bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Medicago truncatula Lysine Motif-Receptor-Like Kinase Gene Family Includes NFP and New Nodule-Expressed Genes
Authors: Arrighi Jean-François , Barre Annick , Ben Amor Besma , Bersoult Anne , Soriano Lidia Campos , Mirabella Rossana , de Carvalho-Niebel Fernanda , Journet Etienne-Pascal , Ghérardi Michèle , Huguet Thierry , Geurts René , Dénarié Jean , Rougé Pierre , Gough Clare 
Published: July 2006

Abstract
Rhizobial Nod factors are key symbiotic signals responsible for starting the nodulation process in host legume plants. Of the six Medicago truncatula genes controlling a Nod factor signaling pathway, Nod Factor Perception (NFP) was reported as a candidate Nod factor receptor gene. Here, we provide further evidence for this by showing that NFP is a lysine motif (LysM)-receptor-like kinase (RLK). NFP was shown both to be expressed in association with infection thread development and to be involved in the infection process. Consistent with deviations from conserved kinase domain sequences, NFP did not show autophosphorylation activity, suggesting that NFP needs to associate with an active kinase or has unusual functional characteristics different from classical kinases. Identification of nine new M. truncatula LysM-RLK genes revealed a larger family than in the nonlegumes Arabidopsis (Arabidopsis thaliana) or rice (Oryza sativa) of at least 17 members that can be divided into three subfamilies. Three LysM domains could be structurally predicted for all M. truncatula LysM-RLK proteins, whereas one subfamily, which includes NFP, was characterized by deviations from conserved kinase sequences. Most of the newly identified genes were found to be expressed in roots and nodules, suggesting this class of receptors may be more extensively involved in nodulation than was previously known.
PoplarFT2Shortens the Juvenile Phase and Promotes Seasonal Flowering
Authors: Hsu Chuan-Yu , Liu Yunxia , Luthe Dawn S. , Yuceer Cetin 
Published: July 2006

AbstractMany woody perennials, such as poplar (Populus deltoides), are not able to form flower buds during the first several years of their life cycle. They must undergo a transition from the juvenile phase to the reproductive phase to be competent to produce flower buds. After this transition, trees begin to form flower buds in the spring of each growing season. The genetic factors that control flower initiation, ending the juvenile phase, are unknown in poplar. The factors that regulate seasonal flower bud formation are also unknown. Here, we report that poplar FLOWERING LOCUS T2 (FT2), a relative of the Arabidopsis thaliana flowering-time gene FT, controls first-time and seasonal flowering in poplar. The FT2 transcript is rare during the juvenile phase of poplar. When juvenile poplar is transformed with FT2 and transcript levels are increased, flowering is induced within 1 year. During the transition between vegetative and reproductive growth in mature trees, FT2 transcripts are abundant during reproductive growth under long days. Subsequently, floral meristems emerge on flanks of the axillary inflorescence shoots. These findings suggest that FT2 is part of the flower initiation pathway in poplar and plays an additional role in regulating seasonal flower initiation that is integrated with the poplar perennial growth habit.
ArabidopsisABA INSENSITIVE4 Regulates Lipid Mobilization in the Embryo and Reveals Repression of Seed Germination by the Endosperm
Authors: Penfield Steven , Li Yi , Gilday Alison D. , Graham Stuart , Graham Ian A. 
Published: July 2006

AbstractRegulation of seed germination requires coordinate action by the embryo and surrounding endosperm. We used Arabidopsis thaliana to establish the relative roles of embryo and endosperm in the control of seed germination and seedling establishment. We previously showed that endospermic oil reserves are used postgerminatively via gluconeogenesis to fuel seedling establishment and that lipid breakdown is repressed by abscisic acid (ABA) in embryo but not endosperm tissues. Here, we use RNA amplification to describe the transcriptome of the endosperm and compare the hormone responses of endosperm and embryo tissues. We show that the endosperm responds to both ABA and gibberellin but that ABA in particular regulates nuclear but not plastid-encoded photosynthetic gene expression in the embryo. We also show that ABA INSENSITIVE4 (ABI4) expression is confined to the embryo, accounts for the major differences in embryo response to ABA, and defines a role for ABI4 as a repressor of lipid breakdown. Furthermore, ABI5 expression in the endosperm defines a second region of altered ABA signaling in the micropylar endosperm cap. Finally, embryo and endosperm ABA signaling mutants demonstrate the spatial specificity of ABA action in seed germination. We conclude that the single cell endosperm layer plays an active role in the regulation of seed germination in Arabidopsis.
Distinct Domains in the ARC Region of the Potato Resistance Protein Rx Mediate LRR Binding and Inhibition of Activation
Authors: Rairdan Gregory J. , Moffett Peter 
Published: July 2006

AbstractPlant nucleotide binding and leucine-rich repeat (NB-LRR) proteins contain a region of homology known as the ARC domain located between the NB and LRR domains. Structural modeling suggests that the ARC region can be subdivided into ARC1 and ARC2 domains. We have used the potato (Solanum tuberosum) Rx protein, which confers resistance to Potato virus X (PVX), to investigate the function of the ARC region. We demonstrate that the ARC1 domain is required for binding of the Rx N terminus to the LRR domain. Domain-swap experiments with Rx and a homologous disease resistance gene, Gpa2, showed that PVX recognition localized to the C-terminal half of the LRR domain. However, inappropriate pairings of LRR and ARC2 domains resulted in autoactive molecules. Thus, the ARC2 domain is required to condition an autoinhibited state in the absence of elicitor as well as for the subsequent elicitor-induced activation. Our data suggest that the ARC region, through its interaction with the LRR, translates elicitor-induced modulations of the C terminus into a signal initiation event. Furthermore, we demonstrate that physical disruption of the LRR–ARC interaction is not required for signal initiation. We propose instead that this activity can lead to multiple rounds of elicitor recognition, providing a means of signal amplification.
Analysis of thePetunia TM6MADS Box Gene Reveals Functional Divergence within theDEF/AP3Lineage
Authors: Rijpkema Anneke S. , Royaert Stefan , Zethof Jan , van der Weerden Gerard , Gerats Tom , Vandenbussche Michiel 
Published: July 2006

AbstractAntirrhinum majus DEFICIENS (DEF) and Arabidopsis thaliana APETALA3 (AP3) MADS box proteins are required to specify petal and stamen identity. Sampling of DEF/AP3 homologs revealed two types of DEF/AP3 proteins, euAP3 and TOMATO MADS BOX GENE6 (TM6), within core eudicots, and we show functional divergence in Petunia hybrida euAP3 and TM6 proteins. Petunia DEF (also known as GREEN PETALS [GP]) is expressed mainly in whorls 2 and 3, and its expression pattern remains unchanged in a blind (bl) mutant background, in which the cadastral C-repression function in the perianth is impaired. Petunia TM6 functions as a B-class organ identity protein only in the determination of stamen identity. Atypically, Petunia TM6 is regulated like a C-class rather than a B-class gene, is expressed mainly in whorls 3 and 4, and is repressed by BL in the perianth, thereby preventing involvement in petal development. A promoter comparison between DEF and TM6 indicates an important change in regulatory elements during or after the duplication that resulted in euAP3- and TM6-type genes. Surprisingly, although TM6 normally is not involved in petal development, 35S-driven TM6 expression can restore petal development in a def (gp) mutant background. Finally, we isolated both euAP3 and TM6 genes from seven solanaceous species, suggesting that a dual euAP3/TM6 B-function system might be the rule in the Solanaceae.
Functional Analyses of Two TomatoAPETALA3Genes Demonstrate Diversification in Their Roles in Regulating Floral Development
Authors: de Martino Gemma , Pan Irvin , Emmanuel Eyal , Levy Avraham , Irish Vivian F. 
Published: July 2006

AbstractThe floral homeotic APETALA3 (AP3) gene in Arabidopsis thaliana encodes a MADS box transcription factor required for specifying petal and stamen identities. AP3 is a member of the euAP3 lineage, which arose by gene duplication coincident with radiation of the core eudicots. Although Arabidopsis lacks genes in the paralogous Tomato MADS box gene 6 (TM6) lineage, tomato (Solanum lycopersicum) possesses both euAP3 and TM6 genes, which have functionally diversified. A loss-of-function mutation in Tomato AP3 (TAP3) resulted in homeotic transformations of both petals and stamens, whereas RNA interference–induced reduction in TM6 function resulted in flowers with homeotic defects primarily in stamens. The functional differences between these genes can be ascribed partly to different expression domains. When overexpressed in an equivalent domain, both genes can partially rescue the tap3 mutant, indicating that relative levels as well as spatial patterns of expression contribute to functional differences. Our results also indicate that the two proteins have differing biochemical capabilities. Together, these results suggest that TM6 and TAP3 play qualitatively different roles in floral development; they also support the ideas that the ancestral role of AP3 lineage genes was in specifying stamen development and that duplication and divergence in the AP3 lineage allowed for the acquisition of a role in petal specification in the core eudicots.
Tobacco Tsip1, a DnaJ-Type Zn Finger Protein, Is Recruited to and Potentiates Tsi1-Mediated Transcriptional Activation
Authors: Ham Byung-Kook , Park Jeong Mee , Lee Suk-Bae , Kim Min Jung , Lee In-Ju , Kim Ki-Jeong , Kwon Chang Seob , Paek Kyung-Hee 
Published: July 2006

AbstractTobacco stress-induced1 (Tsi1) is an ethylene-responsive-element binding protein/APETALA2–type transcription factor that plays an important role in both biotic and abiotic stress signaling pathways. We show that Tsi1-interacting protein1 (Tsip1), a DnaJ-type Zn finger protein, interacts with Tsi1 in vitro and in yeast (Saccharomyces cerevisiae). The transcript level of Tsip1 in tobacco (Nicotiana tabacum) increased upon treatment with salicylic acid (SA), ethylene, gibberellic acid, NaCl, and virus challenge. Tsip1 appeared to be physically associated with the chloroplast surface but dissociated from it after SA treatment. Tsip1 colocalized and coimmunoprecipitated with Tsi1 in plant cells following SA treatment. Tsip1 expression increased Tsi1-mediated transcription and was able to functionally compensate for loss of the Tsi1 transcriptional activation domain through a direct interaction with Tsi1. Transgenic plants simultaneously coexpressing Tsi1 and Tsip1 displayed stronger pathogen resistance and salt tolerance than did transgenic plants expressing either Tsi1 or Tsip1 alone. Concurrent with this, the expression of a subset of stress-related genes was induced in a cooperative manner in Tsi1/Tsip1 transgenic plants. These results together implied that Tsi1 recruits Tsip1 to the promoters of stress-related genes to potentiate Tsi1-mediated transcriptional activation.
General practitioner non‐principals benefit from flexible working
Authors: French Fiona , Andrew Jane , Awramenko Morag , Coutts Helen , Leighton‐Beck Linda , Mollison Jill , Needham Gillian , Scott Anthony , Walker Kim 
Published: July 2006

PurposeThe purpose of this study is to explore non‐principals’ working patterns and attitudes to work.Design/methodology/approachThe article is based on data provided by a questionnaire survey.FindingsGender division was apparent among the non‐principals. Males were more likely to work full‐time, because their spouses modified their working hours.Research limitations/implicationsIt was impossible to identify all non‐principals in Scotland or to compare responders and non‐responders, due to the lack of official data. Hence, the results might not be representative.Practical implicationsMore flexible posts would enable GPs to more easily combine paid work with family commitments. It is anticipated that the new GP contract should deliver this.Originality/valueThis was the first time a study of all non‐principals in Scotland had been attempted. The findings provide a more comprehensive picture of GPs in Scotland and provide valuable information for policymakers.
Dependence in the 2001 One-Number Census Project
Authors: Brown James , Abbott Owen , Diamond Ian 
Published: July 2006

SummaryThe one-number census approach was developed by the Office for National Statistics to adjust the counts from the 2001 census of England and Wales for underenumeration. The method is underpinned by an assumption of independence between the count of the population that was given by the 2001 census and the count that was given by the Census Coverage Survey. Some dependence was, however, detected, and the paper describes the strategy that was used to measure dependence and to adjust the 2001 census population estimates.
Haar–Fisz Estimation of Evolutionary Wavelet Spectra
Authors: Fryzlewicz Piotr , Nason Guy P. 
Published: July 2006

SummaryWe propose a new ‘Haar–Fisz’ technique for estimating the time-varying, piecewise constant local variance of a locally stationary Gaussian time series. We apply our technique to the estimation of the spectral structure in the locally stationary wavelet model. Our method combines Haar wavelets and the variance stabilizing Fisz transform. The resulting estimator is mean square consistent, rapidly computable and easy to implement, and performs well in practice. We also introduce the ‘Haar–Fisz transform’, a device for stabilizing the variance of scaled χ2-data and bringing their distribution close to Gaussianity.
Estimation of a Two-Equation Panel Model with Mixed Continuous and Ordered Categorical Outcomes and Missing Data
Authors: Spiess Martin 
Published: July 2006

Summary
The paper proposes an estimation approach for panel models with mixed continuous and ordered categorical outcomes based on generalized estimating equations for the mean and pseudoscore equations for the covariance parameters. A numerical study suggests that efficiency can be gained in the mean parameter estimators by using individual covariance matrices in the estimating equations for the mean parameters. The approach is applied to estimate the returns to occupational qualification in terms of income and perceived job security in a 9-year period based on the German Socio-Economic Panel. To compensate for missing data, a combined multiple imputation–weighting approach is adopted.
Dopaquinone redox exchange with dihydroxyindole and dihydroxyindole carboxylic acid
Authors: Edge R. , D'Ischia M. , Land E. J. , Napolitano A. , Navaratnam S. , Panzella L. , Pezzella A. , Ramsden C. A. , Riley P. A. 
Published: July 2006

SummaryA pulse radiolytic investigation has been conducted to establish whether a redox reaction takes place between dopaquinone and 5,6‐dihydroxyindole (DHI) and its 2‐carboxylic acid (DHICA) and to measure the rate constants of the interactions. To obviate possible confounding reactions, such as nucleophilic addition, the method employed to generate dopaquinone used the dibromide radical anion acting on dopa to form the semiquinone which rapidly disproportionates to dopaquinone. In the presence of DHI the corresponding indole‐5,6‐quinone (and/or tautomers) was also formed directly but, by judicious selection of suitable relative concentrations of initial reactants, we were able to detect the formation of additional indolequinone from the redox exchange reaction of DHI with dopaquinone which exhibited a linear dependency on the concentration of DHI. Computer simulation of the experimental time profiles of the absorption changes showed that, under the conditions chosen, redox exchange does proceed but not quite to completion, a forward rate constant of 1.4 × 106/M/s being obtained. This is in the same range as the rate constants previously established for reactions of dopaquinone with cyclodopa and cysteinyldopa. In similar experiments carried out with DHICA, the reaction more obviously does not go to completion and is much slower, k (forward) =1.6 × 105/M/s. We conclude that, in the eumelanogenic pathway, DHI oxidation may take place by redox exchange with dopaquinone, although such a reaction is likely to be less efficient for DHICA.
AparAHomolog Selectively Influences Positioning of the Large Chromosome Origin inVibrio cholerae
Authors: Saint-Dic Djenann , Frushour Brian P. , Kehrl Jason H. , Kahng Lyn Sue 
Published: July 2006

ABSTRACTAVibrio choleraedeletion mutant lacking VS2773, aparApartitioning gene homolog located in aparABoperon on the large chromosome, displays altered positioning of the large chromosome origin. Deletion of a secondparAhomolog on the large chromosome (VC2061) does not affect its origin positioning. The origin position of the small chromosome is unchanged by either or both of these deletions, suggesting that VC2773 function is specific to the replicon on which it is carried. VC2773 and VC2772 form aparABSsystem with inverted repeats found near the large chromosome origin.
UvrD Helicase Suppresses Recombination and DNA Damage-Induced Deletions
Authors: Kang Josephine , Blaser Martin J. 
Published: July 2006

ABSTRACT

UvrD, a highly conserved helicase involved in mismatch repair, nucleotide excision repair (NER), and recombinational repair, plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species. In this report, we focus on the UvrD homolog in
Helicobacter pylori
, a genetically diverse organism that lacks many known DNA repair proteins, including those involved in mismatch repair and recombinational repair, and that is noted for high levels of inter- and intragenomic recombination and mutation.
H. pylori
contains numerous DNA repeats in its compact genome and inhabits an environment rich in DNA-damaging agents that can lead to increased rearrangements between such repeats. We find that
H. pylori
UvrD functions to repair DNA damage and limit homologous recombination and DNA damage-induced genomic rearrangements between DNA repeats. Our results suggest that UvrD and other NER pathway proteins play a prominent role in maintaining genome integrity, especially after DNA damage; thus, NER may be especially critical in organisms such as
H. pylori
that face high-level genotoxic stress in vivo.
Identification and Characterization of Bacterial Cysteine Dioxygenases: a New Route of Cysteine Degradation for Eubacteria
Authors: Dominy John E. , Simmons Chad R. , Karplus P. Andrew , Gehring Amy M. , Stipanuk Martha H. 
Published: July 2006

ABSTRACT

In metazoa and fungi, the catabolic dissimilation of cysteine begins with its sulfoxidation to cysteine sulfinic acid by the enzyme cysteine dioxygenase (CDO). In these organisms, CDO plays an important role in the homeostatic regulation of steady-state cysteine levels and provides important oxidized metabolites of cysteine such as sulfate and taurine. To date, there has been no experimental evidence for the presence of CDO in prokaryotes. Using PSI-BLAST searches and crystallographic information about the active-site geometry of mammalian CDOs, we identified a total of four proteins from
Bacillus subtilis
,
Bacillus cereus
, and
Streptomyces coelicolor
A3(2) that shared low overall identity to CDO (13 to 21%) but nevertheless conserved important active-site residues. These four proteins were heterologously expressed and purified to homogeneity by a single-step immobilized metal affinity chromatography procedure. The ability of these proteins to oxidize cysteine to cysteine sulfinic acid was then compared against recombinant rat CDO. The kinetic data strongly indicate that these proteins are indeed bona fide CDOs. Phylogenetic analyses of putative bacterial CDO homologs also indicate that CDO is distributed among species within the phyla of
Actinobacteria
,
Firmicutes
, and
Proteobacteria
. Collectively, these data suggest that a large subset of eubacteria is capable of cysteine sulfoxidation. Suggestions are made for how this novel pathway of cysteine metabolism may play a role in the life cycle of the eubacteria that have it.
Sau1: a Novel Lineage-Specific Type I Restriction-Modification System That Blocks Horizontal Gene Transfer into
Staphylococcus aureus
and between
S. aureus
Isolates of Different Lineages
Authors: Waldron Denise E. , Lindsay Jodi A. 
Published: July 2006

ABSTRACT

The Sau1 type I restriction-modification system is found on the chromosome of all nine sequenced strains of
Staphylococcus aureus
and includes a single
hsdR
(restriction) gene and two copies of
hsdM
(modification) and
hsdS
(sequence specificity) genes. The strain
S. aureus
RN4220 is a vital intermediate for laboratory
S. aureus
manipulation, as it can accept plasmid DNA from
Escherichia coli
. We show that it carries a mutation in the
sau1hsdR
gene and that complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may explain why only four vancomycin-resistant
S. aureus
strains have been identified despite substantial selective pressure in the clinical setting. Using a multistrain
S. aureus
microarray, we show that the two copies of sequence specificity genes (
sau1hsdS1
and
sau1hsdS2
) vary substantially between isolates and that the variation corresponds to the 10 dominant
S. aureus
lineages. Thus, RN4220 complemented with
sau1hsdR
was resistant to bacteriophage lysis but only if the phage was grown on
S. aureus
of a different lineage. Similarly, it could be transduced with DNA from its own lineage but not with the phage grown on different
S. aureus
lineages. Therefore, we propose that Sau1 is the major mechanism for blocking transfer of resistance genes and other mobile genetic elements into
S. aureus
isolates from other species, as well as for controlling the spread of resistance genes between isolates of different
S. aureus
lineages. Blocking Sau1 should also allow genetic manipulation of clinical strains of
S. aureus
.
No Single Irreplaceable Acidic Residues in the
Escherichia coli
Secondary Multidrug Transporter MdfA
Authors: Sigal Nadejda , Molshanski-Mor Shahar , Bibi Eitan 
Published: July 2006

ABSTRACT

The largest family of solute transporters (major facilitator superfamily [MFS]) includes proton-motive-force-driven secondary transporters. Several characterized MFS transporters utilize essential acidic residues that play a critical role in the energy-coupling mechanism during transport. Surprisingly, we show here that no single acidic residue plays an irreplaceable role in the
Escherichia coli
secondary multidrug transporter MdfA.
Lipoprotein Multigene Families in
Mycoplasma pneumoniae
Authors: Hallamaa K. M. , Browning G. F. , Tang S. L. 
Published: July 2006

ABSTRACT

In this study, reverse transcriptase PCR was employed to construct a
transcriptional profile of
Mycoplasma pneumoniae
lipoprotein genes contained in six multigene families. Most genes were
found to be expressed. Many truncated lipoprotein genes were expressed,
often polycistronically with other truncated genes, indicating that
these genes may still be
functional.