bluuebunny/crossref_metadata_2025 huggingface dataset:
Microturbulent drift mode stability before internal transport barrier formation in the Alcator C-Mod radio frequency heated H-mode
Authors: Redi M. H. , Dorland W. , Fiore C. L. , Baumgaertel J. A. , Belli E. M. , Hahm T. S. , Hammett G. W. , Rewoldt G.
Published: July 2005

H -mode experiments on Alcator C-Mod [I. H. Hutchinson, R. L. Boivin, F. Bombarda et al., Phys. Plasmas 1, 1511 (1994)], which exhibit an internal transport barrier (ITB), have been examined with gyrokinetic calculations, before barrier formation. Ion temperature gradient (ITG) and electron temperature gradient (ETG) modes are unstable outside the barrier region and not strongly growing in the core; in the barrier region ITG is only weakly unstable. Linear calculations support the picture that ITG and ETG modes drive high transport outside the ITB, and that weakly unstable ITG modes in the barrier region correlate with reduced particle transport and improved thermal confinement even before the ITB is established, without the need for E×B shear stabilization. Long-wavelength mode stability in the barrier region is analyzed in the context of a phase diagram for ion and electron drift waves by varying the temperature and density scale lengths. Results from the gyrokinetic code GS2 [M. Kotschenreuther, G. Rewoldt, W. M. Tang et al., Comput. Phys. Commun. 88, 128 (1995)] are compared to standard threshold models and benchmark successfully against the experiment in the plasma core.
Electron plasma expansion rate studies on the Electron Diffusion Gauge experimental device
Authors: Morrison Kyle A. , Paul Stephen F. , Davidson Ronald C.
Published: July 2005

The expansion of pure electron plasmas due to collisions with background neutral gas atoms in the Electron Diffusion Gauge experimental device is observed to be in good agreement with the predictions of a macroscopic fluid model with uniform electron temperature. Measurements of the expansion with a two-dimensional (2-D), phosphor-screen density diagnostic suggest that expansion rates measured with the 1-D diagnostic were observed concurrently with substantial changes in the plasma that are not due to electron-neutral collisions. Measurements of the on-axis, parallel plasma temperature evolution support this conclusion and further indicate that the plasmas are continuously losing energy during the expansion, presumably through inelastic collisions with trace background gases.
Integrability of the Bianchi IX system
Authors: Llibre Jaume , Valls Clàudia
Published: July 2005

In this paper we apply the Darboux theory of integrability to the classical Bianchi IX system. Thus, we provide a complete description of the Darboux polynomials, exponential factors, rational first integrals, and Darboux first integrals, for the classical Bianchi IX system.
Magnetocapacitance effect in perovskite-superlattice based multiferroics
Authors: Singh M. P. , Prellier W. , Simon Ch. , Raveau B.
Published: July 2005

We report the structural and magnetoelectrical properties of La0.7Ca0.3MnO3∕BaTiO3 perovskite superlattices grown on (001)-oriented SrTiO3 by the pulsed laser deposition technique. Magnetic hysteresis loops, together with temperature dependent magnetic properties, exhibit well-defined coercivity and magnetic transition temperature (TC) ∼140K. dc electrical studies of films show that the magnetoresistance (MR) is dependent on the BaTiO3 thickness, and negative MR as high as 30% at 100K are observed. The ac electrical studies reveal that the impedance and capacitance in these films vary with the applied magnetic field due to the magnetoelectrical coupling in these structures—a key feature of multiferroics. A negative magnetocapacitance value in the film as high as 3%pertesla at 1kHz and 100K is demonstrated, opening the route for designing novel functional materials.
Effect of multilayer barriers on the optical properties of GaInNAs single quantum-well structures grown by metalorganic vapor phase epitaxy
Authors: Sun H. D. , Clark A. H. , Calvez S. , Dawson M. D. , Kim K. S. , Kim T. , Park Y. J.
Published: July 2005

We report on the effects of combined strain-compensating and strain-mediating layers of various widths on the optical properties of 1.3 μm GaInNAs∕GaAs single quantum well structures grown by metalorganic vapor phase epitaxy (MOVPE). While the emission wavelength of GaInNAs∕GaAs quantum wells can be redshifted by the adoption of strain-compensated GaNAs layers, the material quality is degraded by the increased stress at the well∕barrier interface. This detrimental effect can be cured by inserting a strain-mediating InGaAs layer between them. Contrary to what is expected, however, the emission wavelength is blueshifted by the insertion of the InGaAs layer, which is attributed to the reduced N incorporation due to the improved interface quality. Our results indicate that the optical properties of MOVPE-grown GaInNAs∕GaAs quantum wells can be optimized in quantum efficiency and emission wavelength by combination of strain-compensating and strain-mediating layers with suitable characteristics.
Indirect Oxidation of RDX, HMX, and CL-20 Cyclic Nitramines in Aqueous Solution at Boron-Doped Diamond Electrodes
Authors: Bonin Pascale M. L. , Bejan Dorin , Radovic-Hrapovic Zorana , Halasz Annamaria , Hawari Jalal , Bunce Nigel J.
Published: July 2005

Environmental Context. Nitramine explosives, including RDX, HMX, and the more newly developed CL-20, are the source of groundwater contamination (‘pinkwater’) especially around military installations. These materials all possess an abundance of nitro (NO2) groups, which, like synthetic organohalogens, render them resistant to biodegradation and thereby allows them to persist in the soil and waters. In this study it was shown that these substances can be indirectly oxidized at a boron-doped diamond electrode to small molecules (carboxylic acids and mineralized nitrogen-containing compounds). Abstract. Electrochemical oxidation at boron-doped diamond (BDD) electrodes was examined as a possible technique for the remediation of water contaminated with nitramine explosives. The advantage of BDD is that it promotes indirect oxidation by electrogenerated active intermediates, such as hydroxyl radicals. For the three explosives RDX, HMX, and CL-20, degradation in both acetonitrile/water mixtures and in water alone was suggested to involve an initial denitration, followed by spontaneous decomposition of the molecules, the net result being the complete transformation of the nitramines to small molecules. Although the rate of degradation increased with current density, the current efficiency was highest at low current densities.
Cell wall immobilisation and antioxidant status of Xanthoria parietina thalli exposed to cadmium
Authors: di Toppi Luigi Sanità , Marabottini Rosita , Vattuone Zulema , Musetti Rita , Favali Maria Augusta , Sorgonà Agostino , Badiani Maurizio
Published: July 2005

Total and cell wall-bound cadmium and the major antioxidants were measured in thalli of the lichen Xanthoria parietina (L.) Th. Fr. exposed to two Cd concentrations, namely 4.5 or 9.0 μm, in liquid medium during exposure periods of either 24 or 48 h. Total Cd in the thalli was within the range of previous field measurements and was proportional to the exposure concentration, but less than proportional with respect to exposure duration. More than half of the total Cd was immobilised by the cell wall. The adopted conditions of Cd stress caused: (i) no changes in dry weight and protein concentration; (ii) an increase in the level of ascorbic acid and a decrease in that of reduced glutathione, as well as an increase in guaiacol peroxidase activity; (iii) no changes or moderate decreases in the activities of superoxide dismutase, catalase, dehydroascorbate-, NADPH-dependent glutathione disulfide-, and monodehydroascorbate reductases and of ascorbate peroxidase; (iv) an increase of the level of thiobarbituric acid-reactive substances, assumed to reflect malondialdehyde formation arising from membrane lipid peroxidation. Thus, X. parietina might withstand realistic levels of Cd stress by: (1) intercepting the heavy metal at cell wall level, (2) the intervention of antioxidant metabolites, and (3) a moderate increase in guaiacol peroxidase activity.
Research note: Increasing Amb a 1 content in common ragweed (Ambrosia artemisiifolia) pollen as a function of rising atmospheric CO2 concentration
Authors: Singer Ben D. , Ziska Lewis H. , Frenz David A. , Gebhard Dennis E. , Straka James G.
Published: July 2005

Although the impact of increasing atmospheric carbon dioxide concentration ([CO2]) on production of common ragweed (Ambrosia artemisiifolia L.) pollen has been examined in both indoor and outdoor experiments, the relationship between allergen expression and [CO2] is not known. An enzyme-linked immunosorbent assay (ELISA) was used to quantify Amb a 1, ragweed’s major allergen, in protein extracted from pollen of A. artemisiifolia grown at different [CO2] values in a previous experiment. The concentrations used approximated atmospheric pre-industrial conditions (i.e. at the end of the 19th century), current conditions, and the CO2 concentration projected for the middle of the 21st century (280, 370 and 600 μmol mol–1 CO2, respectively). Although total pollen protein remained unchanged, significant increases in Amb a 1 allergen were observed between pre-industrial and projected future [CO2] and between current and projected future [CO2] (1.8 and 1.6 times, respectively). These data suggest that recent and projected increases in [CO2] could directly increase the allergenicity of ragweed pollen and consequently the prevalence and / or severity of seasonal allergic disease. However, genetic and abiotic factors governing allergen expression will need to be better established to fully understand these data and their implications for public health.
An algorithm for progressive multiple alignment of sequences with insertions
Authors: Löytynoja Ari , Goldman Nick
Published: July 2005

Dynamic programming algorithms guarantee to find the optimal alignment between two sequences. For more than a few sequences, exact algorithms become computationally impractical, and progressive algorithms iterating pairwise alignments are widely used. These heuristic methods have a serious drawback because pairwise algorithms do not differentiate insertions from deletions and end up penalizing single insertion events multiple times. Such an unrealistically high penalty for insertions typically results in overmatching of sequences and an underestimation of the number of insertion events. We describe a modification of the traditional alignment algorithm that can distinguish insertion from deletion and avoid repeated penalization of insertions and illustrate this method with a pair hidden Markov model that uses an evolutionary scoring function. In comparison with a traditional progressive alignment method, our algorithm infers a greater number of insertion events and creates gaps that are phylogenetically consistent but spatially less concentrated. Our results suggest that some insertion/deletion “hot spots” may actually be artifacts of traditional alignment algorithms.
Specific Interaction of the Actin-binding Domain of Dystrophin with Intermediate Filaments Containing Keratin 19
Authors: Stone Michele R. , O'Neill Andrea , Catino Dawn , Bloch Robert J.
Published: July 2005

Cytokeratins 8 and 19 concentrate at costameres of striated muscle and copurify with the dystrophin-glycoprotein complex, perhaps through the interaction of the cytokeratins with the actin-binding domain of dystrophin. We overexpressed dystrophin's actin-binding domain (Dys-ABD), K8 and K19, as well as closely related proteins, in COS-7 cells to assess the basis and specificity of their interaction. Dys-ABD alone associated with actin microfilaments. Expressed with K8 and K19, which form filaments, Dys-ABD associated preferentially with the cytokeratins. This interaction was specific, as the homologous ABD of βI-spectrin failed to interact with K8/K19 filaments, and Dys-ABD did not associate with desmin or K8/K18 filaments. Studies in COS-7 cells and in vitro showed that Dys-ABD binds directly and specifically to K19. Expressed in muscle fibers in vivo, K19 accumulated in the myoplasm in structures that contained dystrophin and spectrin and disrupted the organization of the sarcolemma. K8 incorporated into sarcomeres, with no effect on the sarcolemma. Our results show that dystrophin interacts through its ABD with K19 specifically and are consistent with the idea that cytokeratins associate with dystrophin at the sarcolemma of striated muscle.
Src and FAK Kinases Cooperate to Phosphorylate Paxillin Kinase Linker, Stimulate Its Focal Adhesion Localization, and Regulate Cell Spreading and Protrusiveness
Authors: Brown Michael C. , Cary Leslie A. , Jamieson Jennifer S. , Cooper Jonathan A. , Turner Christopher E.
Published: July 2005

The ArfGAP paxillin kinase linker (PKL)/G protein-coupled receptor kinase-interacting protein (GIT)2 has been implicated in regulating cell spreading and motility through its transient recruitment of the p21-activated kinase (PAK) to focal adhesions. The Nck-PAK-PIX-PKL protein complex is recruited to focal adhesions by paxillin upon integrin engagement and Rac activation. In this report, we identify tyrosine-phosphorylated PKL as a protein that associates with the SH3-SH2 adaptor Nck, in a Src-dependent manner, after cell adhesion to fibronectin. Both cell adhesion and Rac activation stimulated PKL tyrosine phosphorylation. PKL is phosphorylated on tyrosine residues 286/392/592 by Src and/or FAK and these sites are required for PKL localization to focal adhesions and for paxillin binding. The absence of either FAK or Src-family kinases prevents PKL phosphorylation and suppresses localization of PKL but not GIT1 to focal adhesions after Rac activation. Expression of an activated FAK mutant in the absence of Src-family kinases partially restores PKL localization, suggesting that Src activation of FAK is required for PKL phosphorylation and localization. Overexpression of the nonphosphorylated GFP-PKL Triple YF mutant stimulates cell spreading and protrusiveness, similar to overexpression of a paxillin mutant that does not bind PKL, suggesting that failure to recruit PKL to focal adhesions interferes with normal cell spreading and motility.
Theoretical models of selection and mutation on quantitative traits
Authors: Johnson Toby , Barton Nick
Published: July 2005

Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some of the thorny issues that arise when formulating models that describe many traits simultaneously.
Artificial selection and maintenance of genetic variance in the global dairy cow population
Authors: Brotherstone S , Goddard M
Published: July 2005

Genetic improvement of dairy cows, which has increased the milk yield of cows in the UK by 1200 kg per lactation in 12 years, is an excellent example of the application of quantitative genetics to agriculture. The most important traits of dairy cattle are expressed only in females, but the main opportunity for selection is in males. Despite this, genetic improvement was achieved by the invention of a new statistical methodology, called ‘best linear unbiased prediction’ to estimate the breeding value of bulls. Intense selection of the best bulls, combined with the worldwide use of these bulls through artificial insemination and frozen semen, has created a global population and caused concern that the genetic variation available in the future will be reduced. Maintenance of genetic variation and long-term genetic gains would be aided by rational payment systems, use of crossbreeding where profitable, inclusion of all economically important traits in the breeding objective, recognition of genotype by environment interactions and the use of selection algorithms that balance estimated breeding value against the average relationship among the selected animals. Fortunately, all of these things are happening to some degree.
Selection in backcross programmes
Authors: Hospital Frédéric
Published: July 2005

Backcrossing is a well-known and long established breeding scheme where a characteristic is introgressed from a donor parent into the genomic background of a recurrent parent. The various uses of backcrossing in modern genetics, particularly with the help of molecular markers, are reviewed here. Selection in backcross programmes is used to either improve the genetic value of plant and animal populations or fine map quantitative trait loci. Both cases are helpful in our understanding of the genetic bases of quantitative traits variation.
Estimation of quantitative genetic parameters
Authors: Thompson Robin , Brotherstone Sue , White Ian M.S
Published: July 2005

This paper gives a short review of the development of genetic parameter estimation over the last 40 years. This shows the development of more statistically and computationally efficient methods that allow the fitting of more biologically appropriate models. Methods have evolved from direct methods based on covariances between relatives to methods based on individual animal models. Maximum-likelihood methods have a natural interpretation in terms of best linear unbiased predictors. Improvements in iterative schemes to give estimates are discussed. As an example, a recent estimation of genetic parameters for a British population of dairy cattle is discussed. The development makes a connection to relevant work by Bill Hill.
Genotypic probabilities for pairs of inbred relatives
Authors: Liu Wenlei , Weir B.S
Published: July 2005

Expressions for the joint genotypic probabilities of two related individuals are used in many population and quantitative genetic analyses. These expressions, resting on a set of 15 probabilities of patterns of identity by descent among the four alleles at a locus carried by the relatives, are generally well known. There has been recent interest in special cases where the two individuals are both related and inbred, although there have been differences among published results. Here, we return to the original 15-probability treatment and show appropriate reductions for relatives when they are drawn from a population that itself is inbred or when the relatives have parents who are related. These results have application in affected-relative tests for linkage, and in methods for interpreting forensic genetic profiles.
Up hill, down dale: quantitative genetics of curvaceous traits
Authors: Meyer Karin , Kirkpatrick Mark
Published: July 2005

‘Repeated’ measurements for a trait and individual, taken along some continuous scale such as time, can be thought of as representing points on a curve, where both means and covariances along the trajectory can change, gradually and continually. Such traits are commonly referred to as ‘function-valued’ (FV) traits. This review shows that standard quantitative genetic concepts extend readily to FV traits, with individual statistics, such as estimated breeding values and selection response, replaced by corresponding curves, modelled by respective functions. Covariance functions are introduced as the FV equivalent to matrices of covariances.

Considering the class of functions represented by a regression on the continuous covariable, FV traits can be analysed within the linear mixed model framework commonly employed in quantitative genetics, giving rise to the so-called random regression model. Estimation of covariance functions, either indirectly from estimated covariances or directly from the data using restricted maximum likelihood or Bayesian analysis, is considered. It is shown that direct estimation of the leading principal components of covariance functions is feasible and advantageous. Extensions to multi-dimensional analyses are discussed.
Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism
Authors: Wu Gang , Culley David E. , Zhang Weiwen
Published: July 2005

Highly expressed genes in bacteria often have a stronger codon bias than genes expressed at lower levels, due to translational selection. In this study, a comparative analysis of predicted highly expressed (PHX) genes in the Streptomyces coelicolor and Streptomyces avermitilis genomes was performed using the codon adaptation index (CAI) as a numerical estimator of gene expression level. Although it has been suggested that there is little heterogeneity in codon usage in G+C-rich bacteria, considerable heterogeneity was found among genes in these two G+C-rich Streptomyces genomes. Using ribosomal protein genes as references, ∼10 % of the genes were predicted to be PHX genes using a CAI cutoff value of greater than 0·78 and 0·75 in S. coelicolor and S. avermitilis, respectively. The PHX genes showed good agreement with the experimental data on expression levels obtained from proteomic analysis by previous workers. Among 724 and 730 PHX genes identified from S. coelicolor and S. avermitilis, 368 are orthologue genes present in both genomes, which were mostly ‘housekeeping’ genes involved in cell growth. In addition, 61 orthologous gene pairs with unknown functions were identified as PHX. Only one polyketide synthase gene from each Streptomyces genome was predicted as PHX. Nevertheless, several key genes responsible for producing precursors for secondary metabolites, such as crotonyl-CoA reductase and propionyl-CoA carboxylase, and genes necessary for initiation of secondary metabolism, such as adenosylmethionine synthetase, were among the PHX genes in the two Streptomyces species. The PHX genes exclusive to each genome, and what they imply regarding cellular metabolism, are also discussed.
Atomic force microscopy study on specificity and non-specificity of interaction forces between Enterococcus faecalis cells with and without aggregation substance
Authors: Waar Karola , van der Mei Henny C. , Harmsen Hermie J. M. , de Vries Joop , Atema-Smit Jelly , Degener John E. , Busscher Henk J.
Published: July 2005

Enterococcus faecalis is one of the leading causes of hospital-acquired infections, and indwelling medical devices are especially prone to infection. E. faecalis expressing aggregation substance (Agg) adheres to biomaterial surfaces by means of positive cooperativity, i.e. the ability of one adhering organism to stimulate adhesion of other organisms in its immediate vicinity. In this study, atomic force microscopy (AFM) was used to measure the specificity and non-specificity of interaction forces between E. faecalis cells with and without Agg. Bacteria were attached to a substratum surface and a tip-less cantilever. Two E. faecalis strains expressing different forms of Agg showed nearly twofold higher interaction forces between bacterial cells than a strain lacking Agg [adhesive force (F
adh), −1·3 nN]. The strong interaction forces between the strains with Agg were reduced after adsorption of antibodies against Agg from −2·6 and −2·3 nN to −1·2 and −1·3 nN, respectively. This suggests that the non-specific interaction force between the enterococci amounts to approximately 1·2 nN, while the specific force component is only twofold stronger. Comparison of the results of the AFM interaction forces with the positive cooperativity after adhesion to a biomaterial in a parallel-plate flow chamber showed that in the absence of strong interaction forces between the cells, positive cooperativity was also absent. In conclusion, this is believed to be the first time that the influence of specific antibodies on interaction forces between E. faecalis cells has been demonstrated by AFM, thereby experimentally distinguishing between specific and non-specific force components.
Functions of the siderophore esterases IroD and IroE in iron-salmochelin utilization
Authors: Zhu Mingang , Valdebenito Marianne , Winkelmann Günther , Hantke Klaus
Published: July 2005

The siderophore salmochelin is produced under iron-poor conditions bySalmonellaand many uropathogenicEscherichia colistrains. The production of salmochelin, a C-glucosylated enterobactin, is dependent on the synthesis of enterobactin and theiroBCDENgene cluster. AnE. coliIroD protein with an N-terminal His-tag cleaved cyclic salmochelin S4 to the linear trimer salmochelin S2, the dimer salmochelin S1, and the monomers dihydroxybenzoylserine and C-glucosylated dihydroxybenzoylserine (salmochelin SX, pacifarinic acid). The periplasmic IroE protein was purified as a MalE–IroE fusion protein. This enzyme degraded salmochelin S4 and ferric-salmochelin S4 to salmochelin S2 and ferric-salmochelin S2, respectively. InE. coli, uptake of ferric-salmochelin S4 was dependent on the cleavage by IroE, and independent of the FepBDGC ABC transporter in the cytoplasmic membrane. IroC, which has similarities to ABC-multidrug-resistance proteins, was necessary for the uptake of salmochelin S2 from the periplasm into the cytoplasm. IroE did not function as a classical binding protein since salmochelin S2 was taken up in the absence of a functional IroE protein. IroC mediated the uptake of iron via enterobactin in afepBmutant. IroE was also necessary in this case for the uptake of ferric-enterobactin, which indicated that only the linear degradation products of enterobactin were taken up via IroC. PfeE, thePseudomonas aeruginosaIroE homologue, was cloned, and its enzymic activity was shown to be very similar to that of IroE. It is suggested that homologues in other bacteria are also periplasmic IroE-type esterases of siderophores.
Determining the functionality of putative Tat-dependent signal peptides in Streptomyces coelicolor A3(2) by using two different reporter proteins
Authors: Li Haiming , Jacques Pierre-Étienne , Ghinet Mariana Gabriela , Brzezinski Ryszard , Morosoli Rolf
Published: July 2005

The availability of the complete genome sequence ofStreptomyces coelicolorA3(2) has allowed the prediction of the Tat-exported proteins of this Gram-positive bacterium. To predict secreted proteins that potentially use the Tat pathway for their secretion, the TATscan program was developed. This program identified 129 putative Tat substrates. To test the validity of these predictions, nine signal sequences, including three which were not identified by existing prediction programs, were selected and fused to the structuralxlnCgene in place of its native signal sequence. Xylanase C (XlnC) is a cofactorless enzyme which is secreted in an active form exclusively through the Tat-dependent pathway byStreptomyces lividans. Among the nine chosen signal sequences, seven were shown to be Tat-dependent, one was Sec-dependent and one was probably not a signal sequence. The seven Tat-dependent signal sequences comprised two lipoprotein signal sequences and three sequences not predicted by previous programs. Pulse–chase experiments showed that the precursor-processing rate in the seven transformants was generally slower than wild-type XlnC, indicating that these signal peptides were not equivalent in secretion. This suggested that there might be some incompatibility between the signal peptide and the reporter protein fused to it. To test this possibility, the signal peptides were fused to a cofactorless chitosanase (SCO0677), a Tat-dependent protein validated in this work but structurally different from XlnC. With some fluctuations, similar results were obtained with this enzyme, indicating that the type of folding of the reporter protein had little effect on the Tat secretion process.
PorH, a new channel-forming protein present in the cell wall of Corynebacterium efficiens and Corynebacterium callunae
Authors: Hünten Peter , Schiffler Bettina , Lottspeich Friedrich , Benz Roland
Published: July 2005

Corynebacterium callunaeandCorynebacterium efficiensare close relatives of the glutamate-producing mycolata speciesCorynebacterium glutamicum. The properties of the pore-forming proteins, extracted by organic solvents, were studied. The cell extracts contained channel-forming proteins that formed ion-permeable channels with a single-channel conductance of about 2 to 3 nS in 1 M KCl in a lipid bilayer assay. The corresponding proteins from both corynebacteria were purified to homogeneity and were named PorHC.calland PorHC.eff. Electrophysiological studies of the channels suggested that they are wide and water-filled. Channels formed by PorHC.callare cation-selective, whereas PorHC.effforms slightly anion-selective channels. Both proteins were partially sequenced. A multiple sequence alignment search within the known chromosome ofC. efficiensdemonstrated that it contains a gene that fits the partial amino acid sequence of PorHC.eff. PorHC.callshows high homology to PorHC.eff. PorHC.effis encoded in the bacterial chromosome by a gene that is localized within the vicinity of theporAgene ofC. efficiens. PorHC.effhas no signal sequence at the N terminus, which means that it is not exported by the Sec-secretion pathway. The structure of PorH in the cell wall of the corynebacteria is discussed.
Identification and targeted disruption of the gene encoding the main 3-ketosteroid dehydrogenase in Mycobacterium smegmatis
Authors: Brzostek Anna , Śliwiński Tomasz , Rumijowska-Galewicz Anna , Korycka-Machała Małgorzata , Dziadek Jarosław
Published: July 2005

The catabolic potential for sterol degradation of fast-growing mycobacteria is well known. However, no genes or enzymes responsible for the steroid degradation process have been identified as yet in these species. One of the key enzymes required for degradation of the steroid ring structure is 3-ketosteroid Δ1-dehydrogenase (KsdD). The recent annotation of the Mycobacterium smegmatis genome (TIGR database) revealed six KsdD homologues. Targeted disruption of the MSMEG5898 (ksdD-1) gene, but not the MSMEG4855 (ksdD-2) gene, resulted in partial inactivation of the cholesterol degradation pathway and accumulation of the intermediate 4-androstene-3,17-dione. This effect was reversible by the introduction of the wild-type ksdD-1 gene into M. smegmatis ΔksdD-1 or overexpression of ksdD-2. The data indicate that KsdD1 is the main KsdD in M. smegmatis, but that KsdD2 is able to perform the cholesterol degradation process when overproduced.
Distribution and evolution of multiple-step phosphorelay in prokaryotes: lateral domain recruitment involved in the formation of hybrid-type histidine kinases
Authors: Zhang Weiwen , Shi Liang
Published: July 2005

Although most two-component signal transduction systems use a simple phosphotransfer pathway from one histidine kinase (HK) to one response regulator (RR), a multiple-step phosphorelay involving a phosphotransfer scheme of His–Asp–His–Asp was also discovered. Central to this multiple-step-type signal transduction pathway are a hybrid-type HK, containing both an HK domain and an RR receiver domain in a single protein, and a histidine-containing phosphotransfer (HPT) that can exist either as a domain in hybrid-type HKs or as a separate protein. Although multiple-step phosphorelay systems are predominant in eukaryotes, it has been previously suggested that they are less common in prokaryotes. In this study, it was found that putative hybrid-type HKs were present in 56 of 156 complete prokaryotic genomes, indicating that multiple-step phosphorelay systems are more common in prokaryotes than previously appreciated. Large expansions of hybrid-type HKs were observed in 26 prokaryotic species, including photosynthetic cyanobacteria such asNostocsp. PCC 7120, and several pathogenic bacteria such asCoxiella burnetii. Phylogenetic analysis indicated that there was no common ancestor for hybrid-type HKs, and their origin and expansion was achieved by lateral recruitment of a receiver domain into an HK molecule and then duplication as one unit. Lateral recruitment of additional sensory domains such as PAS was also evident. HPT domains or proteins were identified in 32 of the genomes with hybrid-type HKs; however, no significant gene expansion was observed for HPTs even in a genome with a large number of hybrid-type HKs. In addition, fewer HPTs than hybrid-type HKs were identified in all prokaryotic genomes.
The ‘yeast cell wall chip’ – a tool to analyse the regulation of cell wall biogenesis in Saccharomyces cerevisiae
Authors: Rodríguez-Peña Jose M. , Pérez-Díaz Rosa M. , Alvarez Sara , Bermejo Clara , García Raúl , Santiago Catalina , Nombela César , Arroyo Javier
Published: July 2005

Within the field of Saccharomyces cerevisiae functional genomics, DNA microarrays have become a very useful tool to study genome-wide gene-expression changes under diverse experimental conditions. Here, the design and production of a gene microarray, called the ‘yeast cell wall chip’, specifically tailored to investigate cell wall functions, is described. This array has been validated and shown to be useful to address gene involvement in the regulation of the response to cell wall damage in yeast. The advantages of this tailored gene microarray, which contains 390 genes, in terms of reproducibility, accuracy, versatility and ease of use are reported. Importantly, the microarray design permits the performance of a double hybridization process (two experiments) on the same slide. Cell wall stress leads to the transcriptional activation of a set of genes involved in cell wall remodelling. This response has been shown to be strongly controlled by the MAP kinase (MAPK) Slt2p, but other signalling pathways have also been suggested to be involved in this process. Here, using the tailored microarray, the role of the HOG1 pathway in the regulation of the transcriptional compensatory response to cell wall damage was evaluated by comparing the transcriptional profiles of a hog1 mutant and a wild-type strain in the presence of Congo red. Two genes, YFL014W (HSP12) and YLR414C, were found to be dependent on the Hog1p MAPK for their induction, indicating that an additional level of regulation of cell wall functions is mediated by this MAPK.
A putative dual-specific protein phosphatase encoded by YVH1 controls growth, filamentation and virulence in Candida albicans
Authors: Hanaoka Nozomu , Umeyama Takashi , Ueno Keigo , Ueda Kenji , Beppu Teruhiko , Fugo Hajime , Uehara Yoshimasa , Niimi Masakazu
Published: July 2005

In response to stimulants, such as serum, the yeast cells of the opportunistic fungal pathogen Candida albicans form germ tubes, which develop into hyphae. Yvh1p, one of the 29 protein phosphatases encoded in the C. albicans genome, has 45 % identity with the dual-specific phosphatase Yvh1p of the model yeast Saccharomyces cerevisiae. In this study, Yvh1p expression was not observed during the initial step of germ tube formation, although Yvh1p was expressed constitutively in cell cycle progression of yeast or hyphal cells. In an attempt to analyse the function of Yvh1p phosphatase, the complete ORFs of both alleles were deleted by replacement with hph200–URA3–hph200 and ARG4. Although YVH1 has nine single-nucleotide polymorphisms in its coding sequence, both YVH1 alleles were able to complement the YVH1 gene disruptant. The vegetative growth of Δyvh1 was significantly slower than the wild-type. The hyphal growth of Δyvh1 on agar, or in a liquid medium, was also slower than the wild-type because of the delay in nuclear division and septum formation, although germ tube formation was similar between the wild-type and the disruptant. Despite the slow hyphal growth, the expression of several hypha-specific genes in Δyvh1 was not delayed or repressed compared with that of the wild-type. Infection studies using mouse models revealed that the virulence of Δyvh1 was less than that of the wild-type. Thus, YVH1 contributes to normal vegetative yeast or hyphal cell cycle progression and pathogenicity, but not to germ tube formation.
Novel and Mechanical Stress–Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsis
Authors: Lu Shanfa , Sun Ying-Hsuan , Shi Rui , Clark Catherine , Li Laigeng , Chiang Vincent L.
Published: July 2005

MicroRNAs (miRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes by targeting mRNAs for silencing. To test whether miRNAs play roles in the regulation of wood development in tree species, we isolated small RNAs from the developing xylem of Populus trichocarpa stems and cloned 22 miRNAs. They are the founding members of 21 miRNA gene families for 48 miRNA sequences, represented by 98 loci in the Populus genome. A majority of these miRNAs were predicted to target developmental- and stress/defense-related genes and possible functions associated with the biosynthesis of cell wall metabolites. Of the 21 P. trichocarpa miRNA families, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental expression patterns, suggesting that even conserved miRNAs may have different regulatory roles in different species. Most unexpectedly, the remaining 10 miRNAs, for which 17 predicted targets were experimentally validated in vivo, are absent from the Arabidopsis genome, suggesting possible roles in tree-specific processes. In fact, the expression of a majority of the cloned miRNAs was upregulated or downregulated in woody stems in a manner consistent with tree-specific corrective growth against tension and compression stresses, two constant mechanical loads in trees. Our results show that plant miRNAs can be induced by mechanical stress and may function in one of the most critical defense systems for structural and mechanical fitness.
Fucosidosis with angiokeratoma. Immunohistochemical & electronmicroscopic study of a new case and literature review
Authors: Kanitakis Jean , Allombert Carole , Doebelin Bénédicte , Deroo‐Berger Marie‐Charlotte , Grande Sophie , Blanc Sébastien , Claudy Alain
Published: July 2005

Fucosidosis is a rare lysosomal storage disease due to α‐L‐fucosidase deficiency. It presents clinically with neurological, skeletal, and cutaneous findings, including mainly angiokeratoma corporis diffusum. Electronmicroscopic examination reveals characteristic electron‐lucent cytoplasmic vacuolization present in several cell types of the skin and other tissues. We present here a new patient suffering from fucosidosis with angiokeratoma, whose normal and diseased skin was studied by lightmicroscopy and electronmicroscopy. The salient clinicopathological features of this disease are briefly reviewed.
Histopathological review of sebaceous carcinoma of the eyelid
Authors: Pereira Patricia Rusa , Odashiro Alexandre Nakao , Rodrigues‐Reyes Abelardo A , Correa Zelia Maria S , De Souza Filho João Pessoa , Burnier Miguel N
Published: July 2005

Background:  Sebaceous carcinoma of the eyelid can clinically mimic benign conditions, such as recurrent chalazion and inflammation and histopathologically squamous cell and basal cell carcinoma (BCC). This retrospective study was undertaken as an attempt to improve the characterization and consequently the diagnosis of these tumors.

Methods:  Retrospective analysis was performed on eyelid specimens diagnosed as sebaceous carcinoma retrieved from Henry C. Witelson Ophthalmic Pathology Registry, Canada and Hospital Luis S. Bulnes Pathology Registry, Mexico. Two independent, masked pathologists reviewed the H&E microslides.

Results:  Forty‐four cases were retrieved, 31 from Canada and 13 from Mexico. Cytoplasmic vacuoles were observed in 48% of the cases. Eighty‐four percent of the cases were classified as poorly differentiated lesions. Of these, 75% had features similar to squamous cell carcinoma (SqCC), some with dyskeratosis (30%) and 7% resembled BCC. Solid growth pattern was seen in 26.2% of the cases and lobular growth pattern in 26.2%. Superficial spread resembling Bowen‐like disease was observed in 33% of the cases, pagetoid features in 33% and comedocarcinoma in 31.8%.

Conclusion:  Sebaceous carcinoma presented as a poorly differentiated lesion in most cases of this series, which suggests a possibility of misdiagnosis because of its similarities to SqCC.
Kinetics of pulmonary neutrophil recruitment and clearance in a natural and spontaneously resolving model of airway inflammation
Authors: Brazil T. J. , Dagleish M. P. , McGorum B. C. , Dixon P. M. , Haslett C. , Chilvers E. R.
Published: July 2005

BackgroundNeutrophil apoptosis and phagocytic clearance have been proposed as key determinants affecting the resolution of airway inflammation.

ObjectiveTo determine the kinetics of neutrophil priming, recruitment, activation and subsequent clearance in a naturally occurring equine disease model of neutrophilic pulmonary inflammation.

Methods and ResultsA 5 h mouldy hay/straw challenge in hypersensitive horses induced transient pulmonary dysfunction lasting 4 days. At 24 h circulating neutrophils were primed and displayed delayed rates of spontaneous apoptosisin vitro. Neutrophil numbers in the airspaces peaked at 5 h and then fell abruptly, returning to pre‐challenge levels by 4 days. Airspace neutrophils demonstrated increased respiratory burst activity compared with circulating cells and equine neutrophil elastase 2A concentrations increased in parallel with neutrophil numbers indicatingin vivopriming and degranulation. The number of apoptotic neutrophils and proportion of alveolar macrophages containing phagocytosed apoptotic neutrophils increased significantly at 24 h and 4 days post‐challenge corresponding to the period of most rapid neutrophil clearance.

ConclusionThis is the first demonstration of spontaneous neutrophil apoptosis and phagocytic removal in a natural disease model of airway inflammation and provides critical kinetic data to support the hypothesis that this clearance pathway plays a central role in the resolution of neutrophilic inflammation.
Effects of various anti‐asthmatic agents on mite allergen‐pulsed murine bone marrow‐derived dendritic cells
Authors: Machida I. , Matsuse H. , Kondo Y. , Kawano T. , Saeki S. , Tomari S. , Obase Y. , Fukushima C. , Kohno S.
Published: July 2005

Background
Dendritic cells (DCs) play an important role in the immune response and are critically involved in asthma. β2‐agonists could potentially exacerbate type 2 T helper (Th2) cell‐mediated immune response.

Objectives
To determine the effects of various anti‐asthmatic agents on DCs function both in vitro and in vivo.

Methods
Murine bone marrow‐derived DCs were pulsed with mite allergen in the presence of pranlukast, salbutamol, salmeterol or fluticasone. These DCs were then inoculated intranasally into naïve mice to induce allergic airway inflammation in vivo.

Results
Pranlukast reduced IL‐10 and increased IL‐12, while fluticasone reduced both IL‐10 and IL‐12 production by mite allergen‐pulsed DCs. Allergic airway inflammation in pranlukast‐ and fluticasone‐treated and mite allergen pulsed DCs‐harbouring mice was attenuated and such response was associated with inhibition of Th2 response in the airway. Salbutamol did not alter cytokine production, while salmeterol reduced IL‐12 production by mite allergen‐pulsed DCs. Lung pathology in β2‐agonist‐harbouring mice was comparable with those of mite allergen‐pulsed DCs‐harbouring mice.

Conclusions
Our results indicate that leukotriene receptor antagonists and corticosteroids inhibit DCs‐induced Th2 skewed immune response, and that short‐ and long‐acting β2‐agonists do not modify DCs‐induced allergic airway inflammation.
Transgenic mice expressing the T cell antigen receptor specific for an immunodominant epitope of a major allergen of house dust mite develop an asthmatic phenotype on exposure of the airways to allergen
Authors: Jarman E. R. , Tan K. A. L. , Lamb J. R.
Published: July 2005

Background
Current studies on mechanisms underlying allergen‐induced pulmonary inflammation and asthma are hampered by the lack of appropriate physiological in vivo models that reflect the natural route of allergen exposure and sensitization.

Objective
To generate and phenotype a transgenic mouse strain expressing the T cell receptor (TCR) specific for an immunodominant domain of the major inhalant allergen Dermatophagoides pteronyssinus species of house dust mite (Der p 1), for the development of an in vivo model of allergic asthma.

Methods
Der p 1 transgenic mice were generated using TCR‐αβ derived from a CD4+ T cell hybridoma reactive with Der p 1 residues p 110–131. The frequency and functional activity of peripheral T cells were determined and parameters of airway inflammation assessed following allergen challenge of the airways with Der p 1.

Results
CD4+ T cells are functionally active, exhibiting dose‐dependent proliferation and IL‐4 production on primary stimulation with Der p 1 or Der p 1, p 110–131 in vitro, independent of in vivo antigen priming. On sensitization of the airways with allergen, in the absence of systemic priming or the application of adjuvants, the TCR transgenic mice develop airway inflammation characterized by a marked lymphocytic and eosinophilic infiltrate with goblet cell hyperplasia and enhanced mucin production.

Conclusion
The Der p 1 TCR transgenic mice provide a model for investigating the pathophysiological mechanisms of pulmonary inflammation following sensitization by exposure of the airways to allergen and for investigating the mode of action and efficacy of novel immunotherapeutics.
Suppression of inflammatory and fibrotic responses in allergic inflammation by the amniotic membrane stromal matrix
Authors: Solomon A. , Wajngarten M. , Alviano F. , Anteby I. , Elchalal U. , Pe'er J. , Levi‐Schaffer F.
Published: July 2005

Background
The amniotic membrane (AM), which is the innermost layer of the placenta, was shown to possess anti‐inflammatory and anti‐fibrotic properties in various in vitro and clinical studies.

Purpose
To evaluate the anti‐fibrotic and anti‐inflammatory effects of the AM matrix (AMM) on human conjunctival and lung fibroblasts in an in vitro system that tests fibrotic and inflammatory responses at the effector stages of allergic inflammation.

Methods
Human conjunctival or lung fibroblasts were seeded on plastic or on the stromal aspect of the AM, which was mounted on plastic inserts. Sonicates of human peripheral blood eosinophils activated with lipopolysacharide (LPS), or human mast cell (HMC‐1) leukaemia cell sonicates, were added to sub‐confluent fibroblast monolayers. Proliferation of the sub‐confluent fibroblasts was assessed using the [3H]‐thymidine incorporation assay. The production of transforming growth factor (TGF)‐β1, granulocyte–macrophage colony‐stimulating factor (GM‐CSF) and IL‐8 in conjunctival or lung fibroblasts was measured in conditioned media from these cultures by ELISA.

Results
After 4 days in culture, the [3H]‐thymidine incorporation assay indicated a reduced proliferation of activated conjunctival and lung fibroblasts when cultured directly on the AMM. The production of both TGF‐β1 and IL‐8 was significantly suppressed in activated conjunctival fibroblasts cultured on the AMM compared with those cultured on plastic, while the production of both TGF‐β1 and GM‐CSF was decreased in human lung fibroblast cultured on the AMM.

Conclusions
The AMM is capable of suppressing fibrotic responses in an in vitro system of effector stages of ocular allergic inflammation. These data may provide a basis for exploring matrix components in the AM for the treatment of allergic eye disease.