bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrasting effects of soil development on hydrological properties and flow paths
Authors: Lohse Kathleen A. , Dietrich William E.
Published: December 2005

Runoff pathways strongly influence hydrologic and biogeochemical losses and landscape evolution. On an evolving landscape, soil development may alter hydrologic properties and thereby change through time the relative importance of various pathways. Here we report in situ soil water retention, unsaturated and saturated hydraulic conductivity, and flow path characteristics of a 300 year old Andisol and a 4.1 million year old Oxisol, located at the extreme ends of a soil substrate age gradient across the Hawaiian Islands. The two soils contrasted in depth and texture; the young soil was shallow and coarse textured, while the old soil was deep and highly weathered with a near‐surface plinthite horizon overlying numerous clay‐rich subsurface horizons. The young soil drained freely under modest suction, whereas subsurface clay horizons at the old site required significantly more suction to start to drain than the upper horizons. Similarly, saturated hydraulic conductivity (Ks) was high throughout the soil profile at the young site, whereas Ks was two to three orders of magnitude lower through the subsurface clay horizons than the upper ones at the old site. Irrigation experiments with deuterium tracer demonstrated that water was downward advecting at the young site, while water at the old site moved both laterally along the subsurface clay horizon contact and slowly downward through it. Rainfall frequency distributions indicated a high probability of rainfall events exceeding subsurface Ks values in old soil. In Hawaii the addition of dust influences the time evolution of soil, but the tendency for subsoil clay accumulation in older soils leading to alteration in hydrologic flow paths has been proposed in other environments. Our findings together suggest that as soils develop with time, subsurface horizon Ks values decline, impeding rates of vertical water flow but also increasing the importance of shallow subsurface lateral flow.
The baroclinic transport of the Antarctic Circumpolar Current south of Africa
Authors: Legeais Jean‐François , Speich Sabrina , Arhan Michel , Ansorge Isabelle , Fahrbach Eberhard , Garzoli Silvia , Klepikov Alexander
Published: December 2005

Five hydrographic transects at nominal longitudes 0°E and 30°E, and fourteen expendable bathythermograph (XBT) sections near the former longitude are used to study the baroclinic transport of the Antarctic Circumpolar Current (ACC) between Africa and Antarctica. The bottom‐referenced geostrophic transport between the Subtropical Front and the ACC Southern Boundary is 147 ± 10 Sv. Estimating the transport from the XBTs using a technique previously employed south of Australia proves delicate because of an irregular bathymetry and water mass variations. It nevertheless confirms ACC transports around 150 Sv. Gathering these and other estimates from the Atlantic sector suggests that, while North Atlantic Deep Water is injected in the current west of 35°W, a partially compensating loss of Deep Circumpolar Water occurs east of this longitude. Another transport increase from 0°E to 30°E might reflect southward transfer across the Subtropical Front south of the Agulhas retroflection.
Sea‐ice feedbacks on the climatic response to precession and obliquity forcing
Authors: Tuenter E. , Weber S. L. , Hilgen F. J. , Lourens L. J.
Published: December 2005

The possible role of sea‐ice feedbacks in the climatic response to orbital forcing at high northern latitudes is studied with a coupled climate model (ECBilt‐CLIO). It is found that boreal summer insolation is critical for the sea‐ice response. When summer insolation is high (low) the sea‐ice fraction decreases (increases) at the margins of the permanent sea‐ice cover during the whole year. More importantly, rapid shifts in GIN (Greenland‐Iceland‐Norway) Sea ice cover are found to be less (more) frequent for relatively high (low) summer insolation. These events, which are characterized by a sudden expansion in sea‐ice cover, result in reduced GIN Sea convection, a reduction of the Atlantic thermohaline circulation by 5–10 Sverdrups and decreased air temperatures at high latitudes.
Potential predictability of tropical Indian Ocean SST anomalies
Authors: Wajsowicz Roxana C.
Published: December 2005

Retrospective 9‐month 15‐member ensemble forecasts from the National Centers for Environmental Prediction Coupled Forecast System (NCEP CFS) for 1981 to 2003 are used to assess forecast skill and potential predictability of sea‐surface temperature anomalies (SSTAs) over the poles of the Indian Ocean Dipole Mode (IDM). The CFS successfully forecasts through the boreal winter persistence barrier at the east IDM pole capturing the sign change of the SSTAs. Forecasts are skillful up to 3–4 months lead for first half‐year starts, and into the following boreal spring for second half‐year starts. West IDM pole forecasts are skillful up to 6–7 months lead or until mid‐summer; skill returns in fall for forecasts initiated in boreal summer. Potential predictability of boreal fall SSTAs at lead times of 2–3 seasons appears limited by the onset of the boreal summer monsoon at both IDM poles with weak SSTAs, weak ocean‐atmosphere coupling, and lack of good initialization of the subsurface ocean further hampering forecasts initiated in boreal winter at the east IDM pole.
The ‘flickering switch’ of late Pleistocene climate change revisited
Authors: Barker Stephen
Published: December 2005

Extremely rapid fluctuations observed in records of electrical conductivity measurements (ECM) from Greenland ice‐cores provoked the idea that the climate system may be capable of flickering between two states during rapid climate transitions. Here it is shown that in general, the flickers seen in ECM records probably reflect the highly non‐linear response of electrical conductivity as ice approaches acid/base neutrality, rather than significant changes in the climate system. High frequency, relatively low amplitude changes in chemistry, superimposed upon the broader changes typical of climate transitions would be capable of producing the observed characteristics of ECM records. It must be stated that this result does not detract from the observation of extremely rapid changes in, for example, ice core chemistry and isotopes, which clearly demonstrate that Earth's climate is capable of very rapid and major reorganisations.
Erosion of the seafloor at the top of the gas hydrate stability zone on the Hikurangi Margin, New Zealand
Authors: Pecher I. A. , Henrys S. A. , Ellis S. , Chiswell S. M. , Kukowski N.
Published: December 2005

The dissociation of gas hydrates in sediment pores is thought to decrease seafloor strength potentially facilitating submarine slides because of the generation of overpressured gas and the “melting” of load‐bearing or cementing solid hydrate. Here, we present findings that suggest gas hydrates may lead to a previously unknown mechanism of seafloor erosion. Gas‐hydrate‐bearing sub‐sea ridges on the Hikurangi Margin are eroded close to the top of the hydrate stability field in the ocean. We hypothesize that gas hydrate instability may lead to ridge erosion by a combination of two processes; hydrate destabilization caused by depressurization during ridge uplift, and repeated pore volume expansion and contraction from hydrate dissociation and formation triggered by fluctuating water temperatures.
Ocean surface wind prediction in the north Indian Ocean from in situ and satellite observations using genetic algorithm
Authors: Basu Sujit , Satheesan K. , Sarkar Abhijit , Kishtawal C. M.
Published: December 2005

Possibility of predicting surface wind speed in the north Indian Ocean from in situ observations and surface wind components from satellite scatterometer observations using an approach based on genetic algorithm (GA) has been demonstrated in this work. The approach, unlike other prediction methods, provides explicit analytical forecast equation. Predictions made up to 3 days in advance have been found to be significantly superior to those made by persistence and autoregressive techniques.
Macrostructure of collisionless bow shocks: 1. Scale lengths
Authors: Omidi N. , Blanco‐Cano X. , Russell C. T.
Published: December 2005

The global structure of collisionless bow shocks is investigated using a 2.5‐dimensional electromagnetic hybrid code. This allows us to study the macrostructure of the shock while accounting for microphysical processes at the shock. The study entails the interaction of solar wind with magnetic dipoles of varying strength. For very weak dipoles the interaction does not lead to formation of a shock since the obstacle is not strong enough for the flow to become subsonic. For lager dipole strengths, a bow shock/wave is formed due to the presence of a plasma stagnation region in front of the dipole. It is found that the quasi‐perpendicular part of this boundary corresponds to a true shock wave, whereas the quasi‐parallel side consists of a magnetosonic wave followed by a rotational discontinuity. The backstreaming ions in the foreshock of this interaction lead to the generation of parallel propagating sinusoidal waves. These waves result in beam scattering, however, do not affect the solar wind. The formation of quasi‐parallel shock is tightly connected to the generation of oblique compressional waves. These waves are generated by backstreaming ions having a beam‐ring distribution function and are an inherent part of the shock dissipation processes. The results demonstrate that the two classes of 30 s ULF waves observed in the ion foreshock are unrelated. The results also demonstrate that at least in 2.5‐dimensional, plasma scales determine the nature of the bow shock to a large extent although system size can influence both particle acceleration and evolution of ULF waves.
Zonal wind velocity profiles in the equatorial electrojet derived from phase velocities of type II radar echoes
Authors: Shume E. B. , Hysell D. L. , Chau J. L.
Published: December 2005

Zonal wind profiles in the daytime equatorial electrojet are inferred from the Doppler shifts of type II radar echoes observed at the Jicamarca Radio Observatory (JRO) in Perú. The inference is based on a three‐dimensional electrostatic potential model. The model includes anomalous effects and is constrained by radar and magnetometer data. The amplitude and phase of the calculated zonal wind profiles are in general agreement with representative wind profiles measured by the WINDII instrument on board the Upper Atmosphere Research Satellite (UARS). The calculated winds also have the same general characteristics as zonal wind profiles measured by rocket‐borne chemical release experiments. However, the magnitude of the latter are larger than the former. The temporal behavior of the calculated zonal winds suggests a downward phase progression with a roughly semidiurnal period.
Dispersion analysis of low‐frequency waves through the terrestrial bow shock
Authors: Narita Y. , Glassmeier K.‐H.
Published: December 2005

We present dispersion relations of low‐frequency waves observed upstream and downstream of the Earth's bow shock analyzing Cluster magnetometer measurements along an outbound orbit covering four regions: the foreshock, the outer, the middle, and the inner magnetosheath. The aim of our study is to better understand wave transmission, mode conversion, or wave excitation in the bow shock environment. The foreshock waves identified exhibit two wave modes propagating parallel to the magnetic field that are consistent with the right‐hand ion beam instability, whereas the magnetosheath waves exhibit a transition from a mixture of ion cyclotron waves and mirror mode in the outer sheath into primarily mirror mode structures in the middle sheath. Properties of the mirror mode are distorted near the magnetopause probably due to effects of density gradients or plasma flow pattern imposed by the magnetopause. From the viewpoint of the dispersion relation, the propagation angle, and the polarization, the foreshock wave properties are not transmitted into the magnetosheath.
Predicting surface geomagnetic variations using ionospheric electrodynamic models
Authors: Weimer D. R.
Published: December 2005

A technique is described for predicting ground surface geomagnetic variations from measurements of the approaching interplanetary magnetic field (IMF) and solar wind. The method uses twin, empirical representations of the ionospheric electric and magnetic Euler potentials' response to the IMF drivers. The magnetic potential model, originally derived for mapping the large‐scale field‐aligned current structure, describes the curl‐free component of the horizontal ionospheric current, also called the “potential current.” Using approximations that the Hall and Pedersen conductances have a fixed ratio and that there are no conductivity gradients, then the Hall current is derived from the magnetic potentials. In this case the Hall current is the same as the divergence‐free “equivalent current,” which is used to derive the geomagnetic variations at the ground surface. The assumption that the ionospheric conductances have no gradients is avoided if the empirical model for the ionospheric electric potentials is used in addition to the magnetic potentials. In this second method the electric field provides additional information about the direction of the estimated equivalent current. Despite the approximation of a fixed conductance ratio, both calculation methods perform remarkably well for predicting the large‐scale and long‐period geomagnetic variations. The method that includes the electric fields has a slightly better performance, particularly in the polar cap. Corrections for the effects of currents induced underground were not applied for this demonstration. Such corrections could in principle improve the predictions, particularly for the short‐period variations for which the effect is the greatest.
Time variations of cosmic ray electrons and nuclei between 1978 and 2004: Evidence for charge‐dependent modulation organized by changes in solar magnetic polarity and current sheet tilt
Authors: Webber W. R. , Heber B. , Lockwood J. A.
Published: December 2005

We have examined the 52‐day average intensities of 1.2‐GV electrons and positively charged nuclei of the same rigidity during the time period from 1978 to 2004. This time period covers a complete 22‐year solar cycle plus data from 2000 to 2004 that can be used to examine the repetitive nature of the variations. The 11‐year solar modulation changes both the electrons and nuclei intensities by similar overall factors ∼10 at 1.2 GV. Differences in the electron/nuclei modulation as exhibited by the e/nuclei ratios occur mainly between 1980–1984, 1990–1994, and 2000–2004. At these times the e/nuclei ratios increase or decrease by a factor ∼2 at 1.2 GV in close correspondence with the changes in solar magnetic polarity from positive to negative (1980) and negative to positive (1990). The e/nuclei ratio changes in 2000–2004 match those seen in 1980–1984, thus confirming the 22‐year nature of the e/nuclei variations.
Multispacecraft observations of interplanetary shocks: Nonplanarity and energetic particles
Authors: Neugebauer M. , Giacalone J.
Published: December 2005

Numerical simulations of the evolution of interplanetary shocks exhibit growth of distortions of the shock front and nonuniformity of energetic particles from place to place near the shock surface. In this work we use multispacecraft (ACE, Wind, IMP 8, Geotail, Interball‐Tail, SOHO, and Genesis) observations near Earth to search for such effects. On scales of 105 to 106 km, most of the 26 shocks studied were inconsistent with planar structures or with spherical structures with a radius of 1 AU. The average local radius of curvature was ∼3 × 106 km. There were also differences in the intensities and time profiles of energetic particle fluxes seen at both ACE and Wind.
A magnetic fabric study of the Aigoual–Saint Guiral–Liron granite pluton (French Massif Central) and relationships with its associated dikes
Authors: Talbot J.‐Y. , Chen Y. , Faure M.
Published: December 2005

In the southeastern French Massif Central, the Aigoual–Saint Guiral–Liron pluton consists of porphyritic and microgranitic types. The latter is encountered within dikes forming the northern end of the pluton. Both types show prefull crystallization microstructures indicating weak subsolidus deformations. An anisotropy of magnetic susceptibility (AMS) study has been carried out to determine the granite fabric. Biotite, local hornblende, and small grains of magnetite are the main carriers of AMS in both types. Porphyritic granite and dikes display different AMS patterns related to magma dynamics and regional deformation recorded during crystallization. In the porphyritic type, the AMS lineation is mainly consistent with the regional, NW‐SE to E‐W trending, extensional event coeval with emplacement and crystallization of the pluton indicating an influence of regional tectonics on the linear fabric development. The dome shaped foliation pattern of the Saint Guiral massif likely corresponds to internal deformation‐related processes within the pluton. In the microgranite dike swarm, the NNE‐SSW trending lineations with shallow plunges record magmatic flow processes within dikes, i.e., magma injection and filling of dikes from a probable source located southwestward. Regional tectonics played a significant role in the pluton geometry and fabric development. For example, the NE‐SW trend of the dikes suggests that extensional fractures took place in the same extensional strain field as elsewhere in the pluton. Different fabric development modes were therefore responsible for the contrasted fabric patterns between the microgranite and the porphyritic granite.
Numerical modeling of the emplacement of Socompa rock avalanche, Chile
Authors: Kelfoun K. , Druitt T. H.
Published: December 2005

The 7.5 ka Socompa sector collapse emplaced 25 km3 of fragmented rock as a thin, but widespread (500 km2), avalanche deposit, followed by late stage sliding of 11 km3 as Toreva blocks. Most of the avalanche mass was emplaced dry, although saturation of a basal shear layer cannot be excluded. Modeling was carried out using the depth‐averaged granular flow equations in order to provide information on the flow behavior of this well‐preserved, long run‐out avalanche. Results were constrained using structures preserved on the surface of the deposit, as well as by deposit outline and run‐up (a proxy for velocity). Models assuming constant dynamic friction fail to produce realistic results because the low basal friction angles (1 to 3.5°) necessary to generate observed run‐out permit neither adequate deposition on slopes nor preservation of significant morphology on the deposit surface. A reasonable fit is obtained, however, if the avalanche is assumed simply to experience a constant retarding stress of 50–100 kPa during flow. This permits long run‐out as well as deposition on slopes and preservation of realistic depositional morphology. In particular the model explains a prominent topographic escarpment on the deposit surface as the frozen front of a huge wave of debris reflected off surrounding hills. The result that Socompa avalanche experienced a small, approximately constant retarding stress during emplacement is consistent with a previously published analysis of avalanche data.
Deformation‐induced grain boundary wetting and its effects on the acoustic and rheological properties of partially molten rock analogue
Authors: Takei Yasuko
Published: December 2005

An experimental study was performed to investigate the effects of deviatoric stress on the microstructure of partially molten polycrystalline aggregates. Borneol (organic crystal) + melt system having an eutectic temperature of 43°C and a moderate dihedral angle was used as a partially molten rock analogue. Large samples (70 mm cube) having melt fractions of 0.089–0.22 were deformed ductilely under a uniform pure shear stress (shear strain rate of ∼0.8–7×10−7 s−1), while monitoring the sample microstructure in situ using ultrasonic shear waves. Each sample was deformed repeatedly by changing the principal stress direction, resulting in the microstructural changes well detectable under the microscope. The most remarkable features of the stress‐ and/or deformation‐induced microstructural changes are enhanced grain boundary wetting, enhanced grain coarsening, and formation of large (approximately sample scale) melt sheet parallel to the shear plane, which is an assembly of completely wetted two‐grain boundaries at the microscopic scale. Significant changes in the elastic, anelastic, and viscous properties associated with these microstructural changes were observed. The velocity monitoring provided a detailed picture of growth and healing of grain boundary melt films in response to loading cycles. The microstructural changes observed in this study have many similarities with the “dynamic wetting” reported for the partially molten peridotite.
Efficient constitutive expression of Bacillus subtilis xylanase A in Escherichia coli DH5α under the control of the Bacillus BsXA promoter
Authors: Ruller Roberto , Rosa José César , Faça Victor M. , Greene Lewis J. , Ward Richard J.
Published: December 2005

Xylanase A (XynA) is a class G/11 xylanase secreted by Bacillus subtilis. XynA was purified to homogeneity from B. subtilis strain 168 culture supernatants by ethanol precipitation and cation‐exchange chromatography. The DNA fragment encoding the XynA together with the BsXA promoter region was amplified by PCR from B. subtilis 168 genomic DNA, and cloned into the plasmid pT7T3 to give the plasmid pT7BsXA. After transformation of Escherichia coli DH5α with pT7BsXA, a 19‐fold increase in the levels of the secreted XynA was detected in the supernatant as compared with the B. subtilis culture. Correct post‐translation modification of the recombinant protein was confirmed by N‐terminal amino acid sequencing and MS analyses. The pH‐ and temperature‐dependences of the native and recombinant proteins were identical, indicating that the pT7BsXA may be useful for the constitutive expression of heterologous protein in E. coli.
Novel inhibitors of fatty‐acid synthase from green tea (Camellia sinensis Xihu Longjing) with high activity and a new reacting site
Authors: Zhang Rui , Xiao Wenping , Wang Xuan , Wu Xiaodong , Tian Weixi
Published: December 2005

Recent studies have shown that FAS (fatty acid synthase) is a potential therapeutic target of obesity. In the present paper we report that extract of green tea (Camellia sinensis Xihu Longjing) inhibits FAS effectively with an IC50 value of 12.2 μg dry weight/ml. The ability of GTE (green tea extract) to inhibit FAS is more potent than that of two known inhibitors in green tea leaves, EGCG (epigallocatechin gallate) and ECG (epicatechin gallate). We find that (−)‐CG (catechin gallate) is a very potent inhibitor of FAS, with an IC50 of 1.5 μg/ml, and may contribute to the high inhibitory effect of GTE on FAS. The inhibitory mechanism of (−)‐CG is not mainly involved in its binding to the β‐oxoacyl reductase domain to which both (−)‐EGCG and (−)‐ECG mainly bind. By analyses of the inhibitory kinetics and the structure of the gallated catechins, we found that the acyl transferase domain may be the main site reacting with (−)‐CG, the structure consisting of a B ring, a C ring and a gallate ring, which is possibly essential for its inhibitory efficacy. The polyphenols rather than the alkaloids are the main fractions contributing to the inhibitory effect of GTE on FAS. During separation we also found that the total ability of this portion to inhibit FAS increases by 15‐fold, and this may be due to some novel potent inhibitor of FAS other than (−)‐CG being formed.
A multivalent recombinant antibody fragment specific for carcinoembryonic antigen
Authors: Perez Lincidio , Ayala Marta , Pimentel Gilmara , Bell Hanssel , Canaán‐Haden Leonardo , Bequet Mónica , González Luis Javier , Miranda Marlen , Ravelo Rolando , Roque Lourdes , Acevedo Boris , Oliva Juan P. , Gavilondo Jorge V.
Published: December 2005

In the present paper we report the development of a bivalent scFv (single‐chain Fv) antibody fragment, starting from a mouse mAb (monoclonal antibody) specific for CEA (carcinoembryonic antigen) that has received approval for in vivo radioimmunodiagnosis in humans. The diabody is well expressed in Escherichia coli, is easily purified by a combination of immobilized metal ion affinity chromatography and gel filtration and exhibits high affinity and specificity for CEA, comparable with those of the original mAb. Biodistribution experiments in athymic nude mice transplanted with human CEA+ cancer cells showed that the 125I‐labelled diabody preferentially localizes in the tumour tissue and that retention is still high 48 h after injection. The diabody can be advantageous for some in vivo tumour targeting applications, due to the faster clearance derived from its smaller molecular mass.
Synthesis of acylglycerols from ω−3 fatty acids and conjugated linoleic acid isomers
Authors: Zuta Charles P. , Simpson Benjamin K. , Yeboah Faustinus K.
Published: December 2005

n−3 PUFA (ω−3 polyunsaturated fatty acid) concentrate from mackerel oil enriched in EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid) was used to esterify isomers of CLA (conjuated linoleic acid) to produce acylglycerols (glycerides). Catalysis was potentiated by immobilized lipases from the yeast Candida antarctica and the mould Mucor miehei. C. antarctica lipase showed higher reactivity and much faster initial rate of incorporation of CLA into acylglycerols than its M. miehei counterpart. Synthesis with molecular sieves also achieved a better rate of incorporation of fatty acids into acylglycerols than using vacuum or systems without water removal. Esterification achieved at 40 °C with C. antarctica lipase was significantly different from that achieved at 60 or 50 °C. However, there was no significant (P<0.05) difference between esterification at 50 °C and 60 °C. The molar ratio of glycerol to fatty acid was found to influence the initial rate of incorporation, with the lower ratios showing higher initial rates compared with the higher ratios. The present study shows that direct esterification is an effective mechanism for producing acylglycerols from fatty acids in a controlled system.
Increasing the capacity of parvovirus‐retentive membranes: performance of the Viresolve™ Prefilter
Authors: Bolton Glen R. , Spector Shari , LaCasse Dan
Published: December 2005

Removal of small parvoviruses from highly purified proteins can be performed using normal‐flow filters. The entrapment of protein aggregates, denatured proteins and other impurities can cause plugging and a decrease in filter capacity. In the present study a variety of prefilters were investigated for their ability to remove the species that foul Viresolve™ NFP (normal‐flow parvovirus) filters. The Viresolve™ Prefilter, which utilizes entrapped diatomaceous earth to hydrophobically bind fouling species, provided a dramatic increase in virus filter capacity for solutions containing human IgG or a variety of monoclonal antibodies. We found that the component of the human IgG stream that bound to the Prefilter, when analysed using SDS/PAGE, isoelectric‐focusing, size‐exclusion chromatography, CD and ANS (1‐anilinonaphthalene‐8‐sulphonate) titration, consisted of monomeric IgG variants containing more exposed hydrophobic surfaces. The bound component may represent oxidized or otherwise degraded IgG species or a subset of IgG molecules with more hydrophobic antigen‐binding surfaces. The results indicate that NFP membranes do not foul solely as a result of entrapment of protein aggregates in the pore structure. The Viresolve™ Prefilter has a high permeability, did not diminish protein yield and provided consistent performance between different media lots, device lots and device scales.
Expression and characterization of Helicobacter pylori heat‐shock protein A (HspA) protein in transgenic tobacco (Nicotiana tabacum) plants
Authors: Zhang Hongxin , Zhang Xinsheng , Liu Ming , Zhang Jianye , Li Yanjie , Zheng Cheng‐Chao
Published: December 2005

Helicobacter pylori infection is prevalent worldwide, especially in developing countries, and is associated with several upper‐gastrointestinal‐tract diseases. Vaccination is the most effective method to prevent and cure H. pylori infection. By using transgenic plants, plant organs could serve as factories to produce antigens of biotechnological interest. HspA (heat‐shock protein A) is an effective antigen and one common to all strains of H. pylori. In the present study, the PCR technique was employed to amplify the gene fragment of the HspA from H. pylori chromosomal DNA. The pGEM‐T vector was used for the insertion of the gene fragment of the HspA, and the vector pBI121 was used to construct the plant expression vector. After transformation, the regenerated tobacco plants were identified by PCR and by Northern‐ and Western‐blot analyses. The results verified the integration of this gene into the genome of tobacco (Nicotiana tabacum) and the expression of this gene in transgenic tobacco. Mucosal immunization of mice with transgenic tobacco extracts containing the HspA protein elicited anti‐HspA serum antibody that specifically bound to the purified bacterial HspA protein. The present study, using transgenic tobacco plants, provides useful data for the production of an edible plant vaccine.
The potential role of caveolin‐1 in inhibition of aquaporins during the AVD
Authors: Jablonski Elizabeth M. , Hughes Francis M.
Published: December 2005

Background information. During apoptosis, the first morphological change is a distinct cell shrinkage known as the AVD (apoptotic volume decrease). This event is driven by a loss of intracellular K+, which creates an osmotic gradient, drawing water out of the cell through AQPs (aquaporins). Loss of water in balance with K+ would create a shrunken cell with an equivalent intracellular concentration of K+ ([K+]i=140 mM). However, we have previously shown that the [K+]i of the shrunken apoptotic cell is 35 mM, and this level is absolutely essential for the activation of apoptotic enzymes. We have recently found that AQPs are inactivated following the AVD, so that continued loss of K+ will reduce the intracellular concentration to this critical level. Using thymocytes, we have investigated the expression profile and regulation of the AQP family members.

Results. In the present study, we have found that AQP1, AQP8 and AQP9 are present in non‐apoptotic thymocytes and localized primarily to the plasma membrane. Expression and localization did not change when these cells were induced to undergo apoptosis by growth factor withdrawal for 24 h. To explore other possible mechanisms by which these water channels are inactivated, we investigated their association with CAV‐1 (caveolin‐1), binding to which is known to inactivate a variety of proteins. We found that CAV‐1 is present in thymocytes and that this protein co‐localizes with a portion of AQP1 in normal (non‐apoptotic) thymocytes. However, thymocytes induced to undergo apoptosis greatly increase their AQP1/CAV‐1 association.

Conclusions. Taken together, these results indicate that AQPs are localized to the plasma membrane of shrunken apoptotic thymocytes where increased binding to CAV‐1 potentially inactivates them. AQP inactivation, coupled with continued K+ efflux, then allows the [K+]i to decrease to levels conducive for the activation of downstream apoptotic enzymes and the completion of the apoptotic cascade.
Active cathepsins B, H, K, L and S in human inflammatory bronchoalveolar lavage fluids
Authors: Serveau‐Avesque Carole , Martino Michèle Ferrer‐Di , Hervé‐Grépinet Virginie , Hazouard Eric , Gauthier Francis , Diot Elisabeth , Lalmanach Gilles
Published: December 2005

Background information. Chronic inflammation and tissue remodelling result from an imbalance between proteolytic enzymes and their inhibitors in the lungs in favour of proteolysis. While many studies have examined serine proteases (e.g. cathepsin G and neutrophil elastase) and matrix metalloproteases, little is known about the role of papain‐like CPs (cysteine proteases). The present study focuses on the thiol‐dependent cathepsins (CPs) and their specific cystatin‐like inhibitors [CPIs (CP inhibitors)] in human inflammatory BALFs (BAL fluids, where BAL stands for broncho‐alveolar lavage).

Results. Cathepsins B, K and S found were mostly zymogens, whereas cathepsins H and L were predominantly in their mature forms. Little immunoreactive cystatin C was found and the high‐ and low‐molecular‐mass (‘weight’) kininogens were extensively degraded. The BALF procathepsins B and L could be activated autocatalytically, indicating that alveolar fluid pro‐CPs are reservoirs of mature enzymes. Hydrolysis patterns of 7‐amino‐4‐methylcoumarin‐derived peptide substrates showed that extracellular alveolar CPs remain proteolytically active, and that cathepsins B and L are the most abundant thiol‐dependent endoproteases. The CP/CPI balance was significantly tipped in favour of cathepsins (3‐ or 5‐fold), as confirmed by the extensive CP‐dependent degradation of exogenous kininogens by BALFs.

Conclusions. Although their importance for inflammation remains to be clarified, the presence of active cathepsins L, K and S suggests that they contribute to the extracellular breakdown of the extracellular matrix.
Starvation‐induced expression of autophagy‐related genes in Arabidopsis
Authors: Rose Tatiana Lundgren , Bonneau Laurent , Der Christophe , Marty‐Mazars Danièle , Marty Francis
Published: December 2005

Background information. Autophagy is a catabolic process for degradation of cytoplasmic components in the vacuolar apparatus. A genome‐wide survey recently showed evolutionary conservation among autophagy genes in yeast, mammals and plants. To elucidate the molecular and subcellular machinery responsible for the sequestration and subsequent digestion of intracellular material in plants, we utilized a combination of morphological and molecular methods (confocal laser‐scanning microscopy, transmission electron microscopy and real‐time PCR respectively).

Results. Autophagy in Arabidopsis thaliana suspension‐cultured cells was induced by carbon starvation, which triggered an immediate arrest of cell growth together with a rapid degradation of cellular proteins. We followed the onset of these responses and, in this report, provide a clear functional classification for the highly polymorphic autophagosomes by which the cell sequesters and degrades a portion of its own cytoplasm. Quantification of autophagy‐related structures shows that cells respond to the stress signal by a rapid and massive, but transient burst of autophagic activity, which adapts to the stress signal. We also monitored the real‐time expressions of AtATG3, AtATG4a, AtATG4b, AtATG7 and AtATG8a–AtATG8i genes, which are orthologues of yeast genes involved in the Atg8 ubiquitination‐like conjugation pathway and are linked to autophagosome formation. We show that these autophagy‐related genes are transiently up‐regulated in a co‐ordinated manner at the onset of starvation.

Conclusions. Sucrose starvation induces autophagy and up‐regulates orthologues of the yeast Atg8 conjugation pathway genes in Arabidopsis cultured cells. The AtATG3, AtATG4a, AtATG4b, AtATG7 and AtATG8a–AtATG8i genes are expressed in successive waves that parallel the biochemical and cytological remodelling that takes place. These genes thus serve as early markers for autophagy in plants.
Cytochrome P450 expression—induction profile and chemically mediated alterations of the WIF‐B9 cell line
Authors: Biagini Christine , Bender Virginie , Borde Françoise , Boissel Elodie , Bonnet Marie‐Claire , Masson Marie‐Thérèse , Cassio Doris , Chevalier Stephan
Published: December 2005

Background information. WIF‐B9 is a hybrid cell line obtained by fusion of rat hepatoma cells (Fao) and human fibroblasts (WI38). It exhibits the structural and functional characteristics of differentiated hepatocytes, including active bile canaliculi. The aim of the present study was to characterize the WIF‐B9 cell line as a model for analysing drug‐induced hepatic effects. The drug metabolism potential of WIF‐B9 cells was identified by studying the rat and human CYP (cytochrome P450) mRNA constitutive expression profile and induction potential after exposure to reference inducers. The morphological alterations provoked by chemical entities were also characterized.

Results. Competitive reverse transcriptase—PCR revealed that four rat (1A1, 2B1/2, 2E1 and 4A1) and four human (1A1, 2Cs, 2D6 and 2E1) CYP mRNA isoforms were constitutively expressed in WIF‐B9 cells. The rat CYP forms were expressed at levels 2–4 orders of magnitude higher than the human forms. Exposure for 20–72 h to increasing concentrations of CYP reference inducers (β‐naphthoflavone, 3‐methyl cholanthrene, dexamethasone, phenobarbital, clofibrate and pregnenolone 16α‐carbonitrile) revealed that the rat CYP 1A1, 1A2, 3A1, 3A2 and 4A1 and human CYP 1A1 and 2Cs mRNAs were inducible. Rat CYP 1A1 and 1A2 were the most inducible isoforms since they were overexpressed up to 100‐fold after 20–48 h of treatment with β‐naphthoflavone. Human CYP 1A1 and 2Cs mRNAs were induced 3‐fold after 48 h of treatment with phenobarbital. Other mechanisms involved in hepatotoxicity were explored using microscopy and immunofluorescence. The WIF‐B9 cell line exhibited fragmentation and dilatation of bile canaliculi upon exposure to erythromycin, and to isoniazid and cytochalasins, respectively. Monensin promoted cell depolarization and cytoplasmic granulation. Ethionine promoted cytoplasmic vacuolation and dilatation of the Golgi structures.

Conclusions. These results indicate that the CYP expression and induction profiles and the morphological features of WIF‐B9 cells allow prediction in vitro of the induction and hepatotoxicity profiles of chemical entities.
Do Alix and ALG‐2 really control endosomes for better or for worse?
Authors: Sadoul Rémy
Published: December 2005

Alix/AIP1 (ALG‐2‐interacting protein X/apoptosis‐linked‐gene‐2‐interacting protein 1) is an adaptor protein that was first described for its capacity to bind to the calcium‐binding protein ALG‐2 (apoptosis‐linked gene 2), the expression of which seemed necessary for cell death. Over‐expression of truncated forms of Alix blocks caspase‐dependent and ‐independent mechanisms of cell death. Numerous observations in yeast and in mammalian cells suggest that Alix controls the making of and trafficking through endosomes called MVBs (multivesicular bodies), which are crucial intermediates within the endolysosomal system. In particular, deletion of Bro1, one of the yeast homologues of Alix, leads to an impairment in the function of MVBs, leading to mis‐sorting of proteins normally destined to the vacuole. Mammalian Alix may have a similar function and has been shown to bind to lyso(bis)phosphatidic acid, ESCRT (endosomal sorting complex required for transport) proteins, endophilins and CIN85 (Cbl‐interacting protein of 85 kDa), which are all main regulators of the endosomal system. EIAV (equine infectious anaemia virus) and HIV late domains use Alix to recruit the ESCRT machinery in order to bud from the cell surface, underscoring the crucial role of the protein in orchestrating membrane deformation. In this review I develop the hypothesis that the normal function of Alix in the endolysosomal system may be deviated by ALG‐2 towards a destructive role during active cell death.
Effects of simulated acid rain on the growth of five Brazilian tree species and anatomy of the most sensitive species (Joannesia princeps)
Authors: Campos da Silva Luzimar , Azevedo Aristéa Alves , Monteiro da Silva Eldo Antônio , Oliva Marco Antonio
Published: December 2005

Seedlings and young saplings of some woody species were exposed to simulated low-pH acid rain, in order to develop a response screening for tropical tree species by determination of the symptoms of foliar injury and growth responses, as well as to identify anatomical alterations in the leaf blade of the most sensitive species. Gallesia integrifolia (Spreng.) Harms, Genipa americana L., Joannesia princeps Vell., Mimosa artemisiana Heringer & Paula and Spondias dulcis Forst.f. were exposed daily to 20 min of acid rain, pH 3.0, for 10 consecutive days. The degree of leaf damage and the anatomical alterations observed were efficient parameters to determine the sensitivity to acid rain. At the end of the experiment J. princeps was the most sensitive species as determined by foliar injury and seedling growth. The degree of leaf damage was similar among the seedlings, except in S. dulcis, which showed reduced percentage of foliar injury. Necrotic and chlorotic spots on the leaf blade occurred. In the most sensitive species, J. princeps, necrotic blade tissues showed accumulation of phenolic compounds, hypertrophy and collapsed cells. Most of the structural alterations were observed in the adaxial epidermis, the palisade parenchyma and spongy parenchyma and the abaxial epidermis. Long-term experiments with seedlings of S. dulcis and saplings of G. integrifolia are suggested, to characterise the response of these species that presented fewer symptoms but whose growth was affected under acid rain.
Wild harvest of Cycas arnhemica (Cycadaceae): impact on survival, recruitment and growth in Arnhem Land, northern Australia
Authors: Griffiths Anthony D. , Schult H. Julia , Gorman Julian
Published: December 2005

An experimental wild harvest of Cycas arnhemica K.D. Hill, an understorey plant in tropical eucalypt savannas, was conducted in central Arnhem Land, Australia. Replicated harvest treatments were monitored over 2 years with tagged individuals. A range of a priori candidate statistical models were compared to determine the effect of wild harvest and environmental factors such as fire frequency and disturbance from feral animals on survival, recruitment and stem growth. The mean density of C. arnhemica was 1630 ha–1 and ranged from 550 to 2250 ha–1. Harvesting intensity in the 0.04-ha quadrats varied between 10 and 32% of all cycad stems (excluding seedlings). There was no clear effect of harvest treatment on stem survival, seedling abundance and stem growth on the remaining C. arnhemica 2 years after the harvest treatments were applied. Survival of woody stems was higher than that of seedlings but there was considerable overlap among the larger size classes. Seedling abundance was generally low and variable across the three sites, and seedlings were entirely absent from quadrats burnt twice during the study period. Stem growth varied considerably across the three sites and was similar between small and large stems. We suggest that the wild harvest of this abundant Cycas species in a remote region of northern Australia will have minimal impact on wild populations if focused on juvenile stems and return time is extended to 15–40 years at harvested locations. Future harvest management of this and other Cycas species in northern Australia will benefit from further research on stochastic population models to determine the most suitable harvest strategies, particularly for smaller Cycas populations.
Population and phylogenetic analysis of the cinnamoyl coA reductase gene in Eucalyptus globulus (Myrtaceae)
Authors: McKinnon Gay E. , Potts Brad M. , Steane Dorothy A. , Vaillancourt René E.
Published: December 2005

Low-copy number nuclear genes are currently emerging as new markers for phylogenetic and phylogeographic analysis. This study used the single-copy gene for cinnamoyl coA reductase (CCR) to gain insights into the evolutionary history of the forest tree Eucalyptus globulus Labill. (subgenus Symphyomyrtus, section Maidenaria). A population analysis based on CCR restriction fragments from E. globulus was combined with a phylogenetic analysis of 1.5 kb of CCR sequence from the major haplotypes. Two highly divergent CCR lineages were found in E. globulus. One lineage was prominent throughout the species’ range and was identified in 16 other Maidenaria species by restriction analysis. The second lineage, which was prominent in the northern part of the species’ range, was found only in species of the E. globulus complex and surprisingly showed homology to CCR from Eucalyptus saligna Smith (subgenus Symphyomyrtus, section Latoangulatae). This finding may reflect either incomplete lineage sorting in CCR, or reticulate evolution. No statistically significant phylogeographic structure (geographic clustering of closely related haplotypes) was detected. However, patterns of CCR haplotypic diversity were congruent with patterns of chloroplast DNA diversity in several respects, and divided the range of E. globulus into four regions, supporting (1) former gene flow between King Island and western Tasmania, (2) gene flow between northern Tasmania, the Furneaux Group and Victoria, and (3) a genetic disjunction between north-eastern and south-eastern Tasmania, consistent with separate histories for these two regions.
Isozyme diversity in large and isolated populations of Luma apiculata (Myrtaceae) in north-western Patagonia, Argentina
Authors: Caldiz Mayra S. , Premoli Andrea C.
Published: December 2005

We evaluated the amount and distribution of genetic variation in large and small isolated populations of Luma apiculata (DC.) Burret (Myrtaceae) in north-western Patagonia. The hypothesis tested was that isolated smaller populations were more affected by drift and isolation than large stands. Higher genetic diversity was predicted in the latter. Fresh leaf material for isozyme electrophoresis was collected from 30 individuals in four isolated and two large and continuous stands (Quetrihue Peninsula and Punta Norte, Isla Victoria). Five subpopulations were sampled in both large stands, and in addition, three regeneration gaps in Punta Norte. Eleven loci were resolved; 91% were polymorphic in at least one population. Isolated and large populations had similar levels of genetic variation. Reduced observed heterozygosity and elevated inbreeding were measured in subpopulations and regeneration gaps within dense stands. Although small populations consist of a reduced number of individuals they are mostly coastal populations nearby rivers and lakes that may maintain considerable gene flow with other faraway populations counteracting the effects of drift. In addition to potential selfing, increased inbreeding within large populations and regeneration gaps may be due to an intra-population Wahlund effect from local seedling establishment and vegetative spread, resulting in clustered cohorts of similar genotypes.