bluuebunny/crossref_metadata_2025 huggingface dataset:
Case work during the Summer Study Week on ‘Extra‐tropical Cyclones’
Authors: Hewson T D
Published: July 2002

A brief account is given of the case work undertaken as part of the Summer Study Week on ‘Extra‐tropical Cyclones' held in Reading during July 1996. It is shown that different approximate methods of assessing synoptic‐scale vertical velocity can give widely differing results. Computation of the full quasi‐geostrophically forced vertical velocity is recommended as a more informative procedure. Forecasts for the track of an explosively deepening north Atlantic cyclone are compared at different lead times. The comparison encompasses raw model forecasts and model forecasts adjusted by groups of case work participants. The groups achieved a large improvement over a model forecast at the 2–3 day lead time, but only marginal improvements thereafter. It is suggested that improved understanding of development mechanisms would enable the forecaster to appreciate better the range of possible outcomes in cyclogenetic situations. Copyright © 1997 Royal Meteorological Society
How significant is the usual assumption of neutral stability in evapotranspiration estimating models?
Authors: Anadranistakis M , Kerkides P , Liakatas A , Alexandris S , Poulovasilis A
Published: July 2002

The significance of the atmospheric stability approach in models for estimating evapotranspiration is studied by considering the errors encountered when simply adopting neutral instead of actual stability conditions. Maize, cotton and wheat crops grown in 10 hectare fields (central Greece) were used to estimate actual and maximum evapotranspiration for both stability considerations, employing a model based on the equations of Shuttleworth & Wallace (1985). The required meteorological data were recorded in each field continuously, whereas the leaf area index and the plant height were measured weekly. Results show that when estimation of cumulative evapotranspiration losses is attempted, the choice of the atmospheric stability approach is of no importance (error ≤ 2), as over‐ and underestimation of evapotranspiration are counterbalanced when stable and unstable situations are (under the climatic conditions of experimentation) successively interchanged during the cultivating period. When, however, daily estimations are required, the actual stability conditions have to be taken into account, as the daily evapotranspiration rate estimated by regarding the atmospheric stability as neutral may deviate from the corresponding ‘actual’ rate by as much as 50 – 80%. Copyright © 1999 Royal Meteorological Society
An assessment of three automatic depression tracking schemes
Authors: Leonard S R , Turner J , Van Der Wal A
Published: July 2002

The performance of three automatic depression tracking schemes developed by Terry & Atlas (1996), Murray & Simmonds (1991a) and Konig et al. (1993) when applied over one month are assessed. The schemes respectively identify depressions by (a) locating the innermost closed contour in a PMSL field, (b) finding maxima in the curvature in a bi‐cubic spline fitted to the PMSL data and (c) performing a grid point search to identify a minimum in a PMSL field. The largest number of depressions was found by the Murray and Simmonds scheme, with the Atlas and Terry scheme finding the least. The Murray and Simmonds scheme also found the largest number of tracks, with the other two having comparable numbers of tracks. Two possible explanations for the differences in the number of tracks are considered. Firstly, the case where one or more centres identified by one scheme as corresponding to a single track are not found by the other schemes. Secondly, the case where a single track found by one scheme is split into two or more tracks by the other schemes. All three techniques had a similar latitude of cyclogenesis, although the Atlas and Terry and Konig et al. schemes found more lows at high latitudes as a result of using data on a latitude/longitude grid. The longest mean track length was found with the Konig et al. scheme. A comparison of the PMSL fields with satellite imagery shows that the major NWP centres have trouble producing reliable analyses around the Antarctic because of the lack of data. Copyright © 1999 Royal Meteorological Society
Mid‐troposphere variables and their association with daily local precipitation
Authors: Ruiz N E , Vargas W M , Ciappesoni H H
Published: July 2002

This paper describes the meteorological variables directly affecting precipitation in the southern region of South America. Results show the relationships between daily precipitation at Ezeiza, Buenos Aires, and 500 mb dynamic variables (e. g. geopotential heights, relative geostrophic vorticity and its advection, vorticity tendency and zonal and meridional geostrophic wind components) using regional synoptic analyses from the Servicio Meteorológico Nacional of Argentina for 1986. The distribution of significant biserial correlation coefficients reveals the preferred positions for the anomalous wind components which favour the occurrence of rainfall at Ezeiza. In the same way, spatial distributions and temporal lag relations of 500 mb relative vorticity anomalies in relation to precipitation show the positions and relative movement of centres of anomalously cyclonic and anticyclonic vorticity which increase the probability of precipitation at Buenos Aires. Vorticity advection does not yield higher correlations, at least in a daily temporal scale. The geographical distribution of temporal means and standard deviations of geopotential heights and zonal and meridional wind components at the 500 mb level are also shown. Copyright © 1999 Royal Meteorological Society
PET – a platform for experimentation with
efficient HPSG processing techniques
Authors: CALLMEIER ULRICH
Published: July 2002

The PET platform for experimentation with hpsg processing and implementation techniques
is introduced. PET provides an extendible set of building blocks for the implementation of
efficient processors. This enables straightforward comparison of different approaches, rapid
development of new techniques and easy synthesis of known techniques. An overview of the
basic design is given and key aspects of the implementation are discussed. Early empirical
results on the three standard test sets for the LinGO grammar are given. Two improved
expansion strategies are evaluated empirically. The results of fine tuning the quick check
filtering method through empirical study are discussed as an exemplar of the proposed
experimental approach to the development and optimization of processing techniques. An
overview of the progress in processing the LinGO grammar made over a development period
of three years is given.
Differential effects of left and right cerebral vascular
accidents on language competency
Authors: BRYAN KAREN L. , HALE JAMES B.
Published: July 2002

While language facility was once considered to be the sole
province of the “dominant” left hemisphere, clinical
and experimental findings suggest the right hemisphere plays
an equally important role in many language tasks. To elucidate
differential hemispheric language processes, Right Hemisphere
Language Battery and Western Aphasia Battery data from left
(LHD) and right (RHD) hemisphere cerebral vascular accident
(CVA) patients and controls were subjected to multivariate
discriminant analysis. The highly significant group differences
and overall 95% classification rate obtained confirms the utility
of the dependent measures in differential diagnosis. Results
suggest CVA patients experience disparate language deficits,
with the LHD group experiencing concordant-convergent language
deficits and the RHD group displaying discordant–divergent
deficits that interfere with the receptive and expressive language
skills necessary for successful social discourse. (JINS,
2001, 7, 655–664.)
Accounting for the distributional impacts of policy in the green accounts
Authors: HORAN RICHARD D. , HRUBOVCAK JAMES , SHORTLE JAMES S. , BULTE ERWIN H.
Published: July 2002

Green income accounting models are designed to appropriately value changes in a country's natural resource (natural capital) base. However, green NNP is useful as a guide for domestic and international policy only to the extent that it accurately reflects the economic goals and policy options of policy makers. For example, international policy designed to slow natural capital depletion in a developing country is more effective if policy makers recognize the developing country's perceived income effects of the policy. Traditional green accounting models do not satisfy this criterion because they are based on the assumption that policy makers are either not concerned with the distributional consequences of policies, and/or are not limited in the instruments available to them. We present an alternative green NNP measure that reflects distributional goals and policy implementation. Using this measure, the depletion (accumulation) of natural capital stocks in excess of economically efficient rates may increase income.
Environmental considerations in tax policy design
Authors: WHALLEY JOHN
Published: July 2002

This paper discusses how environmental considerations will affect tax policy in the decades ahead. It argues that, in the future, interactions between tax and environmental policy are likely to go well beyond recent discussion of double divided issues, and that internalization of environmental externalities via tax policy will be the goal, which inevitably will involve the particular rather than the general. As a result, notions of neutrality which dominate current thinking on tax design will come under challenge; and in ways which will go well beyond current discussion of special treatment for particular goods and industries on environmental grounds. special treatment of environmentally harmful methods of production, more so than of goods and industries as under present tax policies, will be the name of the game. Moreover, the informational requirements of such an approach to tax policy are likely to be large. The paper concludes by pointing out that if environmental quality is a luxury good, as many suppose, with income elasticity of demand greater than one, then high income households will gain disproportionately from internalization of the externalities at issue. This may fuel pressures for more redistribution elsewhere in the tax system than is currently the case.
Interpolator: a two-dimensional graphical interpolation system for the simultaneous control of digital signal processing parameters
Authors: Spain Martin , Polfreman Richard
Published: July 2002

The musical use of realtime digital audio tools implies the need for simultaneous control of a large number of parameters to achieve the desired sonic results. Often it is also necessary to be able to navigate between certain parameter configurations in an easy and intuitive way, rather than to precisely define the evolution of the values for each parameter. Graphical interpolation systems (GIS) provide this level of control by allocating objects within a visual control space to sets of parameters that are to be controlled, and using a moving cursor to change the parameter values according to its current position within the control space. This paper describes Interpolator, a two-dimensional interpolation system for controlling digital signal processing (DSP) parameters in real time.
An intelligent hybrid model for chord prediction
Authors: CUNHA URAQUITAN SIDNEY , RAMALHO GEBER
Published: July 2002

For a system to be able to generate realtime accompaniment to
previously unknown songs, it must predict their harmonic development,
i.e. the chords to be played. We claim that such a system must combine
long-term experience, to identify typical chord sequences (e.g. II–V
and II–V–I), with ‘on-the-fly’ adaptation to
track-recurrent structures (e.g. choruses and refrains) of the particular
song being played. We have implemented a prediction system using a neural
network model that encompasses prior knowledge about typical chord
sequences. The results achieved are very encouraging, and rather better
than those reported in the literature. However, our predictor could not
adapt its behaviour to the idiosyncrasies of each song, since online
learning is difficult in neural networks. In this paper, we propose an
extension to our previous work by the inclusion of a rule-based sequence
tracker, which detects recurrent chord sequences while the song is being
performed. We show that this hybrid model, which combines a neural network predictor with a rule-based sequence tracker, improves the
system's performance.
Needs Assessment of Children and Adolescents
Authors: Kroll Leopold , Harrington Richard , Bailey Susan
Published: July 2002

Needs assessment is a frequently used term by all agencies involved in the
welfare of children and adolescents, and is a key method in health service
planning (Stevens & Raftery, 1994). However, there is often a lack of
clarity about the meaning of the phrase ‘needs assessment’ (Cohen &
Eastman, 1997). In addition, for CAMHS services there are few established
research or clinical instruments to assess the needs of individuals. This
review sets out first to describe some key concepts and issues and, second,
to describe the development of a needs assessment instrument for
adolescents with complex and multiple problems, and how such an
instrument can be used in clinical and research settings.
Beyond the Phonological Deficit Hypothesis
Authors: Seymour Philip H. K.
Published: July 2002

Snowling and Coltheart and Jackson provide an excellent
overview of the contemporary cognitive and linguistic
approach to the description and definition of dyslexia.
Both contributors consider dyslexia to be a disorder of
written language. Snowling focuses on the origins of the
difficulty in a central ‘phonological deficit’. Coltheart and

Jackson emphasise the internal modular structure of the
reading and spelling systems, suggesting that different
components may be impaired in different individuals,
resulting in distinctive (phonological and surface) patterns
of dyslexia. Both conclude that future research might
focus on implications for effective programmes of treatment.
The Munich Rent Advisor: A success for logic programming on then Internet
Authors: FRÜHWIRTH THOM , ABDENNADHER SLIM
Published: July 2002

Most cities in Germany regularly publish a booklet called the Mietspiegel. It basically contains
a verbal description of an expert system. It allows the calculation of the estimated fair rent for
a flat. By hand, one may need a weekend to do this task. With our computerized version, the
Munich Rent Advisor, the user just fills in a form in a few minutes, and the rent is calculated
immediately. We also extended the functionality and applicability of the Mietspiegel so that
the user need not answer all questions on the form. The key to computing with partial
information using high-level programming was to use constraint logic programming. We rely
on the Internet, and more specifically the World Wide Web, to provide this service to a broad
user group, the citizens of Munich and the people who are planning to move to Munich. To
process the answers from the questionnaire and return its result, we wrote a small simple
stable special-purpose web server directly in ECLiPSe. More than 10,000 people have used
our service in the last three years. This article describes the experiences in implementing and
using the Munich Rent Advisor. Our results suggest that logic programming with constraints
can be an important ingredient in intelligent internet systems.
Active repression and E2F inhibition by pRB are biochemically distinguishable
Authors: Ross John F. , Näär Anders , Cam Hieu , Gregory Richard , Dynlacht Brian David
Published: July 2002

To understand mechanistically how pRB represses transcription, we used a reconstituted transcription assay and compared pRB activity on naked versus chromatin templates. Surprisingly, when pRB was directly recruited to a naked template, no transcriptional repression was observed. However, we observed active repression when the same promoter was assembled into chromatin. Histone deacetylases do not appear to play a role in this observed repression. Further experiments showed repression could occur after preinitiation complex assembly, in contrast with pRB inhibition of E2F, suggesting discrete mechanisms by which pRB directly inhibits an activator such as E2F or actively represses proximally bound transcription factors.
HOBACGEN: Database System for Comparative Genomics in Bacteria
Authors: Perrière Guy , Duret Laurent , Gouy Manolo
Published: July 2002

We present here HOBACGEN, a database system devoted to comparative genomics in bacteria. HOBACGEN contains all available protein genes from bacteria, archaea, and yeast, taken from SWISS-PROT/TrEMBL and classified into families. It also includes multiple alignments and phylogenetic trees built from these families. The database is organized under a client/server architecture with a client written in Java, which may run on any platform. This client integrates a graphical interface allowing users to select families according to various criteria and notably to select homologs common to a given set of taxa. This interface also allows users to visualize multiple alignments and trees associated to families. In tree displays, protein gene names are colored according to the taxonomy of the corresponding organisms. Users may access all information associated to sequences and multiple alignments by clicking on genes. This graphic tool thus gives a rapid and simple access to all data required to interpret homology relationships between genes and distinguish orthologs from paralogs. Instructions for installation of the client or the server are available at http://pbil.univ-lyon1.fr/databases/hobacgen.html.
Comparative Genome Analysis of the Mouse Imprinted GeneImpactand Its Nonimprinted Human HomologIMPACT:Toward the Structural Basis for Species-Specific Imprinting
Authors: Okamura Kohji , Hagiwara-Takeuchi Yuriko , Li Tao , Vu Thanh H. , Hirai Momoki , Hattori Masahira , Sakaki Yoshiyuki , Hoffman Andrew R. , Ito Takashi
Published: July 2002

MouseImpactis a paternally expressed gene encoding an evolutionarily conserved protein of unknown function. Here we identifiedIMPACT, the human homolog ofImpact, on chromosome 18q11.2–12.1, a region syntenic to the mouseImpactlocus.IMPACTwas expressed biallelically in brain and in various tissues from two informative fetuses and in peripheral blood from an informative adult. To reveal the structural basis for the difference in allelic expression between the two species, we elucidated complete genome sequences for both mouseImpact(∼38 kb) and humanIMPACT(∼30 kb). Sequence comparison revealed that the two genes share a well-conserved exon–intron organization but bear significantly different CpG islands. The mouse island lies in the first intron and contains characteristic tandem repeats. Furthermore, this island serves as a differentially methylated region (DMR) consisting of a hypermethylated maternal allele and an unmethylated paternal allele. Intriguingly, this intronic island is missing from the nonimprinted humanIMPACT, whose sole CpG island spans the first exon, lacks any apparent repeats, and escapes methylation on both chromosomes. These results suggest that the intronic DMR plays a role in the imprinting ofImpact.

[The sequence data described in this paper have been submitted to the DDBJ/EMBL/GenBank data library under accession nos.AB026264,AF232228, andAF232229.]
Revisiting the Maturation of Medial Temporal Lobe Memory Functions in Primates
Authors: Alvarado Maria C. , Bachevalier Jocelyne
Published: July 2002

In a review of the literature on the development of the medial temporal lobe region in humans, monkeys, and rodents, Bachevalier and Beauregard indicated that in primates, memory functions subserved by this neural system emerge early in life and increment gradually with further postnatal maturation. Furthermore, they stated that the late-developing memory functions of normal neonates was more likely owing to the slow maturation of the association areas of the cortex than to the slow maturation of the hippocampal formation. This conclusion was based on the limited knowledge concerning the development of hippocampal-dependent memory functions and the maturational events in the medial temporal lobe of monkeys. Over the last decade, however, more information has accumulated about the structural, functional, and behavioral changes occurring throughout ontogeny in monkeys that suggest a refinement of this view. Whereas there is still much to be discovered, we thought it timely to put into perspective the latest findings in hope of shedding light on memory development in general, and particularly, on the role of medial temporal lobe structures in infant and adult memory. [Note: Hippocampal formation refers to the hippocampus proper (Ammon's fields), dentate gyrus, and subicular complex. Hippocampal region refers to the hippocampal formation and the adjacent entorhinal, perirhinal, and parahippocampal cortex.]
Identification and Characterization of a Novel Arabinoxylanase from Wheat Flour
Authors: Cleemput G. , Van Laere K. , Hessing M. , Van Leuven F. , Torrekens S. , Delcour J. A.
Published: July 2002

An endogenous wheat (Triticum aestivum) flour endoxylanase was purified to homogeneity from a crude wheat flour extract by ammonium sulfate precipitation and cation-exchange chromatography. The 30-kD protein had an isoelectric point of 9.3 or higher. A sequence of 19 amino acids at the NH2 terminus showed 84.2% identity with an internal sequence of the 15-kD grain-softness protein, friabilin. High-performance anion-exchange chromatography and gel-permeation analysis of the hydrolysis products indicated the preferential hydrolysis of highly branched structures by the enzyme; wheat arabinoxylan and rye (Secale cereale) arabinoxylan (high arabinose to xylose ratios) were hydrolyzed more efficiently by this enzyme than oat (Avena sativa) spelt xylan (low arabinose to xylose ratios). The release of the hydrolysis products as a function of time suggested that the endoxylanolytic activity was associated with the release of arabinose units from the polysaccharides, suggesting that the enzyme action is similar to that by endoxylanases from Ceratocystis paradoxa, Aspergillus niger, and Neurospora crassa. Although the enzyme released arabinose from arabinoxylan, it did not hydrolyze p-nitrophenyl-α--L-arabinofuranoside. From the above, it follows that the enzyme, called arabinoxylanase, differs from most microbial endoxylanases and from an endoxylanase purified earlier from wheat flour.
The Biosynthesis of Erucic Acid in Developing Embryos ofBrassica rapa1
Authors: Bao Xiaoming , Pollard Mike , Ohlrogge John
Published: July 2002

The prevailing hypothesis on the biosynthesis of erucic acid in developing seeds is that oleic acid, produced in the plastid, is activated to oleoyl-coenzyme A (CoA) for malonyl-CoA-dependent elongation to erucic acid in the cytosol. Several in vivo-labeling experiments designed to probe and extend this hypothesis are reported here. To examine whether newly synthesized oleic acid is directly elongated to erucic acid in developing seeds ofBrassica rapa L., embryos were labeled with [14C]acetate, and the ratio of radioactivity of carbon atoms C-5 to C-22 (de novo fatty acid synthesis portion) to carbon atoms C-1 to C-4 (elongated portion) of erucic acid was monitored with time. If newly synthesized 18:1 (oleate) immediately becomes a substrate for elongation to erucic acid, this ratio would be expected to remain constant with incubation time. However, if erucic acid is produced from a pool of preexisting oleic acid, the ratio of14C in the 4 elongation carbons to 14C in the methyl-terminal 18 carbons would be expected to decrease with time. This labeling ratio decreased with time and, therefore, suggests the existence of an intermediate pool of 18:1, which contributes at least part of the oleoyl precursor for the production of erucic acid. The addition of 2-[{3-chloro-5-(trifluromethyl)-2-pyridinyl}oxyphenoxy] propanoic acid, which inhibits the homodimeric acetyl-CoA carboxylase, severely inhibited the synthesis of [14C]erucic acid, indicating that essentially all malonyl-CoA for elongation of 18:1 to erucate was produced by homodimeric acetyl-CoA carboxylase. Both light and 2-[{3-chloro-5-(trifluromethyl)-2-pyridinyl}oxyphenoxy]-propanoic acid increased the accumulation of [14C]18:1 and the parallel accumulation of [14C]phosphatidylcholine. Taken together, these results show an additional level of complexity in the biosynthesis of erucic acid.
Characterization of a Granule-Bound Starch Synthase Isoform Found in the Pericarp of Wheat
Authors: Nakamura Toshiki , Vrinten Patricia , Hayakawa Kazuhiro , Ikeda Junichi
Published: July 2002

Waxy wheat (Triticum aestivum L.) lacks the waxy protein, which is also known as granule-bound starch synthase I (GBSSI). The starch granules of waxy wheat endosperm and pollen do not contain amylose and therefore stain red-brown with iodine. However, we observed that starch from pericarp tissue of waxy wheat stained blue-black and contained amylose. Significantly higher starch synthase activity was detected in pericarp starch granules than in endosperm starch granules. A granule-bound protein that differed from GBSSI in molecular mass and isoelectric point was detected in the pericarp starch granules but not in granules from endosperm. This protein was designated GBSSII. The N-terminal amino acid sequence of GBSSII, although not identical to wheat GBSSI, showed strong homology to waxy proteins or GBSSIs of cereals and potato, and contained the motif KTGGL, which is the putative substrate-binding site of GBSSI of plants and of glycogen synthase ofEscherichia coli. GBSSII cross-reacted specifically with antisera raised against potato and maize GBSSI. This study indicates that GBSSI and GBSSII are expressed in a tissue-specific manner in different organs, with GBSSII having an important function in amylose synthesis in the pericarp.
Quantitative Control of Inflorescence Formation inImpatiens balsamina
Authors: Pouteau Sylvie , Tooke Fiona , Battey Nicholas
Published: July 2002

We analyzed the process of inflorescence formation in Impatiens balsamina by studying the architecture of the plant under different photoperiod treatments. Floral reversion under noninductive conditions in this species is caused by the lack of persistence of the induced state in the leaf. This can be used to control the amount of inductive signal and to examine its quantitative influence on morphological changes in the plant. The floral transition was characterized by a continuum of variation at the level of meristem identity, primordium initiation, and floral organ identity. This continuum was enhanced during reversion, suggesting that the establishment of a continuum partly reflects limiting amounts of inductive signal exported from the leaf to the meristem. The transcription patterns of two homologs of genes involved in the control of floral meristem identity, Imp-FLO andImp-FIM, were similar in terminal and axillary flowers and may be associated with the continuum exhibited by I. balsamina. By analyzing the fate of axillary meristem primordia initiated before and after the beginning of the inductive period, we showed that de novo initiation of axillary meristem primordia by the evoked meristem is not required and that primordia initiated before evocation can adopt different fates, depending on the amount of inductive signal. The influence of age and/or position on primordium responsiveness to the inductive signal is discussed.
Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Content, Assimilatory Charge, and Mesophyll Conductance in Leaves1
Authors: Eichelmann Hillar , Laisk Agu
Published: July 2002

The content of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) (Et; EC 4.1.1.39) measured in different-aged leaves of sunflower (Helianthus annuus) and other plants grown under different light intensities, varied from 2 to 75 μmol active sites m−2. Mesophyll conductance (μ) was measured under 1.5% O2, as well as postillumination CO2uptake (assimilatory charge, a gas-exchange measure of the ribulose-1,5-bisphosphate pool). The dependence of μ onEt saturated atEt = 30 μmol active sites m−2and μ = 11 mm s−1 in high-light-grown leaves. In low-light-grown leaves the dependence tended toward saturation at similar Et but reached a μ of only 6 to 8 mm s−1. μ was proportional to the assimilatory charge, with the proportionality constant (specific carboxylation efficiency) between 0.04 and 0.075 μm−1s−1. Our data show that the saturation of the relationship between Et and μ is caused by three limiting components: (a) the physical diffusion resistance (a minor limitation), (b) less than full activation of Rubisco (related to Rubisco activase and the slower diffusibility of Rubisco at high protein concentrations in the stroma), and (c) chloroplast metabolites, especially 3-phosphoglyceric acid and free inorganic phosphate, which control the reaction kinetics of ribulose-1,5-bisphosphate carboxylation by competitive binding to active sites.
Dynamic Properties of Endogenous Phytochrome A in Arabidopsis Seedlings
Authors: Hennig Lars , Büche Claudia , Eichenberg Klaus , Schäfer Eberhard
Published: July 2002

The dynamic behavior of phytochrome A (phyA) in seedlings of the model plant Arabidopsis was examined by in vivo spectroscopy and by western and northern blotting. Rapid accumulation of phyA was observed, reaching a steady state after 3 d. Both red and far-red light initiated a rapid destruction of the far-red-light-absorbing form of phytochrome (Pfr); the apparent half-life was only 4-fold longer in far-red than in red light. Furthermore, the Pfr-induced destruction of the red-light-absorbing form of phytochrome (Pr) of phyA occurred in darkness with a rate identical to that of Pfr destruction. A 2-fold decrease in mRNA abundance was observed after irradiation, irrespective of the applied light quality. However, reaccumulation occurred rapidly after far-red but slowly after red irradiation, indicating different modes of regulation of phytochrome expression after light-dark transitions depending on the light quality of the preceding irradiation. The wavelength dependency of the destruction rates was distinct from that of mustard, a close relative of Arabidopsis, and was explained on the basis of Pfr-induced Pr destruction and a simple kinetic two-step model. No dark reversion was detectable in the destruction kinetics after a red pulse. From these data we conclude that Arabidopsis phyA differs significantly in several aspects from other dicot phytochromes.
The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch
Authors: Doan Danny N.P. , Rudi Heidi , Olsen Odd-Arne
Published: July 2002

We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level ofbeps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps andblpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed.
Proline Metabolism in the Wild-Type and in a Salt-Tolerant Mutant of Nicotiana plumbaginifolia Studied by13C-Nuclear Magnetic Resonance Imaging
Authors: Roosens Nancy H. , Willem Rudolph , Li Yan , Verbruggen Ingrid , Biesemans Monique , Jacobs Michel
Published: July 2002

To obtain insight into the link between proline (Pro) accumulation and the increase in osmotolerance in higher plants, we investigated the biochemical basis for the NaCl tolerance of a Nicotiana plumbaginifolia mutant (RNa) that accumulates Pro. Pro biosynthesis and catabolism were investigated in both wild-type and mutant lines. 13C-Nuclear magnetic resonance with [5-13C]glutamate (Glu) as the Pro precursor was used to provide insight into the mechanism of Pro accumulation via the Glu pathway. After 24 h under 200 mm NaCl stress in the presence of [5-13C]Glu, a significant enrichment in [5-13C]Pro was observed compared with non-stress conditions in both the wild type (P2) and the mutant (RNa). Moreover, under the same conditions, [5-13C]Pro was clearly synthesized in higher amounts in RNa than in P2. On the other hand, measurements of enzyme activities indicate that neither the biosynthesis via the ornithine pathway, nor the catabolism via the Pro oxidation pathway were affected in the RNa mutant. Finally, the regulatory effect exerted by Pro on its biosynthesis was evaluated. In P2 plantlets, exogenous Pro markedly reduced the conversion of [5-13C]Glu into [5-13C]Pro, whereas Pro feedback inhibition was not detected in the RNa plantlets. It is proposed that the origin of tolerance in the RNa mutant is due to a mutation leading to a substantial reduction of the feedback inhibition normally exerted in a wild-type (P2) plant by Pro at the level of the Δ-pyrroline-5-carboxylate synthetase enzyme.
Amyloplast Sedimentation Dynamics in Maize Columella Cells Support a New Model for the Gravity-Sensing Apparatus of Roots
Authors: Yoder Thomas L. , Zheng Hui-qiong , Todd Paul , Staehelin L. Andrew
Published: July 2002

Quantitative analysis of statolith sedimentation behavior was accomplished using videomicroscopy of living columella cells of corn (Zea mays) roots, which displayed no systematic cytoplasmic streaming. Following 90° rotation of the root, the statoliths moved downward along the distal wall and then spread out along the bottom with an average velocity of 1.7 μm min−1. When statolith trajectories traversed the complete width or length of the cell, they initially moved horizontally toward channel-initiation sites and then moved vertically through the channels to the lower side of the reoriented cell where they again dispersed. These statoliths exhibited a significantly lower average velocity than those sedimenting on distal-to-side trajectories. In addition, although statoliths undergoing distal-to-side sedimentation began at their highest velocity and slowed monotonically as they approached the lower cell membrane, statoliths crossing the cell's central region remained slow initially and accelerated to maximum speed once they reached a channel. The statoliths accelerated sooner, and the channeling effect was less pronounced in roots treated with cytochalasin D. Parallel ultrastructural studies of high-pressure frozen-freeze-substituted columella cells suggest that the low-resistance statolith pathway in the cell periphery corresponds to the sharp interface between the endoplasmic reticulum (ER)-rich cortical and the ER-devoid central region of these cells. The central region is also shown to contain an actin-based cytoskeletal network in which the individual, straight, actin-like filaments are randomly distributed. To explain these findings as well as the results of physical simulation experiments, we have formulated a new, tensegrity-based model of gravity sensing in columella cells. This model envisages the cytoplasm as pervaded by an actin-based cytoskeletal network that is denser in the ER-devoid central region than in the ER-rich cell cortex and is linked to stretch receptors in the plasma membrane. Sedimenting statoliths are postulated to produce a directional signal by locally disrupting the network and thereby altering the balance of forces acting on the receptors in different plasma membrane regions.
Homeodomain Leucine Zipper Proteins Bind to the Phosphate Response Domain of the SoybeanVspBTripartite Promoter
Authors: Tang Zhijun , Sadka Avi , Morishige Daryl T. , Mullet John E.
Published: July 2002

The soybean (Glycine max L. Merr. cv Williams 82) genes VspA and VspB encode vacuolar glycoprotein acid phosphatases that serve as vegetative storage proteins during seed fill and early stages of seedling growth.VspB expression is activated by jasmonates (JAs) and sugars and down-regulated by phosphate and auxin. Previous promoter studies demonstrated that VspB promoter sequences between −585 and −535 mediated responses to JA, and sequences between −535 and −401 mediated responses to sugars, phosphate, and auxin. In this study, the response domains were further delineated using transient expression of VspBpromoter-β-glucuronidase constructs in tobacco protoplasts. Sequences between −536 and −484 were identified as important for phosphate responses, whereas the region from −486 to −427 mediated sugar responses. Gel-shift and deoxyribonuclease-I footprinting assays revealed four DNA-binding sites between −611 and −451 of the soybeanVspB promoter: one in the JA response domain, two in the phosphate response domain, and one binding site in the sugar response domain. The sequence CATTAATTAG present in the phosphate response domain binds soybean homeodomain leucine zipper proteins, suggesting a role for these transcription factors in phosphate-modulated gene expression.
The Cyclization of Farnesyl Diphosphate and Nerolidyl Diphosphate by a Purified Recombinant δ-Cadinene Synthase
Authors: Benedict Chauncey R. , Lu Jia-Ling , Pettigrew Donald W. , Liu Jinggao , Stipanovic Robert D. , Williams Howard J.
Published: July 2002

The first step in the conversion of the isoprenoid intermediate, farnesyl diphosphate (FDP), to sesquiterpene phytoalexins in cotton (Gossypium barbadense) plants is catalyzed by δ-cadinene (CDN) synthase. CDN is the precursor of desoxyhemigossypol and hemigossypol defense sesquiterpenes. In this paper we have studied the mechanism for the cyclization of FDP and the putative intermediate, nerolidyl diphosphate, to CDN. A purified recombinant CDN synthase (CDN1-C1) expressed in Escherichia colifrom CDN1-C1 cDNA isolated from Gossypium arboreumcyclizes (1RS)-[1-2H](E, E)-FDP to >98% [5-2H]and [11-2H]CDN. Enzyme reaction mixtures cyclize (3RS)-[4,4,13,13,13-2H5]-nerolidyl diphosphate to 62.1% [8,8,15,15,15-2H5]-CDN, 15.8% [6,6,15,15,15-2H5]-α-bisabolol, 8.1% [6,6,15,15,15-2H5]-(β)-bisabolene, 9.8% [4,4,13,13-2H4]-(E)-β-farnesene, and 4.2% unknowns. Competitive studies show that (3R)-nerolidyl diphosphate is the active enantiomer of (3RS)-nerolidyl diphosphate that cyclized to CDN. The kcat/K  m values demonstrate that the synthase uses (E,E)-FDP as effectively as (3R)-nerolidyl diphosphate in the formation of CDN. Cyclization studies with (3R)-nerolidyl diphosphate show that the formation of CDN, (E)-β-farnesene, and β-bisabolene are enzyme dependent, but the formation of α-bisabolol in the reaction mixtures was a Mg2+-dependent solvolysis of nerolidyl diphosphate. Enzyme mechanisms are proposed for the formation of CDN from (E,E)-FDP and for the formation of CDN, (E)-β-farnesene, and β-bisabolene from (3RS)-nerolidyl diphosphate. The primary structures of cotton CDN synthase and tobacco epi-aristolochene synthase show 48% identity, suggesting similar three-dimensional structures. We used the SWISS-MODEL to test this. The two enzymes have the same overall structure consisting of two α-helical domains and epi-aristolochene synthase is a good model for the structure of CDN synthase. Several amino acids in the primary structures of both synthases superimpose. The amino acids having catalytic roles in epi-aristochene synthase are substituted in the CDN synthase and may be related to differences in catalytic properties.
Small-angle X-ray scattering station at the SPring-8 RIKEN beamline
Authors: Fujisawa T. , Inoue K. , Oka T. , Iwamoto H. , Uruga T. , Kumasaka T. , Inoko Y. , Yagi N. , Yamamoto M. , Ueki T.
Published: July 2002

RIKEN beamline I (BL45XU) is an undulator beamline with two branches. One is for protein crystallography (PX) and the other is for small-angle x-ray scattering (SAXS). The beam is split into the two branches by a diamond monochromator so that two experiments can be done simultaneously [Yamamoto et al. (1995) Rev. Sci. Instrum.
66, 1833-1835]. The SAXS branch was designed for studying the weak interaction of proteins or subunits of fibrous or protein solutions especially using hydrostatic pressure. The optics makes use of the good parallelism of the undulator beam in order to reduce parasitic scattering. The beamline consists of a double crystal monochromator and a K-B type focusing mirror system. In order to cope with the high flux of the beam, an x-ray image intensifier (Hamamatsu Photonics, V5445P) with a cooled CCD camera (C4880-82) was used. As a result, decreases in both collection time and sample amount were realized in standard static experiments. These improvements will greatly facilitate SAXS experiments under high pressure.
Accurate cells from area-detector images
Authors: Duisenberg Albert J. M. , Hooft Rob W. W. , Schreurs Antoine M. M. , Kroon Jan
Published: July 2002

A procedure is described, for an Eulerian or Kappa goniostat, to determine the exact spindle value φ at the moment of impact of a reflection on an area detector; such information is essential for the calculation of accurate reflection vectors and, eventually, the unit-cell and lattice orientation. The method is based on a comparison of reflection impact coordinates on two related images. One image is obtained by spindle rotation over a few degrees (`φ scan') and the other by the same φ rotation, but with a superposed rotation (χ) perpendicular to the first (`φ/χ scan'). In both cases, the spindle is kept perpendicular to the primary beam,i.e.ω = 0 or 180°. Therefore, on the second image, exactly the same reflections as on the first will appear, but on a different spot on the detector. From the tangential separation between corresponding reflection impacts, the moment of impact (φ value) is calculated. The method is especially useful in small-molecule work, where rather wide scans are required for a reasonable number of reflections in one image. It is shown that for our purpose the Eulerian φ/χ scan can be simulated practically exactly by simultaneous uniform rotations of the axes ωK, κ and φKof the Kappa goniostat.
Whole-profile structure solution from powder diffraction data using simulated annealing
Authors: Coelho A. A.
Published: July 2002

Techniques and methods to facilitate the solution of structures by simulated annealing have been developed from the starting point of a space group and lattice parameters. The simulated-annealing control parameters have been systematically investigated and optimum values characterized and determined. Most significant is the inclusion of electrostatic-potential penalty functions in a non-linear least-squares Rietveld refinement procedure. The long-range electrostatic potentials are calculated using a general real-space summation which can be used for all space groups. In addition, a general weighting scheme for penalty functions negates the need to determine weighting schemes experimentally. Also investigated and improved is the non-linear least-squares minimization procedure used in the refinement of structural parameters. The behaviour and success of the techniques have been tested on X-ray diffraction powder data against the known structures of AlVO4inP1 with 18 atoms in the asymmetric unit, K2HCr2AsO10inP31with 15 atoms in the asymmetric unit excluding hydrogen, and [Co(NH3)5CO3]NO3.H2O inP121with 15 atoms in the asymmetric unit excluding hydrogen.
A tangent formula derived from Patterson-function arguments. VII. Solution of inorganic structures from powder data with accidental overlap
Authors: Rius J. , Torrelles X. , Miravitlles C. , Ochando L. E. , Reventós M. M. , Amigó J. M.
Published: July 2002

Accidental overlap constitutes one of the principal limitations for the solution of crystal structures from powder diffraction data, since it reduces the number of available intensities for direct-methods application. In this work, the field of application of the direct-methods sum function is extended to cope with powder patterns with relatively large amounts of accidental overlap. This is achieved by refining not only the phases of the structure factors but also the estimated intensities of the severely overlapped peaks during the structure solution process. This procedure has been specifically devised for inorganic compounds with uncertain cell contents and with probable severe atomic disorder, a situation often found when studying complex minerals with limited crystallinity. It has been successfully applied to the solution of the previously unknown crystal structure of the mineral tinticite. Finally, an estimation of the smallest ratio (number of observations to number of variables) for the procedure to be successful is given.
Application of small-angle scattering to the study of graphite-adsorbed hydrocarbons
Authors: Gilbert E. , Reynolds P. , White J.
Published: July 2002

The structure of graphite-adsorbed n-alkanes for 10 ≤ n ≤ 20 has been investigated by SAXS. Below the bulk melting point, Tm, and for alkanes with even n, two distinct diffraction peaks are observed, one associated with the bulk and the other with the surface structure. For alkanes with odd n, only one peak is observed below Tm; above Tm a significant reduction in intensity is found, indicating melting of the bulk, but a peak remains. The intensity at Tm increases with n and correlates with previous pyknometric and calorimetric measurements. The surface-adsorbed structure has a repeat corresponding to the orthorhombic spacing of the bulk alkane crystal.
Quanto: a Rietveld program for quantitative phase analysis of polycrystalline mixtures
Authors: Altomare Angela , Burla Maria Cristina , Giacovazzo Carmelo , Guagliardi Antonietta , Moliterni Anna Grazia Giuseppina , Polidori Giampiero , Rizzi Rosanna
Published: July 2002

Quantitative determination of phase abundance in a multicomponent polycrystalline mixture is a basic goal in materials characterization. Because of several advantages compared with traditional techniques, the Rietveld method has been increasingly applied to this task. Further progress in this direction would be to carry out the analysis automatically. The new Rietveld packageQuantois devoted to the automatic estimation of the weight fraction of each crystalline phase in a mixture. The amorphous content can be estimated by means of the internal-standard method. Corrections for preferred orientation and microabsorption effects are available. A user-friendly graphical interface facilitates interaction. A data bank including several organic and inorganic phases is supplied with the program.