bluuebunny/crossref_metadata_2025 huggingface dataset:
Elastometric Sensing Using Higher Flexural Modes of Microcantilevers
Authors: Spletzer Matthew , Raman Arvind , Reifenberger Ron
Published: May 2009

We present a method to detect the non-uniform elastic property changes of sensor coatings on microcantilever arrays due to radiation, analyte binding or adsorption. The method uses measurements of the resonance frequencies of higher order flexural modes to identify with high sensitivity the location and magnitude of non-uniform elasticity changes in a microcantilever coating. We validate theoretical predictions and demonstrate the method by monitoring the time evolution of resonance frequencies of different flexural modes of microcantilevers functionalized with a small drop of a photosensitive polymer as it is exposed to ultraviolet (UV) radiation. The method is particularly well-suited for measuring quantitatively the time varying elastic properties of thin films or biological materials attached to microcantilevers.
Feedback Control of MEMS Micromirrors Subject to Parametric Uncertainty
Authors: Bronson Jessica R. , Wiens Gloria J.
Published: May 2009

This paper presents research on the development of microelectromechanical systems (MEMS) micromirror arrays with precise and accurate positioning enabled by the use of closed-loop control techniques. The MEMS mirror arrays are one degree-of-freedom, electrostatically actuated and exhibit nonlinear actuation profiles that include pull-in and hysteresis. The device performance is subject to parametric uncertainties from the fabrication process. Preliminary proportional-integrator (PI) controllers are studied in simulation on the nonlinear system to explore issues in the control development. Two different model linearization methods are presented to examine the best way to approximate the nonlinear behaviors using linear models. The effects of parametric uncertainties on the open-loop plant response are considered. It is evident based on these studies that the open-loop response is very sensitive to model uncertainties, while using closed-loop control can achieve input-tracking despite uncertainties in the plant. The work-in-progress includes the development of an optical test bed for the experimental validation of the results presented in this paper.
Uncertainty Bounds of Inertia Properties Required for Vehicle Dynamic Analyses
Authors: Gobbi Massimiliano , Mastinu Giampiero , Mun˜oz Luis E. , Eberhard Peter
Published: May 2009

This paper presents a study on the influence of the inertia properties of the vehicles and their subsystems on both the vehicle dynamics and the powertrain vibrational behaviour. Two different mathematical models have been used, one for the entire vehicle and the other for the powertrain. As result of the whole study, an approach for defining the suitable tolerances for the measurement of the inertia properties of the vehicles and their subsystems is proposed in the paper.
Highly Organized Carbon Nanotube-PDMS Hybrid System for Multifunctional Flexible Devices
Authors: Jung Yung J. , Jaber-Ansari Laila , Xiong Xugang , Mu¨ftu¨ Sinan , Busnaina Ahmed , Kar Swastik , Soldano Caterina , Ajayan Pulickel M.
Published: May 2009

We will present a method to fabricate a new class of hybrid composite structures based on highly organized multiwalled carbon nanotube (MWNT) and singlewalled carbon nanotube (SWNT) network architectures and a polydimethylsiloxane (PDMS) matrix for the prototype high performance flexible systems which could be used for many daily-use applications. To build 1–3 dimensional highly organized network architectures with carbon nanotubes (both MWNT and SWNT) in macro/micro/nanoscale we used various nanotube assembly processes such as selective growth of carbon nanotubes using chemical vapor deposition (CVD) and self-assembly of nanotubes on the patterned trenches through solution evaporation with dip coating. Then these vertically or horizontally aligned and assembled nanotube architectures and networks are transferred in PDMS matrix using casting process thereby creating highly organized carbon nanotube based flexible composite structures. The PDMS matrix undergoes excellent conformal filling within the dense nanotube network, giving rise to extremely flexible conducting structures with unique electromechanical properties. We will demonstrate its robustness under large stress conditions, under which the composite is found to retain its conducting nature. We will also demonstrate that these structures can be directly utilized as flexible field-emission devices. Our devices show some of the best field enhancement factors and turn-on electric fields reported so far.
AFM Indentation and Material Property Identification of Soft Hydrogels
Authors: Tripathy Sakya , Berger Edward , Vemaganti Kumar
Published: May 2009

There is growing evidence of the importance of mechanical deformations on various facets of cell functioning. This asks for a proper understanding of the cell’s characteristics as a mechanical system in different physiological and mechanical loading conditions. Many researchers use atomic force microscopy (AFM) indentation and the Hertz contact model for elastic material property identification under shallow indentation. For larger indentations, many of the Hertz assumptions are not inherently satisfied and the Hertz model is not directly useful for characterizing nonlinear elastic or inelastic material properties. We have used exponential hyperelastic material in FE simulations of the AFM indentation tests. A parameter identification approach is developed for hyperelastic material property determination from the simulated data. We collected AFM indentation data on agarose gel and developed a simple algorithm for contact point detection. The contact point correction improves the prediction of elastic modulus over the case of visual contact point identification. The modulus of 1% agarose gel was found to be about 15 kPa using the proposed correction, with mild but non-trival hardening with deeper indentation. The experimental data is compared with the results from the FE simulations and shows that over the hardening portion of the indentation response, our proposed parameter identification approach successfully captures the experimental data.
Applying Function-Based Failure Propagation in Conceptual Design
Authors: Krus Daniel , Grantham Lough Katie
Published: May 2009

When designing a product, the earlier the potential risks can be identified, the more costs can be saved, as it is easier to modify a design in its early stages. Several methods exist to analyze the risk in a system, but all require a mature design. However, by applying the concept of “common interfaces” to a functional model and utilizing a historical knowledge base, it is possible to analyze chains of failures during the conceptual phase of product design. This paper presents a method based on these “common interfaces” to be used in conjunction with other methods such as Risk in Early Design in order to allow a more complete risk analysis during the conceptual design phase. Finally, application of this method is demonstrated in a design setting by applying it to a thermal control subsystem.
Bifurcations and Chaos in an Experimental Based Quasi-Continuum Nonlinear Dynamical System for the ‘Clapper’ Nanoresonator
Authors: Gottlieb O. , Gemintern A. , Blick R. H.
Published: May 2009

In this paper we formulate and numerically investigate an experimentally based quasi-continuum nonlinear initial-boundary-value problem for the three-field ‘Clapper’ nanoresonator that consistently incorporates the system geometric nonlinearity with nonlinear contributions of both magnetomotive and electrodynamic excitation. The spatio-temporal field equations are then reduced via symmetry and a modal projection to an equivalent quasiperiodically excited, low order, nonlinear dynamical system. The governing parameters of the resulting system are matched with the experimentally measured resonance conditions for small amplitude response. Numerical analysis reveals a complex bifurcation structure of torus doubling culminating with a chaotic strange attractor that exhibits similar features to that previously measured in the ‘Clapper’ experiment.
New Concept of Rollover Resistant Semitrailer for Hydrogen Transport
Authors: Castejo´n Luis , Valladares David , Miralbe´s Ramo´n , Carrera Marco , Cuartero Jesu´s , Marti´n Carlos
Published: May 2009

In this paper a new concept of semitrailer for hydrogen carriers is presented. It has been developed by means of numerical calculations carried out with the finite elements method. This new design of semitrailer incorporates several new functions. The first one is to achieve a rollover resistant vehicle. It has to be taken into account the absence of a specific regulation in Europe for this type of vehicles, so former vehicles were not enough rollover resistant. Nevertheless, in this development process it has been taken into account the European rollover regulation concerning large passenger vehicles “Regulation n° 66 of Geneva”, applied in this case to a vehicle having a much higher mass and a higher centre of gravity than a bus. Therefore a higher kinetic energy will be obtained in case of rollover. The second characteristic inherent to this new design of semitrailer is its lightness. It has achieved a mass reduction of 8500 kg in comparison with former designs, by means of lightening the structure, in charge of supporting the hydrogen cylinders, as well as making lighter these hydrogen cylinders themselves. Numerical models developed have been calculated by explicit integration of the dynamic balance equation. Very complex finite element models have been developed in order to include all geometric details. In these models, the elastic-plastic curves of involved materials have been included as well as its variation due to the strain rate influence. There have also been taken into account non-linear effects from contacts and from large strains that take place.
Design of a Light Semi-Trailer Rear Bumper for Impact Protection According to 79/490/CEE Directive
Authors: Carrera Marco , Castejo´n Luis , Cuartero Jesu´s , Marti´n Carlos
Published: May 2009

In this paper, a new concept of rear bumper for semi trailer has been developed by means of numerical simulation. A semi trailer bumper is a substructure that has a great importance in the whole vehicle. It reduces the effect of a crash impact against another vehicle in the rear part of the semi trailer. Thus, both the vehicle and passengers are protected from impact effects. The design of this kind of structures must show suitable behavior depending upon crash conditions and structure conditions (bumper material, load cases, boundary conditions, impact velocity…). In this study case, 79/490/CEE Directive shows the specific conditions that must be complied by a rear protective device to be approved by an official certifying body. The bumper design has been carried out by means of numerical simulation tools based on the Finite Element Method (FEM). This method provides results in terms of strain and stress of the analyzed structures, subjected to several load cases, boundary conditions, and considering several materials. A new light aluminum bumper structure fulfilling the previous directive is obtained. Finally, a light bumper prototype has been developed based on the previous numerical results and it has been tested according to the homologation conditions specified in 79/490/CEE Directive. Nowadays, Lecitrailer S.A., a Spanish semi trailers manufacturer, has incorporated this new bumper structure to their vehicles.
An Interactive Morphological Matrix Computational Design Tool: A Hybrid of Two Methods
Authors: Bryant Cari R. , Bohm Matt , Stone Robert B. , McAdams Daniel A.
Published: May 2009

This paper builds on previous concept generation techniques explored at the University of Missouri - Rolla and presents an interactive concept generation tool aimed specifically at the early concept generation phase of the design process. Research into automated concept generation design theories led to the creation of two distinct design tools: an automated morphological search that presents a designer with a static matrix of solutions that solve the desired input functionality and a computational concept generation algorithm that presents a designer with a static list of compatible component chains that solve the desired input functionality. The merger of both the automated morphological matrix and concept generation algorithm yields an interactive concept generator that allows the user to select specific solution components while receiving instantaneous feedback on component compatibility. The research presented evaluates the conceptual results from the hybrid morphological matrix approach and compares interactively constructed solutions to those returned by the non-interactive automated morphological matrix generator using a dog food sample packet counter as a case study.
Improving Design Understanding by Analyzing Questions
Authors: Aurisicchio Marco , Ahmed Saeema , Wallace Ken M.
Published: May 2009

This paper describes an interpretation of design activity through investigating design questions. From a number of previous studies two types of question have been identified: 1) reasoning questions; and 2) strategic questions. Strategic questions are part of an experienced designers approach to solving a design task. The paper describes how designers progress their tasks by asking questions at both reasoning and strategic levels. Transcripts of protocol analysis have been examined to identify both reasoning questions and strategic questions. These are discussed together with their relation to a problem solving model. The research aims to contribute to an understanding of design activity.
Non-Dominated Strategies for Decision Based Design for Component Reuse
Authors: Pandey Vijitashwa , Thurston Deborah
Published: May 2009

Component level reuse enables retention of value from products recovered at the end of their first lifecycle. Reuse strategies determined at the beginning of the lifecycle are aimed at maximizing this recovered value. Decision based design can be employed, but there are several difficulties in large scale implementation. First, computational complexities arise. Even with a product with a relatively small number of components, it becomes difficult to find the optimal component level decisions. Second, if there is more than one stakeholder involved, each interested in different attributes, the problem becomes even more difficult, due both to complexity and Arrow’s Impossibility Theorem. However, while the preferences of the stakeholders may not be known precisely, and aggregating those preferences poses difficulties, what is usually known is the partial ordering of alternatives. This paper presents a method for exploiting the features of a solution algorithm to address these difficulties in implementing decision based design. Heuristic methods including non-dominated sorting genetic algorithms (NSGA) can exploit this partial ordering and reject dominated alternatives, simplifying the problem. Including attributes of interest to various stakeholders ensures that the solutions found are practicable. One of the reasons product reuse has not achieved critical acceptance is because the three entities involved, the customers, the manufacturer and the government do not have a common ground. This results in inaccurate aggregating of attributes which the proposed method avoids. We illustrate our approach with a case study of component reuse of personal computers.
Designing the Product Development Process
Authors: Bligh Amanda , Sodhi Manbir
Published: May 2009

Even though the literature on product and process development is extensive, not much attention has been devoted to categorizing the product development process itself. Existing work on product development processes such as Total Design, Integrated Product and Process Design among others advocate common approaches that should be followed throughout the organization, without any consideration of product characteristics. In this paper we review several existing development methodologies. Extensions of these are categorized by their applicability to different classes of products. We propose that development processes should be matched to product attributes and organization goals. Towards this end, we associate development processes along with their components such as House of Quality, Robust Design, TRIZ etc. with goals such as time to market, customer needs satisfaction, intellectual property generation, protection and exploitation, quality, product cost and others. We examine the impact of this association on the development process itself and propose guidelines for constructing specific processes associated with one or more goals. Tools and benchmarks for various applications are discussed, along with some case studies on the design of different development processes.
Including Functional Models of Biological Phenomena as Design Stimuli
Authors: Vakili V. , Chiu I. , Shu L. H. , McAdams D. A. , Stone R. B.
Published: May 2009

This work explores the representation of biological phenomena as stimuli to designers for biomimetic design. We describe a study where participants were asked to solve a micro-assembly problem given a set of biological representations of leaf abscission for inspiration. The visual aids presented to the designers are investigated, and the use of functional models of biological phenomena in particular is critiqued. The designs resulting from the study are classified and theories drawn as to possible influences of the biological representations. Observations, retrospective conversations with participants, and analogical reasoning classifications are used to determine positive qualities as well as areas for improvement in representation of the biological domain. Findings suggest that designers need an explicit list of all possible inherent biological strategies, previously extracted using function structures with objective graph grammar rules. Challenges specific to this type of study are discussed, and possible improvement of representative aids are outlined.
Platform Investment Decisions in Product Family Design
Authors: Zacharias Nicolas A. , Yassine Ali A.
Published: May 2009

The paper proposes an intermediate modeling ground that bridges the gap between engineering design models and marketing models for the development of platform-based product families. In this model, each variant in the product family is assumed to contribute a percentage to the overall market coverage inside a target market segment and we wish to maximize this coverage subject to an available development budget. Following the conceptual engineering design phase of the product family, this model will optimize the initial investment in the platform, the commonality level between variants, and the number of variants to be produced in order to maximize market coverage. An application of the model using a Drill product family is included to demonstrate the usefulness of the proposed model.
Efficacy of Triazoles in a Murine Disseminated Infection by
Candida krusei
Authors: Mariné Marçal , Pastor F. Javier , Serena Carolina , Guarro Josep
Published: May 2009

We evaluated the efficacies of posaconazole and voriconazole in comparison with that of amphotericin B in a systemic murine infection by
Candida krusei.
Posaconazole at 50 mg/kg/day and voriconazole at 40 and 60 mg/kg/day prolonged survival and reduced the fungal tissue burden in the kidneys of mice similarly to amphotericin B at 1.5 mg/kg/day and liposomal amphotericin B at 10 mg/kg/day. None of the treatments tested completely resolved the infection.
Curcumin Modulates Efflux Mediated by Yeast ABC Multidrug Transporters and Is Synergistic with Antifungals
Authors: Sharma Monika , Manoharlal Raman , Shukla Suneet , Puri Nidhi , Prasad Tulika , Ambudkar Suresh V. , Prasad Rajendra
Published: May 2009

Curcumin (CUR), a natural product of turmeric, from rhizomes of
Curcuma longa
, is a known agent of reversal of drug resistance phenotypes in cancer cells overexpressing ATP-binding cassette (ABC) transporters, viz., ABCB1, ABCG2, and ABCC1. In the present study, we evaluated whether CUR could also modulate multidrug transporters of yeasts that belong either to the ABC family or to the major facilitator superfamily (MFS). The effect of CUR on multidrug transporter proteins was demonstrated by examining rhodamine 6G (R6G) efflux in
Saccharomyces cerevisiae
cells overexpressing the
Candida albicans
ABC transporters Cdr1p and Cdr2p (CaCdr1p and CaCdr2p, respectively) and the MFS transporters CaMdr1p and
S. cerevisiae
Pdr5p. CUR decreased the extracellular concentration of R6G in ABC transporter-expressing cells but had no effect on methotrexate efflux mediated through the MFS transporter CaMdr1p. CUR competitively inhibited R6G efflux and the photolabeling of CaCdr1p by [
125
I]iodoarylazidoprazosin, a drug analogue of the substrate prazosin (50% inhibitory concentration, 14.2 μM). Notably, the mutant variants of CaCdr1p that displayed abrogated efflux of R6G also showed reduced modulation by CUR. Drug susceptibility testing of ABC protein-expressing cells by spot assays and checkerboard tests revealed that CUR was selectively synergistic with drug substrates such as R6G, ketoconazole, itraconazole, and miconazole but not with fluconazole, voriconazole, anisomycin, cycloheximide, or FK520. Taken together, our results provide the first evidence that CUR modulates only ABC multidrug transporters and could be exploited in combination with certain conventional antifungal drugs to reverse multidrug resistance in
Candida
cells.
Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1
Authors: Schübbe Sabrina , Williams Timothy J. , Xie Gary , Kiss Hajnalka E. , Brettin Thomas S. , Martinez Diego , Ross Christian A. , Schüler Dirk , Cox B. Lea , Nealson Kenneth H. , Bazylinski Dennis A.
Published: May 2009

The marine bacterium strain MC-1 is a member of the alpha subgroup of the proteobacteria that contains the magnetotactic cocci and was the first member of this group to be cultured axenically. The magnetotactic cocci are not closely related to any other known alphaproteobacteria and are only distantly related to other magnetotactic bacteria. The genome of MC-1 contains an extensive (102 kb) magnetosome island that includes numerous genes that are conserved among all known magnetotactic bacteria, as well as some genes that are unique. Interestingly, certain genes that encode proteins considered to be important in magnetosome assembly (mamJandmamW) are absent from the genome of MC-1. Magnetotactic cocci exhibit polar magneto-aerotaxis, and the MC-1 genome contains a relatively large number of identified chemotaxis genes. Although MC-1 is capable of both autotrophic and heterotrophic growth, it does not appear to be metabolically versatile, with heterotrophic growth confined to the utilization of acetate. Central carbon metabolism is encoded by genes for the citric acid cycle (oxidative and reductive), glycolysis, and gluconeogenesis. The genome also reveals the presence or absence of specific genes involved in the nitrogen, sulfur, iron, and phosphate metabolism of MC-1, allowing us to infer the presence or absence of specific biochemical pathways in strain MC-1. The pathways inferred from the MC-1 genome provide important information regarding central metabolism in this strain that could provide insights useful for the isolation and cultivation of new magnetotactic bacterial strains, in particular strains of other magnetotactic cocci.
Dictyostelium discoideum
CenB Is a Bona Fide Centrin Essential for Nuclear Architecture and Centrosome Stability
Authors: Mana-Capelli Sebastian , Gräf Ralph , Larochelle Denis A.
Published: May 2009

Centrins are a family of proteins within the calcium-binding EF-hand superfamily. In addition to their archetypical role at the microtubule organizing center (MTOC), centrins have acquired multiple functionalities throughout the course of evolution. For example, centrins have been linked to different nuclear activities, including mRNA export and DNA repair.
Dictyostelium discoideum
centrin B is a divergent member of the centrin family. At the amino acid level, DdCenB shows 51% identity with its closest relative and only paralog, DdCenA. Phylogenetic analysis revealed that DdCenB and DdCenA form a well-supported monophyletic and divergent group within the centrin family of proteins. Interestingly, fluorescently tagged versions of DdCenB were not found at the centrosome (in whole cells or in isolated centrosomes). Instead, DdCenB localized to the nuclei of interphase cells. This localization disappeared as the cells entered mitosis, although
Dictyostelium
cells undergo a closed mitosis in which the nuclear envelope (NE) does not break down. DdCenB knockout cells exhibited aberrant nuclear architecture, characterized by enlarged and deformed nuclei and loss of proper centrosome-nucleus anchoring (observed as NE protrusions). At the centrosome, loss of DdCenB resulted in defects in the organization and morphology of the MTOC and supernumerary centrosomes and centrosome-related bodies. The multiple defects that the loss of DdCenB generated at the centrosome can be explained by its atypical division cycle, transitioning into the NE as it divides at mitosis. On the basis of these findings, we propose that DdCenB is required at interphase to maintain proper nuclear architecture, and before delocalizing from the nucleus, DdCenB is part of the centrosome duplication machinery.
Lipophilic Dye Staining ofCryptococcus neoformansExtracellular Vesicles and Capsule
Authors: Nicola André Moraes , Frases Susana , Casadevall Arturo
Published: May 2009

Cryptococcus neoformansis an encapsulated yeast that causes systemic mycosis in immunosuppressed individuals. Recent studies have determined that this fungus produces vesicles that are released to the extracellular environment both in vivo and in vitro. These vesicles contain assorted cargo that includes several molecules associated with virulence and implicated in host-pathogen interactions, such as capsular polysaccharides, laccase, urease, and other proteins. To date, visualization of extracellular vesicles has relied on transmission electron microscopy, a time-consuming technique. In this work we report the use of fluorescent membrane tracers to stain lipophilic structures in cryptococcal culture supernatants and capsules. Two dialkylcarbocyanine probes with different spectral characteristics were used to visualize purified vesicles by fluorescence microscopy and flow cytometry. Dual staining of vesicles with dialkylcarbocyanine and RNA-selective nucleic acid dyes suggested that a fraction of the vesicle population carried RNA. Use of these dyes to stain whole cells, however, was hampered by their possible direct binding to capsular polysaccharide. A fluorescent phospholipid was used as additional membrane tracer to stain whole cells, revealing punctate structures on the edge of the capsule which are consistent with vesicular trafficking. Lipophilic dyes provide new tools for the study of fungal extracellular vesicles and their content. The finding of hydrophobic regions in the capsule ofC. neoformansadds to the growing evidence for a structurally complex structure composed of polysaccharide and nonpolysaccharide components.
CD8 T Cells in Old Mice Contribute to the Innate Immune Response toMycobacterium tuberculosisvia Interleukin-12p70-Dependent and Antigen-Independent Production of Gamma Interferon
Authors: Vesosky Bridget , Rottinghaus Erin K. , Davis Craig , Turner Joanne
Published: May 2009

Elderly individuals have increased morbidity and mortality associated with infectious diseases due in part to the progressive age-associated decline in immune function. Despite this, the old mouse model ofMycobacterium tuberculosisinfection has revealed a CD8- and gamma interferon (IFN-γ)-dependent early resistance to infection. In this study, we investigated the mechanism by which CD8 T cells from old mice contributed to the early immune response toM. tuberculosis. Following a low-dose aerosol infection withM. tuberculosis, CD8 T cells were identified as being a dominant source of IFN-γ expression in the lungs of old mice early after infection, before the typical onset of antigen-specific immunity. In addition,M. tuberculosis-induced IFN-γ production by CD8 T cells isolated from naïve old mice was major histocompatibility complex class I independent but was dependent on interleukin-12p70, confirming an innate role of CD8 T cells duringM. tuberculosisinfection. Moreover, the ability of CD8 T cells from old mice to produce increased innate IFN-γ levels in response toM. tuberculosisinfection was defined as a unique function of CD8 T cells from old mice and not the aged lung environment. Finally, we have identified increased expression of SET as being one possible mechanism by which CD8 T cells from old mice produce enhanced levels of IFN-γ. Additional characterizations of the signaling events that lead to enhanced innate IFN-γ production by CD8 T cells in old mice may lead to novel strategies to further enhance or perpetuate beneficial immune responses in the elderly.
Identification and Gene Disruption of Small Noncoding RNAs in
Streptomyces griseus
Authors: Tezuka Takeaki , Hara Hirofumi , Ohnishi Yasuo , Horinouchi Sueharu
Published: May 2009

Small noncoding RNAs (sRNAs) have been shown to control diverse cellular processes in prokaryotes. To identify and characterize novel bacterial sRNAs, a gram-positive, soil-inhabiting, filamentous bacterium,
Streptomyces griseus
, was examined, on the assumption that
Streptomyces
should express sRNAs as important regulators of morphological and physiological differentiation. By bioinformatics investigation, 54 sRNA candidates, which were encoded on intergenic regions of the
S. griseus
chromosome and were highly conserved in those of both
Streptomyces coelicolor
A3(2) and
Streptomyces avermitilis
, were selected. Of these 54 sRNA candidates, 17 transcripts were detected by Northern blot analysis of the total RNAs isolated from cells grown on solid medium. Then, the direction of transcription of each sRNA candidate gene was determined by S1 nuclease mapping, followed by exclusion of four sRNA candidates that were considered riboswitches of their downstream open reading frames (ORFs). Finally, a further sRNA candidate was excluded because it was cotranscribed with the upstream ORF determined by reverse transcription-PCR. Thus, 12 sRNAs ranging in size from 40 to 300 nucleotides were identified in
S. griseus
. Seven of them were apparently transcribed in a growth phase-dependent manner. Furthermore, of the 12 sRNAs, the expression profiles of 7 were significantly influenced by a mutation of
adpA
, which encodes the central transcriptional regulator of the A-factor regulatory cascade involved in both morphological differentiation and secondary metabolism in
S. griseus
. However, disruption of all 12 sRNA genes showed no detectable phenotypic changes; all the disruptants grew and formed aerial mycelium and spores with the same time course as the wild-type strain on various media and produced streptomycin similarly to the wild-type strain.
OpnS, an Outer Membrane Porin ofXenorhabdus nematophila, Confers a Competitive Advantage for Growth in the Insect Host
Authors: van der Hoeven Ransome , Forst Steven
Published: May 2009

The gammaproteobacteriumXenorhabdus nematophilaengages in a mutualistic association with an entomopathogenic nematode and also functions as a pathogen toward different insect hosts. We studied the role of the growth-phase-regulated outer membrane protein OpnS in host interactions. OpnS was shown to be a 16-stranded β-barrel porin.opnSwas expressed during growth in insect hemolymph and expression was elevated as the cell density increased. When wild-type andopnSdeletion strains were coinjected into insects, the wild-type strain was predominantly recovered from the insect cadaver. Similarly, anopnS-complemented strain outcompeted the ΔopnSstrain. Coinjection of the wild-type and ΔopnSstrains together with uncolonized nematodes into insects resulted in nematode progeny that were almost exclusively colonized with the wild-type strain. Likewise, nematode progeny recovered after coinjection of a mixture of nematodes carrying either the wild-type or ΔopnSstrain were colonized by the wild-type strain. In addition, the ΔopnSstrain displayed a competitive growth defect when grown together with the wild-type strain in insect hemolymph but not in defined culture medium. The ΔopnSstrain displayed increased sensitivity to antimicrobial compounds, suggesting that deletion of OpnS affected the integrity of the outer membrane. These findings show that the OpnS porin confers a competitive advantage for the growth and/or the survival ofX. nematophilain the insect host and provides a new model for studying the biological relevance of differential regulation of porins in a natural host environment.
spr1630 Is Responsible for the Lethality ofclpXMutations inStreptococcus pneumoniae
Authors: Piotrowski Andrew , Burghout Peter , Morrison Donald A.
Published: May 2009

The Clp protease ATPase subunit and chaperone ClpX is dispensable in some bacteria, but it is thought to be essential in others, including streptococci and lactococci. We confirm thatclpXis essential in the Rx strain ofStreptococcus pneumoniaebut show that the requirement forclpXcan be relieved by point mutations, frame shifts, or deletion of the gene spr1630, which is found in many isolates ofS. pneumoniae.Homologs occur frequently inStaphylococcus aureusas well as in a few strains ofListeria monocytogenes,Lactobacillus johnsonii, andLactobacillus rhamnosus. In each case, the spr1630 homolog is accompanied by a putative transcriptional regulator with an HTH DNA binding motif. InS. pneumoniae, the spr1630-spr1629 gene pair, accompanied by a RUP element, occurs as an island inserted between thetrpAandcclAgenes in 15 of 22 sequenced genomes.
The Single Substitution I259T, Conserved in the Plasminogen Activator Pla of PandemicYersinia pestisBranches, Enhances Fibrinolytic Activity
Authors: Haiko Johanna , Kukkonen Maini , Ravantti Janne J. , Westerlund-Wikström Benita , Korhonen Timo K.
Published: May 2009

The outer membrane plasminogen activator Pla ofYersinia pestisis a central virulence factor in plague. The primary structure of the Pla β-barrel is conserved inY. pestisbiovars Antiqua, Medievalis, and Orientalis, which are associated with pandemics of plague. The Pla molecule of the ancestralY. pestislineages Microtus and Angola carries the single amino acid change T259I located in surface loop 5 of the β-barrel. RecombinantY. pestisKIM D34 orEscherichia coliXL1 expressing Pla T259I was impaired in fibrinolysis and in plasminogen activation. Lack of detectable generation of the catalytic light chain of plasmin and inactivation of plasmin enzymatic activity by the Pla T259I construct indicated that Microtus Pla cleaved the plasminogen molecule more unspecifically than did common Pla. The isoform pattern of the Pla T259I molecule was different from that of the common Pla molecule. Microtus Pla was more efficient than wild-type Pla in α2-antiplasmin inactivation. Pla ofY. pestisand PgtE ofSalmonella entericahave evolved from the same omptin ancestor, and their comparison showed that PgtE was poor in plasminogen activation but exhibited efficient antiprotease inactivation. The substitution259IIDKT/TIDKN in PgtE, constructed to mimic the L5 region in Pla, altered proteolysis in favor of plasmin formation, whereas the reverse substitution259TIDKN/IIDKT in Pla altered proteolysis in favor of α2-antiplasmin inactivation. The results suggest that Microtus Pla represents an ancestral form of Pla that has evolved into a more efficient plasminogen activator in the pandemicY. pestislineages.
Complete Genome Sequence of
Lactobacillus plantarum
JDM1
Authors: Zhang Zhuo-Yang , Liu Chang , Zhu Yong-Zhang , Zhong Yi , Zhu Yong-Qiang , Zheng Hua-Jun , Zhao Guo-Ping , Wang Sheng-Yue , Guo Xiao-Kui
Published: May 2009

Lactobacillus plantarum
is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of
Lactobacillus plantarum
JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.
Histological patterns in drug-induced liver disease
Authors: Ramachandran R , Kakar S
Published: May 2009

The diagnosis of drug-induced liver injury (DILI) is a challenging problem, often confounded by incomplete clinical information and the difficulty of eliciting exposure to herbal products, over-the-counter agents and toxins. The task is further rendered difficult on biopsy, as drugs can mimic all the patterns found in primary liver disease. Acute hepatitis, with or without cholestasis, is the most common histological pattern of DILI, and drugs such as acetaminophen are the leading causes of acute liver failure. Most cases of DILI resolve on discontinuation of the drug, but recovery can take months or rarely the disease can progress despite drug withdrawal. Drugs such as methotrexate can lead to chronic hepatitis and cirrhosis, while others such as minocycline, nitrofurantoin and methyldopa are implicated in autoimmune hepatitis. Prolonged cholestasis and ductopenia resembling primary chronic biliary disease can occur. Drug-induced steatohepatitis is also an uncommon pattern, but is well described with drugs such as amiodarone and irinotecan. In the presence of risk factors such as obesity and diabetes, some drugs such as tamoxifen, oestrogens and nifedipine can precipitate or exacerbate steatohepatitis. Other observed patterns include granulomatous hepatitis, vascular injury (eg, sinusoidal obstruction syndrome), Ito cell lipidosis and neoplasms (eg, adenomas).
HER-2/neu analysis in breast cancer bone metastases
Authors: Zustin J , Boddin K , Tsourlakis M C , Burandt E , Mirlacher M , Jaenicke F , Izbicki J , Ruether W , Rueger J M , Bokemeyer C , Simon R , Sauter G
Published: May 2009

Background:

HER-2 is the target for antibody-based treatment of breast cancer (trastuzumab), which is highly successful in both advanced disease and the adjuvant setting. HER-2 can be analysed by fluorescence in situ hybridisation (FISH) for gene amplification or immunohistochemistry (IHC) for protein overexpression.

Aim:

As both methods are known to be influenced by previous tissue processing, to analyse the applicability of both FISH and IHC to decalcified bone metastases of breast cancer.

Methods:

A tissue microarray (TMA) was constructed from 149 breast cancer bone metastases. Consecutive TMA sections were analysed by FISH (PathVysion) and IHC (HercepTest).

Results:

FISH analysis was interpretable in 113 (85.0%) cases. Amplification was seen in 14 (12.4%) interpretable metastases. HER-2 positivity on IHC analysis was 3+ in 9.8% of cases and 2+ in 11.3%. A comparison of the two techniques revealed high concordance. Of the 14 cases of amplification, 10 (71%) showed 3+ IHC staining, two (14%) showed 2+, one (7%) showed 1+, and one (7%) showed 0+. Three of the four amplified cases that did not show 3+ IHC staining had an equivocal FISH result, with a HER-2/centromere 17 ratio of 1.8–2.2. Of the 13 cases that showed IHC 3+ staining, amplification was present in 10 (77%).

Conclusions:

HER-2 FISH analysis has an excellent success rate in highly standardised EDTA-decalcified bone metastases, suggesting that this method is easily applicable to decalcified tissues. The high concordance between IHC and FISH suggests that HER-2 IHC may be equally applicable to EDTA-treated tissues as to the usual formalin-fixed tissues.
CD4 expression by mast cells in mastocytosis: a case report: Figure 1
Authors: Soilleux E J , Bowling J , Hollowood K
Published: May 2009

A 59-year-old man presented with a five-year history of an asymptomatic widespread truncal rash. Cutaneous biopsies showed mastocytosis, which was shown to be CD4-positive immunohistochemically. This potential diagnostic pitfall in the discrimination of mastocytosis from a variety of other haematopoietic neoplasms, particularly mycosis fungoides, is discussed.
A novel system for the reconstruction of a coronary artery lumen profile in real time: a preclinical validation
Authors: Kassab Ghassan S. , Choy Jenny S. , Svendsen Mark , Sinha Anjan K. , Alloosh Mouhamad , Sturek Mike , Huo Yunlong , Sandusky George E. , Hermiller James
Published: May 2009

Accurate sizing of vessel diameter is important for understanding the physiology of blood vessels as well as the treatment of coronary and peripheral artery disease. The objective of this study was to validate a novel catheter-based system [the LumenRECON (LR) system] for the real-time reconstruction of lumen cross-sectional area (CSA) along the length of a vessel segment. A total of 22 swine (20 Yorkshire and 2 atherosclerotic Ossabaw swine) were used to evaluate the accuracy, reproducibility, and safety of the system compared with intravascular ultrasound (IVUS). The CSA of the right coronary artery, left anterior descending coronary artery, and left circumflex artery were determined by IVUS and the LR system over a 3- to 4-cm segment in 12 Yorkshire and 2 atherosclerotic Ossabaw swine and 2 postmortem atherosclerotic human hearts. In eight chronic animals, the effect of the LR catheter on the vessel wall was evaluated at 1 day and 2 wk (4 animals each) after the intervention. A Bland-Altman plot of the LR and IVUS data showed a mean difference between the two measurements of 0.055 mm in diameter, which was not statistically significant from zero, indicating a lack of bias in the comparison of the LR system with IVUS. The root mean square error of the two measurements was 10.2% of the mean IVUS diameter. The repeatability of the LR system was assessed using duplicate measurements. The mean of the difference between the two measurements was nearly zero, and the repeatability coefficient was within 4.5% of the mean of the two measurements. No injury or intimal hyperplasia was found acutely or chronically after the use of the LR system. This study establishes the accuracy, reproducibility, and safety of a nonimaging 2.7-Fr catheter for lumen sizing of coronary arteries. The system provides a continuous quantitative axial profile of the mean vessel lumen in real time and may have significant utility in vascular research and clinically in the catheterization laboratory.
The effects of propofol on vascular function in mesenteric arteries of the aging rat
Authors: Gragasin Ferrante S. , Davidge Sandra T.
Published: May 2009

Hypotension following administration of propofol, an anesthetic agent, is strongly predicted by advanced age and is partly due to direct vasodilation. We hypothesized that propofol increases nitric oxide (NO)-mediated vasodilation by enhancing its bioavailability in the aged adult vasculature, leading to greater vasodilation than in the young adult. Small mesenteric arteries from rats aged 13–15 versus 3 to 4 mo were compared in this study. Reactivity to propofol (1–100 μM) alone and with the addition of acetylcholine (ACh; 0.1–10 μM) in endothelial-intact and dunuded arteries following phenylephrine constriction was assessed using myography. NG-nitro-l-arginine methyl ester (l-NAME) and meclofenamate (Meclo) were used to inhibit NO and prostaglandin synthesis, respectively. Superoxide dismutase (SOD) and catalase were used as antioxidants during ACh relaxation and were compared with propofol in aging arteries. Propofol alone induced greater relaxation in 1) endothelial-intact compared with denuded arteries and 2) aged compared with young arteries, which were inhibited by l-NAME. ACh-induced relaxation was greater in young compared with aged control arteries; however, propofol pretreatment increased this relaxation in aged but not in young arteries. Additionally, propofol inhibited ACh-induced relaxation in arteries treated with l-NAME + Meclo [relaxation attributed to endothelium-derived hyperpolarizing factor (EDHF)]. Pretreatment with SOD and catalase increased relaxation to ACh in aged arteries similar to propofol. In conclusion, propofol causes relaxation in small mesenteric arteries in an endothelial-dependent and independent manner and increases ACh-induced relaxation in aged arteries. Interestingly, propofol inhibits EDHF-mediated relaxation but increases availability of NO, which leads to overall vascular relaxation.
Sustained hypoxia promotes the development of a pulmonary artery-specific chronic inflammatory microenvironment
Authors: Burke Danielle L. , Frid Maria G. , Kunrath Claudia L. , Karoor Vijaya , Anwar Adil , Wagner Brandie D. , Strassheim Derek , Stenmark Kurt R.
Published: May 2009

Recent studies demonstrate that sustained hypoxia induces the robust accumulation of leukocytes and mesenchymal progenitor cells in pulmonary arteries (PAs). Since the factors orchestrating hypoxia-induced vascular inflammation are not well-defined, the goal of this study was to identify mediators potentially responsible for recruitment to and retention and differentiation of circulating cells within the hypoxic PA. We analyzed mRNA expression of 44 different chemokine/chemokine receptor, cytokine, adhesion, and growth and differentiation genes in PAs obtained via laser capture microdissection in adjacent lung parenchyma and in systemic arteries by RT-PCR at several time points of hypoxic exposure (1, 7, and 28 days) in Wistar-Kyoto rats. Analysis of inflammatory cell accumulation and protein expression of selected genes was concomitantly assessed by immunochemistry. We found that hypoxia induced progressive accumulation of monocytes and dendritic cells in the vessel wall with few T cells and no B cells or neutrophils. Upregulation of stromal cell-derived factor-1 (SDF-1), VEGF, growth-related oncogene protein-α (GRO-α), C5, ICAM-1, osteopontin (OPN), and transforming growth factor-β (TGF-β) preceded mononuclear cell influx. With time, a more complex pattern of gene expression developed with persistent upregulation of adhesion molecules (ICAM-1, VCAM-1, and OPN) and monocyte/fibrocyte growth and differentiation factors (TGF-β, endothelin-1, and 5-lipoxygenase). On return to normoxia, expression of many genes (including SDF-1, monocyte chemoattractant protein-1, C5, ICAM-1, and TGF-β) rapidly returned to control levels, changes that preceded the disappearance of monocytes and reversal of vascular remodeling. In conclusion, sustained hypoxia leads to the development of a complex, PA-specific, proinflammatory microenvironment capable of promoting recruitment, retention, and differentiation of circulating monocytic cell populations that contribute to vascular remodeling.