFT and density functional theory/multireference configuration interaction (DFT/MRCI) levels of theory. Generally, the band shapes of the experimental CD spectra are reproduced very well, and also the absolute CD intensities from the simulations are of the right order of magnitude. The sign and the intensity of the CD band are determined by a delicate balance of the contributions of a large number of individual vibronic transitions, and it is found that the vibrational normal modes with a large displacement are dominant. The separation of the calculated CD spectrum into the different contributions due to the overlap of the in-plane and out-of-plane components (regarding the symmetry plane of the unsubstituted molecule) of the electric and magnetic transition dipole moments yields information about the influence of the vibronic coupling effects for the reorientation of the corresponding transition dipole moments. In conclusion, the calculations clearly show that vibronic effects are responsible or at least dominant for the chiroptical properties of isotopically chiral organic molecules.
Cooperativity in ionic liquids
Authors: Koßmann Simone , Thar Jens , Kirchner Barbara , Hunt Patricia A. , Welton Tom
Published: April 2006

Cooperativity in ionic liquids is investigated by means of static quantum chemical calculations. Larger clusters of the dimethylimidazolium cation paired with a chloride anion are calculated within density functional theory combined with gradient corrected functionals. Tests of the monomer unit show that density functional theory performs reasonably well. Linear chain and ring aggregates have been considered and geometries are found to be comparable with liquid phase structures. Cooperative effects occur when the total energy of the oligomer differs from a simple sum of monomer energies. Cooperative effects have been found in the structural motifs examined. A systematic study of linear chains of increasing length (up to nine monomer units) has shown that cooperativity plays a more important role than expected and is stronger than in water. The Cl⋯H distance of the chloride to the most acidic proton increases with an increasing number of monomer units. The average bond distance approaches 218.9pm asymptotically. The dipole moment grows almost linearly and the dipole moment per monomer unit reaches the asymptotic value of 16.3D. The charge on the chloride atoms decreases with an increasing chain length. In order to detect local hydrogen bonding in the clusters a new parametrization of the shared-electron number method is introduced. We find decreasing hydrogen bond energies with an increasing cluster size for both the first hydrogen bond to the most acidic proton and the average hydrogen bond.
Reduced multireference coupled cluster method with singles and doubles: Perturbative corrections for triples
Authors: Li Xiangzhu , Paldus Josef
Published: April 2006

The reduced multireference coupled-cluster method with singles and doubles (RMR CCSD) that employs multireference configuration interaction wave function as an external source for a small subset of approximate connected triples and quadruples, is perturbatively corrected for the remaining triples along the same lines as in the standard CCSD(T) method. The performance of the resulting RMR CCSD(T) method is tested on four molecular systems, namely, the HF and F2 molecules, the NO radical, and the F2+ cation, representing distinct types of molecular structure, using up to and including a cc-pVQZ basis set. The results are compared with those obtained with the standard CCSD(T), UCCSD(T), CCSD(2), and CR CCSD(T) methods, wherever applicable or available. An emphasis is made on the quality of the computed potentials in a broad range of internuclear separations and on the computed equilibrium spectroscopic properties, in particular, harmonic frequencies ωe. It is shown that RMR CCSD(T) outperforms other triply corrected methods and is widely applicable.
Excited-state dynamics and nonlinear optical response of Ge nanocrystals embedded in silica matrix
Authors: Razzari Luca , Gnoli Andrea , Righini Marcofabio , Dâna Aykutlu , Aydinli Atilla
Published: April 2006

We use a dedicated Z-scan setup, arranged to account for cumulative effects, to study the nonlinear optical response of Ge nanocrystals embedded in silica matrix. Samples are prepared with plasma-enchanced chemical-vapor deposition and post-thermal annealing. We measure a third-order nonlinear refraction coefficient of γ=1×10−16m2∕W. The nonlinear absorption shows an intensity-independent coefficient of β=4×10−10m∕W related to fast processes. In addition, we measure a second β component around 10−9m∕W with a relaxation time of 300μs that rises linearly with the laser intensity. We associate its origin to the absorption of excited carriers from a surface-defect state with a long depopulation time.
NIR model development and robustness in prediction of melon fruit total soluble solids
Authors: Guthrie J. A. , Liebenberg C. J. , Walsh K. B.
Published: April 2006

Near infrared spectroscopy (NIRS) can be used for the on-line, non-invasive assessment of fruit for eating quality attributes such as total soluble solids (TSS). The robustness of multivariate calibration models, based on NIRS in a partial transmittance optical geometry, for the assessment of TSS of intact rockmelons (Cucumis melo) was assessed. The mesocarp TSS was highest around the fruit equator and increased towards the seed cavity. Inner mesocarp TSS levels decreased towards both the proximal and distal ends of the fruit, but more so towards the proximal end. The equatorial region of the fruit was chosen as representative of the fruit for near infrared assessment of TSS. The spectral window for model development was optimised at 695–1045 nm, and the data pre-treatment procedure was optimised to second-derivative absorbance without scatter correction. The ‘global’ modified partial least squares (MPLS) regression modelling procedure of WINISI (ver. 1.04) was found to be superior with respect to root mean squared error of prediction (RMSEP) and bias for model predictions of TSS across seasons, compared with the ‘local’ MPLS regression procedure. Updating of the model with samples selected randomly from the independent validation population demonstrated improvement in both RMSEP and bias with addition of approximately 15 samples.
Limitations to the measurement of intact melon total soluble solids using near infrared spectroscopy
Authors: Long Robert L. , Walsh Kerry B.
Published: April 2006

The imposition of a minimum total soluble solids (TSS) value as a quality standard for orange-flesh netted melon fruit (Cucumis melo L. reticulatus group) requires either a batch sampling procedure (i.e. the estimation of the mean and standard deviation of a population), or the individual assessment of fruit [e.g. using a non-destructive procedure such as near infrared (NIR) spectroscopy]. Several potential limitations to the NIR assessment of fruit, including the variation in TSS within fruit and the effect of fruit storage conditions on the robustness of calibration models, were considered in this study. Outer mesocarp TSS was 3 TSS units higher at the stylar end of the fruit compared with the stem end, and the TSS of inner mesocarp was higher than outer tissue and more uniform across spatial positions. The linear relationship between the outer 10 mm and the subsequent middle 10 mm of tissue varied with fruit maturity [e.g. 42 days before harvest (DBH), r 2 = 0.8; 13 DBH, r 2 = 0.4; 0 DBH, r 2 = 0.7], and with cultivars (at fruit maturity, Eastern Star 2001 r 2 = 0.88; Malibu 2001 r 2 = 0.59). This relationship notably affected NIR calibration performance (e.g. based on inner mesocarp TSS; R c 2 = 0.80, root mean standard error of cross-validation (RMSECV) = 0.65, and R c 2 = 0.41, RMSECV = 0.88 for mature Eastern Star and Malibu fruit, respectively). Cold storage of fruit (0–14 days at 5°C) did not affect NIR model performance. Model performance was equivalent when based on either that part of the fruit in contact with the ground or equatorial positions; however, it was improved when based on the stylar end of the fruit.
Construction and analysis of an AFLP molecular linkage map of the silkworm (Bombyx mori)
Authors: Yang-Hu Sima , Bin Li , Da-Xia Chen , De-Bin Sun , Ai-Chun Zhao , Lie Zhang , Cheng Lu , Si-Mei He , Zhong-Huai Xiang
Published: April 2006

An amplification fragment length polymorphism (AFLP) molecular linkage map with a relatively high density for location of quantitative trait loci (QTLs) controlling the quantitative traits of silkworm (Bombyx mori) cocoons, was constructed using 91 individuals of the F2generation. Among the 692 effective loci, 550 were allocated to subgroups a and b, of which 21 linkage groups in subgroup a had 233 molecular markers and 28 linkage groups in subgroup b had 317 markers. The number of markers on each linkage group in subgroups a and b ranged from 4 to 43 and 3 to 35, respectively. The total length of linkage groups for subgroup a was 1868.10 cM, and 2677.50 cM for subgroup b. The length of linkage group varied from 22.3 to 424.3 cM in subgroup a and from 2.4 to 366.5 cM in subgroup b. The average variation in the distance between markers was 3.39–17.43 cM in subgroup a and 0.8–26.96 cM in subgroup b. The average distance between the markers was 8.81 cM in subgroup a and 9.26 cM in subgroup b. There were 14 linkage groups, with an average distance below 10 cM, in subgroup a and 18 linkage groups in subgroup b. There were seven linkage groups with an average distance between 10 and 20 cM in subgroup a and ten linkage groups in subgroup b. Each linkage group in subgroup a had 11.1 loci on average, while there were 11.31 loci on each linkage group on average in subgroup b. The mean length for linkage groups in subgroups a and b was 89 and 95.6 cM, respectively. The total average length for both a and b subgroups was 2272.8, and 9.06 cM for the average marker distance, fulfilling the basic known requirements for locating QTLs.
Regeneration of vgb-transgenic poplar (Populus alba×P. glandulosa) and the primary observation of growth
Authors: Bing-Yu Zhang , Xiao-Hua Su , Yi-Liang Li , Qin-Jun Huang , Xiang-Hua Zhang , Lei Zhang
Published: April 2006

Increasing the growth rate is especially important for low-quality wood applications, so this has become an important goal in poplar breeding. The present study describes the transfer of Vitreoscilla haemoglobin (VHb) gene (vgb) driven by constitutive promoters, by Agrobacterium tumefaciens into poplar (Populus alba×P. glandulosa). From about 450 leaf discs used for transformation, 60 Kan-resistant plants were obtained, and 52 proved to be true transgenic plants. The transgenic nature of these plants was confirmed by polymerase chain reaction (PCR) amplification and Southern dot blot hybridization. The expression of vgb gene in transgenic plants was confirmed by reverse transcriptase-PCR (RT-PCR). The performance of the transgenic lines was evaluated during the first year of growth in a greenhouse. These plants showed no significant stable morphological differences from the untransformed plants. Among them, three vgb-transgenic lines exhibited noticeably higher growth rates in terms of height and diameter.
EGFP expression in goat mammary epithelial cells
Authors: Yue-Mao Zheng , Zhi-Xing An , Xin-Rong Peng , Yu-Qiang Shi , Yong Zhang
Published: April 2006

Primary culture of goat mammary gland cells was achieved by outgrowth of migrating cells from fragments of tissue. The fibroblast and epithelial cells were purified according to their different sensitivity to trypsin and the characteristics of goat mammary epithelial cells were observed under a light microscope. The results showed that the purified goat mammary epithelial cells retained normal characteristics until the 15th passage. The purified mammary epithelial cells propagated and formed a dome-like structure that resembled a nipple and was called a ‘milk orb’. The mammary epithelial cells could produce and secrete milk. There were different cell types: the majority were short shuttle-like or polygons, resembling a beehive; while some were large, flat and round; and others were elongated. The enhanced green fluorescent protein (EGFP) gene was transferred successfully into the goat mammary epithelial cells using electrotransfection, and its expression was observed under a fluoroscope.
Isolation and characterization of endophytic Streptomyces sp. S5 with herbicidal activity from tomato roots
Authors: Zhi-Qi Qiu , Li-Xiang Cao , Hong-Ming Tan , Shi-Ning Zhou
Published: April 2006

Fifty-eight actinomycetes were isolated from surface-sterilized tomato (Lycopersicon esculentum) roots and 43 isolates were screened for herbicidal activities. Isolate S5 was found to have potent herbicidal activity against germination of wheat (Triticum aestivum L.), mung bean (Phaseolus radiatus L.) and grass (Paspalum notatum and Cynodon dactylon) seeds. But the metabolites of isolate S5 showed no influence on the growth of wheat seedlings. The S5 strain was identified as Streptomyces lavendulae var. glaucescens based on its morphological characteristics and physiological properties. The highest herbicidal activity was observed when 2% inocula were applied into S medium (containing 1% glucose, 0.3% beef extract and pH 7.0) and incubated at 25°C on a rotary shaker (160 rpm).
Isolation, cloning and sequence analysis of differentially expressed genes in the backfat tissue between hybrids and parents in pigs
Authors: Zhu-Qing Ren , Yuan-Zhu Xiong , Chang-Yang Deng , Ming-Gang Lei , Bo Zuo , Rong Zheng , Feng-E Li , Si-Wen Jiang , Xun-Ping Jiang
Published: April 2006

In order to reveal the molecular basis of heterosis, Large White (LW), an introduced European pig breed, and Meishan (MS), a Chinese indigenous pig breed, were selected to hybridize directly and reciprocally in the present experiment. mRNA differential display (DD) technique was performed to identify genes that were differentially expressed in the backfat tissues of hybrids (LW×MS, MS×LW) and purebred (LW×LW, MS×MS) pigs. The ten anchor primers in combination with ten arbitrary primers (100 sets in total) were used and nearly 1500 reproducible bands were observed in polyacrylamide gels. The 40 differentially displayed bands were selected for cloning and sequencing. Thirty-six out of 40 expressed sequence tags (ESTs) proved to be novel and the sequences were submitted to GenBank (accession No. CV507051-CV507087); the other four showed similarity to known genes published in GenBank. Three among 36 novel ESTs were chosen for further identification with semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR). The result showed that two ESTs were differentially expressed, and the third showed no obvious difference between hybrids and purebreds. In order to reduce the percentage of false-positive DD, RNA pools of four types of pigs were constructed, by mixing samples from six pigs of the same genotype, and subjected to DD. Stringent annealing temperature was applied and only bands that could be repeated in duplicate PCR were used for further study. The results showed that the expression pattern of these 36 ESTs differed among the four genotypes of pigs, suggesting that the genes corresponding to these differentially expressed ESTs might be related to the heterosis occurring in fat tissue.