bluuebunny/crossref_metadata_2025 huggingface dataset:
A new shock fitting procedure for the MHD Rankine‐Hugoniot relations for the case of small He2+ slippage
Authors: Lin C. C. , Chao J. K. , Lee L. C. , Lyu L. H. , Wu D. J.
Published: September 2006

To study MHD shocks in space, it is important to find the shock frame of reference from the observed plasma and magnetic field parameters. These shock parameters have to satisfy the Rankine‐Hugoniot relations. In this study we present a novel procedure for shock fitting of the one‐fluid anisotropic Rankine‐Hugoniot relations and of the time difference between two spacecraft observations in the case of small He2+ slippage. Here, a Monte‐Carlo calculation and a minimization technique are used. The observed variables including the upstream and downstream magnetic fields, plasma densities, plasma betas, plasma anisotropies, W (the difference between the downstream and upstream velocities, W ≡ V2 − V1), and Δt (the time difference between two spacecraft observations) are used in our procedure where V is defined as the center of mass velocity of plasmas. A loss function based on a difference between the calculated and the observed values is defined, and the best fit solution is found by searching for the minimum loss function value. For shocks that cannot be fitted well, we introduce two new parameters in the modified RH relations, one in the normal momentum flux and the other in the energy flux equations. These two parameters are interpreted as the equivalent “normal momentum” and “heat” fluxes needed in the RH relations. They provide two degrees of freedom in the system, and their amounts can be estimated from our procedure. Several synthetic shocks are given to verify our procedure. We also apply this procedure to two interplanetary shocks observed by both the WIND and Geotail spacecraft. The results demonstrate that our method works for both the synthetic and the real shocks. We have shown that our method can provide accurate shock normal estimations for perpendicular and parallel shocks as well. Given that our model is based on the RH relations that do not include the effect of alpha particle (He2+) slippage, it can only be applied to the cases with an ignorable slippage pressure tensor. We have investigated the pressure tensor due to alpha particle slippage using the WIND spacecraft data. It is found that in general the slippage pressure is small in comparison with the thermal pressure of the system and can be ignored. Thus our model can be applied to most interplanetary shocks observed near the ecliptic plane. However, when the slippage pressure is large, the magnetic coplanarity theorem is not valid any more. A more general model that involves slippage pressure tensor is a major and important development that is beyond the scope of the present study.
High spatial resolution mapping of Mars mesospheric zonal winds by infrared heterodyne spectroscopy of CO2
Authors: Sonnabend G. , Sornig M. , Krötz P. J. , Schieder R. T. , Fast K. E.
Published: September 2006

We present Mars zonal wind measurements by means of infrared heterodyne spectroscopy of CO2 features at 959.3917 cm−1 (10.423 μm). Observations were carried out using the Cologne Tuneable Heterodyne Infrared Spectrometer (THIS) from 5–8 December 2005 shortly after Mars opposition at the McMath‐Pierce Solar Telescope of the National Solar Observatory on Kitt Peak in Arizona with an unprecedented spatial resolution of ∼1.7 arcsec on a ∼16 arcsec Martian disk. Mars was observed at six different latitudes close to the west (evening) limb and zonal winds were retrieved from Doppler shifts between CO2 non‐thermal emission from the mesosphere and absorption features from low atmospheric regions. The season on Mars was late northern winter (LS ≈ 337°). We retrieved retrograde winds at latitude 45°N (−27 ± 17 m/s) that were particularly strong at the equator (up to −80 ± 13 m/s) and prograde winds at high southern latitudes (75°S) up to 51 ± 29 m/s.
Geomagnetic activity indicates large amplitude for sunspot cycle 24
Authors: Hathaway David H. , Wilson Robert M.
Published: September 2006

The level of geomagnetic activity near the time of solar activity minimum has been shown to be a reliable indicator for the amplitude of the following solar activity maximum. The geomagnetic activity index aa can be split into two components: one associated with solar flares, prominence eruptions, and coronal mass ejections which follows the solar activity cycle and a second component associated with recurrent high speed solar wind streams which is out of phase with the solar activity cycle. This second component often peaks before solar activity minimum and has been one of the most reliable indicators for the amplitude of the following maximum. The size of the recent maximum in this second component indicates that solar activity cycle 24 will be much higher than average – similar in size to cycles 21 and 22 with a peak smoothed sunspot number of 160 ± 25.
Episodes of nonlinear internal waves in the northern East China Sea
Authors: Lee Jae Hak , Lozovatsky Iossif , Jang Sung‐Tae , Jang Chan Joo , Hong Chang Su , Fernando H. J. S.
Published: September 2006

Episodes of high‐frequency internal waves, which lasted approximately 3 hours, were detected in the northern East China Sea during a specific phase of the barotropic tide (i.e., low tide at 32°N, 125°E). The observed internal waves influenced the whole water column. The wave packets were presumably generated near the ocean shelf break, approximately 200 km to the southeast of the test site. During several internal wave episodes, which coincided with the neap tide, large‐amplitude solitary wave‐like features emerged preceding higher frequency internal waves. Shear instability of tidal currents is explored as a possible mechanism for sustaining or regenerating internal waves in the packets during the course of their propagation. It is suggested that rotating velocity field of tidal current supports sufficient vertical shear within wave packets to cause outbreaks of K‐H instability. These instabilities may gradually transition to more symmetric Hölmböe waves, following the increase of the bulk Richardson number.
Critical point theory of earthquakes: Observation of correlated and cooperative behavior on earthquake fault systems
Authors: Chen Chien‐chih , Rundle John B. , Li Hsien‐Chi , Holliday James R. , Turcotte Donald L. , Tiampo Kristy F.
Published: September 2006

The critical point theory for earthquakes was originally proposed to explain the scaling relations observed in earthquakes, including the Gutenberg‐Richter frequency‐ magnitude relation and the Omori's law for aftershocks. In this model, main shocks, their foreshocks and aftershocks are all associated with the formation of a correlated, cooperative spatial region with high stress. Until now, only indirect evidence of the existence of these correlated regions has been reported. Here in this paper we present observations and analyses that allow us to directly map the high stress, spatially correlated regions preceding four major earthquakes, i.e. the 1992 Landers (California), 1995 Kobe (Japan), 1999 Chi‐Chi (Taiwan) and 1999 Hector Mine (California) earthquakes. We therefore conclude that the locations and extent of large main shocks and their immediate aftershocks can be determined from seismicity data taken prior to the main shocks, and provide additional evidence in support of the critical point theory for earthquakes.
Self‐consistent formation of electron κ distribution: 1. Theory
Authors: Yoon Peter H. , Rhee Tongnyeol , Ryu Chang‐Mo
Published: September 2006

Since the early days of plasma physics research suprathermal electrons were observed to be generated during beam‐plasma laboratory experiments. Energetic electrons, often modeled by κ distributions, are also ubiquitously observed in space. Various particle acceleration mechanisms have been proposed to explain such a feature, but all previous theories rely on either qualitative analytical method or on non‐self‐consistent approaches. This paper discusses the self‐consistent acceleration of electrons to suprathermal energies by weak turbulence processes which involve the Langmuir/ion‐sound turbulence and the beam‐plasma interaction. It is discussed that the spontaneous scatttering process, which is absent in the purely collisionless theory, is singularly responsible for the generation of κ distributions. The conclusion is that purely collisionless Vlasov theory cannot produce suprathermal population.
Self‐similar scaling of magnetic energy in the inertial range of solar wind turbulence
Authors: Podesta J. J. , Roberts D. A. , Goldstein M. L.
Published: September 2006

Turbulent magnetic field fluctuations in the solar wind undergo an energy cascade in the inertial range with a characteristic Kolmogorov frequency spectrum f−5/3. Using magnetic field measurements from the Wind and ACE spacecraft at 1 AU in the ecliptic plane, probability distributions (PDFs) of time‐delayed differences of magnetic energy density B2(t) are shown to exhibit an approximate self‐similar scaling for time lags τ in the inertial range of the turbulence, that is, from approximately 10 to 1000 s. The scaling is characterized by a single scaling exponent γ, the Hurst exponent, and a universal PDF that is independent of scale for timescales in the inertial range. It is shown that the scaling exponent and the form of the universal PDF change with the 11‐year solar cycle due to the changing nature of the turbulence. The timescale for these changes is roughly estimated to be on the order of 1 or 2 years. Studies of low‐order structure functions are performed in an attempt to corroborate the self‐similar scaling of the PDFs. It is found that the structure functions do not scale in a self‐similar manner indicating that the PDFs are not truly self‐similar. Therefore the claimed self‐similar scaling of the PDFs is only a rough approximation.
Coexistence of two protein folding states in the crystal structure of ribosomal protein L20
Authors: Timsit Youri , Allemand Fréderic , Chiaruttini Claude , Springer Mathias
Published: September 2006

The recent finding of intrinsically unstructured proteins defies the classical structure–function paradigm. However, owing to their flexibility, intrinsically unstructured proteins generally escape detailed structural investigations. Consequently little is known about the extent of conformational disorder and its role in biological functions. Here, we present the X‐ray structure of the unbound ribosomal protein L20, the long basic amino‐terminal extension of which has been previously interpreted as fully disordered in the absence of RNA. This study provides the first detailed picture of two protein folding states trapped together in a crystal and indicates that unfolding occurs in discrete regions of the whole protein, corresponding mainly to RNA‐binding residues. The electrostatic destabilization of the long α‐helix and a structural communication between the two L20 domains are reminiscent of those observed in calmodulin. The detailed comparison of the two conformations observed in the crystal provides new insights into the role of unfolded extensions in ribosomal assembly.
SERRATE: a new player on the plant microRNA scene
Authors: Lobbes Dajana , Rallapalli Ghanasyam , Schmidt Dominik D , Martin Cathie , Clarke Jonathan
Published: September 2006

MicroRNAs (miRNAs) function as sequence‐specific guides that control gene expression by post‐transcriptional gene silencing. Many miRNAs influence plant development by regulating the accumulation of transcripts that encode transcription factors. Mutants defective in miRNA accumulation, such as dcl1, hen1, hyl1 and ago1, have pleiotropic developmental phenotypes. The serrate‐1 (se‐1) mutant of Arabidopsis also shows a highly pleiotropic phenotype, which overlaps with the phenotypes of mutants defective in miRNA accumulation. Although it has been proposed that SERRATE (SE) functions specifically in miRNA‐mediated repression of the leaf polarity genes PHABULOSA and PHAVOLUTA, microarray analysis shows upregulation of many genes known to be the targets of miRNAs in se‐1. We show that SE is a general regulator of miRNA levels affecting the processing of primary miRNA to miRNA.
Generation of suprathermal electrons and Alfvén waves by a high power pulse at the electron plasma frequency
Authors: Van Compernolle B. , Gekelman W. , Pribyl P.
Published: September 2006

The interaction of a short high power pulse at the electron plasma frequency (f=9GHz, pulse length τ=0.5μs or 2.5μs, input power P<80kW) and a magnetized plasma (n0⩽2×1012cm−3, B0=1–2.5kG, helium) capable of supporting Alfvén waves has been studied. The interaction leads to the generation of field aligned suprathermal electrons and shear Alfvén waves. The experiment was performed both in ordinary mode (O mode) and extraordinary mode (X mode), for different background magnetic fields B0 and different power levels of the incoming microwaves.
Bias annealing: A method for obtaining transition paths de novo
Authors: Hu Jie , Ma Ao , Dinner Aaron R.
Published: September 2006

Computational studies of dynamics in complex systems require means for generating reactive trajectories with minimum knowledge about the processes of interest. Here, we introduce a method for generating transition paths when an existing one is not already available. Starting from biased paths obtained from steered molecular dynamics, we use a Monte Carlo procedure in the space of whole trajectories to shift gradually to sampling an ensemble of unbiased paths. Application to basin-to-basin hopping in a two-dimensional model system and nucleotide-flipping by a DNA repair protein demonstrates that the method can efficiently yield unbiased reactive trajectories even when the initial steered dynamics differ significantly. The relation of the method to others and the physical basis for its success are discussed.
State-to-state rotational transitions in H2+H2 collisions at low temperatures
Authors: Lee Teck-Ghee , Balakrishnan N. , Forrey R. C. , Stancil P. C. , Schultz D. R. , Ferland Gary J.
Published: September 2006

We present quantum mechanical close-coupling calculations of collisions between two hydrogen molecules over a wide range of energies, extending from the ultracold limit to the superthermal region. The two most recently published potential energy surfaces for the H2–H2 complex, the so-called Diep-Johnson (DJ) [J. Chem. Phys. 112, 4465 (2000); 113, 3480 (2000)] and Boothroyd-Martin-Keogh-Peterson (BMKP) [J. Chem. Phys. 116, 666 (2002)] surfaces, are quantitatively evaluated and compared through the investigation of rotational transitions in H2+H2 collisions within rigid rotor approximation. The BMKP surface is expected to be an improvement, approaching chemical accuracy, over all conformations of the potential energy surface compared to previous calculations of H2–H2 interaction. We found significant differences in rotational excitation/deexcitation cross sections computed on the two surfaces in collisions between two para-H2 molecules. The discrepancy persists over a large range of energies from the ultracold regime to thermal energies and occurs for several low-lying initial rotational levels. Good agreement is found with experiment B. Maté et al., [J. Chem. Phys. 122, 064313 (2005)] for the lowest rotational excitation process, but only with the use of the DJ potential. Rate coefficients computed with the BMKP potential are an order of magnitude smaller.
Equation of state and sound velocity of a helium plasma by Thomas-Fermi-Dirac molecular dynamics
Authors: Danel J.-F. , Kazandjian L. , Zérah G.
Published: September 2006

A method combining classical molecular dynamics applied to nuclei and Thomas-Fermi-Dirac theory applied to electrons is used to calculate the thermodynamic properties of an helium plasma. Two densities, corresponding to average electronic radii of 1 and 2 Bohr radii, and several temperatures, corresponding to coupling parameters between 0.1 and 100, are considered. Both pressure and internal energy (with a correction for the regularization of the potential) are obtained. Some derivative quantities and sound velocity are computed by numerical differentiation with a careful evaluation of the truncation error and of the statistical error. Pressure and sound velocity are obtained with relative standard deviations, respectively, of less than 0.3% and 2.5%.
Electron plasmas: Confinement and mode structure in a small aspect ratio toroidal experiment
Authors: Pahari S. , Ramachandran H. S. , John P. I.
Published: September 2006

Toroidal electron plasmas have remained less explored due to their poor confinement properties. Their equilibrium, stability, and confinement properties are therefore not entirely understood and continue to remain a topic of intense ongoing research. Large aspect-ratio theory suggests poor confinement in toroidal devices can be overcome by the application of a radial electric field; this has been verified successfully in some of the recent experiments. In the present paper, we report the longest confinement time without these external forces. Increasing the toroidicity has helped us to generate these forces intrinsically. To this end, a trap to confine electron plasmas has been created in a small aspect-ratio (≈1.6) torus. Electrons after being injected from a thermionic source are seen to remain confined with a purely toroidal magnetic field. The confinement time is far more than known single particle drift time scales. Importantly, it is in the absence of any external electric field, additional rotational transform, and/or magnetic fields, which, although not required, in principle, may appear essential particularly due to their role in improving confinement in some of the recent large aspect-ratio traps. The successful confinement in the small aspect-ratio limit has also led to several interesting observations: the evolution of the confined plasma is marked by an interesting nonlinear (large amplitude), electrostatic wave activity. Coherent, periodic, double peak oscillations result from a low-frequency E×B motion of a toroidal vortex in a plasma that closely leans against the inner wall. As many as 16 highly phase-coherent harmonics with dominant power in m=2 suggest that the mode is not merely a center-of-charge motion. Rather, a strong coupling of modes leads to a novel nonlinear state. The predominant energy is present in the shaping of the electron cloud (m=2) and not in the displacement of the center of charge (m=1) seen in large aspect-ratio traps. The absence of any power-law tail suggests absence of any turbulence, at least on time scales longer than the wall-probe resolution (40ns). The frequency, (around 100kHz at 200G) shows an unusual shear in time: it reduces as the mode evolves, but later increases as the mode dies.
Computer simulation of two new solid phases of water: Ice XIII and ice XIV
Authors: Martin-Conde Maria , MacDowell Luis G. , Vega Carlos
Published: September 2006

N p T Monte Carlo simulations have been performed for two recently discovered solid phases of water which have been denoted as ice XIII and ice XIV C. G. Salzmann et al. [Science311, 1758 (2006)]. Several potential models of water were considered, namely, the traditional SPC/E, TIP4P, and TIP5P and the more recent TIP5P-E, TIP4P-Ew, TIP4P/Ice, and TIP4P/2005 models. Significant differences in density and oxygen-oxygen radial distribution functions are found between the predictions of the SPC/E, TIP5P, and the models of the TIP4P family. The models TIP4P/Ice and TIP4P/2005 provide the best estimates of the density.
Regulation of protein tyrosine phosphatase 4a1, B-cell translocation gene 2, nuclear receptor subfamily 4a1 and diacylglycerol O-acyltransferase 1 by follicle stimulating hormone in the rat ovary
Authors: Schmidt Jonathan , de Avila Jeanene , McLean Derek
Published: September 2006

Ovarian response to follicle stimulating hormone (FSH) and luteinising hormone (LH) leads to the formation of a mature follicle that is eventually ovulated. FSH and LH are essential for this process because they direct changes in somatic cells associated with folliculogenesis by regulating the expression of multiple genes. We hypothesised that genes induced by FSH in rat Sertoli cells would also show hormonal regulation during rat folliculogenesis. The objective of this study was to determine the expression patterns of diacylglycerol O-acyltransferase 1 (Dgat1), nuclear receptor subfamily 4a1 (Nr4a1), an anti-proliferative gene (Btg2) and a protein tyrosine phosphatase (Ptp4a1) in the ovaries of pregnant mare serum gonadotrophin (PMSG)-treated and human chorionic gonadotrophin (hCG)-treated rats. Expression of Dgat1, Nr4a1 and Ptp4a1 was induced in ovaries 4 h post PMSG treatment. When rats were treated with hCG, Dgat1, Nr4a1 and Ptp4a1 expression was induced by 12 h. Expression of Nr4a1 protein increases 12–24 h after induction of gene expression. Nr4a1 protein was observed in the granulosa, theca and luteal cells post PMSG and hCG treatment. These findings should increase our knowledge of mechanisms regulating folliculogenesis and luteinisation and demonstrate the diverse proteins that are important in ovarian function.
Oestrous behaviour and development of preovulatory follicles in goats induced to ovulate using the male effect with and without progesterone priming
Authors: Gonzalez-Bulnes A. , Carrizosa J. A. , Urrutia B. , Lopez-Sebastian A.
Published: September 2006

The objective of the current study was to examine follicular dynamics in goats induced to ovulate by using the male effect with or without progesterone pretreatment. Ten Murciano–Granadina goats were treated with a single dose of 25 mg of progesterone in olive oil on the day of male effect induction (Day 0), whereas ten does remained untreated. Changes in the ovarian follicular population and onset of oestrous behaviour were checked daily from Day 0 to the day on which ovulation was detected by ultrasonography. All of the treated goats and only 20% of control goats (P < 0.001) showed oestrous behaviour between 72 and 96 h after the introduction of bucks. Differences in follicle growth were found between the groups. The control goats exhibiting oestrous behaviour during the first 4 days of ovarian screening and all of the goats treated with progesterone had their preovulatory follicles in growing phase. However, the largest follicles in control does not showing oestrus in these first 4 days were in regressing phase, being necessary for the emergence of new preovulatory follicles from a new follicular wave between Days 6 and 7, for exhibition of oestrous behaviour and subsequent ovulation. In conclusion, the appearance of short luteal phases and delayed ovulation in goats treated with the male effect during seasonal anoestrous depends on the stage of follicle development at the time of buck introduction. A single injection of progesterone stimulates the emergence of a new follicular wave, able to grow and give adequate ovulation after induction of the male effect.
Comparison of protocols for cryopreservation of rhesus monkey spermatozoa by post-thaw motility recovery and hyperactivation
Authors: Nichols S. M. , Bavister B. D.
Published: September 2006

Cryopreservation of spermatozoa is useful for gene banking and for in vitro fertilisation (IVF). This study compared several published cryopreservation techniques to find the most efficient for rhesus macaques. Effectiveness was assessed by sperm longevity (post-thaw motility % and duration) and ability to hyperactivate in response to chemical activators (caffeine, dibutyryl cyclic AMP). Each ejaculate from three males was treated with four published cryopreservation protocols (Seier et al. 1993; Sanchez-Partida et al. 2000; Si et al. 2000; Isachenko et al. 2005). Upon thawing, each sub-sample was incubated either at 37°C in 5% CO2 in air with or without activators or at ~22°C in atmospheric air without activators for 0–24 h. Samples cryopreserved using one method showed zero motility and were not included in the 2 × 2 G-test statistical analysis. The other methods all demonstrated good immediate post-thaw motility rates (68%, 73% and 62% respectively) and underwent capacitation after exposure to activators. Sperm motility in each treatment decreased over time at both temperatures but overall, incubation at 22°C preserved motility better in all three methods. In summary, cryopreservation of rhesus spermatozoa using the method published by Sanchez-Partida et al. or Seier et al. appeared best, potentially supporting gene banking as well as allowing for multiple IVF uses from the same sample.
Reproduction in female swamp wallabies, Wallabia bicolor
Authors: Paplinska Justyna Zofia , Moyle Richard L. C. , Temple-Smith Peter D. M. , Renfree Marilyn B.
Published: September 2006

The swamp wallaby (Wallabia bicolor) is a common, medium-sized, browsing macropodid marsupial that is unique in many ways. Relatively little is known about the reproductive biology of this species. Previous studies have proposed that the swamp wallaby has a pre-partum oestrus because the gestation period (

x
¯

-->x = 35.5 days, n = 4) is on average longer than the oestrus period (

x
¯

-->x = 31.0 days, n = 5) and the period from the removal of pouch young (RPY) to mating (

x
¯

-->x = 26.0days, n = 3). In the current study, the period from RPY to birth was confirmed at

x
¯

-->x = 31.25 days (n = 4) in captive animals, consistent with a pre-partum oestrus. A growth curve for swamp wallaby pouch young was constructed from the progeny of captive animals to estimate the age and date of birth of young in a wild, culled population in South Gippsland, Victoria, and the reproduction of females in the wild throughout the year was examined. Young were born in every month of the year, with no statistically significant variation in the number of young born in each month. Females did not have a period of seasonal anoestrus and conceived throughout the year. Female swamp wallabies in South Gippsland bred continuously throughout the period of this study.
Sperm DNA damage is related to field fertility of semen from young Norwegian Red bulls
Authors: Waterhouse K. E. , Haugan T. , Kommisrud E. , Tverdal A. , Flatberg G. , Farstad W. , Evenson D. P. , De Angelis P. M.
Published: September 2006

Flow cytometry was utilised for the first time to independently measure five sperm parameters of individual spermatozoa of bull ejaculates to differentiate between outcome successes after artificial insemination (AI). These parameters included plasma membrane and acrosome integrity, mitochondrial functionality and DNA damage measured by sperm chromatin structure assay (SCSA) and terminal deoxynucleotide transferase-mediated dUTP nick end labelling (TUNEL) assays. For each parameter, results of 142 ejaculates (30 bulls) were ranked into three groups according to their flow cytometric measures: (1) ejaculates with the 25% lowest measures; (2) the 50% middle measures; and (3) the 25% highest measures. In total, 20 272 first-service inseminations (18 × 106 spermatozoa per AI dose) were performed, where fertility was defined as non-return within 60 days after first insemination. While plasma membrane and acrosome integrity, and mitochondrial functionality were not significantly related to fertility, data from SCSA and TUNEL assays were significantly associated with fertility. Ejaculates in SCSA group 1 had higher odds of AI success (1.07, 95% CI = 1.02–1.12), whereas those in group 3 had lower odds of AI success (0.94, 95% CI = 0.89–0.99), compared with the average odds of all three groups. Ejaculates in group 2 did not have significantly higher odds of AI success compared with the average odds. For TUNEL-positive spermatozoa, the odds of AI success was higher in group 1 compared with the average odds (1.10, 95% CI = 1.02–1.13), whereas odds of AI success in groups 2 and 3 were not significant compared with the average odds. In conclusion, despite the high number of spermatozoa per AI dose from high-quality bulls, both SCSA and TUNEL assays were valuable measures in this study for evaluating sperm quality in relation to fertility after AI.
Effects of amino acid supplements and replacement of polyvinyl alcohol with bovine serum albumin in porcine zygote medium
Authors: Suzuki Chie , Yoshioka Koji
Published: September 2006

The effects of glutamine, hypotaurine, taurine and premixed solutions of essential amino acids (EAA) and non-essential amino acids (NEAA) on in vitro development of porcine zygotes were evaluated. The effects of refreshing the medium and replacing polyvinyl alcohol (PVA) with bovine serum albumin (BSA) on embryonic development were also investigated. Porcine zygotes produced by in vitro maturation (IVM) and in vitro fertilisation (IVF) were cultured in porcine zygote medium (PZM), as the basal culture medium, for 5 days after IVF. The total number of cells in blastocysts was significantly increased by the addition of 2 mm glutamine to PZM, as was blastocyst yields after supplementation with 0.25 to 4 mm glutamine. Addition of 1.25 to 10 mm hypotaurine to PZM significantly increased blastocyst yields. Addition of 5 mm taurine to PZM significantly increased blastocyst yield, whereas taurine had no effect on blastocyst yield in cultures already containing 5 mm hypotaurine. Adding 1× EAA significantly increased the rate of blastocyst formation compared with no or 2× EAA, whereas 2× NEAA significantly increased the total cell numbers in blastocysts compared with no NEAA. Refreshing the medium at Day 3 had no effect on blastocyst yields, whereas medium change significantly reduced the total cell numbers in blastocysts. Adjusting the amino acid concentrations of a chemically defined medium can improve the developmental competence of porcine embryo.
Variation of sperm head shape and tail length in a species of Australian hydromyine rodent: the spinifex hopping mouse, Notomys alexis
Authors: Bauer M. , Breed W. G.
Published: September 2006

In Australia, there are around 60 species of murid rodents that occur in the subfamily Hydromyinae, most of which produce highly complex, monomorphic, spermatozoa in which the head has an apical hook together with two ventral processes containing filamentous actin and a long tail of species-specific length. One of the few exceptions to this is the spinifex hopping mouse, Notomys alexis, whose spermatozoa have previously been shown to have pleiomorphic heads. In this study, the structural organisation of the sperm head has been investigated in more detail and the variability in length of the midpiece and total length of the sperm tail has been determined for this species. The findings confirm that pleiomorphic sperm heads are invariably present in these animals and that this variability is associated with that of the nucleus, although nuclear vacuoles were not evident. The total length of the sperm tail, as well as that of the midpiece, was also highly variable both within, as well as between, individual animals. The reason(s) for this high degree of variability in sperm morphology is not known but it may relate to a relaxation of the genetic control of sperm form owing to depressed levels of inter-male sperm competition.
Society for Reproductive Biology Founders' Lecture 2006 Life in the pouch: womb with a view
Authors: Renfree Marilyn B.
Published: September 2006

Marsupials give birth to an undeveloped altricial young after a relatively short gestation period, but have a long and sophisticated lactation with the young usually developing in a pouch. Their viviparous mode of reproduction trades placentation for lactation, exchanging the umbilical cord for the teat. The special adaptations that marsupials have developed provide us with unique insights into the evolution of all mammalian reproduction. Marsupials hold many mammalian reproductive ‘records’, for example they have the shortest known gestation but the longest embryonic diapause, the smallest neonate but the longest sperm. They have contributed to our knowledge of many mammalian reproductive events including embryonic diapause and development, birth behaviour, sex determination, sexual differentiation, lactation and seasonal breeding. Because marsupials have been genetically isolated from eutherian mammals for over 125 million years, sequencing of the genome of two marsupial species has made comparative genomic biology an exciting and important new area of investigation. This review will show how the study of marsupials has widened our understanding of mammalian reproduction and development, highlighting some mechanisms that are so fundamental that they are shared by all today’s marsupial and eutherian mammals.
Field and laboratory study of pesticide leaching in a Motupiko silt loam (Nelson) and in a Waikiwi silt loam (Southland)
Authors: Close M. E. , Sarmah A. K. , Flintoft M. J. , Thomas J. , Hughes B.
Published: September 2006

Selected pesticides were applied to a Motupiko silt loam located near Wakefield, Nelson, and a Waikiwi silt loam located near Invercargill, Southland, New Zealand, along with bromide as a tracer. Atrazine, bromacil, diazinon, hexazinone, and terbuthylazine were applied to both sites, with procymidone also being applied to the Nelson site, and trifluralin being applied to the Southland site. The persistence and transport behaviour of these compounds were monitored for 15 months using a combination of soil sampling down to a maximum of 1 m and 8 suction cups at each site located between 0.2 and 1.3 m down the profile. The bromide tracer had moved below 0.8 m within 9 months at the Nelson site and below 1.0 m within 12 months at the Southland site. Hexazinone was the most mobile of the pesticides, followed by bromacil at both sites. Diazinon and atrazine dissipated rapidly at both sites, while trifluralin and, to a lesser extent, terbuthylazine and bromacil data indicated some volatilisation losses. The diazinon removal was probably a combination of degradation and volatilisation. There was evidence of some preferential flow at the Southland site, as rainfall was heavy at the time of pesticide application. The Koc values from the sorption isotherms were generally similar to literature values for the Waikiwi soil but were much higher for the Motupiko soil. The exception was diazinon, for which the Koc values were much lower than the literature values for both sites.
The sorption and degradation of the rice pesticides fipronil and thiobencarb on two Australian rice soils
Authors: Doran Gregory , Eberbach Philip , Helliwell Stuart
Published: September 2006

The sorption and degradation of the rice pesticides fipronil and thiobencarb on 2 Australian rice-growing soils were investigated. Greater sorption of both pesticides occurred on the soil containing less organic carbon, possibly as a result of the type of organic carbon present, rather than the absolute amount. While sorption tended to appear greater in the 0–10 mm layer than the 10–20 mm layer, analysis showed the difference was not significant (P > 0.05). Under aerobic conditions, a lag period of 20 days in the degradation of thiobencarb occurred on the Yanco soil, but rapid degradation occurred on the Coleambally soil, and, while unlikely, may have been a consequence of preconditioning of the Coleambally soil microbial population. Degradation of thiobencarb under both non-flooded anaerobic and flooded anaerobic conditions differed significantly (P < 0.05) compared to aerobic conditions. Conversely, fipronil degraded rapidly over the first few days and then slowed, and was attributed to the co-metabolism of fipronil by soil microbes. While fipronil sulfide was produced under all oxic/anoxic conditions, its concentration was greatest under flooded anaerobic conditions, possibly as a result of greater exclusion of oxygen from the soil by the floodwater.
Long-term effects of crop rotation, stubble management and tillage on soil phosphorus dynamics
Authors: Bünemann E. K. , Heenan D. P. , Marschner P. , McNeill A. M.
Published: September 2006

The effects of various management practices on soil phosphorus (P) dynamics were investigated in a field experiment in New South Wales, Australia, during 24 years of different crop rotation, stubble management, and tillage treatments. Topsoil samples collected at the beginning of the trial and after 6, 12, 18, and 24 years were analysed for resin-extractable P, inorganic and organic P, and total P. According to the calculated P input–output budget, 9–14 of the 20 kg P/ha added as superphosphate annually remained in the system, depending on the treatment. The measured increase in total P in 0–0.20 m did not differ between treatments, showing an accumulation rate of only 9 ± 2 kg P/ha.year. These results suggest a loss of 4 ± 2 kg P/ha.year, presumably into lower soil layers. Resin-extractable P at 0–0.10 m increased by 1.7 kg P/ha.year, irrespective of the treatment. The increase in total P after 24 years was almost completely accounted for by the increase in total extractable inorganic P. Changes in organic P paralleled changes in organic carbon, with a significant loss in treatments with stubble burning (wheat–lupin rotation and continuous wheat), and a significant accumulation in a wheat–subterranean clover rotation with stubble retention and direct drilling. We conclude that on the time scale of this experiment, the dynamics of carbon and organic P are closely linked.
Minimising off-site movement of contaminants in furrow irrigation using polyacrylamide (PAM). II. Phosphorus, nitrogen, carbon, and sediment
Authors: Oliver Danielle P. , Kookana Rai S.
Published: September 2006

Off-site movement of nutrients and sediment from furrow-irrigated agriculture has been a concern in the Ord River Irrigation Area, Western Australia. After consultation with growers, a range of management strategies were tested to assess the effectiveness of various practices to minimise off-site movement of nutrients during irrigation. This paper reports on the effectiveness of the additions of high molecular weight, anionic, polyacrylamide (PAM) to irrigation water to minimise off-site movement of phosphorus, nitrogen, carbon, and sediment. Surface runoff water quantity and quality from 4 separate irrigation bays, which contained 25 furrows per irrigation bay, was monitored over time for a single irrigation 35 days after sowing.
Addition of PAM as a puck (cylindrical disc 55 mm diameter by 23 mm height) to the head of each irrigation furrow significantly (P < 0.001) decreased the average volume of surface runoff water leaving the irrigation bays by 54%, from 599 kL for the control irrigation bays to 277 kL for the PAM-treated irrigation bays. The addition of PAM also significantly (P < 0.001) decreased the average total suspended sediment load for the duration of the irrigation from 94.9 kg/ha for the control bays to 13.4 kg/ha for the PAM-treated irrigation bays. The concentrations of the different forms of N, P, and C measured in the runoff water were not significantly different between the 2 treatments. The amounts (g) of particulate (>0.45 µm) P and dissolved organic C were significantly (P < 0.01) less from the PAM-treated bays than from the control bays.
There was a consistent trend for the addition of PAM to decrease the cumulative mass loss of all nutrients (N, P, and C) measured. However, significant decreases were only seen for particulate (>0.45 µm) P (by 94%), unfiltered (or total) N (by 56%), and unfiltered (or total) C (by 60%). This experiment demonstrated that the addition of PAM to irrigation waters has the potential to decrease the off-site movement of nutrients bound to colloidal material. However, in this study off-site movement of contaminants present in the ‘soluble’ (<0.45 µm) fraction is unlikely to be mitigated by the addition of PAM to irrigation water. The mode of application of PAM, however, may affect water infiltration and hence vertical movement of ‘soluble’ contaminants and requires further investigation to ensure that while off-site surface transport is being minimised, contamination of groundwater is not being increased. Other strategies to minimise off-site movement for contaminants in the dissolved phase also need investigation.
Rainfall salt accessions in the Queensland Murray - Darling Basin
Authors: Biggs A. J. W.
Published: September 2006

Two east–west transects were established in southern Queensland to quantify rainfall inputs of chloride and associated ions. Electrical conductivity, pH, and major and minor ions were measured at 9 sites within the Queensland Murray–Darling Basin and 1 site to the east. Variability at some sites was high, possibly a function of the sample collection method. Ionic concentrations decreased with distance inland, a trend similar to that observed elsewhere in Australia, although values closer to the coast were higher than observed in southern and western Australia. Equations to predict both annual average rainfall chloride mass deposition and total salt deposition were derived.
Changes on chemical fractions of heavy metals in Chilean soils amended with sewage sludge affected by a thermal impact
Authors: Antilén Mónica , Araya Nadia , Briceno Margarita , Escudey Mauricio
Published: September 2006

Forest fires are frequent in central-southern Chile; high temperatures may affect chemical fractions of heavy metals (Cu, Zn, Ni, Pb, Cd, Mo, Cr, and Mn) naturally present in soils and those coming from sewage sludge amendment. Changes in exchangeable, sorbed, organic, carbonate, and residual heavy metals fractions, evaluated by sequential extraction, were observed after heating at 400°C in 2 amended volcanic soils.
Most significant heavy metals in these samples were Cu, Zn, Pb, and Ni. A significant increment in the total content of organic matter and metal ions, such as Zn and Cu, was observed in amended soils with respect to controls. In all samples, sorbed and exchangeable forms represent <10% of the total amount, while organic and carbonate fractions represent 24 and 48%, respectively. The thermal treatment of amended soil samples results in a redistribution of the organic fraction, mainly into more insoluble carbonate and residual fractions such as oxides. Finally, the thermal impact is much more important on sewage sludge amended soils if a heavy metal remediation process is considered, reducing the mobility and solubility of heavy metals supported by sewage sludge, minimising leaching and promoting accumulations in surface horizons.
Quantitative phase tomography of
Arabidopsis
seeds reveals intercellular void network
Authors: Cloetens Peter , Mache Régis , Schlenker Michel , Lerbs-Mache Silva
Published: September 2006

We used quantitative phase tomography with synchrotron radiation to elucidate the 3D structure of
Arabidopsis
seeds in their native state. The cells are clearly distinguished, and their internal structure is revealed through local variations in electron density. We visualized a 3D network of intercellular air space that might allow immediate gas exchange for energy supply during germination and/or serve for rapid water uptake and distribution during imbibition.
First-principles, quantum-mechanical simulations of electron solvation by a water cluster
Authors: Herbert John M. , Head-Gordon Martin
Published: September 2006

Despite numerous experiments and static electronic structure calculations, the nature of hydrated-electron clusters, (H
2
O)

n

−
, remains poorly understood. Here, we introduce a hybrid
ab initio
molecular dynamics scheme, balancing accuracy against feasibility, to simulate vibrational and photoelectron spectra of (H
2
O)

n

−
, treating all electrons quantum-mechanically. This methodology provides a computational tool for understanding the spectra of weakly bound and supramolecular anions and for elucidating the fingerprint of dynamics in these spectra. Simulations of (H
2
O)

4

−
provide quantitative agreement with experimental spectra and furnish direct evidence of the nonequilibrium nature of the cluster ensemble that is probed experimentally. The simulations also provide an estimate of the cluster temperature (
T
≈ 150–200 K) that is not available from experiment alone. The “double acceptor” electron-binding motif is found to be highly stable with respect to thermal fluctuations, even at
T
= 300 K, whereas the extra electron stabilizes what would otherwise be unfavorable water configurations.
Genome reduction inLeptospira borgpeterseniireflects limited transmission potential
Authors: Bulach Dieter M. , Zuerner Richard L. , Wilson Peter , Seemann Torsten , McGrath Annette , Cullen Paul A. , Davis John , Johnson Matthew , Kuczek Elizabeth , Alt David P. , Peterson-Burch Brooke , Coppel Ross L. , Rood Julian I. , Davies John K. , Adler Ben
Published: September 2006

Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. Most infections are caused by eitherLeptospira borgpeterseniiorLeptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. We report the complete genomic sequences of two strains ofL. borgpeterseniiserovar Hardjo that have distinct phenotypes and virulence. These two strains have nearly identical genetic content, with subtle frameshift and point mutations being a common form of genetic variation. Starkly limited regions of synteny are shared between the large chromosomes ofL. borgpeterseniiandL. interrogans, probably the result of frequent recombination events between insertion sequences. TheL. borgpeterseniigenome is ≈700 kb smaller and has a lower coding density thanL. interrogans, indicating it is decaying through a process of insertion sequence-mediated genome reduction. Loss of gene function is not random but is centered on impairment of environmental sensing and metabolite transport and utilization. These features distinguishL. borgpeterseniifromL. interrogans, a species with minimal genetic decay and that survives extended passage in aquatic environments encountering a mammalian host. We conclude thatL. borgpeterseniiis evolving toward dependence on a strict host-to-host transmission cycle.
RETRACTED: The herpesvirus glycoproteins B and H·L are sequentially recruited to the receptor-bound gD to effect membrane fusion at virus entry
Authors: Gianni Tatiana , Forghieri Cristina , Campadelli-Fiume Gabriella
Published: September 2006

Four glycoproteins (gD, gB, gH, and gL) are required for herpes simplex virus entry into the cell or for cell–cell fusion in transfected cells. gD serves as the receptor-binding glycoprotein and as the trigger of fusion; the other three execute fusion between the viral envelope and the plasma and endocytic membranes or the membranes of adjacent cells and are highly conserved among members of the herpesvirus family. Details of the interaction of gD with gB, gH, and gL were not known. Here, we report that the four glycoproteins assemble into a complex initiated by the interaction of gD with its cellular receptor. gB is recruited to the gD–receptor complex next, even in the absence of gH·gL. gH·gL is recruited next, but only to the receptor–gD–gB ensemble. A complex with the composition receptor–gD–gB–gH·gL is assembled transiently with a life span of 15–30 min in cells exposed to virus but can also be found in infected cells and in cells committed to form polykaryocytes after transfection of the glycoprotein quartet. The results indicate that the complex assembly is a critical step in the process of virus entry and fusion, and that no viral protein other than those that participate in the complex itself is required for complex assembly. These findings imply critical protein–protein interactions among the quartet as herpes simplex virions enter the cells and at cell–cell fusion, define a specific order of recruitment, and place gH·gL as the last link in the process of glycoprotein recruitment to the complex.