bluuebunny/crossref_metadata_2025 huggingface dataset:
Datamining Protein Structure Databanks for Crystallization Patterns of Proteins
Authors: VALAFAR HOMAYOUN , PRESTEGARD JAMES H. , VALAFAR FARAMARZ
Published: July 2009

Abstract: A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One‐ and two‐dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two‐dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two‐dimensional Bayesian analysis succeeded with a performance of about 75%.
Achieving Congruency of Phylogenetic Trees Generated by W‐Curves of Genomic Sequences
Authors: CORK DOUGLAS J. , HUTCH THOMAS B. , MARLAND ELIZABETH , ZMUDA JORY
Published: July 2009

Abstract:Comparative genomic analysis at its most fundamental level involves alignment and analysis of linear strings of DNA. Many useful and powerful tools, such asBlastNandClustalWare able to respectively, search for, and align similar strings of DNA from a variety of species. However, interesting genomic patterns cannot be immediately visualized within the information contact embedded in long genomic strings without extensivea prioriknowledge. More problematic is the question of whether we will be able to crystallize long genomic sequences and analyze their true secondary and tertiary structures. It is, of course, these putative motifs that are binding to the three‐dimensional structures of proteins and inducing replication and transcription events. The W‐curve is a numerical mapping algorithm that allows one to geometrically visualize the information content of genomic motifs. Patterns of ALU, LINES, SINEs, and duplication sequences may be easily visualized with the W‐curve. It is our hope that this pattern recognition algorithm will lead to visualization tools to track the evolutionary history of motif patterns. The combinatorics of DNA motif crossover‐recombination events will be more easily followed as we continue to sequence more and more genomes. In our laboratory we are currently collaborating with mathematicians and computer scientists to develop and test tools, such as the W‐curve, for analyzing patterns of long genomic sequences. In this paper, we examine the limitations of using the W‐curve to infer the phylogenetic history of species.
Functional Magnetic Resonance of Human Breast Tumors
Authors: SINHA SHANTANU , SINHA USHA
Published: July 2009

Abstract: This review is focused on two relatively new developments in magnetic resonance imaging (MRI) and their application to breast lesion characterization: diffusion and perfusion MRI. Diffusion MRI measures the mobility of the water protons and thus provides a window to tissue microstructure. Perfusion MRI measures the rate at which blood is delivered to tissue and thus provides information about microvasculature. Because both tissue structure and vasculature are likely to change in disease states, measurement of diffusion and perfusion may have direct physiologic relevance. This review covers topics related to the imaging sequences, image analysis, and clinical studies for diffusion and perfusion breast MRI. Preliminary studies show that the apparent diffusion coefficient (ADC) is a marker of cell density and can distinguish malignant from benign lesions. Perfusion MR also shows promise for breast tumor characterization: malignant tumors have consistently higher relative tissue blood volumes (rTBV) than normal and benign tumors. Additional research is required with large patient cohorts to establish these two techniques on a clinical footing.
Higher Order Statistics in Computer Vision
Authors: FARHADI ALI , SHAHSHAHANI MEHRDAD
Published: July 2009

Abstract: The aim of this work is to present methods for classifying images and locating extraneous objects within images. Our methods make use of higher order statistics, transforms of data into the frequency domain, and characteristics of the resulting clusters.
Volume Reconstruction for Health Care
Authors: MASERO VALENTÍN , LEÓN‐ROJAS JUAN M. , MORENO JOSÉ
Published: July 2009

Abstract:In many scientific and technical applications, a three‐dimensional (3D) object must be reconstructed, either to assist in understanding the object's structure or to ease its automatic handling and analysis. Volume reconstruction has been used in health care to diagnose, simulate, facilitate surgical planning, develop image‐guided surgery, facilitate telemedicine, and to assist in many other applications. This paper presents a survey of computational methods used to achieve volume reconstruction. First, we review 3D imaging techniques. Second, since we consider image segmentation the most important and difficult phase of 3D reconstruction, we focus on this topic. Subsequently, we concentrate on some of the most successful techniques of segmentation used for 3D reconstruction, such as active contours. We also review computer graphics and visualization methods used with volume reconstruction. Finally, we indicate future lines for research in volume reconstruction and 3D imaging for health care.
Decision Support System for the Analysis of Hospital Operation Indicators
Authors: WU FAN , LIN JIUNN RONG , TSAI WEN‐CHEN
Published: July 2009

Abstract: The inauguration of national health insurance (NHI) in many countries and their worsening financial condition has increased the sensitivity to operational cost and efficiency in hospitals. For several years, hospitals have been monitoring their operations by analyzing the financial and operational reports that are provided. Because of the rapidly changing character of the medical industry, statistical data shown on paper are no longer sufficient for decision makers. This paper describes a decision support system (DSS) for hospital administrators to assist in analyzing their operations efficiently and precisely. In hospitals, operational data of outpatients and inpatients are now stored on computers, resulting in much easier and faster data acquisition for administrators. The proposed system makes suggestions to hospital administrators and is able to self‐learn to improve its future usefulness. With the dual capabilities of integrating evaluations and data collecting, the system can assist administrators in discovering and resolving problems quickly. The system provides multidimensional and multilevel analyses, by using data warehousing techniques, and generates appropriate advice to users by employing decision‐making methodology. The self‐learning function of the system makes it work like an expert, continually modifying its content (knowledge) and generating advice that is promptly updated to accord with changes in the medical industry.
Epicenter Location by Analysis of Interictal Spikes
Authors: HAND CHARLES
Published: July 2009

Abstract: Artificial neural network (ANN) technology is finding increasing application in medicine and biomedical engineering. This paper supplies necessary background in ANN technology for researchers unfamiliar with this rapidly emerging discipline. This introduction to ANN application is cast in the context of epileptic seizure epicenter location. This is a very real problem faced by neurosurgeons every day. Precise location of the area of excision is currently determined with a network of surgically implanted subdural electrodes. This means that the cure entails two surgical procedures: one to implant the electrode array that precisely locates the epicenter, and another to remove the epicenter. This paper outlines an experimental diagnostic software system (DSS) that uses artificial neural network (ANN) analysis of magnetoencephalographic (MEG) data to eliminate the first of these surgical procedures. The MEG recording is a quick and painless process that requires no surgery. This approach has the potential to save time, reduce patient discomfort, and eliminate a painful and potentially dangerous surgical step in the treatment procedure.
Structures of Solid and Liquid during Melting and Solidification of Indium
Authors: COSTANZA G. , GAUZZI F. , MONTANARI R.
Published: July 2009

Abstract: During melting and solidification of polycrystalline indium the structures of the solid and liquid phases were investigated by X‐ray diffractometry (XRD) in 1g conditions. The experiments showed that melting is immediately preceded and accompanied by an abnormal increase of vacancy concentration in the solid that enhances the diffusion. At the melting point (TM) the lattice planes facing the first formed liquid appear to be {0 02} and {101}; that is, those planes allocating first and second neighbors around a given atom, with shell radii very close to the mean distance of nearest neighbors in liquid as obtained from the radial distribution function (RDF). On this basis some types of solid‐liquid interface (sharp or diffuse) are discussed; the possibility of a sudden texture change in the solid is also considered. On the other hand, the evolution of RDF curve of liquid indium, cooled down through TM, shows that there are correlations between the structure of the liquid and of the forming solid during solidification. To avoid convective motions in the liquid and to achieve the best experimental conditions, we discuss the possibility of repeating the measurements in microgravity (μg) using thin oxide films as containers. This technique was already successfully tested by one of the investigators in the experiment ES 311 A‐B carried out during the mission SPACELAB‐1.
Dielectricin SituMonitoring of Microgravity Polymerizations
Authors: KENNEDY ALVIN P. , TADESSE SOLOMON
Published: July 2009

Abstract:The objective of the research described here is to develop dielectric spectroscopy to monitor polymerization reactions and processes in microgravity. Ground based measurements have been made on both neat thermoset resins and solution polymerization reactions. Polymerization of diglycidyl ether of bisphenol A (DGEBA) using two curing agents,m‐phenylenediamine (m‐PDA), and 4,4′‐diamino‐diphenyl‐methane (DDM) were investigated to determine the relationship between the dielectric spectra and the thermoset polymer network and morphology. The results for the epoxy thermosets indicate that this technique can be used to monitor the extent of polymerization and the qualitative nature of polymer network. The photopolymerization of 6‐(2‐methyl‐4‐nitroanilino)‐2,4‐hexadiyn‐1‐ol (DAMNA) in solution was also investigated to determine if gravitational effects could be observed using dielectric spectroscopy. The technique is able to distinguish between surface and solution polymerizations during formation of the polydiacetylene thin films. In addition, it is capable of monitoring convective effects during solution polymerization.
Microgravity Effects on Thermodynamic and Kinetic Properties of Colloidal Dispersions
Authors: OKUBO TSUNEO , TSUCHIDA AKIRA
Published: July 2009

Abstract: Microgravity experiments on the physicochemical properties of colloidal dispersions reported hitherto have been reviewed. In microgravity, reliability and reproducibility of experimental data have been improved significantly by the elimination of convection in the suspension. Vanishment of the excess downward diffusion in microgravity has also produced a significant effect on properties of colloidal suspensions. For example, colloidal crystallization rates decreased in microgravity, whereas colloidal alloy crystallization rates increased. These results demonstrate the important role of the segregation effect in normal gravity. Colloidal silica formation reactions are retarded in microgravity, a phenomenon that is correlated deeply with disappearance of the downward diffusion of heavy products.
Optical Measurement of Concentration Gradient Near Miscible Interfaces
Authors: RASHIDNIA N. , BALASUBRAMANIAM R.
Published: July 2009

Abstract: A common path interferometer (CPI) system was developed to measure the diffusivity of transparent liquid pairs. The CPI is an optical technique that can be used to measure changes in the gradient of refractive index of transparent materials. The CPI is a shearing interferometer that shares the same optical path from a laser light source to the final imaging plane. Molecular diffusivity of liquids can be determined by using physical relations between changes in optical path length and liquid phase properties. In this paper, we present results obtained when the diffusivity depends on the local concentration of the miscible fluids.
Coupled Mean Flow‐Amplitude Equations for Nearly Inviscid Parametrically Driven Surface Waves
Authors: KNOBLOCH EDGAR , MARTEL CARLOS , VEGA JOSE M.
Published: July 2009

Abstract: Nearly inviscid parametrically excited surface gravity‐capillary waves in two‐dimensional periodic domains of finite depth and both small and large aspect ratio are considered. Coupled equations describing the evolution of the amplitudes of resonant left‐ and right‐traveling waves and their interaction with a mean flow in the bulk are derived, and the conditions for their validity established. In general the mean flow consists of an inviscid part together with a viscous streaming flow driven by a tangential stress due to an oscillating viscous boundary layer near the free surface and a tangential velocity due to a bottom boundary layer. These forcing mechanisms are important even in the limit of vanishing viscosity, and provide boundary conditions for the Navier‐Stokes equation satisfied by the mean flow in the bulk. The streaming flow is responsible for several instabilities leading to pattern drift.
Thermocapillary Convection Around Gas Bubbles
Authors: BETZ J. , STRAUB J.
Published: July 2009

Abstract: In the presence of a temperature gradient at a liquid—gas or liquid—liquid interface, thermocapillary or Marangoni convection develops. This convection is a special type of natural convection that was not paid much attention in heat transfer for a long time, although it is strong enough to drive liquids against the direction of buoyancy on Earth. In a microgravity environment, however, it is the remaining mode of natural convection and supports heat and mass transfer. During boiling in microgravity it was observed at subcooled liquid conditions. Therefore, the question arises about its contribution to heat transfer without phase change. Thermocapillary convection was quantitatively studied at single gas bubbles in various liquids, both experimentally and numerically. A two‐dimensional mathematical model described in this article was developed. The coupled mechanism of heat transfer and fluid flow in pure liquids around a single gas bubble was simulated with a control‐volume FE‐method. The simulation was accompanied and compared with experiments on Earth. The numerical results are in good accordance with the experiments performed on Earth at various Marangoni numbers using various alcohols of varying chain length and Prandtl numbers. As well as calculations on Earth, the numerical method also allows simulations at stationary spherical gas bubbles in a microgravity environment. The results demonstrate that thermocapillary convection is a natural heat transfer mechanism that can partially replace the buoyancy in a microgravity environment, if extreme precautions are taken concerning the purity of the liquids, because impurities accumulate predominantly at the interface. Under Earth conditions, an enhancement of the heat transfer in a liquid volume is even found in the case where thermocapillary flow is counteracted by buoyancy. In particular, the obstructing influence of surface active substances could be observed during the experiments on Earth in water and also in some cases with alcohols.
Numerical Simulations of Bubble Motion in a Vibrated Cell Under Microgravity Using Level Set and VOF Algorithms
Authors: FRIESEN TIMOTHY J. , TAKAHIRA HIROYUKI , ALLEGRO LISA , YASUDA YOSHITAKA , KAWAJI MASAHIRO
Published: July 2009

Abstract:Understanding the stability of fluid interfaces subjected to small vibrations under microgravity conditions is important for designing future materials science experiments to be conducted aboard orbiting spacecraft. During the STS‐85 mission, experiments investigating the motion of a large bubble resulting from small, controlled vibrations were performed aboard the Space Shuttle Discovery. To better understand the experimental results, two‐and three‐dimensional simulations of the experiment were performed using level set and volume‐of‐fluid interface tracking algorithms. The simulations proved capable of predicting accurately the experimentally determined bubble translation behavior. Linear dependence of the bubble translation amplitude on the container translation amplitude was confirmed. In addition, the simulation model was used to confirm predictions of a theoretical inviscid model of bubble motion developed in a previous study.
High Heat Flux Cooling by Microbubble Emission Boiling
Authors: SUZUKI KOICHI , SAITOH HIROSHI , MATSUMOTO KAZUAKI
Published: July 2009

Abstract:In subcooled flow boiling of water in a horizontal rectangular channel, microbubble emission boiling occurred at higher subcooling of liquid in transition boiling, and the heat flux increased more than the critical heat flux. The maximum heat flux reached 10 MW/m2for a channel with 12 mm × 14mm cross‐section at 40K liquid subcooling and 0.5 m/sec liquid velocity. For smaller rectangular channels with 14 mm × 5mm, 14mm × 3mm, and 14mm × 1mm cross‐sections, the maximum heat flux was 7 MW/m2—more than 20 times the cooling limit of a present day CPU. Microbubble emission boiling is expected to realize high heat flux cooling for electronic devices. In convection boiling with subcooled water jet, the same boiling regime and heat flux were obtained for a downward heating surface and an upward heating surface. In subcooled flow boiling with strong convection, the hydrodynamic force is predominant for vapor‐liquid exchange. Accordingly, microbubble emission boiling is expected for high heat flux cooling or high heat flux heat transfer in microgravity.
Heat Transfer Mechanisms in Microgravity Flow Boiling
Authors: OHTA HARUHIKO
Published: July 2009

Abstract:The objective of this paper is to clarify the mechanisms of heat transfer and dryout phenomena in flow boiling under microgravity conditions. Liquid—vapor behavior in annular flow, encountered in the moderate quality region, has extreme significance for practical application in space. To clarify the gravity effect on the heat transfer observed for an upward flow in a tube, the research described here started from the measurement of pressure drop for binary gas—liquid mixture under various gravity conditions. The shear stress acting on the surface of the annular liquid film was correlated by an empirical method. Gravity effects on the heat transfer due to two‐phase forced convection were investigated by the analysis of velocity and temperature profiles in the film. The results reproduce well the trends of heat transfer coefficients varying with the gravity level, quality, and mass velocity. Dryout phenomena in the moderate quality region were observed in detail by the introduction of a transparent heated tube. At heat fluxes just lower and higher than CHF value, a transition of the heat transfer coefficient was calculated from oscillating wall temperature, where a series of opposing heat transfer trends—the enhancement due to the quenching of dried areas or evaporation from thin liquid films and the deterioration due to the extension of dry patches—were observed between the passage of disturbance waves. The CHF condition that resulted from the insufficient decrease of wall temperature in the period of enhanced heat transfer was overcome by a temperature increase in the deterioration period. No clear effect of gravity on the mechanisms of dryout was observed within the range of experiments.
Criteria for Approximating Certain Microgravity Flow Boiling Characteristics in Earth Gravity
Authors: MERTE HERMAN , PARK JAESEOK , SHULTZ WILLIAM W. , KELLER ROBERT B.
Published: July 2009

Abstract: The forces governing flow boiling, aside from system pressure, are buoyancy, liquid momentum, interfacial surface tensions, and liquid viscosity. Guidance for approximating certain aspects of the flow boiling process in microgravity can be obtained in Earth gravity research by the imposition of a liquid velocity parallel to a flat heater surface in the inverted position, horizontal, or nearly horizontal, by having buoyancy hold the heated liquid and vapor formed close to the heater surface. Bounds on the velocities of interest are obtained from several dimensionless numbers: a two‐phase Richardson number, a two‐phase Weber number, and a Bond number. For the fluid used in the experimental work here, liquid velocities in the range U= 5‐10cm/sec are judged to be critical for changes in behavior of the flow boiling process. Experimental results are presented for flow boiling heat transfer, concentrating on orientations that provide the largest reductions in buoyancy parallel to the heater surface, varying ±5 degrees from facing horizontal downward. Results are presented for velocity, orientation, and subcooling effects on nucleation, dryout, and heat transfer. Two different heater surfaces were used: a thin gold film on a polished quartz substrate, acting as a heater and resistance thermometer, and a gold‐plated copper heater. Both transient and steady measurements of surface heat flux and superheat were made with the quartz heater; only steady measurements were possible with the copper heater. R‐113 was the fluid used; the velocity varied over the interval 4‐16cm/sec; bulk liquid subcooling varied over 2‐20°C; heat flux varied over 4‐8W/cm2.
Microgravity Studies of Cells and Tissues
Authors: VUNJAK‐NOVAKOVIC GORDANA , SEARBY NANCY , DE LUIS JAVIER , FREED LISA E.
Published: July 2009

Abstract: Controlled in vitro studies of cells and tissues under the conditions of microgravity (simulated on Earth, or actual in space) can improve our understanding of gravity sensing, transduction, and responses in living cells and tissues. This paper discusses the scientific results and practical implications of three NASA‐related biotechnology projects: ground and space studies of microgravity tissue engineering (JSC‐Houston), and the development of the cell culture unit for use aboard the International Space Station (ARC‐Ames).
Bioactive, Degradable Composite Microspheres
Authors: QIU QING‐QING , DUCHEYNE PAUL , AYYASWAMY PORTONOVO S.
Published: July 2009

Abstract: Composite microspheres with two different fillers were developed using a solid‐in‐oil‐in‐water (s/o/w) emulsion solvent removal method. Two types of bioactive ceramic powders, specifically calcium hydroxyapatite (HA) and modified bioactive glass (MBG), were incorporated into degradable poly(lactic acid) (PLA) polymer matrix to form composite microspheres. For each filler material, microspheres with three different weight ratios of filler material to polymer, namely, 1: 1, 1: 3, and 1: 9, were synthesized. In vitro immersion using simulated physiological fluid (SPF) was employed to evaluate the surface reactivity of the microspheres. SEM analysis revealed that after a 14‐day immersion the surface of the microspheres containing 50% MBG was fully transformed into a bone‐like apatite. In contrast, a limited number of mineral nodules were present on the surface of microspheres containing HA. The solution chemical analyses performed to determine changes of Ca, P, and Si concentrations as a function of the immersion time showed that the ion concentration profiles were similar for all microspheres, except the [Si] profile. A higher Si concentration was detected in the SPF immersed with MBG‐containing microspheres. These data show that the MBG filler significantly enhances the surface reactivity of the composite microspheres. This observation enables us to conclude that the composite MBG‐containing microspheres are the preferable microspheres for three‐dimensional bone tissue engineering.
Gene Profiling Approach to Establish the Molecular Bases for Partial versus Full Activation of Naïve CD8 T Lymphocytes
Authors: VERDEIL GRÉGORY , PUTHIER DENIS , NGUYEN CATHERINE , SCHMITT‐VERHULST ANNE‐MARIE , AUPHAN‐ANEZIN NATHALIE
Published: July 2009

Abstract: When initial antigen encounter involves optimal antigenic and costimulatory stimuli, naïve CD8 T cells undergo a developmental program that leads to their activation, expansion and acquisition of effector functions (including production of IL‐2, IFNγ and expression of cytolytic effector molecules). A subset of the activated CD8 T cells thrives as long‐lived memory cells. Encounter of tissue‐associated, and in particular tumor‐associated antigen, may often be suboptimal in terms of antigenicity and costimulation, however. We previously developed a model of naïve CD8 T cells from transgenic mice expressing an alloreactive TCR for which a mutant alloantigen behaved as a partial agonist, inducing only some of the effector functions induced by the native alloantigen. To ascertain the molecular bases for the establishment of divergent fates within the same naïve CD8 T cells, we have used cDNA microarrays to monitor sequential gene expression patterns in conditions of full or partial response of these naïve CD8 T cells. Of the 5000 different genes monitored on the array, 18% showed changes in expression in activated versus naïve CD8 T cells, independent of whether stimulation was with full or partial agonist. These included antigen‐induced upregulated as well as downregulated genes. Clusters of genes that were differentially expressed were also identified, being either (i) weakly versus strongly, or (ii) transiently versus stably expressed in response to partial and full agonist, respectively. They included (i) genes encoding costimulatory molecules and (ii) genes controlling cytolytic function, cytokine production, and chemokines. Therefore, the cDNA microarray approach was a sensitive tool to provide an exhaustive picture of T cell activation as it could discriminate quantitative, qualitative and dynamic differences in mRNA expression profiles between fully or partially activated T cells.
Integrated Genomic and Proteomic Analysis of Signaling Pathways in Dendritic Cell Differentiation and Maturation
Authors: RICHARDS JOHN , LE NAOUR FRANÇOIS , HANASH SAMIR , BERETTA LAURA
Published: July 2009

Abstract:Dendritic cells (DCs) are antigen‐presenting cells that play a major role in initiating primary immune responses. Their phenotypic and functional characteristics are intimately linked to their stage of maturation. The specific biochemical pathways and genes whose expression mediates differentiation of progenitors to DCs and their maturation are largely undefined. We recently utilized two approaches, DNA microarrays and proteomics, to analyze the expression profile of human CD14+blood monocytes and their derived DCs. Approximately 4% of the genes or proteins expressed were found to be regulated during DC differentiation. Most of these genes were not previously associated with DCs and included genes highly relevant to DC functions (genes involved in antigen presentation, cell adhesion and motility, lipid metabolism). Genes involved in specific signaling pathways, including IκBα, PPAR‐γ and C/EBPα as well as two members of the family of transcription factors, interferon regulatory factors (IRFs), were also modified. Modulation of IRF gene expression is of particular interest because of their functional roles in innate and adaptive immune responses. IRF‐family members control the expression of proteins that include type‐1 interferons, interleukin‐12, interleukin‐15, MHC molecules and adhesion molecules. They have also been found to play an important role in lymphocyte development. In contrast to DC differentiation, very few genes were modified at the transcript level during DC maturation as determined by microarray experiments. Further analysis suggested that DC maturation is largely controlled by posttranscriptional and posttranslational modifications. The use of proteomics is therefore necessary for a full comprehension of DC maturation process.
Stronger Correlation of bcl‐3 than bcl‐2, bcl‐xL, Costimulation, or Antioxidants with Adjuvant‐Induced T Cell Survival
Authors: MITCHELL THOMAS C. , TEAGUE T. KENT , HILDEMAN DAVID A. , BENDER JEREMY , REES WILLIAM A. , KEDL ROSS M. , SWANSON BRAD , KAPPLER JOHN W. , MARRACK PHILIPPA
Published: July 2009

Abstract: A set of signals separate from those needed for T cell activation and clonal expansion acts to sustain a T cell response once it has begun. Immunologic adjuvants can initiate these signals in a process we designate adjuvant‐induced survival (AIS). Here, the natural adjuvant LPS was used in a super‐antigen model of AIS to understand which factors are needed to sustain T cell survival after activation. Flow cytometric stains for antiapoptotic Bcl‐2 and Bcl‐xL showed that neither factor was well correlated with AIS, although both were increased transiently upon T cell activation. T cells protected via AIS showed no increased ability to resist death caused by reactive oxygen species, and cellular division was not accelerated as might be expected if AIS were to operate through co‐stimulatory pathways. Finally, microarray analyses were performed that showed increased expression of Bcl‐3, an NFκB/IκB factor, was correlated with AIS. It is proposed that T cell survival during productive immune responses occurs by successive activities of Bcl‐2, Bcl‐xL and Bcl‐3, with Bcl‐3 requiring innate immune responses to adjuvants for its expression.
Unlocking the Mysteries of Virus‐Host Interactions
Authors: KORTH MARCUS J. , KATZE MICHAEL G.
Published: July 2009

Abstract: The interactions between viruses and the cells they infect are complex and multifaceted. While viruses strive to usurp cellular functions to their advantage, the cell strives to thwart these efforts by mounting a variety of defensive responses. These responses may include the induction of interferon, stress response, or apoptotic pathways, all of which are accompanied by changes in gene expression. Some viruses consistently win this tug of war, whereas others succumb to cellular defense mechanisms. The viral and cellular factors that determine the outcome are for the most part still unknown. With the advent of functional genomics, potent new technologies are now available to probe the complexities of virus‐host interactions in ever increasing depth and detail. We describe here our efforts to use microarrays, proteomics, and bioinformatics to focus in on the changes in gene expression and protein production that occur in a virus‐infected cell and to use these technologies to unlock the mysteries of virus‐host interactions.
Chlamydiae Host Cell Interactions Revealed Using DNA Microarrays
Authors: MAHONY JAMES B.
Published: July 2009

Abstract: Chlamydiae are obligate intracellular bacterial parasites that infect eukaryotic cells and live their entire life cycle within a cytoplasmic vacuole or inclusion. We have employed cDNA microarray and conventional biological approaches to study the pathogen‐host cell interaction during C. pneumoniae infection of eukaryotic cells. Two host cell signaling pathways, MEK/ERK and PI 3‐kinase/Akt, were activated within 5 and 20 minutes, respectively, following infection with chlamydiae. Pharmacological inhibition of these pathways blocked invasion of HEp2 cells indicating that activation of these pathways was required for infection. Rho family GTPase activity was essential for invasion, since the pan‐Rho GTPase inhibitor, compactin, blocked infection of HEp2 cells. cDNA microarrays and reverse transcriptase PCR were used to study host cell and chlamydial gene expression during the replication cycle. Analysis of host cell gene expression following infection with C. pneumoniae indicated that genes coding for cytokines, growth factors, and signaling molecules were upregulated, as early as 2 hours postinfection. Analysis of chlamydial gene expression indicated a temporal regulation of transcription with distinct early‐, mid‐, and late‐cycle classes of RNA transcripts. Newly discovered genes encoding three Ser/Thr protein kinases and one protein phosphatase were upregulated 6‐12 hours postinfection. One protein kinase, designated CpnPK1, was first detected at 12 hours postinfection, accumulated in the inclusion throughout the replication cycle, and may be a type III effector molecule. An increased understanding of chlamydial host cell interactions, in particular the role of various chlamydial proteins in infection and identification of essential virulence factors should provide novel targets for the development of new antimicrobials.
Gene Expression Profile in Neisseria meningitidis and Neisseria lactamica upon Host‐Cell Contact
Authors: GRIFANTINI R. , BARTOLINI E. , MUZZI A. , DRAGHI M. , FRIGIMELICA E. , BERGER J. , RANDAZZO F. , GRANDI G.
Published: July 2009

Abstract: Differential gene regulation in the human pathogen Neisseria meningitidis group B (MenB) and in Neisseria lactamica, a human commensal species, was studied by whole genome microarray after bacterial interaction with epithelial cells. Host‐cell contact induced changes in the expression of 347 and 285 genes in MenB and N. lactamica, respectively. Of these, only 167 were common to MenB and N. lactamica, suggesting that a different subset of genes is activated by pathogens and commensals. Change in gene expression was stable over time in N. lactamica, but short‐lived in MenB. A large part (greater than 30%) of the regulated genes encoded proteins with unknown function. Among the known genes, those coding for pili, capsule, protein synthesis, nucleotide synthesis, cell wall metabolism, ATP synthesis, and protein folding were down‐regulated in MenB. Transporters for iron, chloride and sulfate, some known virulence factors, GAPDH and the entire pathway of selenocysteine biosynthesis were upregulated. Gene expression profiling indicates that approximately 40% of the regulated genes encode putative surface‐associated proteins, suggesting that upon cell contact Neisseria undergoes substantial surface remodeling. This was confirmed by FACS analysis of adhering bacteria using mouse sera against a subset of recombinant proteins. Finally, a few surface‐located, adhesion‐activated antigens were capable of inducing bactericidal antibodies, indicating that microarray technology can be exploited for the identification of new vaccine candidates.
Prognosis of Breast Cancer and Gene Expression Profiling Using DNA Arrays
Authors: BERTUCCI FRANÇOIS , HOULGATTE RÉMI , GRANJEAUD SAMUEL , NASSER VALÉRY , LORIOD BÉATRICE , BEAUDOING EMMANUEL , HINGAMP PASCAL , JACQUEMIER JOCELYNE , VIENS PATRICE , BIRNBAUM DANIEL , NGUYEN CATHERINE
Published: July 2009

Abstract: Breast cancer is a complex genetic disease characterized by the accumulation of multiple molecular alterations. The resulting clinical heterogeneity makes current therapeutic strategies—based on clinicopathlogical factors—less than perfectly adapted to each patient. Today, DNA arrays, by allowing the simultaneous and quantitative analysis of the mRNA expression levels of thousands of genes in a single assay, provide novel tools to tackle this complexity. Potential applications are multiple in the cancer field and the first research results are promising. Using home‐made DNA arrays in an approach easily compatible with academic research—nylon support and radioactive detection—we identified a predictor set of 23 genes whose expression patterns differentiated two groups of breast cancer patients with different survival after adjuvant chemotherapy. We then validated and further extended these results in a larger, independent and homogeneous series of poor prognosis primary breast cancers treated with adjuvant anthracyclin‐based chemotherapy. We confirmed the prognostic classification provided by the 23‐gene set predictor. We then improved the predictor set and refined the classification by sorting the tumors into three classes with significantly different long‐term survival. These results show the potential of the technology with an accessible approach for academic research teams. We also showed that nylon DNA arrays with radioactive detection are associated with excellent sensitivity, an advantage in clinical situations where the amount of available material is limited.
Identifying Immunotherapeutic Targets for Prostate Carcinoma through the Analysis of Gene Expression Profiles
Authors: NELSON PETER S.
Published: July 2009

Abstract: Carcinoma of the prostate represents one of the most frequently diagnosed cancers in men. If detected at an early stage, prostate cancer is highly treatable. However, cancers identified at a late stage are rarely cured with contemporary medical therapies. Early detection strategies presently center on the identification of prostate‐specific proteins in the serum, and emerging therapeutics have utilized genes and proteins with prostate‐restricted expression for tissue‐selective immunological regimens incorporating vaccines, dendritic cell therapy, gene therapy, and antibody‐based cell targeting. In order to develop improved therapeutic procedures, efforts have been directed toward the identification of genes exhibiting prostate‐restricted expression profiles, or altered expression levels in neoplastic cells relative to their normal counterparts. Comprehensive expression profiling approaches such as the analysis of oligonucleotide‐ or complementary DNA (cDNA)‐microarrays have greatly enhanced these efforts. Genes and their cognate proteins identified using such methods offer additional diagnostic and therapeutic targets that may aid in the understanding and treatment of prostate carcinoma.
Humoral Links between Sleep and the Immune System
Authors: KRUEGER JAMES M. , MAJDE JEANNINE A.
Published: July 2009

Abstract: In the last twenty years we have realized that the immune system synthesizes a class of peptides, termed cytokines, that play a central role in alerting the brain to ongoing inflammation in peripheral tissues. Among the brain's responses to proinflammatory cytokines, or agents that induce these cytokines, are certain alterations in sleep profiles. Characteristically there is an increase in non‐rapid eye movement sleep (NREMS), and NREMS intensity is often accompanied by a decrease in rapid eye movement sleep (REMS). Cytokines appear to play a role in normal sleep regulation; during pathology, higher levels of cytokines amplify the physiological cytokine sleep mechanisms. In this review we summarize the extensive literature on the roles of interleukin‐1 (IL‐1) and tumor necrosis factor‐α (TNF‐α) in sleep regulation, and their interactions with the neuropeptides growth hormone‐releasing hormone (GHRH) and corticotropin‐releasing hormone (CRH). We reach the tentative conclusion that the sleep‐promoting actions of IL‐1 and GHRH are mediated via anterior hypothalamic neurons that are receptive to these substances. It also seems likely that TNF‐α and CRH also influence these neurons. In addition, we discuss an array of research issues raised by these studies that remain to be resolved.
HPA Axis Activation and Neurochemical Responses to Bacterial Translocation from the Gastrointestinal Tract
Authors: DUNN ADRIAN J. , ANDO TETSUYA , BROWN RHONDA F. , BERG RODNEY D.
Published: July 2009

Abstract:Stress can cause migration of indigenous bacterial flora from the gut to the peritoneum, a phenomenon known as bacterial translocation. Destruction of the cell walls of gram‐negative bacteria can result in the production of endotoxin (lipopolysaccharide, LPS), which is the likely cause of sepsis. Exogenously administered LPS can activate the hypothalamo‐pituitary‐adrenal (HPA) axis as well as brain noradrenergic and indoleaminergic systems. Thus, it is possible that activations of these systems associated with laboratory stressors in rats and mice could be attributed to bacterial translocation and LPS production. To test this hypothesis we conducted experiments on the time course of bacterial translocation in response to restraint in mice, while measuring HPA and neurochemical responses. These experiments failed to show good correlations between the occurrence of bacterial translocation and HPA and neurochemical activations, suggesting that the later responses were not linked to bacterial translocation. This conclusion was supported by the observation of normal neurochemical responses to restraint in germ‐free mice. In further experiments, translocation ofSalmonella typhimurium, a bacterium that readily translocates in unstressed animals, was associated with HPA activation and noradrenergic and indoleaminergic responses, indicating that bacterial translocation can indeed activate the HPA axis and brain amines. However, the above experiments suggest that this is not the mechanism by which restraint activates these systems.
Role of Nitric Oxide in Regulating the Rat Hypothalamic‐Pituitary‐Adrenal Axis Response to Endotoxemia
Authors: RIVIER CATHERINE
Published: July 2009

Abstract:This work examines the role of nitric oxide (NO) in the periphery (i.e., on the pituitary) and the brain (particularly on corticotropin‐releasing factor [CRF] and vasopressin [VP] neurons in the paraventricular nucleus [PVN] of the hypothalamus) as a modulator of the ACTH response to lipopolysaccharide. We previously showed that NO restricted the pituitary response to VP while it facilitated the synthesis of PVN CRF and VP. In our experience, only relatively high doses of lipopolysaccharide (>50 μg/kg, injected intravenously [iv]) cause detectable increases in PVN neuronal activation. Our hypothesis, therefore, was that pituitary NO‐VP interactions would predominate in rats injected with a low dose of lipopolysaccharide (0.5 μg/kg, iv) while the stimulatory influence of the gas on PVN neuronal activity would play an important role following iv injection of a large dose of lipopolysaccharide (50 μg/kg, iv). We observed that the ability of 0.5 μg/kg lipopolysaccharide to release ACTH was significantly enhanced by the subcutaneous (sc), but not the intracerebroventricular (icv) injection of L‐NAME, an arginine derivative that blocks NO synthesis. The effect of sc L‐NAME was reversed by immunoneutralization of endogenous VP, which indicated that in this model, the ability of lipopolysaccharide to release ACTH depended, at least in part, on the influence exerted by NO on the pituitary response to VP. In rats injected with the high lipopolysaccharide dose, the sc injection of L‐NAME decreased plasma ACTH levels compared to those in rats pretreated with the vehicle. The effect of sc L‐NAME was not significantly altered by VP antibodies. These results indicate that in this model, the primary influence of NO was exerted in the PVN and/or its afferents and that it did not depend on a peripheral, VP‐mediated effect of the gas. On the one hand, these data are at odds with our finding that the icv injection of L‐NAME only marginally altered the ACTH response to the large dose of lipopolysaccharide. As icv injected L‐NAME should have primarily decreased hypothalamic, but not pituitary NOS, its only modest influence on ACTH release may have been due to a balance between stimulating and inhibiting effects of NO within the brain. As high doses of lipopolysaccharide increase brain levels of prostaglandin, monoamine, and proinflammatory cytokines, it will be important to investigate the influence exerted by NO on these secretagogues and on their interactions with PVN CRF and VP neurons, which may help us resolve the issues raised by our results. Collectively, these data support our hypothesis that the mechanisms mediating the ACTH response to a low lipopolysaccharide concentration involve the inhibitory VP‐mediated influence of NO on pituitary activity. By contrast, the stimulatory effect of high doses of lipopolysaccharide on ACTH release depends, at least in part, on the ability of NO to upregulate PVN neuronal activity.
The Hypothalamo‐Pituitary‐Adrenal Axis in Multiple Sclerosis
Authors: HUITINGA INGE , ERKUT ZEYNEL A. , Van BEURDEN DENIS , SWAAB DICK F.
Published: July 2009

Abstract: During multiple sclerosis (MS), an inflammatory demyelinating disease of the central nervous system (CNS), activation of the hypothalamo‐pituitary‐adrenal (HPA) axis is considered to modulate the immune system in such a way that the probability of recovery from a relapse is increased. In a series of postmortem studies we observed a significant activation of corticotropin releasing hormone (CRH) neurons and increased cortisol in the cerebrospinal fluid (CSF) of MS patients, indicating activation of the HPA axis in this disease. On the other hand, sepsis, while elevating cortisol in control subjects, did not associate with a further increase of cortisol in MS patients. Thus, the activated HPA‐system in MS does not respond to an acute inflammatory stimulus. In order to investigate the role of chronic inflammation in the CNS in the activation of the HPA axis in MS, MS lesions in the hypothalamus were quantified and interleukin (IL)‐6 levels in the CSF were determined. There was no difference in IL‐6 levels between MS and control patients. A positive correlation was found between cortisol and IL‐6 in control subjects with sepsis, but not in MS patients with sepsis or MS and control groups without sepsis. Thus, IL‐6 in the CSF of MS patients is not the cause of the activation of the HPA system in MS. We found a remarkably high incidence (95% of the patients) of MS lesions in the hypothalamus, of which the majority (60%) were active. The more active lesions were present in the hypothalamus, the shorter the disease duration to the moment of death, indicative of a worse disease course. Preliminary data show suppression of the activation of CRH neurons by active hypothalamic MS lesions. We propose that this suppression of CRH neurons by active hypothalamic MS lesions causes the concomitant unfavorable disease course via an inadequate cortisol response during relapses of MS.
Effects ofin Vitroandin VivoOpioids on the Production of IL‐12 and IL‐10 by Murine Macrophages
Authors: SACERDOTE PAOLA
Published: July 2009

Abstract:We evaluated the ability of the specific μ opioid receptor agonist DAMGO, the κ‐specific agonist U‐50488in vitro, and exogenous opioid morphine administeredin vivoboth acutely and chronically to modulate IL‐12 and IL‐10 production by murine peritoneal macrophages. Damgo and U‐50488 at the concentrations of 10−6and 10−8M decreased the production of IL‐12 without affecting IL‐10. One hour after the acute administration of 5, 10, and 20 mg/kg of morphine a dose‐related decrease of both IL‐10 and IL‐12 levels was present. The pretreatment with naltrexone at doses up to 20 mg/kg did not prevent the decrease of IL‐10 and IL‐12 induced by morphine. When the drug was administered chronically, a differential development of tolerance to the immune effects was observed. After 3 days of treatment the effect of the acute challenge with 20 mg/kg of morphine on IL‐12 was lost. In contrast, morphine‐induced inhibition of IL‐10 disappeared between 10 and 12 days of treatment, in parallel with tolerance to the antinociceptive effect. These results suggest that opioids modulate macrophage cytokine production. However, the effects exerted by thein vivoadministration of morphine are not superimposable onto those induced by thein vitroadministration of specific opioid agonists.