bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in the sensitivity of parasitic weed seeds to germination stimulants
Authors: Matusova Radoslava , Mourik Tom van , Bouwmeester Harro J.
Published: December 2004

The effects of preconditioning temperature and preconditioning period on the sensitivity of parasitic weed seeds to the synthetic germination stimulant GR24 were studied under laboratory and field conditions. The temperature during preconditioning ofOrobanche cumanaandStriga hermonthicaseeds strongly affected the responsiveness of the seeds to the applied germination stimulant. Preconditioning at an optimal temperature (21°C forO. cumanaand 30°C forS. hermonthica) rapidly released dormancy and increased the sensitivity to GR24 by several orders of magnitude. After reaching maximum sensitivity, prolonged preconditioning rapidly induced secondary dormancy, i.e. decreased sensitivity ofO. cumanaandS. hermonthicato GR24. The rapid change in sensitivity of preconditioned seeds to germination stimulants during prolonged preconditioning was particularly visible at low concentrations of GR24. GR24 at higher concentrations (0.1 and 1 mg l1) usually induced high germination of both species, regardless of the preconditioning period. The striking similarities between the response of parasitic weed seeds to GR24, described here, and results in the literature on non-parasitic wild plant seeds are discussed. Our results show that parasitic weed seeds are highly sensitive to the germination stimulant for a short period of time only, and then enter into secondary dormancy relatively quickly. The similar germination pattern ofS. hermonthicaseeds preconditioned for prolonged periods of time under laboratory and field conditions suggests that the mechanism observed is of ecological significance.
Effects of five different salts on seed germination and seedling growth of Haloxylon ammodendron (Chenopodiaceae)
Authors: Tobe Kazuo , Li Xiaoming , Omasa Kenji
Published: December 2004

Saline soils contain multiple types of salt, each of which may exert a different effect on seed germination and seedling growth of plants. The effects of five types of salt on the initial growth ofHaloxylon ammodendron, a shrub found on both saline and non-saline areas in deserts of China, were investigated. Seeds were incubated at 20°;C in the dark in a solution (0 to –5.1 MPa) of a salt (NaCl, MgCl2, CaCl2, Na2SO4or MgSO4) or polyethylene glycol (PEG)-6000, or in a salt (NaCl or MgCl2) or PEG solution containing a low concentration of CaCl2. Seed germination, seedling growth and cation (Na+, Mg2+, Ca2+and K+) contents of seedlings were examined. Each salt had a different effect on seed germination, seedling growth and influx and outflux of cations in the seedlings. In both NaCl and MgCl2treatments, the addition of low concentrations of CaCl2favoured seed germination and seedling growth, and reduced K+outflux from seedlings, but caused no appreciable decrease in the influx of Na+or Mg2+into seedlings. Marked abnormalities in seedlings were found only in treatments with Mg2+salts, but these effects were completely alleviated by a low concentration of Ca2+(Ca2+/Mg2+= 0.012). The different responses of the initial growth inH. ammodendronto different isotonic salt solutions were attributed to differences among salt components in membrane permeability, toxicity and effects on functions of the plasma membrane and/or the cell wall.
Characterization of germinating and non-viable soybean seeds by nuclear magnetic resonance (NMR) spectroscopy
Authors: Krishnan P. , Joshi D.K. , Nagarajan Shantha , Moharir A.V.
Published: December 2004

The changes in water status of germinating and non-viable soybean (Glycine maxL. Merr.) seeds were characterized by nuclear magnetic resonance (NMR) spectroscopy. There were distinct changes in water status between viable and non-viable soybean seeds. In dry seeds, there were only two components, bound and bulk water, as revealed by component analysis of NMR (T2) data. On the contrary, a three-component water proton system (bound, bulk and free water) was observed in both germinating and non-viable soybeans during Phase I of hydration. The bulk water component of non-viable seeds disappeared completely during the lag phase (Phase II) of hydration, resulting in a two-component water proton system. In contrast, the three-component water proton system in Phase II was observed in the germinating seeds. Rapid hydration (Phase III), following Phase II, was observed in germinating soybean seeds only. Due to reorganization of water protons, there was a concomitant increase in bulk and free water, but a decrease in bound water. The physical state of water in these seeds (analysed by NMR spectroscopy) and the measurements of tissue leachate conductivity suggest that non-viable soybean seeds were more affected by the disorganized cell structure in the seed membrane system. The present study also provides evidence that physical reorganization of water is essential in germinating soybean seeds during hydration.
HIV-specific Cytotoxic T Cells from Long-Term Survivors Select a Unique T Cell Receptor
Authors: Dong Tao , Stewart-Jones Guillaume , Chen Nan , Easterbrook Philippa , Xu Xiaoning , Papagno Laura , Appay Victor , Weekes Michael , Conlon Chris , Spina Celsa , Little Susan , Screaton Gavin , van der Merwe Anton , Richman Douglas D. , McMichael Andrew J. , Jones E. Yvonne , Rowland-Jones Sarah L.
Published: December 2004

HIV-specific cytotoxic T lymphocytes (CTL) are important in controlling HIV replication, but the magnitude of the CTL response does not predict clinical outcome. In four donors with delayed disease progression we identified Vβ13.2 T cell receptors (TCRs) with very similar and unusually long β-chain complementarity determining region 3 (CDR3) regions in CTL specific for the immunodominant human histocompatibility leukocyte antigens (HLA)-B8–restricted human immunodeficiency virus-1 (HIV-1) nef epitope, FLKEKGGL (FL8). CTL expressing Vβ13.2 TCRs tolerate naturally arising viral variants in the FL8 epitope that escape recognition by other CTL. In addition, they expand efficiently in vitro and are resistant to apoptosis, in contrast to FL8–specific CTL using other TCRs. Selection of Vβ13.2 TCRs by some patients early in the FL8-specific CTL response may be linked with better clinical outcome.
Down-regulation of Plasminogen Activator Inhibitor 1 Expression Promotes Myocardial Neovascularization by Bone Marrow Progenitors
Authors: Xiang Guosheng , Schuster Michael D. , Seki Tetsunori , Kocher Alfred A. , Eshghi Shawdee , Boyle Andrew , Itescu Silviu
Published: December 2004

Human adult bone marrow–derived endothelial progenitors, or angioblasts, induce neovascularization of infarcted myocardium via mechanisms involving both cell surface urokinase-type plasminogen activator, and interactions between β integrins and tissue vitronectin. Because each of these processes is regulated by plasminogen activator inhibitor (PAI)-1, we selectively down-regulated PAI-1 mRNA in the adult heart to examine the effects on postinfarct neovascularization and myocardial function. Sequence-specific catalytic DNA enzymes inhibited rat PAI-1 mRNA and protein expression in peri-infarct endothelium within 48 h of administration, and maintained down-regulation for at least 2 wk. PAI-1 inhibition enhanced vitronectin-dependent transendothelial migration of human bone marrow–derived CD34+ cells, and resulted in a striking augmentation of angioblast-dependent neovascularization. Development of large, thin-walled vessels at the peri-infarct region was accompanied by induction of proliferation and regeneration of endogenous cardiomyocytes and functional cardiac recovery. These results identify a causal relationship between elevated PAI-1 levels and poor outcome in patients with myocardial infarction through mechanisms that directly inhibit bone marrow–dependent neovascularization. Strategies that reduce myocardial PAI-1 expression appear capable of enhancing cardiac neovascularization, regeneration, and functional recovery after ischemic insult.
CD8 Epitope Escape and Reversion in Acute HCV Infection
Authors: Timm Joerg , Lauer Georg M. , Kavanagh Daniel G. , Sheridan Isabelle , Kim Arthur Y. , Lucas Michaela , Pillay Thillagavathie , Ouchi Kei , Reyor Laura L. , zur Wiesch Julian Schulze , Gandhi Rajesh T. , Chung Raymond T. , Bhardwaj Nina , Klenerman Paul , Walker Bruce D. , Allen Todd M.
Published: December 2004

In the setting of acute hepatitis C virus (HCV) infection, robust HCV-specific CD8+ cytotoxic T lymphocyte (CTL) responses are associated with initial control of viremia. Despite these responses, 70–80% of individuals develop persistent infection. Although viral escape from CD8 responses has been illustrated in the chimpanzee model of HCV infection, the effect of CD8 selection pressure on viral evolution and containment in acute HCV infection in humans remains unclear. Here, we examined viral evolution in an immunodominant human histocompatibility leukocyte antigen (HLA)-B8–restricted NS3 epitope in subjects with acute HCV infection. Development of mutations within the epitope coincided with loss of strong ex vivo tetramer and interferon γ enzyme-linked immunospot responses, and endogenous expression of variant NS3 sequences suggested that the selected mutations altered processing and presentation of the variant epitope. Analysis of NS3 sequences from 30 additional chronic HCV-infected subjects revealed a strong association between sequence variation within this region and expression of HLA-B8, supporting reproducible allele-specific selection pressures at the population level. Interestingly, transmission of an HLA-B8–associated escape mutation to an HLA-B8 negative subject resulted in rapid reversion of the mutation. Together, these data indicate that viral escape from CD8+ T cell responses occurs during human HCV infection and that acute immune selection pressure is of sufficient magnitude to influence HCV evolution.
Role of Dok-1 and Dok-2 in Myeloid Homeostasis and Suppression of Leukemia
Authors: Yasuda Tomoharu , Shirakata Masaki , Iwama Atsushi , Ishii Asuka , Ebihara Yasuhiro , Osawa Mitsujiro , Honda Kazuho , Shinohara Hisaaki , Sudo Katsuko , Tsuji Kohichiro , Nakauchi Hiromitsu , Iwakura Yoichiro , Hirai Hisamaru , Oda Hideaki , Yamamoto Tadashi , Yamanashi Yuji
Published: December 2004

Dok-1 and Dok-2 are closely related rasGAP-associated docking proteins expressed preferentially in hematopoietic cells. Although they are phosphorylated upon activation of many protein tyrosine kinases (PTKs), including those coupled with cytokine receptors and oncogenic PTKs like Bcr-Abl, their physiological roles are largely unidentified. Here, we generated mice lacking Dok-1 and/or Dok-2, which included the double-deficient mice succumbed to myeloproliferative disease resembling human chronic myelogenous leukemia (CML) and chronic myelomonocytic leukemia. The double-deficient mice displayed medullary and extramedullary hyperplasia of granulocyte/macrophage progenitors with leukemic potential, and their myeloid cells showed hyperproliferation and hypo-apoptosis upon treatment and deprivation of cytokines, respectively. Consistently, the mutant myeloid cells showed enhanced Erk and Akt activation upon cytokine stimulation. Moreover, loss of Dok-1 and/or Dok-2 induced blastic transformation of chronic phase CML-like disease in mice carrying the bcr-abl gene, a cause of CML. These findings demonstrate that Dok-1 and Dok-2 are key negative regulators of cytokine responses and are essential for myeloid homeostasis and suppression of leukemia.
Role of Dok-1 and Dok-2 in Leukemia Suppression
Authors: Niki Masaru , Di Cristofano Antonio , Zhao Mingming , Honda Hiroaki , Hirai Hisamaru , Van Aelst Linda , Cordon-Cardo Carlos , Pandolfi Pier Paolo
Published: December 2004

Chronic myelogenous leukemia (CML) is characterized by the presence of the chimeric p210bcr/abl oncoprotein that shows elevated and constitutive protein tyrosine kinase activity relative to the normal c-abl tyrosine kinase. Although several p210bcr/abl substrates have been identified, their relevance in the pathogenesis of the disease is unclear. We have identified a family of proteins, Dok (downstream of tyrosine kinase), coexpressed in hematopoietic progenitor cells. Members of this family such as p62dok(Dok-1) and p56dok-2(Dok-2) associate with the p120 rasGTPase-activating protein (rasGAP) upon phosphorylation by p210bcr/abl as well as receptor and nonreceptor tyrosine kinases. Here, we report the generation and characterization of single and double Dok-1 or Dok-2 knockout (KO) mutants. Single KO mice displayed normal steady-state hematopoiesis. By contrast, concomitant Dok-1 and Dok-2 inactivation resulted in aberrant hemopoiesis and Ras/MAP kinase activation. Strikingly, all Dok-1/Dok-2 double KO mutants spontaneously developed transplantable CML-like myeloproliferative disease due to increased cellular proliferation and reduced apoptosis. Furthermore, Dok-1 or Dok-2 inactivation markedly accelerated leukemia and blastic crisis onset in Tec-p210bcr/abl transgenic mice known to develop, after long latency, a myeloproliferative disorder resembling human CML. These findings unravel the critical and unexpected role of Dok-1 and Dok-2 in tumor suppression and control of the hematopoietic compartment homeostasis.
Mycobacterium tuberculosis pks12 Produces a Novel Polyketide Presented by CD1c to T Cells
Authors: Matsunaga Isamu , Bhatt Apoorva , Young David C. , Cheng Tan-Yun , Eyles Stephen J. , Besra Gurdyal S. , Briken Volker , Porcelli Steven A. , Costello Catherine E. , Jacobs William R. , Moody D. Branch
Published: December 2004

CD1c-mediated T cells are activated by a mycobacterial phospholipid antigen whose carbohydrate structure precisely corresponds to mammalian mannosyl β-1-phosphodolichol (MPD), but contains an unusual lipid moiety. Here, we show that this T cell antigen is a member of a family of branched, alkane lipids that vary in length (C30-34) and are produced by medically important mycobacteria such as M. tuberculosis and M. bovis Bacille-Calmette-Guerin. The alkane moiety distinguished these mycobacterial lipid antigens from mammalian MPDs and was necessary for activation of CD1c-restricted T cells, but could not be accounted for by any known lipid biosynthetic pathway. Metabolic labeling and mass spectrometric analyses suggested a mechanism for elongating lipids using alternating C2 and C3 units, rather than C5 isopentenyl pyrophosphate. Inspection of the M. tuberculosis genome identified one candidate gene, pks12, which was predicted to encode the largest protein in M. tuberculosis, consisting of 12 catalytic domains that correspond to key steps in the proposed pathway. Genetic deletion and complementation showed that Pks12 was necessary for antigen production, but did not affect synthesis of true isoprenols. These studies establish the genetic and enzymatic basis for a previously unknown type of polyketide, designated mycoketide, which contains a lipidic pathogen-associated molecular pattern.
A note on the weighted Hilbert’s inequality
Authors: Li Xian-Jin
Published: December 2004

A finite Hilbert transformation associated with a polynomial is the analogue of a Hilbert transformation associated with an entire function which is a generalization of the classical Hilbert transformation. The weighted Hilbert inequality, which has applications in analytic number theory, is closely related to the finite Hilbert transformation associated with a polynomial. In this note, we study a relation between the finite Hilbert transformation and the weighted Hilbert’s inequality. A question is posed about the finite Hilbert transformation, of which an affirmative answer implies the weighted Hilbert inequality.
Real 3𝑥+1
Authors: Misiurewicz Michał , Rodrigues Ana
Published: December 2004

The famous

3
x
+
1

3x+1

problem involves applying two maps:

T
0

(
x
)
=
x

/

2

T_0(x)=x/2

and

T
1

(
x
)
=
(
3
x
+
1
)

/

2

T_1(x)=(3x+1)/2

to positive integers. If

x
x

is even, one applies

T
0

T_0

, if it is odd, one applies

T
1

T_1

. The conjecture states that each trajectory of the system arrives to the periodic orbit

{
1
,
2
}

\{1,2\}

. In this paper, instead of choosing each time which map to apply, we allow ourselves more freedom and apply both

T
0

T_0

and

T
1

T_1

independently of

x
x

. That is, we consider the action of the free semigroup with generators

T
0

T_0

and

T
1

T_1

on the space of positive real numbers. We prove that this action is minimal (each trajectory is dense) and that the periodic points are dense. Moreover, we give a full characterization of the group of transformations of the real line generated by

T
0

T_0

and

T
1

T_1

.
Characterization of scaling functions in a multiresolution analysis
Authors: Cifuentes P. , Kazarian K. , San Antolín A.
Published: December 2004

We characterize the scaling functions of a multiresolution analysis in a general context, where instead of the dyadic dilation one considers the dilation given by a fixed linear map

A
:

R

n

→

R

n

A: \mathbb {R}^n\rightarrow \mathbb {R}^n

such that

A
(

Z

n

)
⊂

Z

n

A(\mathbb {Z}^n) \subset \mathbb {Z}^n

and all (complex) eigenvalues of

A
A

have absolute value greater than

1.
1.

In the general case the conditions depend on the map

A
.

A.

We identify some maps for which the obtained condition is equivalent to the dyadic case, i.e., when

A
A

is a diagonal matrix with all numbers in the diagonal equal to

2.
2.

There are also easy examples of expanding maps for which the obtained condition is not compatible with the dyadic case. The complete characterization of the maps for which the obtained conditions are equivalent is out of the scope of the present note.
Restricted weak type versus weak type
Authors: Grafakos Loukas , Mastyło Mieczysław
Published: December 2004

We prove that translation invariant multilinear operators of restricted weak type

(
1
,
1
,
…
,
1
,
q
)

(1,1,\dots , 1,q)

must necessarily be of weak type

(
1
,
1
,
…
,
1
,
q
)

(1,1,\dots , 1,q)

. We give applications.
Subelliptic Cordes estimates
Authors: Domokos András , Manfredi Juan
Published: December 2004

We prove Cordes type estimates for subelliptic linear partial differential operators in non-divergence form with measurable coefficients in the Heisenberg group. As an application we establish interior horizontal

W

2
,
2

W^{2,2}

-regularity for p-harmonic functions in the Heisenberg group

H

1

{\mathbb H}^1

for the range

17

−
1

2

≤
p
>

5
+

5

2

\frac {\sqrt {17}-1}{2} \leq p > \frac {5+\sqrt {5}}{2}

.
Clustering of diverse genomic data using information fusion
Authors: Kasturi Jyotsna , Acharya Raj
Published: December 2004

Motivation: Genome sequencing projects and high-through-put technologies like DNA and Protein arrays have resulted in a very large amount of information-rich data. Microarray experimental data are a valuable, but limited source for inferring gene regulation mechanisms on a genomic scale. Additional information such as promoter sequences of genes/DNA binding motifs, gene ontologies, and location data, when combined with gene expression analysis can increase the statistical significance of the finding. This paper introduces a machine learning approach to information fusion for combining heterogeneous genomic data. The algorithm uses an unsupervised joint learning mechanism that identifies clusters of genes using the combined data.

Results: The correlation between gene expression time-series patterns obtained from different experimental conditions and the presence of several distinct and repeated motifs in their upstream sequences is examined here using publicly available yeast cell-cycle data. The results show that the combined learning approach taken here identifies correlated genes effectively. The algorithm provides an automated clustering method, but allows the user to specify apriori the influence of each data type on the final clustering using probabilities.

Availability: Software code is available by request from the first author.

Contact:  jkasturi@cse.psu.edu
An architecture for biological information extraction and representation
Authors: Vailaya Aditya , Bluvas Peter , Kincaid Robert , Kuchinsky Allan , Creech Michael , Adler Annette
Published: December 2004

Motivations: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data.

Results: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation.

Contact:  aditya_vailaya@agilent.com
Multidimensional support vector machines for visualization of gene expression data
Authors: Komura D. , Nakamura H. , Tsutsumi S. , Aburatani H. , Ihara S.
Published: December 2004

Motivation: Since DNA microarray experiments provide us with huge amount of gene expression data, they should be analyzed with statistical methods to extract the meanings of experimental results. Some dimensionality reduction methods such as Principal Component Analysis (PCA) are used to roughly visualize the distribution of high dimensional gene expression data. However, in the case of binary classification of gene expression data, PCA does not utilize class information when choosing axes. Thus clearly separable data in the original space may not be so in the reduced space used in PCA.

Results: For visualization and class prediction of gene expression data, we have developed a new SVM-based method called multidimensional SVMs, that generate multiple orthogonal axes. This method projects high dimensional data into lower dimensional space to exhibit properties of the data clearly and to visualize a distribution of the data roughly. Furthermore, the multiple axes can be used for class prediction. The basic properties of conventional SVMs are retained in our method: solutions of mathematical programming are sparse, and nonlinear classification is implemented implicitly through the use of kernel functions. The application of our method to the experimentally obtained gene expression datasets for patients' samples indicates that our algorithm is efficient and useful for visualization and class prediction.

Contact:  komura@hal.rcast.u-tokyo.ac.jp
Finding differentially expressed genes for pattern generation
Authors: Abul Osman , Alhajj Reda , Polat Faruk , Barker Ken
Published: December 2004

Motivation: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.

Results: We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second method, one for error minimization and the other for confidence bounding. Also, we show how the method called Patterns from Gene Expression (PaGE) (Grant et al., 2000) can benefit from q-values. Finally, we conducted some experiments to demonstrate the effectiveness of the proposed methods; experimental results on a selected dataset (BRCA1 vs BRCA2 tumor types) are provided.

Contact:  alhajj@cpsc.ucalgary.ca
An integrated tool for microarray data clustering and cluster validity assessment
Authors: Bolshakova Nadia , Azuaje Francisco , Cunningham Pádraig
Published: December 2004

Summary: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations.

Availability: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html

Contact:  Nadia.Bolshakova@cs.tcd.ie
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Authors: Stamatakis A. , Ludwig T. , Meier H.
Published: December 2004

Motivation: The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining. Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa.

Results: In this paper we present the latest release of our program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor. We compare RAxML-III to the currently fastest implementations for maximum likelihood and bayesian inference: PHYML and MrBayes. Whereas RAxML-III performs worse than PHYML and MrBayes on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values.

Availability Supplementary information: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http://wwwbode.cs.tum/~stamatak

Contact:  stamatak@cs.tum.edu
Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-Citrate Lyase in Arabidopsis
Authors: Fatland Beth L. , Nikolau Basil J. , Wurtele Eve Syrkin
Published: December 2004

Acetyl-CoA provides organisms with the chemical flexibility to biosynthesize a plethora of natural products that constitute much of the structural and functional diversity in nature. Recent studies have characterized a novel ATP-citrate lyase (ACL) in the cytosol of Arabidopsis thaliana. In this study, we report the use of antisense RNA technology to generate a series of Arabidopsis lines with a range of ACL activity. Plants with even moderately reduced ACL activity have a complex, bonsai phenotype, with miniaturized organs, smaller cells, aberrant plastid morphology, reduced cuticular wax deposition, and hyperaccumulation of starch, anthocyanin, and stress-related mRNAs in vegetative tissue. The degree of this phenotype correlates with the level of reduction in ACL activity. These data indicate that ACL is required for normal growth and development and that no other source of acetyl-CoA can compensate for ACL-derived acetyl-CoA. Exogenous malonate, which feeds into the carboxylation pathway of acetyl-CoA metabolism, chemically complements the morphological and chemical alterations associated with reduced ACL expression, indicating that the observed metabolic alterations are related to the carboxylation pathway of cytosolic acetyl-CoA metabolism. The observations that limiting the expression of the cytosolic enzyme ACL reduces the accumulation of cytosolic acetyl-CoA–derived metabolites and that these deficiencies can be alleviated by exogenous malonate indicate that ACL is a nonredundant source of cytosolic acetyl-CoA.
Cytosolic Ascorbate Peroxidase 1 Is a Central Component of the Reactive Oxygen Gene Network of Arabidopsis
Authors: Davletova Sholpan , Rizhsky Ludmila , Liang Hongjian , Shengqiang Zhong , Oliver David J. , Coutu Jesse , Shulaev Vladimir , Schlauch Karen , Mittler Ron
Published: December 2004

Reactive oxygen species (ROS), such as O2  − and H2O2, play a key role in plant metabolism, cellular signaling, and defense. In leaf cells, the chloroplast is considered to be a focal point of ROS metabolism. It is a major producer of O2  − and H2O2 during photosynthesis, and it contains a large array of ROS-scavenging mechanisms that have been extensively studied. By contrast, the function of the cytosolic ROS-scavenging mechanisms of leaf cells is largely unknown. In this study, we demonstrate that in the absence of the cytosolic H2O2-scavenging enzyme ascorbate peroxidase 1 (APX1), the entire chloroplastic H2O2-scavenging system of Arabidopsis thaliana collapses, H2O2 levels increase, and protein oxidation occurs. We further identify specific proteins oxidized in APX1-deficient plants and characterize the signaling events that ensue in knockout-Apx1 plants in response to a moderate level of light stress. Using a dominant-negative approach, we demonstrate that heat shock transcription factors play a central role in the early sensing of H2O2 stress in plants. Using knockout plants for the NADPH oxidase D protein (knockout-RbohD), we demonstrate that RbohD might be required for ROS signal amplification during light stress. Our study points to a key role for the cytosol in protecting the chloroplast during light stress and provides evidence for cross-compartment protection of thylakoid and stromal/mitochondrial APXs by cytosolic APX1.
The Inheritance of Apomixis inPoa pratensisConfirms a Five Locus Model with Differences in Gene Expressivity and Penetrance
Authors: Matzk Fritz , Prodanovic Sanja , Bäumlein Helmut , Schubert Ingo
Published: December 2004

The genetic control of apomixis was studied in numerous segregating progenies originated from intercrossing and selfing of obligate sexual and facultative apomictic parents in Poa pratensis by means of the flow cytometric seed screen. The data support a novel model with five major genes required to control asexual seed formation: the Apospory initiator (Ait) gene, the Apospory preventer (Apv) gene, a Megaspore development (Mdv) gene, the Parthenogenesis initiator (Pit) gene, and the Parthenogenesis preventer (Ppv) gene. Differences in expressivity and interactions of these genes are responsible for the wide variation of the mode of reproduction. Apospory and parthenogenesis as well as the initiator and preventer genes of these components segregate independently. The genotypes with the highest expressivity of apospory and parthenogenesis were assigned as Ait-/apvapv/Pit-/ppvppv, those with intermediate expressivity as Ait-/Apv-/Pit-/Ppv-, and those with low expressivity as aitait/apvapv/pitpit/ppvppv. Among the self progenies of obligate sexual individuals, plants with a low capacity for apospory and/or parthenogenesis occurred, indicating that the sexual parents were heterozygous for the preventer genes and homozygous for the recessive initiator alleles (aitait/Apv-/pitpit/Ppv-). The dominant allele Ait exhibits incomplete penetrance. The degree of expressivity of apospory and parthenogenesis was constant among several harvest years of F1 plants.
Two Plant–Viral Movement Proteins Traffic in the Endocytic Recycling Pathway
Authors: Haupt Sophie , Cowan Graham H. , Ziegler Angelika , Roberts Alison G. , Oparka Karl J. , Torrance Lesley
Published: December 2004

Many plant viruses exploit a conserved group of proteins known as the triple gene block (TGB) for cell-to-cell movement. Here, we investigated the interaction of two TGB proteins (TGB2 and TGB3) of Potato mop-top virus (PMTV), with components of the secretory and endocytic pathways when expressed as N-terminal fusions to green fluorescent protein or monomeric red fluorescent protein (mRFP). Our studies revealed that fluorophore-labeled TGB2 and TGB3 showed an early association with the endoplasmic reticulum (ER) and colocalized in motile granules that used the ER-actin network for intracellular movement. Both proteins increased the size exclusion limit of plasmodesmata, and TGB3 accumulated at plasmodesmata in the absence of TGB2. TGB3 contains a putative Tyr-based sorting motif, mutations in which abolished ER localization and plasmodesmatal targeting. Later in the expression cycle, both fusion proteins were incorporated into vesicular structures. TGB2 associated with these structures on its own, but TGB3 could not be incorporated into the vesicles in the absence of TGB2. Moreover, in addition to localization to the ER and motile granules, mRFP-TGB3 was incorporated into vesicles when expressed in PMTV-infected epidermal cells, indicating recruitment by virus-expressed TGB2. The TGB fusion protein-containing vesicles were labeled with FM4-64, a marker for plasma membrane internalization and components of the endocytic pathway. TGB2 also colocalized in vesicles with Ara7, a Rab5 ortholog that marks the early endosome. Protein interaction analysis revealed that recombinant TGB2 interacted with a tobacco protein belonging to the highly conserved RME-8 family of J-domain chaperones, shown to be essential for endocytic trafficking in Caenorhabditis elegans and Drosophila melanogaster. Collectively, the data indicate the involvement of the endocytic pathway in viral intracellular movement, the implications of which are discussed.
New Subunits NDH-M, -N, and -O, Encoded by Nuclear Genes, Are Essential for Plastid Ndh Complex Functioning in Higher Plants
Authors: Rumeau Dominique , Bécuwe-Linka Noëlle , Beyly Audrey , Louwagie Mathilde , Garin Jérôme , Peltier Gilles
Published: December 2004

In higher plants, the Ndh complex reduces plastoquinones and is involved in cyclic electron flow around photosystem I, supplying extra-ATP for photosynthesis, particularly under environmental stress conditions. Based on plastid genome sequences, the Ndh complex would contain 11 subunits (NDH-A to -K), but homologies with bacterial complex indicate the probable existence of additional subunits. To identify missing subunits, tobacco (Nicotiana tabacum) NDH-H was His tagged at its N terminus using plastid transformation. A functional Ndh subcomplex was purified by Ni2+ affinity chromatography and its subunit composition analyzed by mass spectrometry. Five plastid encoded subunits (NDH-A, -H, -I, -J, and -K) were identified as well as three new subunits (NDH-M, -N, and -O) homologous to cyanobacterial and higher plant proteins. Arabidopsis thaliana mutants missing one of these new subunits lack a functional Ndh complex, and NDH-M and NDH-N are not detected in a tobacco transformant lacking the Ndh complex. We discuss the involvement of these three nuclear-encoded subunits in the functional integrity of the plastidial complex.
Arabidopsis Membrane Steroid Binding Protein 1 Is Involved in Inhibition of Cell Elongation
Authors: Yang Xiao-Hua , Xu Zhi-Hong , Xue Hong-Wei
Published: December 2004

A putative Membrane Steroid Binding Protein (designated MSBP1) was identified and functionally characterized as a negative regulator of cell elongation in Arabidopsis thaliana. The MSBP1 gene encodes a 220–amino acid protein that can bind to progesterone, 5-dihydrotestosterone, 24-epi-brassinolide (24-eBL), and stigmasterol with different affinities in vitro. Transgenic plants overexpressing MSBP1 showed short hypocotyl phenotype and increased steroid binding capacity in membrane fractions, whereas antisense MSBP1 transgenic plants showed long hypocotyl phenotypes and reduced steroid binding capacity, indicating that MSBP1 negatively regulates hypocotyl elongation. The reduced cell elongation of MSBP1-overexpressing plants was correlated with altered expression of genes involved in cell elongation, such as expansins and extensins, indicating that enhanced MSBP1 affected a regulatory pathway for cell elongation. Suppression or overexpression of MSBP1 resulted in enhanced or reduced sensitivities, respectively, to exogenous progesterone and 24-eBL, suggesting a negative role of MSBP1 in steroid signaling. Expression of MSBP1 in hypocotyls is suppressed by darkness and activated by light, suggesting that MSBP1, as a negative regulator of cell elongation, plays a role in plant photomorphogenesis. This study demonstrates the functional roles of a steroid binding protein in growth regulation in higher plants.
Modeling Conditional Yield Densities
Authors: Ker Alan P. , Coble Keith
Published: December 2004

Given the increasing interest in agricultural risk, many have sought improved methods to characterize conditional crop‐yield densities. While most have postulated the Beta as a flexible alternative to the Normal, others have chosen nonparametric methods. Unfortunately, yield data tends not to be sufficiently abundant to invalidate many reasonable parametric models. This is problematic because conclusions from economic analyses, which require estimated conditional yield densities, tend not to be invariant to the modeling assumption. We propose a semiparametric estimator that, because of its theoretical properties and our simulation results, enables one to empirically proceed with a higher degree of confidence.
Stochastic Technology, Risk Preferences, and Adoption of Site‐Specific Technologies
Authors: Isik Murat , Khanna Madhu
Published: December 2004

A model of farmer decision making is developed to determine the extent to which uncertainties about soil fertility and weather affect the value of site‐specific technologies (SSTs) using jointly estimated risk and technology parameters. Uncertainty can lead risk‐averse farmers to apply more fertilizers and generate more pollution than in the certainty case. Ignoring uncertainty and risk aversion would overestimate the economic and environmental benefits of SSTs and underestimate the subsidy required to induce adoption. Accounting for uncertainties and risk preferences might explain the low observed adoption rates of SSTs. Improving the accuracy of SSTs would increase the incentives for adoption.
Crop Insurance in a Political Economy: An Alternative Perspective on Agricultural Policy
Authors: Innes Robert
Published: December 2004

Lawmakers often subsidize farmers in times of financial distress. This article models this political impulse as a constraint on government farm policy, describing how ex ante government farm insurance can deter ex post“disaster relief” and improve production incentives by countering the moral hazard that otherwise prevails. Absent ex ante government policy, ex post relief takes the form of revenue insurance, which prompts excessive entry into farm production and under‐production by operating farmers. Ex ante government policy can raise economic and political welfare by buying out low productivity farmers and offering profitable farmers a combination of revenue insurance, price supports, and a program participation fee.
Price Stabilization and the Risk‐Averse Firm
Authors: Chambers Robert G. , Quiggin John
Published: December 2004

An analytically simple and tractable approach to firm‐level welfare analysis of complete and partial mean‐preserving price stabilization for producers with general risk‐averse preferences facing a stochastic technology is developed. Necessary and sufficient conditions for price stabilization to be welfare enhancing are derived under different assumptions of the producer's preferences and the producer's technology. Existing stabilization results for the risk‐averse firm are shown to be corollaries of these more general results.
Distinguishing Errors in Measurement from Errors in Optimization
Authors: Pope Rulon D. , Just Richard E.
Published: December 2004

Typical econometric production practices under duality ignore the source of disturbances. We show that, depending on the source, a different approach to estimation is required. The typical approach applies under errors in factor input measurement rather than errors in optimization. An approach to the identification of disturbance sources is suggested. We find credible evidence in U.S. agriculture of errors in optimization compared to errors of measurement, and thus reject the typical specification.
Fertilizer Use, Risk, and Off‐Farm Labor Markets in the Semi‐Arid Tropics of India
Authors: Lamb Russell L.
Published: December 2004

A two‐period model is developed in which a risk‐averse farmer uses off‐farm labor to smooth consumption, leading to greater use of fertilizer. Fertilizer demand is shown to increase with the depth of the off‐farm labor market. Controlling for exogenous weather risk, farmers use more fertilizer the lower the unemployment rate and the higher the share of nonagricultural work in total off‐farm labor. The results suggest that off‐farm labor markets and own‐farm production may be complementary in risky production environments, so that policies which promote the depth of the off‐farm labor market in low‐income areas may also bolster farm productivity.
Specialization and Diversification in Agricultural Transformation: The Case of West Punjab, 1903–92
Authors: Kurosaki Takashi
Published: December 2004

In this article, the role of crop specialization and diversification in agricultural transformation is investigated empirically. Changes in aggregate land productivity are associated structurally with inter‐crop and inter‐district reallocation of land use. Results from a region with the oldest history of agricultural commercialization in developing countries show that cropping patterns of subsistence agriculture changed substantially, with rising concentration of crop acreage in districts with higher and growing productivity. Rapid specialization in crop production was observed at the district level recently, after a phase with sporadic specialization. These changes reflected comparative advantage and contributed to the improvement in aggregate land productivity.
Market Transparency and Market Structure: The Livestock Mandatory Reporting Act of 1999
Authors: Azzam Azzeddine
Published: December 2004

The premise of the Livestock Mandatory Reporting Act of 1999 is that enhanced transparency promotes competition. This article provides a theoretical study of the consequences of such transparency for the structure, conduct, and performance of the livestock industry. I conclude that the usefulness of the Act to the livestock industry may not be in the value of reported information to feeders, as the supporters of the Act claim. Rather, by forcing packers to pool information at negligible marginal cost, the Act may foster more competitive conduct in the procurement of livestock.
Development of the Interactive Broiler Income Spreadsheet
Authors: Shofner Tara
Published: December 2004

The poultry industry has experienced unprecedented efficiencies since 1960 in large part due to vertical integration facilitated by production contracts between growers and integrators. As growers seek information about contract production they need to be well informed about all aspects of the process, especially potential income. Recent poultry grower complaints have surfaced as a result of incorrect expense and revenue expectations. The Interactive Broiler Income Spreadsheet (IBIS) is developed to enable current and prospective poultry producers to better estimate income. IBIS, an unbiased Excel spreadsheet tool to assist in decision‐making regarding broiler production profitability, uses actual grower expense and revenue information or, alternatively, grower‐panel default data to assess income under various grower‐specified production, expense, and price scenarios.

Poultry integrator grower service personnel, lenders, and Cooperative Extension professionals will utilize IBIS to assist growers in operational planning and risk tolerance identification in varying economic situations. Growers may also gauge effects of capital improvements, equipment upgrades, chick placements, and time between flocks on income.
A Note on Estimating Nested Constant Elasticity of Substitution Preferences for Outdoor Recreation
Authors: von Haefen Roger H. , Phaneuf Daniel J.
Published: December 2004

A generalized version of a well‐known statistical result is used to suggest an alternative strategy for estimating nested constant elasticity of substitution preferences for recreation demand. Parameter and welfare estimates from nested constant elasticity of substitution count data demand system models are presented and compared to estimates from the multinomial approaches developed previously. A significant advantage of the count data estimation strategy over the multinomial‐based approaches is that the analyst avoids the difficulties associated with choice occasion specification and interpretation.
Estimating Willingness to Pay for Improved Water Quality in the Presence of Item Nonresponse Bias
Authors: Brox James A. , Kumar Ramesh C. , Stollery Kenneth R.
Published: December 2004

This article deals with the problem of item nonresponse in contingent valuation surveys using a payment‐card method, by applying a grouped‐data sample‐selection estimation technique that is capable of imputing the missing values conditional upon a respondent's decision to answer a willingness‐to‐pay question. The advantage of the technique lies in its ability to utilize all of the information in the sample, permitting a more efficient estimation in the presence of item nonresponse bias. The major determinants of willingness to pay appear to be household income, number of children, education, perception of existing water quality, and identification with environmental issues.
Valuing Pre‐Commercial Genetic Resources: A Maximum Entropy Approach
Authors: Zohrabian Armineh , Traxler Greg , Caudill Steven , Smale Melinda
Published: December 2004

Genetic improvement has been a major contributor to agricultural productivity in the United States, but many questions about the economics of crop breeding, such as the value of pre‐commercial germplasm, remain unanswered. This study estimates the marginal value of poorly characterized materials contained in the U.S. national germplasm system. Within the search theoretic framework, we apply a maximum entropy method to estimate the probability and the expected level of improvement in pest susceptibility relative to its best previously observed level. The results indicate that the lower‐bound estimate of benefit is significantly higher than the upper‐bound cost of conserving an accession.
Preservation of Species and Genetic Diversity
Authors: Önal Hayri
Published: December 2004

This article presents a mathematical programming approach to determine a conservation strategy that maximizes preserved species' diversity under limited resource availability. Diversity is defined as the negative of total diversity loss given by the sum of genetic distances between extinct species and their closest surviving relatives. The model incorporates both species richness and genetic diversity as the conservation criteria when determining species preservation and site selection decisions. The article also presents two empirical applications to the conservation of 15 crane species and 208 genera including most of the endangered or threatened North American bird species.