bluuebunny/crossref_metadata_2025 huggingface dataset:
On the spectral sequence constructors of Guichardet and Stefan
Authors: Barnes Donald
Published: April 2003

The concept of a spectral sequence constructor is generalised to Hopf Galois extensions. The spectral sequence constructions that are given by Guichardet for crossed product algebras are also generalised and shown to provide examples. It is shown that all spectral sequence constructors for Hopf Galois extensions construct the same spectral sequence.
The almost-disjointness number may have countable cofinality
Authors: Brendle Jörg
Published: April 2003

We show that it is consistent for the almost-disjointness numbera\mathfrak {a}to have countable cofinality. For example, it may be equal toℵω\aleph _\omega.
Composition operators acting on holomorphic Sobolev spaces
Authors: Choe Boo , Koo Hyungwoon , Smith Wayne
Published: April 2003

We study the action of composition operators on Sobolev spaces of analytic functions having fractional derivatives in some weighted Bergman space or Hardy space on the unit disk. Criteria for when such operators are bounded or compact are given. In particular, we find the precise range of orders of fractional derivatives for which all composition operators are bounded on such spaces. Sharp results about boundedness and compactness of a composition operator are also given when the inducing map is polygonal.
Criteria for large deviations
Authors: Comman Henri
Published: April 2003

We give the general variational form of
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="limit sup left-parenthesis integral Underscript upper X Endscripts e Superscript h left-parenthesis x right-parenthesis slash t Super Subscript alpha Superscript Baseline mu Subscript alpha Baseline left-parenthesis d x right-parenthesis right-parenthesis Superscript t Super Subscript alpha">

lim sup
(

∫
X

e

h
(
x
)

/

t

α

μ

α

(
d
x
)

)

t

α

\limsup (\int _X e^{h(x)/t_{\alpha }}\mu _{\alpha }(dx))^{t_{\alpha }}

\]
for any bounded above Borel measurable function

h
h

on a topological space

X
X

, where

(

μ

α

)

(\mu _{\alpha })

is a net of Borel probability measures on

X
X

, and

(

t

α

)

(t_{\alpha })

a net in

]
0
,
∞
[

]0,\infty [

converging to

0
0

. When

X
X

is normal, we obtain a criterion in order to have a limit in the above expression for all

h
h

continuous bounded, and deduce new criteria of a large deviation principle with not necessarily tight rate function; this allows us to remove the tightness hypothesis in various classical theorems.
Large rectangular semigroups in Stone-Cech compactifications
Authors: Hindman Neil , Strauss Dona , Zelenyuk Yevhen
Published: April 2003

We show that large rectangular semigroups can be found in certain Stone-Čech compactifications. In particular, there are copies of the

2

c

×

2

c

2^{\mathfrak {c}}\times 2^{\mathfrak {c}}

rectangular semigroup in the smallest ideal of

(
β

N

,
+
)

(\beta \mathbb {N},+)

, and so, a semigroup consisting of idempotents can be embedded in the smallest ideal of

(
β

N

,
+
)

(\beta \mathbb {N},+)

if and only if it is a subsemigroup of the

2

c

×

2

c

2^{\mathfrak {c}}\times 2^{\mathfrak {c}}

rectangular semigroup. In fact, we show that for any ordinal

λ
\lambda

with cardinality at most

c

\mathfrak {c}

,

β

N

\beta {\mathbb {N}}

contains a semigroup of idempotents whose rectangular components are all copies of the

2

c

×

2

c

2^{\mathfrak {c}}\times 2^{\mathfrak {c}}

rectangular semigroup and form a decreasing chain indexed by

λ
+
1

\lambda +1

, with the minimum component contained in the smallest ideal of

β

N

\beta \mathbb {N}

. As a fortuitous corollary we obtain the fact that there are

≤

L

\leq _{L}

-chains of idempotents of length

c

\mathfrak {c}

in

β

N

\beta \mathbb {N}

. We show also that there are copies of the direct product of the

2

c

×

2

c

2^{\mathfrak {c}}\times 2^{\mathfrak {c}}

rectangular semigroup with the free group on

2

c

2^{\mathfrak {c}}

generators contained in the smallest ideal of

β

N

\beta \mathbb {N}

.
Stability of small amplitude boundary layers for mixed hyperbolic-parabolic systems
Authors: Rousset F.
Published: April 2003

We consider an initial boundary value problem for a symmetrizable mixed hyperbolic-parabolic system of conservation laws with a small viscosity

ε
\varepsilon

,
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="u Subscript t Superscript epsilon Baseline plus upper F left-parenthesis u Superscript epsilon Baseline right-parenthesis Subscript x Baseline equals epsilon left-parenthesis upper B left-parenthesis u Superscript epsilon Baseline right-parenthesis u Subscript x Superscript epsilon Baseline right-parenthesis Subscript x Baseline period">

u
t
ε

+
F
(

u
ε

)
x

=
ε
(
B
(

u
ε

)

u
x
ε

)
x

.

u^\varepsilon _t+F(u^\varepsilon )_x =\varepsilon (B(u^\varepsilon ) u^\varepsilon _x )_x .

When the boundary is noncharacteristic for both the viscous and the inviscid system, and the boundary condition dissipative, we show that

u
ε

u^\varepsilon

converges to a solution of the inviscid system before the formation of shocks if the amplitude of the boundary layer is sufficiently small. This generalizes previous results obtained for

B
B

invertible and the linear study of Serre and Zumbrun obtained for a pure Dirichlet’s boundary condition.
Galois groups of quantum group actions and regularity of fixed-point algebras
Authors: Yamanouchi Takehiko
Published: April 2003

It is shown that, for a minimal and integrable action of a locally compact quantum group on a factor, the group of automorphisms of the factor leaving the fixed-point algebra pointwise invariant is identified with the intrinsic group of the dual quantum group. It is proven also that, for such an action, the regularity of the fixed-point algebra is equivalent to the cocommutativity of the quantum group.
Cyclicity of CM elliptic curves modulo 𝑝
Authors: Cojocaru Alina
Published: April 2003

Let

E
E

be an elliptic curve defined over

Q

\mathbb {Q}

and with complex multiplication. For a prime

p
p

of good reduction, let

E
¯

\overline {E}

be the reduction of

E
E

modulo

p
.

p.

We find the density of the primes

p
≤
x

p \leq x

for which

E
¯

(

F

p

)

\overline {E}(\mathbb {F}_p)

is a cyclic group. An asymptotic formula for these primes had been obtained conditionally by J.-P. Serre in 1976, and unconditionally by Ram Murty in 1979. The aim of this paper is to give a new simpler unconditional proof of this asymptotic formula and also to provide explicit error terms in the formula.
Feature selection and transduction for
prediction of molecular bioactivity for drug design
Authors: Weston Jason , Pérez-Cruz Fernando , Bousquet Olivier , Chapelle Olivier , Elisseeff André , Schölkopf Bernhard
Published: April 2003

Motivation: In drug discovery a key task is to identify characteristics that separate active (binding) compounds from inactive (non-binding) ones. An automated prediction system can help reduce resources necessary to carry out this task.

Results: Two methods for prediction of molecular bioactivity for drug design are introduced and shown to perform well in a data set previously studied as part of the KDD (Knowledge Discovery and Data Mining) Cup 2001. The data is characterized by very few positive examples, a very large number of features (describing three-dimensional properties of the molecules) and rather different distributions between training and test data. Two techniques are introduced specifically to tackle these problems: a feature selection method for unbalanced data and a classifier which adapts to the distribution of the the unlabeled test data (a so-called transductive method). We show both techniques improve identification performance and in conjunction provide an improvement over using only one of the techniques. Our results suggest the importance of taking into account the characteristics in this data which may also be relevant in other problems of a similar type.

Availability: Matlab source code is available at http://www.kyb.tuebingen.mpg.de/bs/people/weston/kdd/kdd.html

Contact: jason.weston@tuebingen.mpg.de

Supplementary information: Supplementary material is available at http://www.kyb.tuebingen.mpg.de/bs/people/weston/kdd/kdd.html.

* To whom correspondence should be addressed.
Protein structure comparison by probability-based matching of secondary
structure elements
Authors: Shih Edward S.C. , Hwang Ming-Jing
Published: April 2003

Motivation: Protein structure comparison (PSC) has been used widely in studies of structural and functional genomics. However, PSC is computationally expensive and as a result almost all of the PSC methods currently in use look only for the optimal alignment and ignore many alternative alignments that are statistically significant and that may provide insight into protein evolution or folding.

Results: We have developed a new PSC method with efficiency to detect potentially viable alternative alignments in all-against-all database comparisons. The efficiency of the new PSC method derives from the ability to directly home in on a limited number of viable and ranked alignment solutions based on intuitively derived SSE (secondary structure element)-matching probabilities.

Availability: The new PSC tool is accessible at our lab website http://gln.ibms.sinica.edu.tw/software.php

Contact: mjhwang@ibms.sinica.edu.tw

Supplementary Information: Supplementary tables and figures for this paper can be found at the same website.

* To whom correspondence should be addressed.
RECSIM and INDSTATS: probabilities of identity in general genealogies
Authors: Dimitropoulou Polixeni , Cannings Chris
Published: April 2003

Summary: RECSIM takes a general genealogy and simulates the transmission of chromosomes through that genealogy. INDSTATS extracts some basic statistics from the output of RECSIM

Availability: The RECSIM and INDSTATS programs together with readme files READMESIM and READMESTATS can be downloaded from http://www.shef.ac.uk/mmge/chris/inbred.html

Contact: c.cannings@shef.ac.uk

* To whom correspondence should be addressed.
Genome-wide analysis of Bkm sequences (GATA repeats):
predominant association with sex chromosomes and potential role
in higher order chromatin organization and function
Authors: Subramanian Subbaya , Mishra Rakesh K. , Singh Lalji
Published: April 2003

Motivation: Bkm (Banded krait minor) satellite DNA sequences (GATA repeats) have been shown to be associated with the sex determining chromosomes of various eukaryotes and have been implicated in the evolution and differentiation of sex chromosomes in snakes. The objective of the study is to analyze the GATA repeats of human genome specifically, the Y-chromosome, and other model organisms to understand the possible function and potential role in higher order chromatin organization.

Results: Our extensive analysis of GATA repeats in the prokaryotic and eukaryotic genomes, which have been completely sequenced so far, has revealed that GATA repeats are absent in prokaryotes and have been gradually accumulated in higher organisms during the course of evolution. In human, the Y-chromosome has the highest GATA repeat density, which predominantly exists in the Yq centromeric region. Generally, occurrence of repeats in the genomes decreases steadily as the length of the repeat increases. In contrast, we report, that the occurrence of GATA repeats increases as the length of the repeat increases from six tandem repeats onwards and peaks at (GATA)10–12. This has not been observed with any other simple repeat. Distribution of (GATA)10–12 along the chromosome and their close proximity to Matrix Associated Regions (GATA-MAR) suggests that it may be demarking chromatin domains for a coordinated expression of genes residing in these domains. Supplementary data is available at http://www.ccmb.res.in/bkm/gata.htm.

Contact: lalji@ccmb.res.in

* To whom correspondence should be addressed.
Statistical tests for identifying differentially
expressed genes in time-course microarray experiments
Authors: Park Taesung , Yi Sung-Gon , Lee Seungmook , Lee Seung Yeoun , Yoo Dong-Hyun , Ahn Jun-Ik , Lee Yong-Sung
Published: April 2003

Motivation: Microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. In time-course experiments in which gene expression is monitored over time, we are interested in testing gene expression profiles for different experimental groups. However, no sophisticated analytic methods have yet been proposed to handle time-course experiment data.

Results: We propose a statistical test procedure based on the ANOVA model to identify genes that have different gene expression profiles among experimental groups in time-course experiments. Especially, we propose a permutation test which does not require the normality assumption. For this test, we use residuals from the ANOVA model only with time-effects. Using this test, we detect genes that have different gene expression profiles among experimental groups. The proposed model is illustrated using cDNA microarrays of 3840 genes obtained in an experiment to search for changes in gene expression profiles during neuronal differentiation of cortical stem cells.

Availability: A set of programs written by R will be electronically sent upon request.

Contact: tspark@stats.snu.ac.kr

* To whom correspondence should be addressed.
Computer simulation of the cellular arrangement using physical
model in early cleavage of the nematode Caenorhabditis elegans
Authors: Kajita Atsushi , Yamamura Masayuki , Kohara Yuji
Published: April 2003

Motivation: The ultimate goal of bioinformatics is to reconstruct biological systems in the computer. Since biological systems have many levels, it is important to focus on an appropriate level. In our first application of computer modeling to the early development of the nematode Caenorhabditis elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell–cell interaction, and is regarded as a system, one level higher than the system of gene regulation within cells. It is largely restricted by physical conditions that seemed feasible to model by computer.

Results: We constructed a computer model of the C.elegans embryo, currently up to the 4-cell stage, using a deformable and dividable triangulated network. The model is based solely on cellular-level dynamics. We found that the optimal ranges of three parameters that affect the elongation of dividing cells led, in computer simulations, to almost the same cellular arrangements as in real embryos. The nature of the model and the relationship with real embryos are discussed.

Availability: The software is available upon request.

Contact: akajita@lab.nig.ac.jp

* To whom correspondence should be addressed.
Construction of reliable protein–protein interaction networks
with a new interaction generality measure
Authors: Saito Rintaro , Suzuki Harukazu , Hayashizaki Yoshihide
Published: April 2003

Motivation: Recent screening techniques have made large amounts of protein–protein interaction data available, from which biologically important information such as the function of uncharacterized proteins, the existence of novel protein complexes, and novel signal-transduction pathways can be discovered. However, experimental data on protein interactions contain many false positives, making these discoveries difficult. Therefore computational methods of assessing the reliability of each candidate protein–protein interaction are urgently needed.

Results: We developed a new ‘interaction generality’ measure (IG2) to assess the reliability of protein–protein interactions using only the topological properties of their interaction-network structure. Using yeast protein–protein interaction data, we showed that reliable protein–protein interactions had significantly lower IG2 values than less-reliable interactions, suggesting that IG2 values can be used to evaluate and filter interaction data to enable the construction of reliable protein–protein interaction networks.

Availability: The protein–protein interaction data used in this study along with the associated IG2 values are available at http://genome.gsc.riken.go.jp.

Contact: rgscerg@gsc.riken.go.jp

* To whom correspondence should be addressed.

† Present address: Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.
Using multiple interdependency
to separate functional from phylogenetic correlations in protein alignments
Authors: Tillier Elisabeth R.M. , Lui Thomas W.H.
Published: April 2003

Motivation: Multiple sequence alignments of homologous proteins are useful for inferring their phylogenetic history and to reveal functionally important regions in the proteins. Functional constraints may lead to co-variation of two or more amino acids in the sequence, such that a substitution at one site is accompanied by compensatory substitutions at another site. It is not sufficient to find the statistical correlations between sites in the alignment because these may be the result of several undetermined causes. In particular, phylogenetic clustering will lead to many strong correlations.

Results: A procedure is developed to detect statistical correlations stemming from functional interaction by removing the strong phylogenetic signal that leads to the correlations of each site with many others in the sequence. Our method relies upon the accuracy of the alignment but it does not require any assumptions about the phylogeny or the substitution process. The effectiveness of the method was verified using computer simulations and then applied to predict functional interactions between amino acids in the Pfam database of alignments.

Availability: The program and supplementary figures tables are available from the site http://www.uhnres.utoronto.ca/tillier/depend2/dependency.html.

Contact: e.tillier@utoronto.ca

* To whom correspondence should be addressed.
Automated generation and refinement of protein signatures:
case study with G-protein coupled receptors
Authors: Sadowski Michael I. , Parish John Howard
Published: April 2003

Motivation: Previous work had established that it was possible to derive sparse signatures (essentially sequence-length motifs) by examining points of contact between residues in proteins of known three-dimensional (3D) structure. Many interesting protein families have very little tertiary structural information. Methods for deriving signatures using only primary and secondary-structural information were therefore developed.

Results: Two methods for deriving protein signatures using protein sequence information and predicted secondary structures are described. One method is based on a scoring approach, the other on the Genetic Algorithm (GA). The effectiveness of the method was tested on the superfamily of GPCRs and compared with the established hidden Markov model (HMM) method. The signature method is shown to perform well, detecting 68% of superfamily members before the first false positive sequence and detecting several distant relationships. The GA population was used to provide information on alignment regions of particular importance for selection of key residues.

Contact: howard@bmb.leeds.ac.uk

Supplementary information: Software developed for this project and further data are available online (http://bbsrc-bioinf.leeds.ac.uk/BIOINF/jhp/)

* To whom correspondence should be addressed.
GoFish finds genes with combinations of Gene Ontology attributes
Authors: Berriz Gabriel F. , White James V. , King Oliver D. , Roth Frederick P.
Published: April 2003

Summary: GoFish is a Java application that allows users to search for gene products with particular gene ontology (GO) attributes, or combinations of attributes. GoFish ranks gene products by the degree to which they satisfy a Boolean query. Four organisms are currently supported: Saccaromyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and M.musculus.

Availability: GoFish can be used freely through the www as a Java applet for Windows, Mac OS X, or Unix: http://llama.med.harvard.edu/Software.html.

Contact: fritz_roth@hms.harvard.edu

* To whom correspondence should be addressed.
EPPS: mining the COG database by an extended phylogenetic
patterns search
Authors: Reichard Klaus , Kaufmann Michael
Published: April 2003

Summary: EPPS runs under Microsoft Windows. It is an extended version of the phylogenetic patterns search (PPS). The output condition of PPS is the exact match of a user defined phylogenetic pattern with the pattern represented by the respective cluster of orthologous groups (COG). In contrast, the software described here is less restrictive. The user may define the accuracy of the search by the number of genomes that are allowed not to match the predefined phylogenetic pattern. Thus, EPPS has the advantage to detect COGs even if organisms defined to be included are not or organisms defined to be excluded are present in the output COGs.

Availability: EPPS is free and both windows executable and source code are available at http://www.uni-wh.de/de/nawi/institut/protein/epps.html

Contact: mika@uni-wh.de

* To whom correspondence should be addressed.
AFLPinSilico, simulating AFLP fingerprints
Authors: Rombauts Stephane , Van de Peer Yves , Rouzé Pierre
Published: April 2003

Summary: A drawback of the Amplified Fragment Length Polymorphism (AFLP) fingerprinting method is the difficulty to correlate the different fragments with their DNA sequence. The AFLPinSilico application presented here simulates AFLP experiments run on either cDNA or genomic sequences, producing virtual fingerprints that allow high throughput identification of AFLP fragments. The program also enables biologists to manage experiments through simulations done beforehand, thereby reducing the number of experiments that have to be run. AFLPinSilico is available through the www or as a stand-alone version, through a command line executable (available upon request, for any platform running PERL).

Availability: For academic use http://www.psb.rug.ac.be/bioinformatics/AFLPinSilico.html

Contact: strom@gengenp.rug.ac.be

* To whom correspondence should be addressed.
Symplastic Continuity between Companion Cells and the Translocation Stream: Long-Distance Transport Is Controlled by Retention and Retrieval Mechanisms in the Phloem
Authors: Ayre Brian G. , Keller Felix , Turgeon Robert
Published: April 2003

Substantial symplastic continuity appears to exist between companion cells (CCs) and sieve elements of the phloem, which suggests that small solutes within the CC are subject to indiscriminate long-distance transport via the translocation stream. To test this hypothesis, the distributions of exotic and endogenous solutes synthesized in the CCs of minor veins were studied. Octopine, a charged molecule derived from arginine and pyruvate, was efficiently transported through the phloem but was also transferred in substantial amounts to the apoplast, and presumably other non-phloem compartments. The disaccharide galactinol also accumulated in non-phloem compartments, but long-distance transport was limited. Conversely, sucrose, raffinose, and especially stachyose demonstrated reduced accumulation and efficient transport out of the leaf. We conclude that small metabolites in the cytosol of CCs do enter the translocation stream indiscriminately but are also subject to distributive forces, such as nonselective and carrier-mediated membrane transport and symplastic dispersal, that may effectively clear a compound from the phloem or retain it for long-distance transport. A model is proposed in which the transport of oligosaccharides is an adaptive strategy to improve photoassimilate retention, and consequently translocation efficiency, in the phloem.
Natural Abundance Carbon Isotope Composition of Isoprene Reflects Incomplete Coupling between Isoprene Synthesis and Photosynthetic Carbon Flow
Authors: Affek Hagit P. , Yakir Dan
Published: April 2003

Isoprene emission from leaves is dynamically coupled to photosynthesis through the use of primary and recent photosynthate in the chloroplast. However, natural abundance carbon isotope composition (δ13C) measurements in myrtle (Myrtus communis), buckthorn (Rhamnus alaternus), and velvet bean (Mucuna pruriens) showed that only 72% to 91% of the variations in the δ13C values of fixed carbon were reflected in the δ13C values of concurrently emitted isoprene. The results indicated that 9% to 28% carbon was contributed from alternative, slow turnover, carbon source(s). This contribution increased when photosynthesis was inhibited by CO2-free air. The observed variations in the δ13C of isoprene under ambient and CO2-free air were consistent with contributions to isoprene synthesis in the chloroplast from pyruvate associated with cytosolic Glc metabolism. Irrespective of alternative carbon source(s), isoprene was depleted in 13C relative to mean photosynthetically fixed carbon by 4‰ to 11‰. Variable13C discrimination, its increase by partially inhibiting isoprene synthesis with fosmidomicin, and the associated accumulation of pyruvate suggested that the main isotopic discrimination step was the deoxyxylulose-5-phosphate synthase reaction.
Vulnerability of Xylem Vessels to Cavitation in Sugar Maple. Scaling from Individual Vessels to Whole Branches
Authors: Melcher Peter J. , Zwieniecki Maciej A. , Holbrook N. Michele
Published: April 2003

The relation between xylem vessel age and vulnerability to cavitation of sugar maple (Acer saccharum Marsh.) was quantified by measuring the pressure required to force air across bordered pit membranes separating individual xylem vessels. We found that the bordered pit membranes of vessels located in current year xylem could withstand greater applied gas pressures (3.8 MPa) compared with bordered pit membranes in vessels located in older annular rings (2.0 MPa). A longitudinal transect along 6-year-old branches indicated that the pressure required to push gas across bordered pit membranes of current year xylem did not vary with distance from the growing tip. To understand the contribution of age-related changes in vulnerability to the overall resistance to cavitation, we combined data on the pressure thresholds of individual xylem vessels with measurements of the relative flow rate through each annual ring. The annual ring of the current year contributed only 16% of the total flow measured on 10-cm-long segments cut from 6-year-old branches, but it contributed more than 70% of the total flow when measured through 6-year-old branches to the point of leaf attachment. The vulnerability curve calculated using relative flow rates measured on branch segments were similar to vulnerability curves measured on 6-year-old branches (pressure that reduces hydraulic conductance by 50% = 1.6–2.4 MPa), whereas the vulnerability curve calculated using relative flow rates measured on 6-year-old branches were similar to ones measured on the extension growth of the current year (pressure that reduces hydraulic conductance by 50% = 3.8 MPa). These data suggest that, in sugar maple, the xylem of the current year can withstand larger xylem tensions than older wood and dominates water delivery to leaves.
Freezing Sensitivity in the sfr4 Mutant of Arabidopsis Is Due to Low Sugar Content and Is Manifested by Loss of Osmotic Responsiveness
Authors: Uemura Matsuo , Warren Gareth , Steponkus Peter L.
Published: April 2003

Protoplasts were tested to determine whether the freezing sensitivity of the sfr4 (sensitive to freezing) mutant of Arabidopsis was due to the mutant's deficiency in soluble sugars after cold acclimation. When grown under nonacclimated conditions,sfr4 protoplasts possessed freezing tolerance similar to that of wild type, with the temperature at which 50% of protoplasts are injured (LT50) of −4.5°C. In both wild-type andsfr4 protoplasts, expansion-induced lysis was the predominant lesion between −2°C and −4°C, but its incidence was low (approximately 10%); below −5°C, loss of osmotic responsiveness (LOR) was the predominant lesion. After cold acclimation, the LT50 was decreased to only −5.6°C forsfr4 protoplasts, compared with −9.1°C for wild-type protoplasts. Although expansion-induced lysis was precluded in both types of protoplasts, the sfr4 protoplasts remained susceptible to LOR. After incubation of seedlings in Suc solution in the dark at 2°C, freezing tolerance and the incidence of freeze-induced lesions in sfr4 protoplasts were examined. The freezing tolerance of isolated protoplasts (LT50 of −9°C) and the incidence of LOR were now similar for wild type and sfr4. These results indicate that the freezing sensitivity of cold-acclimated sfr4 is due to its continued susceptibility to LOR (associated with lyotropic formation of the hexagonal II phase) and associated with the low sugar content of its cells.
Disruption of Apyrases Inhibits Pollen Germination in Arabidopsis
Authors: Steinebrunner Iris , Wu Jian , Sun Yu , Corbett Ashley , Roux Stanley J.
Published: April 2003

In Arabidopsis, we previously identified two highly similar apyrases, AtAPY1 and AtAPY2. Here, T-DNA knockout (KO) mutations of each gene were isolated in a reverse genetic approach. The single KO mutants lacked a discernible phenotype. The double KO mutants, however, exhibited a complete inhibition of pollen germination, and this correlated with positive β-glucuronidase staining in the pollen of apyrase promoter:β-glucuronidase fusion transgenic lines. The vast majority of the pollen grains of these mutants were identical to wild type in size, shape, and nuclear state and were viable as assayed by metabolic activity and plasma membrane integrity. Complementation with either AtAPY1 or AtAPY2 cDNA rescued pollen germination, confirming that the phenotype was apyrase specific. Despite the redundancy of the two apyrases in rescue potential, transmission analyses suggested a greater role for AtAPY2 in male gamete success. The effect of mutant apyrase on the transmission through the female gametophyte was only marginal, and embryo development appeared normal in the absence of apyrases. The male-specific double KO mutation is fully penetrant and shows that apyrases play a crucial role in pollen germination.
Ethylene Rapidly Up-Regulates the Activities of Both Monomeric GTP-Binding Proteins and Protein Kinase(s) in Epicotyls of Pea
Authors: Moshkov Igor E. , Novikova Galina V. , Mur Luis A.J. , Smith Aileen R. , Hall Michael A.
Published: April 2003

It is demonstrated that, in etiolated pea (Pisum sativum) epicotyls, ethylene affects the activation of both monomeric GTP-binding proteins (monomeric G-proteins) and protein kinases. For monomeric G-proteins, the effect may be a rapid (2 min) and bimodal up-regulation, a transiently unimodal activation, or a transient down-regulation. Pretreatment with 1-methylcyclopropene abolishes the response to ethylene overall. Immunoprecipitation studies indicate that some of the monomeric G-proteins affected may be of the Rab class. Protein kinase activity is rapidly up-regulated by ethylene, the effect is inhibited by 1-methylcyclopropene, and the activation is bimodal. Immunoprecipitation indicates that the kinase(s) are of the MAP kinase ERK1 group. It is proposed that the data support the hypothesis that a transduction chain exists that is separate and antagonistic to that currently revealed by studies on Arabidopsis mutants.
Functional Analysis of Cystathionine γ-Synthase in Genetically Engineered Potato Plants
Authors: Kreft Oliver , Hoefgen Rainer , Hesse Holger
Published: April 2003

In plants, metabolic pathways leading to methionine (Met) and threonine diverge at the level of their common substrate, O-phosphohomoserine (OPHS). To investigate the regulation of this branch point, we engineered transgenic potato (Solanum tuberosum) plants affected in cystathionine γ-synthase (CgS), the enzyme utilizing OPHS for the Met pathway. Plants overexpressing potato CgS exhibited either: (a) high transgene RNA levels and 2.7-fold elevated CgS activities but unchanged soluble Met levels, or (b) decreased transcript amounts and enzyme activities (down to 7% of wild-type levels). In leaf tissues, these cosuppression lines revealed a significant reduction of soluble Met and an accumulation of OPHS. Plants expressing CgS antisense constructs exhibited reductions in enzyme activity to as low as 19% of wild type. The metabolite contents of these lines were similar to those of the CgS cosuppression lines. Surprisingly, neither increased nor decreased CgS activity led to visible phenotypic alterations or significant changes in protein-bound Met levels in transgenic potato plants, indicating that metabolic flux to Met synthesis was not greatly affected. Furthermore, in vitro feeding experiments revealed that potato CgS is not subject to feedback regulation by Met, as reported for Arabidopsis. In conclusion, our results demonstrate that potato CgS catalyzes a near-equilibrium reaction and, more importantly, does not display features of a pathway-regulating enzyme. These results are inconsistent with the current hypothesis that CgS exerts major Met metabolic flux control in higher plants.
Structural and Functional Vein Maturation in Developing Tobacco Leaves in Relation to AtSUC2 Promoter Activity
Authors: Wright Kathryn M. , Roberts Alison G. , Martens Helle J. , Sauer Norbert , Oparka Karl J.
Published: April 2003

Transgenic tobacco (Nicotiana tabacum) plants expressing green fluorescent protein (GFP) from theAtSUC2 promoter were used to study the function of different vein classes in developing leaves. In sink leaves, unloading capacity occurred acropetally, with the class I (midrib) and class II veins becoming functional in phloem unloading before the maturation of the class III veinal network. In contrast, in developing cotyledons and source leaves, loading capacity occurred in a basipetal direction. There was a strong correlation between loading capacity, as assessed by14C Suc uptake and companion cell expression of AtSUC2-GFP. Developing cotyledons were shown to utilize all available vein classes for loading. A second line of transgenic plants was produced in which GFP, expressed from theAtSUC2 promoter, was targeted to the endoplasmic reticulum instead of the cytoplasm. In these AtSUC2-GFP-ER plants, GFP was unable to traffic into the sieve element and was restricted solely to the companion cells of source leaf tissues. Partial shading of leaves undergoing the sink-source transition demonstrated that the activation of the AtSUC2 promoter in tobacco was influenced by light. Functional and structural maturation of the minor veins required light or a product of light. The activation of theAtSUC2 promoter within major veins appears to be regulated differently from that in the minor veins. The relationship between AtSUC2 activation and the activity of endogenous tobacco Suc transporters is discussed.
The Evolution of CONSTANS-Like Gene Families in Barley, Rice, and Arabidopsis
Authors: Griffiths Simon , Dunford Roy P. , Coupland George , Laurie David A.
Published: April 2003

The CO (CONSTANS) gene of Arabidopsis has an important role in the regulation of flowering by photoperiod. CO is part of a gene family with 17 members that are subdivided into three classes, termed Group I to III here. All members of the family have a CCT (CO,CO-like, TOC1) domain near the carboxy terminus. Group I genes, which include CO, have two zinc finger B-boxes near the amino terminus. Group II genes have one B-box, and Group III genes have one B-box and a second diverged zinc finger. Analysis of rice (Oryza sativa) genomic sequence identified 16 genes (OsA–OsP) that were also divided into these three groups, showing that their evolution predates monocot/dicot divergence. Eight Group I genes (HvCO1–HvCO8) were isolated from barley (Hordeum vulgare), of which two (HvCO1and HvCO2) were highly CO like.HvCO3 and its rice counterpart (OsB) had one B-box that was distantly related to Group II genes and was probably derived by internal deletion of a two B-box Group I gene. Sequence homology and comparative mapping showed that HvCO1 was the counterpart of OsA (Hd1), a major determinant of photoperiod sensitivity in rice. Major genes determining photoperiod response have been mapped in barley and wheat (Triticum aestivum), but none corresponded toCO-like genes. Thus, selection for variation in photoperiod response has affected different genes in rice and temperate cereals. The peptides of HvCO1, HvCO2(barley), and Hd1 (rice) show significant structural differences from CO, particularly amino acid changes that are predicted to abolish B-box2 function, suggesting an evolutionary trend toward a one-B-box structure in the most CO-like cereal genes.
Cytokinin Inhibits a Subset of Diageotropica-Dependent Primary Auxin Responses in Tomato
Authors: Coenen Catharina , Christian May , Lüthen Hartwig , Lomax Terri L.
Published: April 2003

Many aspects of plant development are regulated by antagonistic interactions between the plant hormones auxin and cytokinin, but the molecular mechanisms of this interaction are not understood. To test whether cytokinin controls plant development through inhibiting an early step in the auxin response pathway, we compared the effects of cytokinin with those of the dgt(diageotropica) mutation, which is known to block rapid auxin reactions of tomato (Lycopersicon esculentum) hypocotyls. Long-term cytokinin treatment of wild-type seedlings phenocopied morphological traits of dgt plants such as stunting of root and shoot growth, reduced elongation of internodes, reduced apical dominance, and reduced leaf size and complexity. Cytokinin treatment also inhibited rapid auxin responses in hypocotyl segments: auxin-stimulated elongation, H+ secretion, and ethylene synthesis were all inhibited by cytokinin in wild-type hypocotyl segments, and thus mimicked the impaired auxin responsiveness found in dgt hypocotyls. However, cytokinin failed to inhibit auxin-induced LeSAUR gene expression, an auxin response that is affected by the dgt mutation. In addition, cytokinin treatment inhibited the auxin induction of only one of two 1-aminocyclopropane-1-carboxylic acid synthase genes that exhibited impaired auxin inducibility in dgt hypocotyls. Thus, cytokinin inhibited a subset of the auxin responses impaired indgt hypocotyls, suggesting that cytokinin blocks at least one branch of the DGT-dependent auxin response pathway.
Water Relations Link Carbon and Oxygen Isotope Discrimination to Phloem Sap Sugar Concentration inEucalyptus globulus
Authors: Cernusak Lucas A. , Arthur David J. , Pate John S. , Farquhar Graham D.
Published: April 2003

A strong correlation was previously observed between carbon isotope discrimination (Δ13C) of phloem sap sugars and phloem sap sugar concentration in the phloem-bleeding tree Eucalyptus globulus Labill. (J. Pate, E. Shedley, D. Arthur, M. Adams [1998] Oecologia 117: 312–322). We hypothesized that correspondence between these two parameters results from covarying responses to plant water potential. We expected Δ13C to decrease with decreasing plant water potential and phloem sap sugar concentration to increase, thereby maintaining turgor within sieve tubes. The hypothesis was tested with analyses of E. globulus trees growing on opposite ends of a rainfall gradient in southwestern Australia. The Δ13C of phloem sap sugars was closely related to phloem sap sugar concentration (r = −0.90,P < 0.0001, n = 40). As predicted, daytime shoot water potential was positively related to Δ13C (r = 0.70, P< 0.0001, n = 40) and negatively related to phloem sap sugar concentration (r = −0.86,P < 0.0001, n = 40). Additional measurements showed a strong correspondence between predawn shoot water potential and phloem sap sugar concentration measured at midday (r = −0.87, P < 0.0001, n = 30). The Δ13C of phloem sap sugars collected from the stem agreed well with that predicted from instantaneous measurements of the ratio of intercellular to ambient carbon dioxide concentrations on subtending donor leaves. In accordance, instantaneous ratio of intercellular to ambient carbon dioxide concentrations correlated negatively with phloem sap sugar concentration (r = −0.91, P < 0.0001, n = 27). Oxygen isotope enrichment (Δ18O) in phloem sap sugars also varied with phloem sap sugar concentration (r = 0.91,P < 0.0001, n = 39), consistent with predictions from a theoretical model of Δ18O. We conclude that drought induces correlated variation in the concentration of phloem sap sugars and their isotopic composition in E. globulus.
Identification, Expression, and Import of Components 17 and 23 of the Inner Mitochondrial Membrane Translocase from Arabidopsis,
Authors: Murcha Monika W. , Lister Ryan , Ho Angela Y. Y. , Whelan James
Published: April 2003

Characterization of components 17 and 23 of the inner mitochondrial membrane translocase (TIM17:23) from Arabidopsis indicated that there were three genes present for TIM17 andTIM23 and two for TIM44.AtTIM17 differed from the yeast (Saccharomyces cerevisiae) and mammalian homologs in that two genes encoded proteins that were longer and one gene encoded a shorter protein. All Arabidopsis TIM23 predicted proteins appeared to lack the first 34 amino acids compared with yeast TIM23. All AtTIM17 andAtTIM23 genes were expressed but displayed different tissue and developmental profiles. Complementation of deletion mutants in yeast indicated that for AtTIM17, the extension at the C terminus not present in yeast had to be removed to achieve complementation, whereas for TIM23, a preprotein and amino acid transporter domain had to be present for complementation. Import assays with AtTIM17 and AtTIM23 indicated that they both contained internal signals for integration into the inner mitochondrial membrane in a membrane potential-dependent manner. The C terminus of imported AtTIM17-2 was susceptible to degradation by externally added protease with intact mitochondria. Removal of the 85 C-terminal amino acids resulted in import and full protection of the truncated protein. This suggests that the novel extension at the C terminus of AtTIM17-2 links the outer and inner membrane in a manner analogous to yeast TIM23.
Phloem Metabolism and Function Have to Cope with Low Internal Oxygen
Authors: van Dongen Joost T. , Schurr Ulrich , Pfister Michelle , Geigenberger Peter
Published: April 2003

We have investigated the consequences of endogenous limitations in oxygen delivery for phloem transport in Ricinus communis. In situ oxygen profiles were measured directly across stems of plants growing in air (21% [v/v] oxygen), using a microsensor with a tip diameter of approximately 30 μm. Oxygen levels decreased from 21% (v/v) at the surface to 7% (v/v) in the vascular region and increased again to 15% (v/v) toward the hollow center of the stem. Phloem sap exuding from small incisions in the bark of the stem was hypoxic, and the ATP to ADP ratio (4.1) and energy charge (0.78) were also low. When 5-cm stem segments of intact plants were exposed to zero external oxygen for 90 min, oxygen levels within the phloem decreased to approximately 2% (v/v), and ATP to ADP ratio and adenylate energy charge dropped further to 1.92 and 0.68, respectively. This was accompanied by a marked decrease in the phloem sucrose (Suc) concentration and Suc transport rate, which is likely to be explained by the inhibition of retrieval processes in the phloem. Germinating seedlings were used to analyze the effect of a stepwise decrease in oxygen tension on phloem transport and energy metabolism in more detail. Within the endosperm embedding the cotyledons—next to the phloem loading sites—oxygen decreased from approximately 14% (v/v) in 6-d-old seedlings down to approximately 6% (v/v) in 10-d-old seedlings. This was paralleled by a similar decrease of oxygen inside the hypocotyl. When the endosperm was removed and cotyledons incubated in a 100 mm Suc solution with 21%, 6%, 3%, or 0.5% (v/v) oxygen for 3 h before phloem sap was analyzed, decreasing oxygen tensions led to a progressive decrease in phloem energy state, indicating a partial inhibition of respiration. The estimated ratio of NADH to NAD+ in the phloem exudate remained low (approximately 0.0014) when oxygen was decreased to 6% and 3% (v/v) but increased markedly (to approximately 0.008) at 0.5% (v/v) oxygen, paralleled by an increase in lactate and ethanol. Suc concentration and translocation decreased when oxygen was decreased to 3% and 0.5% (v/v). Falling oxygen led to a progressive increase in amino acids, especially of alanine, γ-aminobutyrat, methionine, and isoleucine, a progressive decrease in the C to N ratio, and an increase in the succinate to malate ratio in the phloem. These results show that oxygen concentration is low inside the transport phloem in planta and that this results in adaptive changes in phloem metabolism and function.
Glucosylglycerol, a Compatible Solute, Sustains Cell Division under Salt Stress
Authors: Ferjani Ali , Mustardy Laszlo , Sulpice Ronan , Marin Kay , Suzuki Iwane , Hagemann Martin , Murata Norio
Published: April 2003

The cyanobacterium Synechocystis sp. PCC 6803 accumulates the compatible solute glucosylglycerol (GG) and sucrose under salt stress. Although the molecular mechanisms for GG synthesis including regulation of the GG-phosphate synthase (ggpS) gene, which encodes GgpS, has been intensively investigated, the role of GG in protection against salt stress remains poorly understood. In our study of the role of GG in the tolerance to salt stress, we found that salt stress due to 450 mm NaCl inhibited cell division and significantly increased cell size in ΔggpS mutant cells, whereas the inhibition of cell division and increase in cell size were observed in wild-type cells at high concentrations of NaCl, such as 800 mm. Electron microscopy revealed that, in ΔggpS cells, separation of daughter cells was incomplete, and aborted division could be recognized by the presence of a structure that resembled a division ring. The addition of GG to the culture medium protected ΔggpS cells against salt stress and reversed the adverse effects of NaCl on cell division and cell size. These observations suggest that GG is important for salt tolerance and thus for the proper division of cells under salt stress conditions.
Analysis of the Competence to Respond to KNOTTED1 Activity in Arabidopsis Leaves Using a Steroid Induction System
Authors: Hay Angela , Jackson David , Ori Naomi , Hake Sarah
Published: April 2003

Expression of KNOX(KNOTTED1-like homeobox) genes in the shoot apical meristem of Arabidopsis is required for maintenance of a functional meristem, whereas exclusion of KNOX gene expression from leaf primordia is required for the elaboration of normal leaf morphology. We have constructed a steroid-inducible system to regulate both the amount and timing of KN1(KNOTTED1) misexpression in Arabidopsis leaves. We demonstrate that lobed leaf morphology is produced in a dose-dependent manner, indicating that the amount of KN1 quantitatively affects the severity of lobing. The KN1-glucocorticoid receptor fusion protein is not detected in leaves in the absence of steroid induction, suggesting that it is only stable when associated with steroid in an active state. By using a second inducible fusion protein to mark exposure of leaf primordia to the steroid, we determined the stage of leaf development that produces lobed leaves in response to KN1. Primordia as old as plastochron 7 and as young as plastochron 2 were competent to respond to KN1.