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PubMed2006

Differential regulation of hyaluronan-induced IL-8 and IP-10 in airway epithelial cells.

Airway epithelium is emerging as a regulator of local inflammation and immune responses. However, the cellular and molecular mechanisms responsible for the immune modulation by these cells have yet to be fully elucidated. At the cellular level, the hallmarks of airway inflammation are mucus gland hypertrophy with excess mucus production, accumulation of inflammatory mediators, inflammation in the airway walls and lumen, and breakdown and turnover of the extracellular matrix. We demonstrate that fragments of the extracellular matrix component hyaluronan induce inflammatory chemokine production in primary airway epithelial cells grown at an air-liquid interface. Furthermore, hyaluronan fragments use two distinct molecular pathways to induce IL-8 and IFN-gamma-inducible protein 10 (IP-10) chemokine expression in airway epithelial cells. Hyaluronan-induced IL-8 requires the MAP kinase pathway, whereas hyaluronan-induced IP-10 utilizes the NF-kappaB pathway. The induction is specific to low-molecular-weight hyaluronan fragments as other glycosaminoglycans do not induce IL-8 and IP-10 in airway epithelial cells. We hypothesize that not only is the extracellular matrix a target of destruction in airway inflammation but it plays a critical role in perpetuating inflammation through the induction of cytokines, chemokines, and modulatory enzymes in epithelial cells. Furthermore, hyaluronan, by inducing IL-8 and IP-10 by distinct pathways, provides a unique target for differential regulation of key inflammatory chemokines.

Binding Sites↗

PubMed1985

Distribution of a fatty acid spin probe in sarcoplasmic reticulum. Evidence of membrane asymmetry.

The distribution of a lipophilic spin probe, 5-doxyl stearate, between the inner and outer halves of the sarcoplasmic reticulum (SR) bilayer was determined by titration with Ni X EDTA, a spin broadening agent. Titrations were also performed with Fe(CN)3-6 and with the solvated Ni2+ cation. Ni X EDTA titrations reached a clearly defined asymptote at 35% signal reduction. Fe(CN)3-6 and Ni2+ titrations gave biphasic curves but showed 35% of the signal to be readily eliminated at low concentrations. When the Ni2+ cation was used with ionophore, titrations indicated that 96% of the probe is aligned in the bilayer with the spin moiety at either the inner or outer interface. It was concluded that the spin probe distribution between the outer and inner halves of the SR bilayer is 35:65, respectively. Titrations performed on vesicles of purified SR lipids gave a ratio of 60 exposed:40 protected, consistent with the vesicular geometry. In addition the spin probe distribution in SR vesicles did not vary as a function of temperature, salt concentration, or spin probe concentration. On this basis it was concluded that the spin probe distribution gives a reasonable estimation of the volume of fluid lipids available to readily solubilize the probe in each half of the bilayer and that the observed asymmetry in distribution is due to the presence of SR proteins which were eliminated in the pure lipid vesicles. Furthermore, as EDTA is unique in its ability to chelate transition metals, Ca2+ and EGTA can be used in Ni X EDTA titrations without altering the chelation of Ni2+. Known changes in ATPase conformation accompanying Ca2+ and adenyl-5'-yl imidodiphosphate X Mg binding did not affect the spin probe distribution. However, phosphorylation of the enzyme by Pi gave a small, but clearly discernible, protection of spin probe signal. Chemical reduction with ascorbate indicated that this was due to occlusion of a small fraction of spin probes and thus possibly SR lipids.

Adenosine Triphosphatases↗

PubMed2005

Accident prediction model for railway-highway interfaces.

Considerable past research has explored relationships between vehicle accidents and geometric design and operation of road sections, but relatively little research has examined factors that contribute to accidents at railway-highway crossings. Between 1998 and 2002 in Korea, about 95% of railway accidents occurred at highway-rail grade crossings, resulting in 402 accidents, of which about 20% resulted in fatalities. These statistics suggest that efforts to reduce crashes at these locations may significantly reduce crash costs. The objective of this paper is to examine factors associated with railroad crossing crashes. Various statistical models are used to examine the relationships between crossing accidents and features of crossings. The paper also compares accident models developed in the United States and the safety effects of crossing elements obtained using Korea data. Crashes were observed to increase with total traffic volume and average daily train volumes. The proximity of crossings to commercial areas and the distance of the train detector from crossings are associated with larger numbers of accidents, as is the time duration between the activation of warning signals and gates. The unique contributions of the paper are the application of the gamma probability model to deal with underdispersion and the insights obtained regarding railroad crossing related vehicle crashes.

Accidents↗

PubMed2004

Delivery systems for small molecule drugs, proteins, and DNA: the neuroscience/biomaterial interface.

Manipulation of cellular processes in vivo by the delivery of drugs, proteins or DNA is of paramount importance to neuroscience research. Methods for the presentation of these molecules vary widely, including direct injection (either systemic or stereotactic), osmotic pump-mediated chronic delivery, or even implantation of cells engineered to indefinitely secrete a factor of interest. Biomaterial-based delivery systems represent an alternative to more traditional approaches, with the possibility of increased efficacy. Drug-releasing biomaterials, either as injectable microspheres or as three-dimensional implants, can deliver a molecule of interest (including small molecule drugs, biologically active proteins, or DNA) over a more prolonged period of time than by standard bolus injection, avoiding the need for repeated administration. Furthermore, sustained-release systems can maintain therapeutic concentrations at a target site, thus reducing the chance for toxicity. This review summarizes applications of polymer-based delivery of small molecule drugs, proteins, and DNA specifically relevant to neuroscience research. We detail the fabrication procedures for the polymeric systems and their utility in various experimental models. The biomaterial field offers unique experimental tools with downstream clinical application for the study and treatment of neurologic disease.

Animals↗

PubMed2006

Genetic and dopaminergic modulation of reversal learning in a touchscreen-based operant procedure for mice.

Mice are uniquely suited as experimental subjects for various approaches to the study of the molecular and genetic basis of behavior, and there has been a corresponding explosion in the use of mice in behavioral neuroscience. Rats and monkeys, however, remain the preferred species for high-order cognitive models largely due to the unavailability of valid, reliable and translatable endpoint measures of behavior in the mouse. Here we present further development and validation of a touchscreen-based operant method for measuring cognition that is comparable to methods used in other species and human patients. C57BL/6J mice were found to show good performance on visual discrimination and reversal learning using this method. Demonstrating the sensitivity of the paradigm to genetic factors, C57BL/6J and DBA/2J mice exhibited marked differences in discrimination and reversal learning. Systemic treatment with the selective D1-like agonist, SKF81297, produced an impairment in the early phase of reversal learning, but did not alter visual discrimination, in C57BL/6J mice. The same treatment impaired spatial working memory on the T-maze delayed alternation task, but did not alter control measures of behavior including motivation and locomotor activity. These data demonstrate the sensitivity of visual discrimination and reversal learning measured by this method to genetic factors and pharmacological challenge, and thereby provide an extension and further validation of the method for measuring cognition in mice. When combined with emerging molecular techniques uniquely suited to this species such as genetic engineering and RNA modification this paradigm could provide a powerful new tool for behavioral neuroscience.

Analysis of Variance↗

PubMed2003

Designing a knowledge management system for distributed activities: a human centered approach.

In this study we use the principles of distributed cognition and the methodology of human-centered distributed information design to analyze a complex distributed human-computer system, identify its problems, and generate design requirements and implementation specifications of a replacement prototype for effective organizational memory and knowledge management. We argue that a distributed human-computer information system has unique properties, structures and processes that are best described in the language of distributed cognition. Distributed cognition provides researchers a richer theoretical understanding of human-computer interactions and enables re-searchers to capture the phenomenon that emerges in social interactions as well as the interactions between people and structures in their environment.

Artificial Intelligence↗

PubMed2002

Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins.

2-Cys peroxiredoxins (Prxs) are a large and diverse family of peroxidases which, in addition to their antioxidant functions, regulate cell signaling pathways, apoptosis, and differentiation. These enzymes are obligate homodimers (alpha(2)), utilizing a unique intermolecular redox-active disulfide center for the reduction of peroxides, and are known to form two oligomeric states: individual alpha(2) dimers or doughnut-shaped (alpha(2))(5) decamers. Here we characterize both the oligomerization properties and crystal structure of a bacterial 2-Cys Prx, Salmonella typhimurium AhpC. Analytical ultracentrifugation and dynamic light scattering show that AhpC's oligomeric state is redox linked, with oxidization favoring the dimeric state. The 2.5 A resolution crystal structure (R = 18.5%, R(free) = 23.9%) of oxidized, decameric AhpC reveals a metastable oligomerization intermediate, allowing us to identify a loop that adopts distinct conformations associated with decameric and dimeric states, with disulfide bond formation favoring the latter. This molecular switch contains the peroxidatic cysteine and acts to buttress the oligomerization interface in the reduced, decameric enzyme. A structurally detailed catalytic cycle incorporating these ideas and linking activity to oligomeric state is presented. Finally, on the basis of sequence comparisons, we suggest that the enzymatic and signaling activities of all 2-Cys Prxs are regulated by a redox-sensitive dimer to decamer transition.

Amino Acid Sequence↗

PubMed2006

Kallikrein-mediated proteolysis regulates the antimicrobial effects of cathelicidins in skin.

The presence of cathelicidin antimicrobial peptides provides an important mechanism for prevention of infection against a wide variety of microbial pathogens. The activity of cathelicidin is controlled by enzymatic processing of the proform (hCAP18 in humans) to a mature peptide (LL-37 in human neutrophils). In this study, elements important to the processing of cathelicidin in the skin were examined. Unique cathelicidin peptides distinct from LL-37 were identified in normal skin. Through the use of selective inhibitors, SELDI-TOF-MS, Western blot, and siRNA, the serine proteases stratum corneum tryptic enzyme (SCTE, kallikrein 5) and stratum corneum chymotryptic protease (SCCE, kallikrein 7) were shown to control activation of the human cathelicidin precursor protein hCAP18 and also influence further processing to smaller peptides with alternate biological activity. The importance of this serine protease activity to antimicrobial activity in vivo was illustrated in SPINK5-deficient mice that lack the serine protease inhibitor LEKTI. Epidermal extracts of these animals show a significant increase in antimicrobial activity compared with controls, and immunoabsorption of cathelicidin diminished antimicrobial activity. These observations demonstrate that the balance of proteolytic activity at an epithelial interface will control innate immune defense.

Animals↗

PubMed2004

Hydrophobic core repacking in a coiled-coil dimer via phage display: insights into plasticity and specificity at a protein-protein interface.

The coiled-coil, which consists of two or more interwoven amphiphilic alpha-helices, is formed by sequences that have a characteristic heptad repeat (abcdefg) where a and d are hydrophobic residues. Most efforts to elucidate the origins of coiled-coil pairing selectivity have focused on electrostatic interactions among side chains that flank the core (positions e and g) and on polar side chains that occur occasionally at core positions. We have used phage display to explore another source of coiled-coil specificity: steric matching among nonpolar side chains in the core. We introduced a destabilizing Leu-->Ala mutation into the core of one helix in a known heterodimer and then screened a phage-based library of potential partner helices in search of compensating mutations. We identified a new heterodimer pair (30 residues/helix) that is comparable in stability to the GCN4-p1 homodimer (33 residues/helix). Furthermore, the Leu-->Ala mutant shows specificity for its phage-derived partner over the original partner despite their similar sequences. These results show that a phage-based approach can provide unique insights on coiled-coil pairing preferences that should facilitate both the analysis of natural sequences and the development of specific dimerization motifs that are orthogonal to one another.

Alanine↗

PubMed1997

The PDZ domain of human erythrocyte p55 mediates its binding to the cytoplasmic carboxyl terminus of glycophorin C. Analysis of the binding interface by in vitro mutagenesis.

The PDZ domain, also known as the GLGF repeat/DHR domain, is an approximately 90-amino acid motif discovered in a recently identified family of proteins termed MAGUKs (membrane-associated guanylate kinase homologues). Sequence comparison analysis has since identified PDZ domains in over 50 proteins. Like SH2 and SH3 domains, the PDZ domains mediate specific protein-protein interactions, whose specificities appear to be dictated by the primary structure of the PDZ domain as well as its binding target. Using recombinant fusion proteins and a blot overlay assay, we show that a single copy of the PDZ domain in human erythrocyte p55 binds to the carboxyl terminus of the cytoplasmic domain of human erythroid glycophorin C. Deletion mutagenesis of 21 amino acids at the amino terminus of the p55 PDZ domain completely abrogates its binding activity for glycophorin C. Using an alanine scan and surface plasmon resonance technique, we identify residues in the cytoplasmic domain of glycophorin C that are critical for its interaction with the PDZ domain. The recognition specificity of the p55 PDZ domain appears to be unique, since the three PDZ domains of hDlg (human lymphocyte homologue of the Drosophila discs large tumor suppressor) do not bind the cytoplasmic domain of glycophorin C. Taken together with our previous studies, these results complete the identification of interacting domains in the ternary complex between p55, glycophorin C, and protein 4.1. Implications of these findings are discussed in terms of binding specificity and the regulation of cytoskeleton-membrane interactions.

Amino Acid Sequence↗

PubMed1999

Guiding a docking mode by phage display: selection of correlated mutations at the staphylokinase-plasmin interface.

During co-evolution of interacting proteins, functionally disruptive mutations on one side of the interface may be compensated by local amino acid changes on the other to restore binding affinity. This information can be useful for geometry-based docking approaches by reducing the translational and rotational space available to the proteins. Here, we demonstrate that correlated mutations at a protein-protein interface can be rapidly identified by selecting a phage-displayed library of a randomly mutated component of the complex for complementation of mutations that decreased binding in the interacting partner. This approach was used to deduce the binding mode of staphylokinase (Sak), a 15.5 kDa "indirect" plasminogen activator on microplasmin (microPli), the 28 kDa serine protease domain of plasmin. Biopanning indicated that residues Arg94 and Gly174 in microPli are located in close proximity to Glu75 and the Glu88:Ile128 pair in Sak, respectively. The coupled mutations Glu94<-->Lys75 reversed and Gly174<-->Lys88:Val128 introduced a salt bridge, whereby the binding affinities (with coupling energies of 1.8 to 2.3 kcal mol-1, respectively) and the plasminogen activation ability of the mutated complexes were partially restored. These findings suggested a unique docking mode of Sak at the western rim of the active-site cleft of microPli, that is in agreement with the structure of the Sak-microPli complex as recently derived by other methods.

Amino Acid Substitution↗

PubMed2005

The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.

The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.

Animals↗

PubMed2002

An alternative accident prediction model for highway-rail interfaces.

Safety levels at highway/rail interfaces continue to be of major concern despite an ever-increasing focus on improved design and appurtenance application practices. Despite the encouraging trend towards improved safety, accident frequencies remain high, many of which result in fatalities. More than half of these accidents occur at public crossings, where active warning devices (i.e. gates, lights, bells, etc.) are in place and functioning properly. This phenomenon speaks directly to the need to re-examine both safety evaluation (i.e. accident prediction) methods and design practices at highway-rail crossings. With respect to earlier developed accident prediction methods, the Peabody Dimmick Formula, the New Hampshire Index and the National Cooperative Highway Research Program (NCHRP) Hazard Index, all lack descriptive capabilities due to their limited number of explanatory variables. Further, each has unique limitations that are detailed in this paper. The US Department of Transportation's (USDOT) Accident Prediction Formula, which is most widely, also has limitations related to the complexity of the three-stage formula and its decline in accident prediction model accuracy over time. This investigation resulted in the development of an alternate highway-rail crossing accident prediction model, using negative binomial regression that shows great promise. The benefit to be gained through the application of this alternate model is (1) a greatly simplified, one-step estimation process; (2) comparable supporting data requirements and (3) interpretation of both the magnitude and direction of the effect of the factors found to significantly influence highway-rail crossing accident frequencies.

Accidents, Traffic↗

PubMed2003

Spiral magnetic resonance coronary angiography with rapid real-time localization.

A spiral high-resolution coronary artery imaging sequence (SH) interfaced with real-time localization system (RT) has been developed. A clinical study of 40 patients suspected of coronary artery disease (CAD) was conducted. Segmented k-space acquisition techniques have dominated magnetic resonance coronary angiography (MRCA) over the last decade. Although a recent multicenter trial using this technique demonstrated encouraging results, the technique was hampered by low specificity. Spiral k-space acquisition had demonstrated several advantages for MRCA. Therefore, a first clinical trial implementing spiral high-resolution coronary imaging sequence with real-time localization (SH-RT) was performed.A clinical study of 40 patients suspected of CAD undergoing X-ray angiography was conducted to analyze the clinical reliability of this novel imaging system. The SH-RT had been designed to exploit the unique capability of two imaging sequences. The RT allowed a rapid localization of the coronary arteries. Then SH achieved multislice acquisition during a short breath-hold with submillimeter resolution. The MRCA data were analyzed for scan time, anatomic coverage, image quality, and accuracy in detecting CAD. In 40 subjects, SH achieved 0.7 to 0.9 mm resolution with 14-heartbeat breath-holds. Excellent or good image quality was achieved in 78% (263/337) of the coronary segments. Blinded consensus reading among three observers generated sensitivity of 76% and specificity of 91% in the detection of CAD compared with X-ray angiography. The MRCA imaging sequence implementing a novel spiral k-space acquisition technique enabled rapid and reliable imaging of the CAD in submillimeter resolution with short breath-holds.

Adult↗

PubMed2005

Depth profiling of peptide films with TOF-SIMS and a C60 probe.

A buckminsterfullerene ion source is employed to characterize peptide-doped trehalose thin films. The experiments are designed to utilize the unique sputtering properties of cluster ion beams for molecular depth profiling. The results show that trehalose films with high uniformity can be prepared on Si by a spin-coating technique. Bombardment of the film with C60+ results in high quality time-of-flight secondary ion mass spectrometry spectra, even during ion doses of up to 3 x 10(14) ions/cm2. This result is in contrast to atomic bombardment experiments in which the dose of incident ions must be kept below 10(12) ions/cm2 so as to retain mass spectral information. Moreover, since the films are of uniform thickness, it is possible to depth-profile through the film and into the Si substrate. This experimental protocol allows the yield of trehalose molecular equivalents and the degree of interface mixing to be evaluated in detail. When doped with a variety of small peptides up to a molecular weight of m/z 500, we find that the peptide molecular ion intensity remains stable under continuous C60+ bombardment, although some decrease in intensity is observed. The results are interpreted in terms of a model whereby the high trehalose yield and low damage depth of the C60 projectile combine to prevent damage accumulation. In general, the peptide-trehalose system provides a valuable model for evaluating the parameters that lead to effective 3-dimensional characterization of biomaterials.

Fullerenes↗

PubMed2003

The influence of the src-family kinases, Lck and Fyn, on T cell differentiation, survival and activation.

The src-family kinases p56lck (Lck) and p59fyn (Fyn) are expressed in T cells and are among the first signaling molecules to be activated downstream of the T cell receptor (TCR). Evidence is emerging that although closely related, these signaling molecules have discrete functions during development, maintenance and activation of peripheral T cells. For example, during thymopoiesis Lck is uniquely able to provide all the signals required for pre-TCRbeta selection, although Fyn can substitute for a subset of these. Positive selection of CD4 single-positive (SP) cells is also critically dependent on the expression of Lck but not Fyn, while differentiation of CD8 SP cells proceeds relatively efficiently in the absence of Lck. In naïve peripheral T cells either Lck or Fyn can transmit TCR-mediated survival signals, and yet only Lck is able to trigger TCR-mediated expansion signals under conditions of lymphopenia. Stimulation of naïve T cells by antigenic stimuli is also severely compromised in the absence of Lck, but more subtly impaired by the absence of Fyn. We discuss recent experiments addressing how these two src-kinase family members interface with downstream signaling pathways to regulate these diverse aspects of T cell behavior.

Animals↗

PubMed2005

Structural basis for activation of the thiamin diphosphate-dependent enzyme oxalyl-CoA decarboxylase by adenosine diphosphate.

Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate-dependent enzyme that plays an important role in the catabolism of the highly toxic compound oxalate. We have determined the crystal structure of the enzyme from Oxalobacter formigenes from a hemihedrally twinned crystal to 1.73 A resolution and characterized the steady-state kinetic behavior of the decarboxylase. The monomer of the tetrameric enzyme consists of three alpha/beta-type domains, commonly seen in this class of enzymes, and the thiamin diphosphate-binding site is located at the expected subunit-subunit interface between two of the domains with the cofactor bound in the conserved V-conformation. Although oxalyl-CoA decarboxylase is structurally homologous to acetohydroxyacid synthase, a molecule of ADP is bound in a region that is cognate to the FAD-binding site observed in acetohydroxyacid synthase and presumably fulfils a similar role in stabilizing the protein structure. This difference between the two enzymes may have physiological importance since oxalyl-CoA decarboxylation is an essential step in ATP generation in O. formigenes, and the decarboxylase activity is stimulated by exogenous ADP. Despite the significant degree of structural conservation between the two homologous enzymes and the similarity in catalytic mechanism to other thiamin diphosphate-dependent enzymes, the active site residues of oxalyl-CoA decarboxylase are unique. A suggestion for the reaction mechanism of the enzyme is presented.

Adenosine Diphosphate↗

PubMed2006

MASQOT-GUI: spot quality assessment for the two-channel microarray platform.

UNLABELLED: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated. AVAILABILITY: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at http://masqot-gui.sourceforge.net/

Computer Graphics↗