bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation of nanocones for immobilizing DNA probe by a low-temperature plasma plume
Authors: Chen Guangliang , Zhao Wenjun , Chen Shihua , Zhou Mingyan , Feng Wenran , Gu Weichao , Yang Si-ze
Published: September 2006

Using allylamine monomer, a matrix of nanocones was fabricated by applying a low-temperature plasma plume without any catalysts and template. This nanocone acted as an adhesion layer immobilizing DNA probe for DNA hybridization assay. A simple conceptual model to describe the growth of the nanocones was also developed. The highest density of amino-labeled DNA probe was about 1.6pM∕cm2 confirmed by the dyed oligonucleotide, and each nanocone contained nearly 3×102 amine groups. This strategy provides a robust procedure to immobilize DNA, which is a very useful substrate for fabricating nanobiosensors.
Ralstonia solanacearum
requires F-box-like domain-containing type III effectors to promote disease on several host plants
Authors: Angot Aurélie , Peeters Nemo , Lechner Esther , Vailleau Fabienne , Baud Catherine , Gentzbittel Laurent , Sartorel Elodie , Genschik Pascal , Boucher Christian , Genin Stéphane
Published: September 2006

The phytopathogenic bacterium
Ralstonia solanacearum
encodes a family of seven type III secretion system (T3SS) effectors that contain both a leucine-rich repeat and an F-box domain. This structure is reminiscent of a class of typical eukaryotic proteins called F-box proteins. The latter, together with Skp1 and Cullin1 subunits, constitute the SCF-type E3 ubiquitin ligase complex and control specific protein ubiquitinylation. In the eukaryotic cell, depending on the nature of the polyubiquitin chain, the ubiquitin-tagged proteins either see their properties modified or are doomed for degradation by the 26S proteasome. This pathway is essential to many developmental processes in plants, ranging from hormone signaling and flower development to stress responses. Here, we show that these previously undescribed T3SS effectors are putative bacterial F-box proteins capable of interacting with a subset of the 19 different
Arabidopsis
Skp1-like proteins like bona fide
Arabidopsis
F-box proteins. A
R. solanacearum
strain in which all of the seven
GALA
effector genes have been deleted or mutated was no longer pathogenic on
Arabidopsis
and less virulent on tomato. Furthermore, we found that GALA7 is a host-specificity factor, required for disease on
Medicago truncatula
plants. Our results indicate that the GALA T3SS effectors are essential to
R. solanacearum
to control disease. Because the F-box domain is essential to the virulence function of GALA7, we hypothesize that these effectors act by hijacking their host SCF-type E3 ubiquitin ligases to interfere with their host ubiquitin/proteasome pathway to promote disease.
Structural insights into methyltransfer reactions of a corrinoid iron–sulfur protein involved in acetyl-CoA synthesis
Authors: Svetlitchnaia Tatiana , Svetlitchnyi Vitali , Meyer Ortwin , Dobbek Holger
Published: September 2006

The cobalt- and iron-containing corrinoid iron–sulfur protein (CoFeSP) is functional in the acetyl-CoA (Ljungdahl–Wood) pathway of autotrophic carbon fixation in various bacteria and archaea, where it is essential for the biosynthesis of acetyl-CoA. CoFeSP acts in two methylation reactions: the transfer of a methyl group from methyltransferase (MeTr)-bound methyltetrahydrofolate to the cob(I)amide of CoFeSP and the transfer of the methyl group of methyl-cob(III)amide to the reduced Ni-Ni-[4Fe-4S] active site cluster A of acetyl-CoA synthase (ACS). We have solved the crystal structure of as-isolated CoFeSP
Ch
from the CO-oxidizing hydrogenogenic bacterium
Carboxydothermus hydrogenoformans
at 1.9-Å resolution. The heterodimeric protein consists of two tightly interacting subunits with pseudo-twofold symmetry. The large CfsA subunit comprises three domains, of which the N-terminal domain binds the [4Fe-4S] cluster, the middle domain is a (βα)
8
-barrel, and the C-terminal domain shows an open fold and binds
Co
β-aqua-(5,6-dimethylbenzimidazolylcobamide) in a “base-off” state without a protein ligand at the cobalt ion. The small CfsB subunit also displays a (βα)
8
-barrel fold and interacts with the upper side of the corrin macrocycle. Structure-based alignments show that both (βα)
8
-barrel domains are related to the MeTr in the acetyl-CoA pathway and to the folate domain of methionine synthase. We suggest that the C-terminal domain of the large subunit is the mobile element that allows the necessary interaction of CoFeSP
Ch
with the active site of ACS
Ch
and the methyltetrahydrofolate carrying MeTr. The conformation in the crystal structure shields the two open coordinations of cobalt and likely represents a resting state.
Sex-biased maternal effects reduce ectoparasite-induced mortality in a passerine bird
Authors: Badyaev Alexander V. , Hamstra Terri L. , Oh Kevin P. , Acevedo Seaman Dana A.
Published: September 2006

Duration of developmental stages in animals evolves under contrasting selection pressures of age-specific mortality and growth requirements. When relative importance of these effects varies across environments, evolution of developmental periods is expected to be slow. In birds, maternal effects on egg-laying order and offspring growth, two proximate determinants of nestling period, should enable rapid adjustment of developmental periods to even widely fluctuating mortality rates. We test this hypothesis in a population of house finches (Carpodacus mexicanus) breeding under two contrasting mortality risks: (i) a nest mite-free condition when selection on offspring survival favors a longer time in the nest; and (ii) a mite infestation when selection favors a shorter nest tenure. Mites affected survival of sons more than daughters, and females breeding under mite infestation laid male eggs last and female eggs first in the clutch, thereby reducing sons' exposure to mites and associated mortality. Strong sex bias in laying order and growth patterns enabled mite-infested offspring to achieve similar fledging size, despite a shorter nest tenure, compared with mite-free conditions. In mite-infested nests, male nestlings hatched at larger sizes, completed growth earlier, and had faster initial growth compared with mite-free nests, whereas mite-infested females grew more slowly but for a longer period of time. A combination of heavily sex-biased laying order and sex differences in growth patterns lowered mite-induced mortality by >10% in both sexes. Thus, strong maternal effects can account for frequently observed, but theoretically unexpected, concordance of mortality risks and growth patterns, especially under fluctuating ecological conditions.
Regulation of gene expression in the mammalian eye and its relevance to eye disease
Authors: Scheetz Todd E. , Kim Kwang-Youn A. , Swiderski Ruth E. , Philp Alisdair R. , Braun Terry A. , Knudtson Kevin L. , Dorrance Anne M. , DiBona Gerald F. , Huang Jian , Casavant Thomas L. , Sheffield Val C. , Stone Edwin M.
Published: September 2006

We used expression quantitative trait locus mapping in the laboratory rat (
Rattus norvegicus
) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F
2
rats generated from an SR/JrHsd × SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (α = 0.001; estimated empirical false discovery rate = 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5′ flanking sequence of the
Abca4
gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor β2 associated with a decreased expression level of the gene encoding short-wavelength sensitive opsin (
Opn1sw
). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet–Biedl syndrome. These data and analytical approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.
An α
2
-macroglobulin-like protein is the cue to gregarious settlement of the barnacle
Balanus amphitrite
Authors: Dreanno Catherine , Matsumura Kiyotaka , Dohmae Naoshi , Takio Koji , Hirota Hiroshi , Kirby Richard R. , Clare Anthony S.
Published: September 2006

Many benthic marine invertebrates, like barnacles, have a planktonic larval stage whose primary purpose is dispersal. How these species colonize suitable substrata is fundamental to understanding their evolution, population biology, and wider community dynamics. Unlike larval dispersal, settlement occurs on a relatively small spatial scale and involves larval behavior in response to physical and chemical characteristics of the substratum. Biogenic chemical cues have been implicated in this process. Their identification, however, has proven challenging, no more so than for the chemical basis of barnacle gregariousness, which was first described >50 years ago. We now report that a biological cue to gregarious settlement, the settlement-inducing protein complex (SIPC), of the major fouling barnacle
Balanus amphitrite
is a previously undescribed glycoprotein. The SIPC shares a 30% sequence homology with the thioester-containing family of proteins that includes the α
2
-macroglobulins. The cDNA (5.2 kb) of the
SIPC
encodes a protein precursor comprising 1,547 aa with a 17-residue signal peptide region. A number of structural characteristics and the absence of a thioester bond in the SIPC suggest that this molecule is a previously undescribed protein that may have evolved by duplication from an ancestral α
2
-macroglobulin gene. Although the SIPC is regarded as an adult cue that is recognized by the cyprid at settlement, it is also expressed in the juvenile and in larvae, where it may function in larva–larva settlement interactions.
An intracellular lamellar–nonlamellar phase transition rationalizes the superior performance of some cationic lipid transfection agents
Authors: Koynova Rumiana , Wang Li , MacDonald Robert C.
Published: September 2006

Two cationic phospholipid derivatives with asymmetric hydrocarbon chains were synthesized: ethyl esters of oleoyldecanoyl-ethylphosphatidylcholine (C18:1/C10-EPC) and stearoyldecanoyl-ethylphosphatidylcholine (C18:0/C10-EPC). The former was 50 times more effective as a DNA transfection agent (human umbilical artery endothelial cells) than the latter, despite their similar chemical structure and virtually identical lipoplex organization. A likely reason for the superior effectiveness of C18:1/C10-EPC relative to C18:0/C10-EPC (and to many other cationic lipoids) was suggested by the phases that evolved when these lipoids were mixed with negatively charged membrane lipid formulations. The saturated C18:0/C10-EPC remained lamellar in mixtures with biomembrane-mimicking lipid formulations [e.g., dioleoyl-phosphatidylcholine/dioleoyl-phosphatidylethanolamine/dioleoyl-phosphatidylserine/cholesterol at 45:20:20:15 (wt/wt)]; in contrast, the unsaturated C18:1/C10-EPC exhibited a lamellar–nonlamellar phase transition in such mixtures, which took place at physiological temperatures, ≈37°C. As is well known, lipid vehicles exhibit maximum leakiness and contents release in the vicinity of phase transitions, especially those involving nonlamellar phase formation. Moreover, nonlamellar phase-forming compositions are frequently highly fusogenic. Indeed, FRET experiments showed that C18:1/C10-EPC exhibits lipid mixing with negatively charged membranes that is several times more extensive than that of C18:0/C10-EPC. Thus, C18:1/C10-EPC lipoplexes are likely to easily fuse with membranes, and, as a result of lipid mixing, the resultant aggregates should exhibit extensive phase coexistence and heterogeneity, thereby facilitating DNA release and leading to superior transfection efficiency. These results highlight the phase properties of the carrier lipid/cellular lipid mixtures as a decisive factor for transfection success and suggest a strategy for the rational design of superior cationic lipid carriers.
Differences in vertebrate microRNA expression
Authors: Ason Brandon , Darnell Diana K. , Wittbrodt Beate , Berezikov Eugene , Kloosterman Wigard P. , Wittbrodt Jochen , Antin Parker B. , Plasterk Ronald H. A.
Published: September 2006

MicroRNAs (miRNAs) attenuate gene expression by means of translational inhibition and mRNA degradation. They are abundant, highly conserved, and predicted to regulate a large number of transcripts. Several hundred miRNA classes are known, and many are associated with cell proliferation and differentiation. Many exhibit tissue-specific expression, which aids in evaluating their functions, and it has been assumed that their high level of sequence conservation implies a high level of expression conservation. A limited amount of data supports this, although discrepancies do exist. By comparing the expression of ≈100 miRNAs in medaka and chicken with existing data for zebrafish and mouse, we conclude that the timing and location of miRNA expression is not strictly conserved. In some instances, differences in expression are associated with changes in miRNA copy number, genomic context, or both between species. Variation in miRNA expression is more pronounced the greater the differences in physiology, and it is enticing to speculate that changes in miRNA expression may play a role in shaping the physiological differences produced during animal development.
Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units
Authors: Chan Yolande A. , Boyne Michael T. , Podevels Angela M. , Klimowicz Amy K. , Handelsman Jo , Kelleher Neil L. , Thomas Michael G.
Published: September 2006

Combinatorial biosynthesis of type I polyketide synthases is a promising approach for the generation of new structural derivatives of polyketide-containing natural products. A target of this approach has been to change the extender units incorporated into a polyketide backbone to alter the structure and activity of the natural product. One limitation to these efforts is that only four extender units were known: malonyl-CoA, methylmalonyl-CoA, ethylmalonyl-CoA, and methoxymalonyl-acyl carrier protein (ACP). The chemical attributes of these extender units are quite similar, with the exception of the potential hydrogen bonding interactions by the oxygen of the methoxy moiety. Furthermore, the incorporated extender units are not easily modified by using simple chemical approaches when combinatorial biosynthesis is coupled to semisynthetic chemistry. We recently proposed the existence of two additional extender units, hydroxymalonyl-ACP and aminomalonyl-ACP, involved in the biosynthesis of zwittermicin A. These extender units offer unique possibilities for combinatorial biosynthesis and semisynthetic chemistry because of the introduction of free hydroxyl and amino moieties into a polyketide structure. Here, we present the biochemical and mass spectral evidence for the formation of these extender units. This evidence shows the formation of ACP-linked extender units for polyketide synthesis. Interestingly, aminomalonyl-ACP formation involves enzymology typically found in nonribosomal peptide synthesis.
Epistasis correlates to genomic complexity
Authors: Sanjuán Rafael , Elena Santiago F.
Published: September 2006

Whether systematic genetic interactions (epistasis) occur at the genomic scale remains a challenging topic in evolutionary biology. Epistasis should make a significant contribution to variation in complex traits and influence the evolution of genetic systems as sex, diploidy, dominance, or the contamination of genomes with deleterious mutations. We have collected data from widely different organisms and quantified epistasis in a common, per-generation scale. Simpler genomes, such as those of RNA viruses, display antagonistic epistasis (mutations have smaller effects together than expected); bacterial microorganisms do not apparently deviate from independent effects, whereas in multicellular eukaryotes, a transition toward synergistic epistasis occurs (mutations have larger effects together than expected). We propose that antagonistic epistasis might be a property of compact genomes with few nonpleiotropic biological functions, whereas in complex genomes, synergism might emerge from mutational robustness.
Synergistic inhibition of growth of lung carcinomas by antagonists of growth hormone-releasing hormone in combination with docetaxel
Authors: Hohla Florian , Schally Andrew V. , Szepeshazi Karoly , Varga Jozsef L. , Buchholz Stefan , Köster Frank , Heinrich Elmar , Halmos Gabor , Rick Ferenc G. , Kannadka Chandrika , Datz Christian , Kanashiro Celia A.
Published: September 2006

We investigated the effect of antagonists of growth hormone-releasing hormone (GHRH) MZ-J-7-138 and JV-1-92 on H460 human non-small cell lung carcinoma (NSCLC) xenografted orthotopically into nude mice. Treatment with MZ-J-7-138 or JV-1-92 inhibited orthotopic growth of H460 NSCLC by 52–65% (
P
< 0.001) and was associated with a significant decrease in protein expression of K-Ras, cyclooxygenase-2 (Cox-2) and phospho-Akt (pAkt). In other experiments, treatment with MZ-J-7-138 or docetaxel reduced tumor volume of s.c. xenografted H460 human NSCLC by 30–36% (
P
< 0.01). The combination of MZ-J-7-138 and docetaxel resulted in a synergistic growth inhibition of H460 NSCLC xenografts of 63%. MZ-J-7-138 alone or in combination with docetaxel significantly reduced protein levels of K-Ras, Cox-2, and pAkt by 56–63%. Docetaxel given singly diminished the protein levels only of Cox-2 and did not affect K-Ras and pAkt. High-affinity binding sites, mRNA, and protein expression of pituitary GHRH receptors and its splice variant (SV) 1 were found in H460. H460 NSCLC cells contained GHRH peptide, and its growth was significantly inhibited
in vitro
by 10 μM MZ-J-7-138 (
P
< 0.001). Serum insulin-like growth factor 1 (IGF1) was not reduced by either GHRH antagonists. These findings suggest that antiproliferative effects of GHRH antagonists in H460 NSCLC are associated with down-regulation of K-Ras, Cox-2, and pAkt. In conclusion, GHRH antagonists in combination with docetaxel synergistically inhibit growth of H460 NSCLC and the expression of K-ras, Cox-2, and pAkt, which might abrogate the signal transduction pathways for cell growth stimulation and therapeutic resistance.
Cardiac myosin missense mutations cause dilated cardiomyopathy in mouse models and depress molecular motor function
Authors: Schmitt Joachim P. , Debold Edward P. , Ahmad Ferhaan , Armstrong Amy , Frederico Andrea , Conner David A. , Mende Ulrike , Lohse Martin J. , Warshaw David , Seidman Christine E. , Seidman J. G.
Published: September 2006

Dilated cardiomyopathy (DCM) leads to heart failure, a leading cause of death in industrialized nations. Approximately 30% of DCM cases are genetic in origin, with some resulting from point mutations in cardiac myosin, the molecular motor of the heart. The effects of these mutations on myosin's molecular mechanics have not been determined. We have engineered two murine models characterizing the physiological, cellular, and molecular effects of DCM-causing missense mutations (S532P and F764L) in the α-cardiac myosin heavy chain and compared them with WT mice. Mutant mice developed morphological and functional characteristics of DCM consistent with the human phenotypes. Contractile function of isolated myocytes was depressed and preceded left ventricular dilation and reduced fractional shortening. In an
in vitro
motility assay, both mutant cardiac myosins exhibited a reduced ability to translocate actin (
V
actin
) but had similar force-generating capacities. Actin-activated ATPase activities were also reduced. Single-molecule laser trap experiments revealed that the lower
V
actin
in the S532P mutant was due to a reduced ability of the motor to generate a step displacement and an alteration of the kinetics of its chemomechanical cycle. These results suggest that the depressed molecular function in cardiac myosin may initiate the events that cause the heart to remodel and become pathologically dilated.
The
Arabidopsis thaliana
vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3
Authors: Wood Craig C. , Robertson Masumi , Tanner Greg , Peacock W. James , Dennis Elizabeth S. , Helliwell Chris A.
Published: September 2006

In
Arabidopsis thaliana
, the promotion of flowering by cold temperatures, vernalization, is regulated via a floral-repressive MADS box transcription factor, FLOWERING LOCUS C (FLC). Vernalization leads to the epigenetic repression of
FLC
expression, a process that requires the polycomb group (PcG) protein VERNALIZATION 2 (VRN2) and the plant homeodomain protein VERNALIZATION INSENSITIVE 3 (VIN3). We demonstrate that the repression of
FLC
by vernalization requires homologues of other Polycomb Repressive Complex 2 proteins and VRN2. We show
in planta
that VRN2 and VIN3 are part of a large protein complex that can include the PcG proteins FERTILIZATION INDEPENDENT ENDOSPERM, CURLY LEAF, and SWINGER. These findings suggest a single protein complex is responsible for histone deacetylation at
FLC
and histone methylation at
FLC
in vernalized plants. The abundance of the complex increases during vernalization and declines after plants are returned to higher temperatures, consistent with the complex having a role in establishing
FLC
repression.
The X-linked lymphoproliferative disease gene product SAP associates with PAK-interacting exchange factor and participates in T cell activation
Authors: Gu Cuiping , Tangye Stuart G. , Sun Xiaoqing , Luo Ying , Lin Zhixin , Wu Jun
Published: September 2006

SLAM (signaling lymphocyte activation molecule)-associated protein (SAP) is a Src homology 2 (SH2) domain-containing adaptor expressed in T cells and natural killer cells. Its essential role in immune responses is underscored by the recent finding that mutations in SAP result in a rare but fatal X-linked lymphoproliferative disease (XLP). Although SAP is known to associate with SLAM-family receptors, the exact molecular mechanism by which SAP regulates lymphocyte signaling remains elusive. We here report that in T cells, SAP associates with the PAK-interacting exchange factor (PIX), a guanine nucleotide exchange factor (GEF) specific for Rac/Cdc42 GTPases. Moreover, SAP, PIX, and an activated form of Cdc42 form a complex in mammalian cells. We demonstrate that the SAP-PIX interaction is specific and is mediated by the C-terminal region of the SAP SH2 domain and the PIX SH3 domain. We further show that SAP is required for the recruitment of PIX to the SLAM-family receptors. Interestingly, overexpression of SAP, but not its homolog EAT-2, leads to a synergistic activation of nuclear factor of activating T cells (NFAT) in combination with a calcium signal in T cells. This SAP-mediated activation appears to be receptor-dependent and can be blocked by a dominant negative form of PIX. Taken together, our data strongly suggest that, in addition to the known SAP-interacting kinase Fyn, PIX may be another key player in SAP-mediated T cell activation.
The von Hippel–Lindau tumor suppressor gene product represses oncogenic β-catenin signaling in renal carcinoma cells
Authors: Peruzzi Benedetta , Athauda Gagani , Bottaro Donald P.
Published: September 2006

Loss of von Hippel–Lindau (
VHL
) tumor suppressor gene function occurs in familial and most sporadic clear cell renal cell carcinoma (RCC), resulting in the aberrant expression of genes that control cell proliferation, invasion, and angiogenesis. The molecular mechanisms by which
VHL
loss leads to tumorigenesis are not yet fully defined.
VHL
loss has been shown to allow robust RCC cell motility, invasiveness, and morphogenesis in response to hepatocyte growth factor (HGF) stimulation, processes that are known to contribute to tumor invasiveness and metastatic potential. Among the most likely intracellular mediators of these HGF-driven activities is β-catenin, a structural link between cadherens and the actin cytoskeleton, as well as a gene transactivator. We show that reconstitution of
VHL
expression in RCC cells repressed HGF-stimulated β-catenin tyrosyl phosphorylation, adherens junction disruption, cytoplasmic β-catenin accumulation, and reporter gene transactivation in RCC cells. Ectopic expression of a ubiquitination-resistant β-catenin mutant specifically restored HGF-stimulated invasion and morphogenesis in
VHL
-transfected RCC cells.
VHL
gene silencing in non-RCC renal epithelial cells phenotypically mimicked
VHL
loss in RCC, and HGF-driven invasiveness was blocked by the expression of a dominant-negative mutant of Tcf. We conclude that, unlike many other cancers, where HGF pathway activation contributes to malignancy through the acquisition of autocrine signaling, receptor overexpression, or mutation, in RCC cells
VHL
loss enables HGF-driven oncogenic β-catenin signaling. These findings identify β-catenin as a potential target in biomarker and drug development for RCC.
The Impact of Path Crossing on Visuo-Spatial Serial Memory: Encoding or Rehearsal Effect?
Authors: Parmentier Fabrice B. R. , Andrés Pilar
Published: September 2006

The determinants of visuo-spatial serial memory have been the object of little research, despite early evidence that not all sequences are equally remembered. Recently, empirical evidence was reported indicating that the complexity of the path formed by the to-be-remembered locations impacted on recall performance, defined for example by the presence of crossings in the path formed by successive locations (Parmentier, Elford, & Maybery, 2005). In this study, we examined whether this effect reflects rehearsal or encoding processes. We examined the effect of a retention interval and spatial interference on the ordered recall of spatial sequences with and without path crossings. Path crossings decreased recall performance, as did a retention interval. In line with the encoding hypothesis, but in contrast with the rehearsal hypothesis, the effect of crossing was not affected by the retention interval nor by tapping. The possible nature of the impact of path crossing on encoding mechanisms is discussed.
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
Authors: Hong Fangxin , Breitling Rainer , McEntee Connor W. , Wittner Ben S. , Nemhauser Jennifer L. , Chory Joanne
Published: September 2006

Summary: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004)FEBS Lett., 573, 83–92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements.

Availability: RankProd is available at Bioconductor . A web-based interface will soon be available at

Contact:  fhong@salk.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS)
Authors: Vanselow Katja , Vanselow Jens T. , Westermark Pål O. , Reischl Silke , Maier Bert , Korte Thomas , Herrmann Andreas , Herzel Hanspeter , Schlosser Andreas , Kramer Achim
Published: September 2006

PERIOD (PER) proteins are central components within the mammalian circadian oscillator, and are believed to form a negative feedback complex that inhibits their own transcription at a particular circadian phase. Phosphorylation of PER proteins regulates their stability as well as their subcellular localization. In a systematic screen, we have identified 21 phosphorylated residues of mPER2 including Ser 659, which is mutated in patients suffering from familial advanced sleep phase syndrome (FASPS). When expressing FASPS-mutated mPER2 in oscillating fibroblasts, we can phenocopy the short period and advanced phase of FASPS patients’ behavior. We show that phosphorylation at Ser 659 results in nuclear retention and stabilization of mPER2, whereas phosphorylation at other sites leads to mPER2 degradation. To conceptualize our findings, we use mathematical modeling and predict that differential PER phosphorylation events can result in opposite period phenotypes. Indeed, interference with specific aspects of mPER2 phosphorylation leads to either short or long periods in oscillating fibroblasts. This concept explains not only the FASPS phenotype, but also the effect of the tau mutation in hamster as well as the doubletime mutants (dbtS and dbtL) in Drosophila.
Evolution and biogeography of native Hawaiian Hylaeus bees (Hymenoptera: Colletidae)
Authors: Magnacca Karl N. , Danforth Bryan N.
Published: September 2006

The only bees native to the Hawaiian Islands form a single clade of 60 species in the genus Hylaeus. The group is understudied and relatively poorly known. A data set consisting of 1201 base pairs of the mitochondrial genes cytochrome oxidase I and II and tRNA‐Leucine, and 14 morphological characters was used to construct a phylogenetic tree for 48 of the 60 known species. Genetic variation was high, including amino acid changes, and a number of species showed evidence of heteroplasmy. Tree support was low due to high levels of homoplasy. Biogeographical analysis using DIVA indicates that early radiation took place on the island of Hawaii. This places an upper age limit of only 0.4–0.7 Myr for the group, an unusually short time for such a large radiation. Moreover, it is an unusual biogeographical pattern among the Hawaiian biota. © The Willi Hennig Society 2006.
Effect of multiple doses of montelukast on the pharmacokinetics of rosiglitazone, a CYP2C8 substrate, in humans
Authors: Kim Kyoung‐Ah , Park Pil‐Whan , Kim Kyong Rae , Park Ji‐Young
Published: September 2006

Aims

To investigate the effect of multiple dosing with montelukast, a selective leukotriene‐receptor antagonist, on the pharmacokinetics of rosiglitazone, a CYP2C8 substrate, in humans.

Methods

A two‐period, randomized crossover study was conducted in 10 healthy subjects. After administration of oral doses of placebo or 10 mg montelukast daily for 6 days, 4 mg rosiglitazone was administered and plasma samples were obtained for 24 h and analyzed for rosiglitazone and N‐desmethylrosiglitazone using high‐performance liquid chromatography with fluorescence detection.

Results

During the montelukast phase, the total area under the time‐concentration curve (AUC) and peak plasma concentration of rosiglitazone were 102% (90% CI 98, 107%) and 98% (90% CI 92, 103%) of the corresponding values during the placebo phase, respectively. Multiple dosing with montelukast did not affect the oral clearance of rosiglitazone significantly (90% CI 94, 105%; P = 0.50). The AUC ratio and plasma concentration ratios of N‐desmethylrosiglitazone : rosiglitazone were not changed by multiple dosing with montelukast (90% CI 90, 103%; P = 0.14).

Conclusions

Multiple doses of montelukast do not inhibit CYP2C8‐mediated rosiglitazone metabolism in vivo despite in vitro findings indicating that montelukast is a selective CYP2C8 inhibitor.
High dose calcitriol may reduce thrombosis in cancer patients
Authors: Beer Tomasz M. , Venner Peter M. , Ryan Christopher W. , Petrylak Daniel P. , Chatta Gurkamal , Dean Ruether J. , Chi Kim N. , Curd John G. , DeLoughery Thomas G.
Published: September 2006

The incidence of venous and arterial thrombosis in a placebo‐controlled randomised trial of DN‐101 (high dose calcitriol) with docetaxel versus docetaxel was compared. Of the 13 thrombotic events observed in the 250 patients enroled in this study, two occurred in DN‐101 and 11 in placebo‐treated patients (P = 0·01). This difference remained significant after adjustment for baseline history of thrombosis, atrial fibrillation and use of anti‐thrombotic agents. In vitro and vitamin D receptor (VDR) knockout mouse studies predict that nanomolar concentrations of calcitriol may act as an antithrombotic agent. We report the first clinical observation that supports this hypothesis in humans.
Impalement injuries of the oral cavity in children: a case report and survey of the literature
Authors: YOUNESSI O. JAMES , ALCAINO EDUARDO A.
Published: September 2006

Background.  Impalement injuries of the soft palate and oropharynx are common in children, especially those of preschool age. These injuries are particularly common in toddlers, given their propensity to fall easily while carrying objects in their mouths. Although most of these injuries do not have lasting sequelae, some can have devastating neurological complications, and consequently, careful assessment of the patient during the early stages of trauma is imperative. Close follow‐up for up to 72 h, and parental counselling and instruction should be considered as part of their immediate care.

Case report.  A case of toothbrush impalement in a 4‐year‐old child is presented. The foreign body was noted to be lodged in the cheek. After careful triaging, history taking and appropriate imaging, surgical removal of this brush was carried out uneventfully under general anaesthesia. No further complications were noted postoperatively, and because of the type of injury, the patient was discharged within 24 h and reviewed as an outpatient.

Conclusion.  A survey of the literature confirms that most injuries of this kind can be treated conservatively, and in many cases, without surgical intervention. However, careful assessment by an experienced clinician is necessary to rule out other complications. The present paper discusses the prevalence, management and complications associated with impalement injuries of the oral cavity in children.
Validity and reliability of the Arabic translation of the child oral‐health‐related quality of life questionnaire (CPQ11−14) in Saudi Arabia
Authors: BROWN A. , AL‐KHAYAL Z.
Published: September 2006

Summary.  Aim.  The purpose of this study was to test the validity and reliability of an Arabic translation and adaptation of the child oral‐health‐related quality of life questionnaire (CPQ11−14) in Saudi Arabia.

Design.  The modified questionnaire included two global ratings (oral health and oral‐health‐related well‐being), and a battery of 36 questions in four domains (oral symptoms, functional limitations, emotional well‐being and social well‐being). The study population consisted of 174, 11–14‐year‐old children (65% healthy and 35% medically compromised). Clinical data on caries status and malocclusion were collected for 138 of the children, and 47 completed the questionnaire a second time.

Results.  There was a significant difference in mean total scale scores between children with and without malocclusions (P < 0·05). Significant relationships were identified between caries status and oral symptoms subscale scores, and between malocclusion and total scale and social well‐being subscale scores (P < 0·05). Correlation was highly significant between scale scores and global ratings (P < 0·01). Cronbach's alpha was 0·81 and the test–retest reliability was substantial (r = 0·65, P < 0·001). However, problems were encountered in Saudi Arabia regarding self‐reporting of age, and the questionnaire was too long for many of the medically compromised patients.

Conclusions.  The questionnaire is valid and reliable for use in Saudi Arabia, although development of a shorter version is recommended.
The effects of a long wait for children's dental general anaesthesia
Authors: NORTH SARAH , DAVIDSON LESLEY E. , BLINKHORN ANTHONY S. , MACKIE IAIN C.
Published: September 2006

Objectives.   The purpose of this study was to monitor the effect of an interruption in a service for children who were scheduled to have dental extractions under general anaesthesia (GA). The reasons for offering GA and the treatment given while the service was not available, together with the history of the pain, antibiotic usage and alterations to the number of teeth extracted were recorded.

Methods.   When the GA extraction service stopped, the children who were scheduled to have their teeth extracted were placed on a waiting list. When the service recommenced 6 months later, the children were invited to attend a reassessment. Relevant data were collected at this visit using a proforma.

Results.   A total of 321 children had their extractions delayed. Only 249 of these attended for a reassessment. During the waiting period, 102 parents (41.0%) reported that their children required analgesics, 71 (28.5%) stated that their children's sleep was disturbed and 82 (32.9%) recorded problems with eating. One hundred and twenty‐three children (49.4%) had received antibiotics, with 49 (19.6%) having been prescribed two or more courses. The majority of treatment plans (85.5%) remained unchanged.

Conclusions.   Many children who had had their extractions delayed suffered further pain and disruption to their life.
Patient satisfaction with NHS elective tonsillectomy outsourced to the private sector under the Patient Choice Programme
Authors: Patiar Shalini , Lo Stephen , Duvvi Shyam , Spraggs Paul Dr
Published: September 2006

Rationale, aims and objectives  An interim goal of the NHS ‘Extending choice for patients’ initiative was that, by 2004, patients who had been on the NHS waiting list for elective surgery for 6 months were provided with a choice of staying on the waiting list or being treated faster by opting to have their operation with an alternative provider. The aim of this study was to examine patient satisfaction in a cohort of patients who travelled out‐of‐region to undergo routine tonsillectomy performed by an NHS consultant at a private hospital.

Method  A questionnaire survey was conducted of adult patients undergoing elective tonsillectomy in 2002 and 2003 at The Hampshire Clinic, Basingstoke, UK.

Results  Our results showed that 95% (n = 123) of patients were happy to travel considerable distances from their local hospital to have their operation. Overall 71% (n = 92) of patients rated the overall experience of having the operation performed at the private hospital as excellent and 25% (n = 32) rated it as satisfactory.

Conclusion  We conclude that tonsillectomy performed by a consultant in an out‐of‐region private hospital is associated with a high level of patient satisfaction and is an acceptable way to reduce waiting times for tonsillectomy provided clear guidelines and safeguards are in place.
Review and evaluation of the Dutch guidelines for osteoporosis
Authors: Geusens Piet P. , Lems Willem F. , Verhaar Harald J. J. , Leusink Geraline , Goemaere Stefan , Zmierczack Hans , Compston Jullet
Published: September 2006

Rationale  At the request of a Dutch governmental organization, a multidisciplinary group of osteoporosis experts in the Netherlands published in 2002 a guideline on case finding, diagnosis, prevention and treatment of osteoporosis. These guidelines were evaluated for their validity and applicability.

Methods  Analysis by 5 external osteoporosis experts using the ‘Appraisal of Guidelines for Research & Evaluation’ (‘AGREE’) instrument.

Results  The score for the 6 domains of AGREE was 88% for the scope and purpose domain, 76% for stakeholder involvement, 81% for rigour of development, 84% for clarity and presentation, 77% for applicability and 73% for editorial independence. For single components of the domains of AGREE, highest scores were found for systematic methods used to search for evidence (100%), inclusion of individuals from all the relevant professional groups (95%) and ease of identifying key recommendations (95%). Lowest scores to single components of the several domains were given for piloting among target users (44%). All experts recommended the guidelines for use in practice.

Conclusions  The AGREE instrument scored high for development, clarity and presentation but low for piloting among target users and implementation. Based on the guideline, algorithms from case finding to treatment were constructed that could be tested for piloting among target users and for implementation of the guideline.
The comparison of different dyspnoea scales in patients with COPD
Authors: Ozalevli Sevgi , Ucan Eyup S.
Published: September 2006

Objectives  (i) to compare the relationship between different dyspnoea scales and physical and clinical parameters of patients with chronic obstructive pulmonary disease (COPD); and (ii) to determine the most suitable scale among these scales for this patient group.

Methods  Forty patients with COPD [mean 1st second forced expiratory volume (FEV1), 49.16 ± 2.33% predicted], aged 53–85 participated in this study. The severity of dyspnoea was assessed with different five scales [Modified Borg Scale (MBS), Visual Analogue Scale (VAS), Medical Research Council Dyspnoea Scale (MRCS), Baseline Dyspnoea Index (BDI) and Oxygen Cost Diagram (OCD)]. As clinical parameters, respiratory function was measured by means of pulmonary function test and arterial blood gas analysis. As physical parameters, age and body mass index was recorded.

Results  Patient’s dyspnoea severities were 1.59 ± 2.75, 2.03 ± 2.82, 2.14 ± 1.44, 6.81 ± 4.07, 4.56 ± 2.47 for MBS, VAS, MRCS, BDI, OCD, respectively (P = 0.08). It was proven that only %FEV1 had a correlation with MRCS (r = −0.67, P = 0.01) and BDI (r = 0.58, P = 0.02). In addition to these determinations MRCS, MBS and VAS had a strong correlation defining their relationships with each other (P < 0.05).

Conclusions  MRCS and BDI could assess dyspnoea during daily activities, so these scales showed strength correlation with physical and clinical values. Briefly MRCS is the most suitable dyspnoea scale for the patients with COPD, moreover, BDI, as the second suitable scale, is correlated only with MRCS. Based on these findings, we recommended that MRCS and BDI are appropriate scales for evaluation of dyspnoea in the patients with COPD.
Members of the Arabidopsis AtTPK/KCO family form homomeric vacuolar channels in planta
Authors: Voelker Camilla , Schmidt Diana , Mueller‐Roeber Bernd , Czempinski Katrin
Published: September 2006

The Arabidopsis thaliana K+ channel family of AtTPK/KCO proteins consists of six members including a ‘single‐pore’ (Kir‐type) and five ‘tandem‐pore’ channels. AtTPK4 is currently the only ion channel of this family for which a function has been demonstrated in planta. The protein is located at the plasma membrane forming a voltage‐independent K+ channel that is blocked by extracellular calcium ions. In contrast, AtTPK1 is a tonoplast‐localized protein, that establishes a K+‐selective, voltage‐independent ion channel activated by cytosolic calcium when expressed in a heterologous system, i.e. yeast. Here, we provide evidence that other AtTPK/KCO channel subunits, i.e. AtTPK2, AtTPK3, AtTPK5 and AtKCO3, are also targeted to the vacuolar membrane, opening the possibility that they interact at the target membrane to form heteromeric ion channels. However, when testing the cellular expression patterns of AtTPK/KCO genes we observed distinct expression domains that overlap in only a few tissues of the Arabidopsis plant, making it unlikely that different channel subunits interact to form heteromeric channels. This conclusion was substantiated by in planta expression of combinations of selected tonoplast AtTPK/KCO proteins. Fluorescence resonance energy transfer assays indicate that protein interaction occurs between identical channel subunits (most efficiently between AtTPK1 or AtKCO3) but not between different channel subunits. The finding could be confirmed by bimolecular fluorescence complementation assays. We conclude that tonoplast‐located AtTPK/KCO subunits form homomeric ion channels in vivo.
Distribution of Shigella enterotoxin genes and secreted autotransporter toxin gene among diverse species and serotypes of shigella isolated from Andaman Islands, India
Authors: Roy Subarna , Thanasekaran K. , Dutta Roy Anita R. , Sehgal Subhash C.
Published: September 2006

We studied the prevalence and distribution of the newly described genes for Shigella enterotoxins (ShET1 and ShET2, encoded by set and sen genes) and secreted auto‐transporter toxin (encoded by sat gene) in clinical isolates from the Andaman Islands, India. A total of 153 Shigella isolates obtained from hospitalized patients during 1994–2004 were analysed. These isolates included all the four species of Shigella (S. dyseteriae– 29, S. flexneri– 75, S. sonnei– 38, S. boydii– 5) that belonged to diverse serotypes (including serologically untypable – 6) and each serotype included a wide variety of genotypes. Each isolate underwent polymerase chain reaction (PCR) for detection of set, sen and sat genes employing specific primers. We found the set gene in all S. flexneri 2a and 2b isolates (41 of 41, 100%) but not outside S. flexneri serotype 2. The sen gene was well distributed among all species and serotypes but its presence was apparently low at 49.1% (75 of 153), probably because of the loss of the large plasmid that harbours the gene in 76 of the 78 (97.4%) sen negative isolates. Also, all S. flexneri 2 isolates (including 2a and 2b serotypes) had the sat gene. It was present in 96% (72 of 75) of S. flexneri, in 6.9% (2 of 29) of S. dysenteriae, in 20% (1 of 5) of S. boydii, and in 33.3% (2 of 6) of untypable Shigella, but not in (0 of 38) S. sonnei. This study provides initial data on the prevalence and distribution of of the set, sen and sat genes in a wide variety of Shigella isolated over a 10‐year period. Our results suggest a greater prevalence of the set and sat genes in S. flexneri 2 isolates than previously thought and might help in future pathochip designs.
The role of the mitochondrion in plant responses to biotic stress
Authors: Amirsadeghi Sasan , Robson Christine A. , Vanlerberghe Greg C.
Published: September 2006

Recent studies suggest that the plant mitochondrion may play a role during biotic stress responses, such as those occurring during incompatible plant–pathogen interactions. There are indications that signal molecules or pathways initiated by such interactions may directly or indirectly target mitochondrial components and that an important consequence of this targeting is an early disruption of mitochondrial homeostasis, resulting in an increased generation of mitochondrial reactive oxygen species (mROS). These mROS may then initiate further mitochondrial dysfunction and further mROS generation in a self‐amplifying manner. The mROS, as well as the graded dysfunction of the mitochondrion may act as cellular signals that initiate graded cellular responses ranging from defense gene induction to initiation of programmed cell death. However, these events may be attenuated by the unique components of the plant electron transport chain that act to substitute for dysfunctional components, dampen mROS generation or facilitate in defining the cellular level of ROS and antioxidant defense systems.