bluuebunny/crossref_metadata_2025 huggingface dataset:
Orphan nuclear receptor TLX recruits histone deacetylases to repress transcription and regulate neural stem cell proliferation
Authors: Sun GuoQiang , Yu Ruth T. , Evans Ronald M. , Shi Yanhong
Published: September 2007

TLX is a transcription factor that is essential for neural stem cell proliferation and self-renewal. However, the molecular mechanism of TLX-mediated neural stem cell proliferation and self-renewal is largely unknown. We show here that TLX recruits histone deacetylases (HDACs) to its downstream target genes to repress their transcription, which in turn regulates neural stem cell proliferation. TLX interacts with HDAC3 and HDAC5 in neural stem cells. The HDAC5-interaction domain was mapped to TLX residues 359–385, which contains a conserved nuclear receptor–coregulator interaction motif IXXLL. Both HDAC3 and HDAC5 have been shown to be recruited to the promoters of TLX target genes along with TLX in neural stem cells. Recruitment of HDACs led to transcriptional repression of TLX target genes, the cyclin-dependent kinase inhibitor,

p21
CIP1/WAF1
(p21)

, and the tumor suppressor gene,
pten
. Either inhibition of HDAC activity or knockdown of HDAC expression led to marked induction of p21 and pten gene expression and dramatically reduced neural stem cell proliferation, suggesting that the TLX-interacting HDACs play an important role in neural stem cell proliferation. Moreover, expression of a TLX peptide containing the minimal HDAC5 interaction domain disrupted the TLX–HDAC5 interaction. Disruption of this interaction led to significant induction of p21 and pten gene expression and to dramatic inhibition of neural stem cell proliferation. Taken together, these findings demonstrate a mechanism for neural stem cell proliferation through transcriptional repression of p21 and pten gene expression by TLX–HDAC interactions.
Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance
Authors: Brouard Sophie , Mansfield Elaine , Braud Christophe , Li Li , Giral Magali , Hsieh Szu-chuan , Baeten Dominique , Zhang Meixia , Ashton-Chess Joanna , Braudeau Cécile , Hsieh Frank , Dupont Alexandre , Pallier Annaik , Moreau Anne , Louis Stéphanie , Ruiz Catherine , Salvatierra Oscar , Soulillou Jean-Paul , Sarwal Minnie
Published: September 2007

Long-term allograft survival generally requires lifelong immunosuppression (IS). Rarely, recipients display spontaneous “operational tolerance” with stable graft function in the absence of IS. The lack of biological markers of this phenomenon precludes identification of potentially tolerant patients in which IS could be tapered and hinders the development of new tolerance-inducing strategies. The objective of this study was to identify minimally invasive blood biomarkers for operational tolerance and use these biomarkers to determine the frequency of this state in immunosuppressed patients with stable graft function. Blood gene expression profiles from 75 renal-transplant patient cohorts (operational tolerance/acute and chronic rejection/stable graft function on IS) and 16 healthy individuals were analyzed. A subset of samples was used for microarray analysis where three-class comparison of the different groups of patients identified a “tolerant footprint” of 49 genes. These biomarkers were applied for prediction of operational tolerance by microarray and real-time PCR in independent test groups. Thirty-three of 49 genes correctly segregated tolerance and chronic rejection phenotypes with 99% and 86% specificity. The signature is shared with 1 of 12 and 5 of 10 stable patients on triple IS and low-dose steroid monotherapy, respectively. The gene signature suggests a pattern of reduced costimulatory signaling, immune quiescence, apoptosis, and memory T cell responses. This study identifies in the blood of kidney recipients a set of genes associated with operational tolerance that may have utility as a minimally invasive monitoring tool for guiding IS titration. Further validation of this tool for safe IS minimization in prospective clinical trials is warranted.
Plasmodium falciparum
ookinetes require mosquito midgut chondroitin sulfate proteoglycans for cell invasion
Authors: Dinglasan Rhoel R. , Alaganan Aditi , Ghosh Anil K. , Saito Akio , van Kuppevelt Toin H. , Jacobs-Lorena Marcelo
Published: September 2007

Malaria transmission entails development of the
Plasmodium
parasite in its insect vector, the
Anopheles
mosquito. Parasite invasion of the mosquito midgut is the critical first step and involves adhesion to host epithelial cell ligands. Partial evidence suggests that midgut oligosaccharides are important ligands for parasite adhesion; however, the identity of these glycans remains unknown. We have identified a population of chondroitin glycosaminoglycans along the apical midgut microvilli of
Anopheles gambiae
and further demonstrated ookinete recognition of these glycans
in vitro
. By repressing the expression of the peptide-
O
-xylosyltransferase homolog of
An. gambiae
by means of RNA interference, we blocked glycosaminoglycan chain biosynthesis, diminished chondroitin sulfate levels in the adult midgut, and substantially inhibited parasite development. We provide evidence for the
in vivo
role of chondroitin sulfate proteoglycans in
Plasmodium falciparum
invasion of the midgut and insight into the molecular mechanisms mediating parasite–mosquito interactions.
Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin
Authors: Pukatzki Stefan , Ma Amy T. , Revel Andrew T. , Sturtevant Derek , Mekalanos John J.
Published: September 2007

Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In
Vibrio cholerae
, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin
in vitro
, and this activity was used to demonstrate that
V. cholerae
can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. Protein structure search algorithms predict that VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate “tail spike” of
Escherichia coli
bacteriophage T4. VgrG-1 was shown to interact with itself, VgrG-2, and VgrG-3, suggesting that such a complex does form. Because the phage tail spike protein complex acts as a membrane-penetrating structure as well as a conduit for the passage of DNA into phage-infected cells, we propose that the VgrG components of the T6SS apparatus may assemble a “cell-puncturing device” analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells.
Processing and function of CFTR-ΔF508 are species-dependent
Authors: Ostedgaard Lynda S. , Rogers Christopher S. , Dong Qian , Randak Christoph O. , Vermeer Daniel W. , Rokhlina Tatiana , Karp Philip H. , Welsh Michael J.
Published: September 2007

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis. The most common mutation, a deletion of the phenylalanine at position 508 (ΔF508), disrupts processing of the protein. Nearly all human CFTR-ΔF508 is retained in the endoplasmic reticulum and degraded, preventing maturation to the plasma membrane. In addition, the F508 deletion reduces the activity of single CFTR channels. Human CFTR-ΔF508 has been extensively studied to better understand its defects. Here, we adopted a cross-species comparative approach, examining human, pig, and mouse CFTR-ΔF508. As with human CFTR-ΔF508, the ΔF508 mutation reduced the single-channel activity of the pig and mouse channels. However, the mutant pig and mouse proteins were at least partially processed like their wild-type counterparts. Moreover, pig and mouse CFTR-ΔF508 partially restored transepithelial Cl
−
transport to CF airway epithelia. Our data, combined with earlier work, suggest that there is a gradient in the severity of the CFTR-ΔF508 processing defect, with human more severe than pig or mouse. These findings may explain some previously puzzling observations in CF mice, they have important implications for evaluation of potential therapeutics, and they suggest new strategies for discovering the mechanisms that disrupt processing of human CFTR-ΔF508.
Crystallographic trapping in the rebeccamycin biosynthetic enzyme RebC
Authors: Ryan Katherine S. , Howard-Jones Annaleise R. , Hamill Michael J. , Elliott Sean J. , Walsh Christopher T. , Drennan Catherine L.
Published: September 2007

The biosynthesis of rebeccamycin, an antitumor compound, involves the remarkable eight-electron oxidation of chlorinated chromopyrrolic acid. Although one rebeccamycin biosynthetic enzyme is capable of generating low levels of the eight-electron oxidation product on its own, a second protein, RebC, is required to accelerate product formation and eliminate side reactions. However, the mode of action of RebC was largely unknown. Using crystallography, we have determined a likely function for RebC as a flavin hydroxylase, captured two snapshots of its dynamic catalytic cycle, and trapped a reactive molecule, a putative substrate, in its binding pocket. These studies strongly suggest that the role of RebC is to sequester a reactive intermediate produced by its partner protein and to react with it enzymatically, preventing its conversion to a suite of degradation products that includes, at low levels, the desired product.
Dmbx1 is essential in agouti-related protein action
Authors: Fujimoto Wakako , Shiuchi Tetsuya , Miki Takashi , Minokoshi Yasuhiko , Takahashi Yoshihisa , Takeuchi Ayako , Kimura Kazuhiro , Saito Masayuki , Iwanaga Toshihiko , Seino Susumu
Published: September 2007

Dmbx1 is a paired-class homeodomain transcription factor. We show here that mice deficient in
Dmbx1
exhibit severe leanness associated with hypophagia and hyperactivity and that isolation of a
Dmbx1
−/−
mouse from its cohabitants induces self-starvation, sometimes leading to death, features similar to those of anorexia nervosa in humans. Interestingly, overexpression of agouti in
Dmbx1
−/−
mice failed to induce aspects of the

A
y
/a

phenotype, including hyperphagia, obesity, and diabetes mellitus. In
Dmbx1
−/−
mice, administration of agouti-related protein increased cumulative food intake for the initial 6 h but significantly decreased it over 24- and 48-h periods. In addition, Dmbx1 was shown to be expressed at embryonic day 15.5 in the lateral parabrachial nucleus, the rostral nucleus of the tractus solitarius, the dorsal motor nucleus of the vagus, and the reticular nucleus in the brainstem, all of which receive melanocortin signaling, indicating involvement of Dmbx1 in the development of the neural network for the signaling. Thus, Dmbx1 is essential for various actions of agouti-related protein and plays a role in normal regulation of energy homeostasis and behavior.
Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event
Authors: Bhandari Rashna , Saiardi Adolfo , Ahmadibeni Yousef , Snowman Adele M. , Resnick Adam C. , Kristiansen Troels Z. , Molina Henrik , Pandey Akhilesh , Werner J. Kent , Juluri Krishna R. , Xu Yong , Prestwich Glenn D. , Parang Keykavous , Snyder Solomon H.
Published: September 2007

In a previous study, we showed that the inositol pyrophosphate diphosphoinositol pentakisphosphate (IP
7
) physiologically phosphorylates mammalian and yeast proteins. We now report that this phosphate transfer reflects pyrophosphorylation. Thus, proteins must be prephosphorylated by ATP to prime them for IP
7
phosphorylation. IP
7
phosphorylates synthetic phosphopeptides but not if their phosphates have been masked by methylation or pyrophosphorylation. Moreover, IP
7
phosphorylated peptides are more acid-labile and more resistant to phosphatases than ATP phosphorylated peptides, indicating a different type of phosphate bond. Pyrophosphorylation may represent a novel mode of signaling to proteins.
Censoring the Word
Authors: Petley Julian
Published: September 2007

FROM JOHN MILTON TO RUPERT MURDOCH: A BRIEF HISTORY OF EVERYTHING YOU NEED TO KNOW ABOUT FREE SPEECH
Mutations in α-Tubulin Confer Dinitroaniline Resistance at a Cost to Microtubule Function
Authors: Ma Christopher , Li Catherine , Ganesan Lakshmi , Oak Jean , Tsai Susan , Sept David , Morrissette Naomi S.
Published: September 2007

Protozoan microtubules are sensitive to disruption by dinitroanilines, compounds that kill intracellular Toxoplasma gondii parasites without affecting microtubules in vertebrate host cells. We previously isolated a number of resistant Toxoplasma lines that harbor mutations to the α1-tubulin gene. Some of the mutations are localized in or near the M and N loops, domains that coordinate lateral interactions between protofilaments. Other resistance mutations map to a computationally identified binding site beneath the N loop. Allelic replacement of wild-type α1-tubulin with the individual mutations is sufficient to confer dinitroaniline resistance. Some mutations seem to increase microtubule length, suggesting that they increase subunit affinity. All mutations are associated with replication defects that decrease parasite viability. When parasites bearing the N loop mutation Phe52Tyr are grown without dinitroaniline selection, they spontaneously acquired secondary mutations in the M loop (Ala273Val) or in an α-tubulin–specific insert that stabilizes the M loop (Asp367Val). Parasites with the double mutations have both reduced resistance and diminished incidence of replication defects, suggesting that the secondary mutations decrease protofilament affinity to increase parasite fitness.
Log-linear model-based multifactor dimensionality reduction method to detect gene–gene interactions
Authors: Yeoun Lee Seung , Chung Yujin , Elston Robert C. , Kim Youngchul , Park Taesung
Published: September 2007

Motivation: The identification and characterization of susceptibility genes that influence the risk of common and complex diseases remains a statistical and computational challenge in genetic association studies. This is partly because the effect of any single genetic variant for a common and complex disease may be dependent on other genetic variants (gene–gene interaction) and environmental factors (gene–environment interaction). To address this problem, the multifactor dimensionality reduction (MDR) method has been proposed by Ritchie et al. to detect gene–gene interactions or gene–environment interactions. The MDR method identifies polymorphism combinations associated with the common and complex multifactorial diseases by collapsing high-dimensional genetic factors into a single dimension. That is, the MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups based on a comparison of the ratios of the numbers of cases and controls. When a high-order interaction model is considered with multi-dimensional factors, however, there may be many sparse or empty cells in the contingency tables. The MDR method cannot classify an empty cell as high risk or low risk and leaves it as undetermined.

Results: In this article, we propose the log-linear model-based multifactor dimensionality reduction (LM MDR) method to improve the MDR in classifying sparse or empty cells. The LM MDR method estimates frequencies for empty cells from a parsimonious log-linear model so that they can be assigned to high-and low-risk groups. In addition, LM MDR includes MDR as a special case when the saturated log-linear model is fitted. Simulation studies show that the LM MDR method has greater power and smaller error rates than the MDR method. The LM MDR method is also compared with the MDR method using as an example sporadic Alzheimer's disease.

Contact:  tspark@stats.snu.ac.kr
IGG: A tool to integrate GeneChips for genetic studies
Authors: Li M.-X. , Jiang L. , Ho S.-L. , Song Y.-Q. , Sham P.-C.
Published: September 2007

Summary: To facilitate genetic studies using high-throughput genotyping technologies, we have developed an open source tool to integrate genotype data across the Affymetrix and Illumina platforms. It can efficiently integrate a large amount of data from various GeneChips, add genotypes of the HapMap Project into a specific project, flexibly trim and export the integrated data with different formats of popular genetic analysis tools, and highly control the quality of genotype data. Furthermore, this tool has sufficiently simplified its usage through its user-friendly graphic interface and is independent of third-party databases. IGG has successfully been applied to a genome-wide linkage scan in a Charcot-Marie-Tooth disease pedigree by integrating three types of GeneChips and HapMap project genotypes.

Availability:  http://bioinfo.hku.hk/iggweb (version 0.9).

Contact:  limx54@yahoo.com and songy@hku.hk
EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography
Authors: Bilbao-Castro J. R. , García I. , Fernández J. J.
Published: September 2007

Summary: Electron tomography is the leading technique to elucidate the structure of complex biological specimens. Due to the resolution needs, huge reconstructions are required. Grid computing has the potential to face the significant computational demands involved. However, there are a number of key issues, such as stability or difficult user-grid interaction, that currently preclude fully exploitation of its potential. EGEETomo is a user-friendly application that facilitates the interaction with the grid for the non-specialized user and automates job submission and supervision. In addition, EGEETomo is supplied with an automated fault recovery mechanism, which is key to make all the work transparent to the user. EGEETomo significantly accelerates tomographic reconstruction by exploiting the computational resources in the EGEE grid with minimal user intervention.

Availability:  http://www.ace.ual.es/~jrbcast/EGEETomo.tar.gz

Contact:  jrbcast@ace.ual.es or jose@ace.ual.es
Graph-based consensus clustering for class discovery from gene expression data
Authors: Yu Zhiwen , Wong Hau-San , Wang Hongqiang
Published: September 2007

Motivation: Consensus clustering, also known as cluster ensemble, is one of the important techniques for microarray data analysis, and is particularly useful for class discovery from microarray data. Compared with traditional clustering algorithms, consensus clustering approaches have the ability to integrate multiple partitions from different cluster solutions to improve the robustness, stability, scalability and parallelization of the clustering algorithms. By consensus clustering, one can discover the underlying classes of the samples in gene expression data.

Results: In addition to exploring a graph-based consensus clustering (GCC) algorithm to estimate the underlying classes of the samples in microarray data, we also design a new validation index to determine the number of classes in microarray data. To our knowledge, this is the first time in which GCC is applied to class discovery for microarray data. Given a pre specified maximum number of classes (denoted as Kmax in this article), our algorithm can discover the true number of classes for the samples in microarray data according to a new cluster validation index called the Modified Rand Index. Experiments on gene expression data indicate that our new algorithm can (i) outperform most of the existing algorithms, (ii) identify the number of classes correctly in real cancer datasets, and (iii) discover the classes of samples with biological meaning.

Availability: Matlab source code for the GCC algorithm is available upon request from Zhiwen Yu.

Contact:  yuzhiwen@cs.cityu.edu.hk and cshswong@cityu.edu.hk

Supplementary information: Supplementary data are available at Bioinformatics online.
The Constrained Instability of Majority Rule: Experiments on the Robustness of the Uncovered Set
Authors: Bianco William T. , Lynch Michael S. , Miller Gary J. , Sened Itai
Published: September 2007

The uncovered set has frequently been proposed as a solution concept for majority rule settings. This paper tests this proposition using a new technique for estimating uncovered sets and a series of experiments, including five-player computer-mediated experiments and 35-player paper-format experiments. The results support the theoretic appeal of the uncovered set. Outcomes overwhelmingly lie in or near the uncovered set. Furthermore, when preferences shift, outcomes track the uncovered set. Although outcomes tend to occur within the uncovered set, they are not necessarily stable; majority dominance relationships still produce instability, albeit constrained by the uncovered set.
CIRCADIAN CLOCK ASSOCIATED1 Transcript Stability and the Entrainment of the Circadian Clock in Arabidopsis
Authors: Yakir Esther , Hilman Dror , Hassidim Miriam , Green Rachel M.
Published: September 2007

The circadian clock is an endogenous mechanism that generates rhythms with an approximately 24-h period and enables plants to predict and adapt to daily and seasonal changes in their environment. These rhythms are generated by molecular oscillators that in Arabidopsis (Arabidopsis thaliana) have been shown to consist of interlocking feedback loops involving a number of elements. An important characteristic of circadian oscillators is that they can be entrained by daily environmental changes in light and temperature. Previous work has shown that one possible entrainment point for the Arabidopsis oscillator is the light-mediated regulation of expression of one of the oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 (CCA1). In this article, we have used transgenic plants with constitutive CCA1 expression to show that light also regulates CCA1 transcript stability. Our experiments show that CCA1 messenger RNA is relatively stable in the dark and in far-red light but has a short half-life in red and blue light. Furthermore, using transgenic plants expressing chimeric CCA1 constructs, we demonstrate that the instability determinants in CCA1 transcripts are probably located in the coding region. We suggest that the combination of light regulation of CCA1 transcription and CCA1 messenger RNA degradation is important for ensuring that the Arabidopsis circadian oscillator is accurately entrained by environmental changes.
Transcription Factor RAP2.2 and Its Interacting Partner SINAT2: Stable Elements in the Carotenogenesis of Arabidopsis Leaves
Authors: Welsch Ralf , Maass Dirk , Voegel Tanja , DellaPenna Dean , Beyer Peter
Published: September 2007

The promoter of phytoene synthase, the first specific enzyme of carotenoid biosynthesis, shows two main regulatory regions: a G-box-containing region located near the TATA box, and a TATA box distal region containing the cis-acting element ATCTA, which mediates strong basal promoter activity. This second element was also present in the promoter of phytoene desaturase, the next step of the carotenoid pathway, suggesting a common regulatory mechanism. In this work, we demonstrate that AtRAP2.2, a member of the APETALA2 (AP2)/ethylene-responsive element-binding protein transcription factor family, binds to the ATCTA element. In Arabidopsis (Arabidopsis thaliana) leaves, AtRAP2.2 transcript and protein levels were tightly controlled as indicated by unchanged transcript and protein levels in T-DNA insertion mutants in the AtRAP2.2 promoter and 5′ untranslated region and the lack of change in AtRAP2.2 protein levels in lines strongly overexpressing the AtRAP2.2 transcript. Homozygous loss-of-function mutants could not be obtained for the AtRAP2.2 5′ untranslated region T-DNA insertion line indicating a lethal phenotype. In AtRAP2.2 overexpression lines, modest changes in phytoene synthase and phytoene desaturase transcripts were only observed in root-derived calli, which consequently showed a reduction in carotenoid content. The RING finger protein SEVEN IN ABSENTIA OF ARABIDOPSIS2 (SINAT2) was identified as an AtRAP2.2 interaction partner using a two-hybrid approach. The structure of SINAT2 and related proteins of Arabidopsis show homology to the SEVEN IN ABSENTIA protein of Drosophila that is involved in proteasome-mediated regulation in a variety of developmental processes. The action of SINAT2 may explain the recalcitrance of AtRAP2.2 protein levels to change by altering AtRAP2.2 transcription.
Vitamer Levels, Stress Response, Enzyme Activity, and Gene Regulation of Arabidopsis Lines Mutant in the Pyridoxine/Pyridoxamine 5′-Phosphate Oxidase (PDX3) and the Pyridoxal Kinase (SOS4) Genes Involved in the Vitamin B6 Salvage Pathway
Authors: González Eugenia , Danehower David , Daub Margaret E.
Published: September 2007

PDX3 and SALT OVERLY SENSITIVE4 (SOS4), encoding pyridoxine/pyridoxamine 5′-phosphate oxidase and pyridoxal kinase, respectively, are the only known genes involved in the salvage pathway of pyridoxal 5′-phosphate in plants. In this study, we determined the phenotype, stress responses, vitamer levels, and regulation of the vitamin B6 pathway genes in Arabidopsis (Arabidopsis thaliana) plants mutant in PDX3 and SOS4. sos4 mutant plants showed a distinct phenotype characterized by chlorosis and reduced plant size, as well as hypersensitivity to sucrose in addition to the previously noted NaCl sensitivity. This mutant had higher levels of pyridoxine, pyridoxamine, and pyridoxal 5′-phosphate than the wild type, reflected in an increase in total vitamin B6 observed through HPLC analysis and yeast bioassay. The sos4 mutant showed increased activity of PDX3 as well as of the B6 de novo pathway enzyme PDX1, correlating with increased total B6 levels. Two independent lines with T-DNA insertions in the promoter region of PDX3 (pdx3-1 and pdx3-2) had decreased PDX3 activity. Both also had decreased activity of PDX1, which correlated with lower levels of total vitamin B6 observed using the yeast bioassay; however, no differences were noted in levels of individual vitamers by HPLC analysis. Both pdx3 mutants showed growth reduction in vitro and in vivo as well as an inability to increase growth under high light conditions. Increased expression of salvage and some of the de novo pathway genes was observed in both the pdx3 and sos4 mutants. In all mutants, increased expression was more dramatic for the salvage pathway genes.
TheArabidopsisBEL1-LIKE HOMEODOMAIN Proteins SAW1 and SAW2 Act Redundantly to RegulateKNOXExpression Spatially in Leaf Margins
Authors: Kumar Ravi , Kushalappa Kumuda , Godt Dietmute , Pidkowich Mark S. , Pastorelli Sandro , Hepworth Shelley R. , Haughn George W.
Published: September 2007

In Arabidopsis  thaliana, the BEL1-like TALE homeodomain protein family consists of 13 members that form heterodimeric complexes with the Class 1 KNOX TALE homeodomain proteins, including SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS (BP). The BEL1-like protein BELLRINGER (BLR) functions together with STM and BP in the shoot apex to regulate meristem identity and function and to promote correct shoot architecture. We have characterized two additional BEL1-LIKE HOMEODOMAIN (BLH) proteins, SAWTOOTH1 (BLH2/SAW1) and SAWTOOTH2 (BLH4/SAW2) that, in contrast with BLR, are expressed in lateral organs and negatively regulate BP expression. saw1 and saw2 single mutants have no obvious phenotype, but the saw1 saw2 double mutant has increased leaf serrations and revolute margins, indicating that SAW1 and SAW2 act redundantly to limit leaf margin growth. Consistent with this hypothesis, overexpression of SAW1 suppresses overall growth of the plant shoot. BP is ectopically expressed in the leaf serrations of saw1 saw2 double mutants. Ectopic expression of Class 1 KNOX genes in leaves has been observed previously in loss-of-function mutants of ASYMMETRIC LEAVES (AS1). Overexpression of SAW1 in an as1 mutant suppresses the as1 leaf phenotype and reduces ectopic BP leaf expression. Taken together, our data suggest that BLH2/SAW1 and BLH4/SAW2 establish leaf shape by repressing growth in specific subdomains of the leaf at least in part by repressing expression of one or more of the KNOX genes.
LITTLE NUCLEIGenes Affecting Nuclear Morphology inArabidopsis thaliana
Authors: Dittmer Travis A. , Stacey Nicola J. , Sugimoto-Shirasu Keiko , Richards Eric J.
Published: September 2007

Efforts to understand nuclear organization in plant cells have received little assistance from the better-studied animal nuclei, because plant proteomes do not contain recognizable counterparts to the key animal proteins involved in nuclear organization, such as lamin nuclear intermediate filament proteins. Previous studies identified a plant-specific insoluble nuclear protein in carrot (Daucus carota), called Nuclear Matrix Constituent Protein1 (NMCP1), which contains extensive coiled-coil domains and localizes to the nuclear periphery. Here, we describe a genetic characterization of two NMCP1-related nuclear proteins in Arabidopsis thaliana, LITTLE NUCLEI1 (LINC1) and LINC2. Disruption of either gene caused a reduction in nuclear size and altered nuclear morphology. Moreover, combining linc1 and linc2 mutations had an additive effect on nuclear size and morphology but a synergistic effect on chromocenter number (reduction) and whole-plant morphology (dwarfing). The reduction in nuclear size in the linc1 linc2 double mutant was not accompanied by a corresponding change in endopolyploidy. Rather, the density of DNA packaging at all endopolyploid levels in the linc1 linc2 mutants was increased significantly. Our results indicate that the LINC coiled-coil proteins are important determinants of plant nuclear structure.
Crystal Structures of Flax Rust Avirulence Proteins AvrL567-A and -D Reveal Details of the Structural Basis for Flax Disease Resistance Specificity
Authors: Wang Ching-I A. , Gunčar Gregor , Forwood Jade K. , Teh Trazel , Catanzariti Ann-Maree , Lawrence Gregory J. , Loughlin Fionna E. , Mackay Joel P. , Schirra Horst Joachim , Anderson Peter A. , Ellis Jeffrey G. , Dodds Peter N. , Kobe Boštjan
Published: September 2007

The gene-for-gene mechanism of plant disease resistance involves direct or indirect recognition of pathogen avirulence (Avr) proteins by plant resistance (R) proteins. Flax rust (Melampsora lini) AvrL567 avirulence proteins and the corresponding flax (Linum usitatissimum) L5, L6, and L7 resistance proteins interact directly. We determined the three-dimensional structures of two members of the AvrL567 family, AvrL567-A and AvrL567-D, at 1.4- and 2.3-Å resolution, respectively. The structures of both proteins are very similar and reveal a β-sandwich fold with no close known structural homologs. The polymorphic residues in the AvrL567 family map to the surface of the protein, and polymorphisms in residues associated with recognition differences for the R proteins lead to significant changes in surface chemical properties. Analysis of single amino acid substitutions in AvrL567 proteins confirm the role of individual residues in conferring differences in recognition and suggest that the specificity results from the cumulative effects of multiple amino acid contacts. The structures also provide insights into possible pathogen-associated functions of AvrL567 proteins, with nucleic acid binding activity demonstrated in vitro. Our studies provide some of the first structural information on avirulence proteins that bind directly to the corresponding resistance proteins, allowing an examination of the molecular basis of the interaction with the resistance proteins as a step toward designing new resistance specificities.
Nucleocytoplasmic Shuttling of BZR1 Mediated by Phosphorylation Is Essential inArabidopsisBrassinosteroid Signaling
Authors: Ryu Hojin , Kim Kangmin , Cho Hyunwoo , Park Joonghyuk , Choe Sunghwa , Hwang Ildoo
Published: September 2007

Phytohormone brassinosteroids (BRs) play critical roles in plant growth and development. BR acts by modulating the phosphorylation status of two key transcriptional factors, BRI1 EMS SUPPRESSOR1 and BRASSINAZOLE RESISTANT1 (BZR1), through the action of BRASSINOSTEROID INSENSITIVE1/BRI1 ASSOCIATED RECEPTOR KINASE1 receptors and a GSK3 kinase, BRASSINOSTEROID INSENSITIVE2 (BIN2). It is still unknown how the perception of BR at the plasma membrane connects to the expression of BR target genes in the nucleus. We show here that BZR1 functions as a nucleocytoplasmic shuttling protein and GSK3-like kinases induce the nuclear export of BZR1 by modulating BZR1 interaction with the 14-3-3 proteins. BR-activated phosphatase mediates rapid nuclear localization of BZR1. Besides the phosphorylation domain for 14-3-3 binding, another phosphorylation domain in BZR1 is required for the BIN2-induced nuclear export of BZR1. Mutations of putative phosphorylation sites in two distinct domains enhance the nuclear retention of BZR1 and BR responses in transgenic plants. We propose that the spatial redistribution of BZR1 is critical for proper BR signaling in plant growth and development.
TheArabidopsis CLASPGene Encodes a Microtubule-Associated Protein Involved in Cell Expansion and Division
Authors: Ambrose J. Christian , Shoji Tsubasa , Kotzer Amanda M. , Pighin Jamie A. , Wasteneys Geoffrey O.
Published: September 2007

Controlling microtubule dynamics and spatial organization is a fundamental requirement of eukaryotic cell function. Members of the ORBIT/MAST/CLASP family of microtubule-associated proteins associate with the plus ends of microtubules, where they promote the addition of tubulin subunits into attached kinetochore fibers during mitosis and stabilize microtubules in the vicinity of the plasma membrane during interphase. To date, nothing is known about their function in plants. Here, we show that the Arabidopsis thaliana CLASP protein is a microtubule-associated protein that is involved in both cell division and cell expansion. Green fluorescent protein–CLASP localizes along the full length of microtubules and shows enrichment at growing plus ends. Our analysis suggests that CLASP promotes microtubule stability. clasp-1 T-DNA insertion mutants are hypersensitive to microtubule-destabilizing drugs and exhibit more sparsely populated, yet well ordered, root cortical microtubule arrays. Overexpression of CLASP promotes microtubule bundles that are resistant to depolymerization with oryzalin. Furthermore, clasp-1 mutants have aberrant microtubule preprophase bands, mitotic spindles, and phragmoplasts, indicating a role for At CLASP in stabilizing mitotic arrays. clasp-1 plants are dwarf, have significantly reduced cell numbers in the root division zone, and have defects in directional cell expansion. We discuss possible mechanisms of CLASP function in higher plants.
Privatization in agro‐food sector: the case of Turkish dairy industry
Authors: Gönenç Sertaç , Rehber Erkan
Published: September 2007

Purpose

This article aims to focus on the issue of privatization movement in the agro‐food sector, in the light of the Turkish Dairy Industry Enterprises (TSEK) case, and the effects on the sector following privatization. In order to make an appropriate evaluation, the background of the privatization movement and the general structure of the dairy sector in Turkey are examined first.

Design/methodology/approach

After a brief evaluation, the privatization process of TSEK and its effects on the sector are discussed in the light of the results of empirical data that obtain from the ANOVA model.

Findings

It has been concluded that the liberalization process has been adopted without the setting up of market regulatory policies, thus, the price balance in the dairy sector has changed to the disadvantage of both producers and consumers, while market concentration has increased and regional differentials have become more apparent.

Originality/value

This article may be relevant for other countries where privatization or liberalization movement in the agro‐food sector is in process.
Intentions of New Zealanders to purchase lamb or beef made using nanotechnology
Authors: Cook Andrew J. , Fairweather John R.
Published: September 2007

Purpose

This paper aims to provide an early assessment of key influences on intentions to purchase low fat lamb or beef made using nanotechnology.

Design/methodology/approach

Data was gathered using a national postal survey of New Zealanders (N=565).

Findings

The new product was more acceptable than GM food. Most had a positive attitude and intention to purchase and were the type of person who would purchase (self‐identity). Most considered they had the support of people whose views are important to them (subjective norm) and few felt an impediment to purchasing (perceived behavioural control). Attitude, subjective norm, perceived behavioural control and self‐identity explained a good deal of intention (R2=0.64). There was also a strong link between a sum of beliefs about the risks and benefits of the new product and attitude (r=0.79).

Research limitations/implications

Differences between the sample and the population could marginally affect projections of the descriptive results onto the population.

Practical implications

Identifies a range of potentially dynamic factors that affect intentions. These have implications for informing the public and informing technology development.

Originality/value

This paper is of immediate value for those interested in public reactions to the new topic of the use of nanotechnology in food production.
Stairways to heaven or treadmills to oblivion?
Authors: Cox Andrew , Chicksand Daniel , Palmer Martin
Published: September 2007

Purpose

This paper aims to assess the findings of a research project that investigates the scope for lean strategies to be adopted in beef, lamb and pig supply chains.

Design/methodology/approach

The paper reports on action research carried out in three red meat supply chains. The methodology is inductive and qualitative, using a multi‐case, multi‐site approach. Each of the supply chains was analysed from farm gate to consumer, interviewing multiple participants at each stage of the supply chain.

Findings

The analysis demonstrates that, although a lean approach has been introduced in the pig supply chain, it is much more problematic in beef and lamb supply chains. Furthermore, the majority of participants in the UK pig supply chain – the first to adopt lean strategies – have not received the commercial improvement (the “stairway to heaven” of higher returns) that was anticipated. On the contrary, the majority of participants in this supply chain are experiencing a strategic “treadmill to oblivion” of continuous lean operational efficiency, but with low commercial returns.

Research limitations/implications

The research is based upon three red meat supply chains – beef, lamb and pig. It would be beneficial if further in‐depth studies could be undertaken in other agri‐food supply chains to further validate the findings.

Practical implications

If government agencies and/or multiple retailers develop lean strategies in UK beef and lamb supply chains, it is not at all clear that this will benefit all parties in these chains. This raises important questions about the efficacy and appropriateness of lean strategies in supply chains that do not have the same demand, supply and power and leverage characteristics as those in which lean principles were first developed.

Originality/value

This paper should be of value to researchers in this area and to managers responsible for strategy formation in UK agri‐food supply chains.
Maslow's hierarchy and food tourism in Finland: five cases
Authors: Tikkanen Irma
Published: September 2007

Purpose

The purpose of this paper is to explore the sectors of food tourism in Finland by using Maslow's hierarchy of needs in the classification.

Design/methodology/approach

Previous research on food tourism concentrates on the role of food as an attraction, as a cultural phenomenon, and as an experience. Moreover, food from productional and motivational viewpoints is reviewed briefly. The empirical data consists both of the secondary data and an interview.

Findings

The findings introduce five sectors of food tourism where the needs and motivations are linked with Maslow's hierarchy of needs.

Practical implications

The practical implications are that the food tourism promoters could emphasize the needs and motivations when marketing food tourism services.

Originality/value

Sectors of food tourism in Finland classified by the hierarchy of needs are presented, providing practical implications for food tourism promoters and thus offering motivations for food tourism.
Physiological analysis of lactobacillus rhamnosus VTT E‐97800
Authors: Sunny‐Roberts E.O. , Knorr D.
Published: September 2007

Purpose

This paper aims to describe the physiological analysis of L. rhamnosus VTT E‐97800 and its adaptive response to osmotic stress induced by trehalose.

Design/methodology/approach

Cells of L. rhamnosus E800 in the stationary phase of growth were subjected to osmotic stress induced by trehalose treatments. The effects of osmotic stress on the viability of the study strain were determined by conducting flow cytometric analysis with carboxyfluorescein diacetate (cFDA) and propidium iodide (PI) and by observing the corresponding cells growth on MRS agar plates. Osmotic‐induced changes of esterase activity and membrane integrity were monitored. Ability to extrude intracellular accumulated cF (additional vitality marker) was taken into consideration.

Findings

The fluorescence‐based approach gave additional insights on osmotic induced changes of cellular events, which could not be explicitly assessed by culture techniques. Trehalose treatments caused a transient membrane permeabilization as revealed by a gradual decrease in esterase activity (a measure of enzyme activity and thus of viability) with increase in trehalose molarity. However, culturability on MRS agar was not significantly affected. Membrane integrity was maintained and there was an improvement in the ability of cells to extrude intracellular accumulated cF.

Originality/value

The paper provides a comparative study of the conventional culture techniques and the flow cytometric viability assessment which showed that esterase activity cannot be relied on to ascertain the culturability and viability status of an organism.
Internet identity and public libraries: communicating service values through web presence
Authors: McMenemy David
Published: September 2007

Purpose

To discuss the nature of public library websites and what they communicate about the values of the sector.

Design/methodology/approach

The article examines a range of Scottish public library websites to determine domain and quality of information resources provided.

Findings

That many public libraries in Scotland have a virtual identity problem brought about by being part of larger websites for their parent bodies. It is argued that this identity problem is to the detriment of the service, and that models of good practice should be urgently considered by public librarians.

Practical implications

The article should be of interest to librarians considering how best to present their websites and the potential challenges in doing so as part of a larger umbrella organisation.

Originality/value

This is the first article to examine all sites from Scottish public libraries in terms of their origins and content.
Professional values in a bureaucratic structure:
Authors: Usherwood R.C.
Published: September 2007

Purpose

This archive paper is presented as part of the 80th birthday celebrations of Library Review. It examines concepts of professionalism and bureaucracy in the early 1980s public library service.

Design/methodology/approach

The paper provides a reflective viewpoint.

Findings

That challenges to professionalism existed in 1980 and that librarians needed to contemplate professional values more fully.

Practical implications

Raises issues about professional values in management structures.

Originality/value

This is part of an anniversary celebration and as such revisits some old arguments.
Cultural issues, organizational hierarchy and information fulfilment
Authors: Burke Maria E.
Published: September 2007

Purpose

The purpose of this paper is to present the cultural results of a three year study into the concept of information fulfilment and considers the impact of culture on levels of information fulfilment.

Design/methodology/approach

Ethnographic studies were undertaken within higher education institutions in four countries, by examining each organization's shape and comparing it with the level of achievement of information fulfilment. The social and symbolic meanings that underpinned the culture of information in the chosen institutions are presented. The cultural frameworks are analysed and followed by a section of “raw data” from the ethnographic field.

Findings

Culture impacted significantly in all the studies, and each study had its own unique character which provided rich insights into the culture, atmosphere and contexts of the fields.

Originality/value

The relationships between the cultures and the levels of information fulfilment are reported with a view to helping build knowledge management systems that deliver higher levels of information fulfilment.
Community analysis needs ethnography: an example from Romania
Authors: Whipple Mindy , Nyce James M.
Published: September 2007

Purpose

The purpose of this paper is to demonstrate the importance of using qualitative research methods, such as ethnography, in community analysis within the library and information science (LIS) community.

Design/methodology/approach

The authors review the LIS literature on community analysis up to May 2004, critique a representative case study and compare its results to what emerged from the research carried out in rural Romania summer of 2004. Students and faculty from Emporia State University and Ball State University in May 2004 gathered qualitative data on the rural information infrastructure and the information needs and of residents in the Romanian community of Lunca Ilvei. The research team used ethnographic methods to collect data and found this method to be effective in the analysis and understanding of the community's information behavior.

Findings

Community analysis in LIS has relied primarily on quantitative methods. While quantitative methods can give the researcher some information about a given community, these methods cannot always produce community sensitive and appropriate statements. Ethnography can produce this kind of data which can be used to assess and plan library services.

Research limitations/implications

The argument rests on a single village study. However, the paper's review of the literature and its analysis of a key example of community analysis strengthen the argument.

Originality/value

As libraries strive to serve communities and remain relevant to their users research methodologies, like ethnography, that are effective in revealing information needs, wants, behaviors, and fulfillment need be accepted as legitimate and distributed throughout the library community.