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PubMed2002

Compartmentalized Eph receptor and ephrin expression in the thymus.

The maturation of T cells is an intricate process involving the interaction of developing thymocytes with discrete microenvironments within the thymus. Numerous studies have indicated that distinct thymic compartments provide signals required for each stage of thymocyte maturation. In this study we performed a comprehensive analysis of the expression patterns of Eph-A receptors and ephrins-A in the thymus using in situ hybridization and reverse transcription-polymerase chain reaction, and show that expression of these molecules is highly compartmentalized. Based on these expression patterns and the known mechanisms of action of Eph receptor/ephrin interactions in other organs, these data suggest that differential Eph receptor expression on discrete subsets of thymic stromal cells may be important in establishing compartment boundaries and preventing intermingling of stromal cell subtypes. Further, together with chemotactic signals such as those provided by chemokines, regulated Eph receptor/ephrin expression on thymocytes may play a role in thymocyte migration.

Animals↗
PubMed2002

Functional proteomics; current achievements.

This review presents the current improvements in functional proteomic strategies and their research applications. Proteomics has emerged as an indispensable methodology for large-scale and high-throughput protein analyses in the post-genome era. Functional proteomics, the comprehensive analysis of proteins with special attention to their functions, is a powerful and useful approach for investigations in the life and medical sciences. Various methods have been developed for this purpose, expanding the field further. This important technology will not only provide a wealth of information on proteins, but also contribute synergistically to the understanding of life with other systematic technologies such as gene chips.

Protein Processing, Post-Translational↗
PubMed1995

Prediction of thoracic and lumbar vertebral body compressive strength: correlations with bone mineral density and vertebral region.

The bone density of thoracolumbar vertebral columns (T1 to L5) from 18 individuals was measured using quantitative computed tomography and dual energy x-ray absorptiometry. Three hundred six isolated vertebral bodies were tested in a materials test device to determine their compressive strength. Between T1 and L5 the mean segmental increase in bone mineral content was 0.3 g, while the corresponding mean decrease in trabecular density was 4.7 HU. Midvertebral body cross-sectional area increased by an average of 46 mm2 per segment and the mean segmental increase in compressive strength was 0.17 kN. Compressive strength was significantly correlated with bone mineral density measured with dual energy x-ray absorptiometry (r = 0.86). Vertebral trabecular density samples measured with quantitative computed tomography were poorly correlated with compressive strength (r = 0.28); however, this was improved when the trabecular density was multiplied by the midvertebral body cross-sectional area (r = 0.83). This study provides information concerning the relationships between density and mechanical properties of all thoracic and lumbar vertebral bodies across a wide age range. While the load-bearing capacity of the vertebral bodies is largely dependent on their geometry and bone density, this relationship has been only extensively tested for the lumbar spine. This study extends these observations over the lumbar and thoracic regions to provide a comprehensive analysis of the strength characteristics of each vertebral body. This is particularly important given the paucity of data on the thoracic spine where age-related vertebral fractures predominate. These data provide a basis for the development of models to predict the potential for thoracolumbar fractures in the elderly vertebral column.

Absorptiometry, Photon↗
PubMed1989

How does gender influence age at first hospitalization for schizophrenia? A transnational case register study.

Numerous studies have reported a lower mean age at first hospitalization for schizophrenia in males than in females. For this finding not only a gender difference in age at first onset of schizophrenia, but also other factors can be responsible. With the aim of providing a comprehensive analysis of gender differences in onset, symptomatology and course of schizophrenia, we started by testing the hypothesis postulating a gender difference in mean age at first hospitalization. By using the Danish and the Mannheim psychiatric case registers we analysed all hospital admissions for schizophrenia and related diagnoses and all previous admissions for other diagnoses of the Danish population in 1976 and those of the inhabitants of the German city of Mannheim in the period of 1978-80. Artefacts were controlled for systematically. The impact of intervening variables such as selection factors as well as the influence of gender on the ascription of a diagnosis of schizophrenia for the first time were assessed. We found a mean difference of 5 to 6 years in age at first hospitalization between males and females in both countries when a broad definition of the diagnosis was used and of 4 to 5 years when a restrictive definition was applied. The higher mean age at first hospitalization among females is not attributable to artefacts, diagnostic procedures or to any essential extent to gender differences in help-seeking behaviour or occupational status. When a distinction was made between 'single' and 'married', the significant difference in age at first hospitalization between the sexes disappeared in singles. With case register data and without knowing the chronological order of marriage and onset of the disease, it remains an open question whether this finding can be explained by purely correlative associations between sex, marital status and age of onset or by causal effects.

Adolescent↗
PubMed1988

Health technology development in Japan.

This article provides a comprehensive analysis of the social, cultural and economic factors which have led to the present pattern of technology utilization in Japan. It is divided into five sections. The first provides the historical framework; the second, an overview of the health care delivery context and its economic incentive structure; the third, an analysis of the various contenders involved in the process of resource allocation; the fourth, a description of the technology areas which have been emphasized in Japan; and the fifth, an examination of future issues.

Communication↗
PubMed1994

Changing epidemiology of human salmonellosis in Hong Kong, 1982-93.

A comprehensive analysis of the epidemiology of salmonellosis in a major hospital in Hong Kong from 1982-93 is reported. The trend of salmonella isolations over the past 12 years and changes in the occurrence of individual serotypes are delineated. A total of 5328 isolates were analyzed. Groups B (Salmonella typhimurium and S. derby) and E (S. anatum) were the commonest serogroups isolated from the intestinal tract in all age groups. A significant increase in the isolation of group D salmonellae has been observed since 1989. This is accounted for by a substantial rise in S. enteritidis isolation as seen in Western countries, despite a concomitant decrease of S. typhi. The extraintestinal isolation index (EII) is proposed as an index of the virulence potential of individual serotypes and serogroups. Group D salmonella was found to be the most invasive serogroup. While group D was the predominant serogroup isolated from extraintestinal sites in patients older than 1 year, group B serotypes (especially S. typhimurium) were more frequently seen in infants younger than 12 months.

Adolescent↗
PubMed2002

Transcript abundance supercedes editing efficiency as a factor in developmental variation of chloroplast gene expression.

In maize plastids, transcripts are known to be modified at 27 C-to-U RNA editing sites, affecting the expression-of 15 different genes. The relative contribution of editing efficiency versus transcript abundance in regulation of chloroplast gene expression has previously been analyzed for only a few genes. We undertook a comprehensive analysis of the editing efficiency of each of the 27 maize editing sites in 10 different maize tissues, which contain a range of plastid types including chloroplasts, etioplasts, and amyloplasts. Using a reproducible poisoned primer extension assay, we detected variation between RNA editing extent of different sites in the same transcript in the same tissue, and between the same site in different tissues. The most striking editing deficiency is in an editing site in ndhB that is edited at only 8% and 1% in roots and callus plastids respectively, whereas green leaf chloroplasts edit this site at 100%. Editing efficiencies of some sites are not affected by the developmental stages we examined and are always edited close to 80-100%. The relative amounts of transcripts of each of the 10 genes that exhibited variable editing extents were determined by real-time PCR. Seven genes exhibited over 100 times lower transcript abundance in either roots or tissue-cultured cells relative to green leaf tissue. The quantitative analysis indicates that a particular editing site can be efficiently edited over a large range of transcript abundance, resulting in no general correlation of transcript abundance and editing extent. The independent variation of editing efficiency of different sites within the same transcript fits with a model that postulates individual trans-acting factors specific to each editing site. Because tissues where editing efficiency at certain sites is low invariably also exhibited greatly decreased abundance of the transcripts carrying those sites, decrease in the amounts of particular RNAs rather than a lack of editing is predicted to have the most significant impact on gene expression under steady-state conditions. Our data is consistent with the hypothesis that the role of editing in angiosperm plastids is to correct otherwise detrimental mutations rather than to generate significant protein diversity.

Amino Acid Sequence↗
PubMed2002

Treatment non-response in OCD: methodological issues and operational definitions.

While controlled trials with SRIs have demonstrated a selective efficacy in obsessive-compulsive disorder (OCD), up to 40-60% of patients do not have a satisfactory outcome. Non-response to treatment in OCD is associated with serious social disability. There are a large number of non-responsive patients, and they are difficult to cluster due to ambiguities in the diagnostic criteria, possibility of subtypes, and a high rate of comorbidity. Moreover, the findings of current studies of so-called 'non-responsive' cases are currently non-generalizable because of the lack of an operational definition of non-response. The result has been that a cumulative body of data on a reasonably homogeneous sample of non-responders has not been developed. The aims of this paper are to clarify some of the obstacles in defining stages of response and levels of non-response and, through a comprehensive analysis, to propose a systematic nosology for this rather common condition. Better characterization of which patients respond and do not respond to various treatments will enable more accurate clustering of patients, and help facilitate multi-site data collection for future research trials.

Drug Resistance↗
PubMed2002

A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics.

One of the strategies of functional proteomics, research aiming to discover gene function at the protein level, is the comprehensive analysis of protein-protein interactions related to the functional linkage among proteins and analysis of functional cellular machinery to better understand the basis of cell functions. Here, we describe the direct nanoflow LC (DNLC) system, which is equipped with a fritless high-resolution electrospray interface column packed with 1-microm reversed-phase (RP) beads and a novel splitless nanoflow gradient elution system to operate the column. Using RP-DNLC at an extremely slow flow rate, <50 nL/min, combined with data-dependent collision-induced dissociation tandem MS (MS/MS) and computer-assisted retrieval of spectra, we identified approximately 100 protein components in a biological complex such as a premature mammalian ribosome pull-down from cultured cells when we used an epitope-tagged protein as bait. Because this analysis is most sensitive, requires approximately 0.2 microg of total protein, and is a fully automated 1-h process, we anticipated that it should be an excellent tool for analyzing a limited amount of functional multi-protein complexes in cells.

Amino Acid Sequence↗
PubMed2004

A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography.

Extensive prefractionation is now considered to be a necessary prerequisite for the comprehensive analysis of complex proteomes where the dynamic range of protein abundances can vary from approximately 10(6) for cells to approximately 10(10) for tissues such as blood. Here, we describe a high-resolution 2D protein separation system that uses a continuous free-flow electrophoresis (FFE) device to fractionate complex protein mixtures by solution-phase isoelectric focusing (IEF) into 96 well-defined pools, each separated by approximately 0.02-0.10 pH unit depending on the gradient created, followed by rapid (approximately 6 min per analysis) reversed-phase high-performance liquid chromatography (RP-HPLC) of each FFE pool. Fractionated proteins are readily visualized in a virtual 2D format using software that plots protein loci, pI in the first dimension and relative hydrophobicity (i.e., RP-HPLC retention time) in the second dimension. By coupling a diode-array detector in line with a multiwavelength fluorescence detector, separated proteins can be monitored in the RP-HPLC eluent by both UV absorbance and intrinsic fluorescence simultaneously from a single experiment. Triplicate analyses of standard proteins using a pH 3-10 gradient conducted over a 3-day period revealed a high system reproducibility with a SD of 0.57 (0.05 pH unit) within the FFE pools and 0.003 (0.18 s) for protein retention times in the second-dimension RP-HPLC step. In addition, we demonstrate that the FFE-IEF/RP-HPLC separation strategy can also be applied to complex mixtures of low molecular weight compounds such as peptides. With the facile ability to measure the pH of the isoelectric focused pools, peptide pI values can be estimated and used to qualify peptide identifications made using either MS/MS sequencing approaches or pI discriminated peptide mass fingerprinting. The calculated peak capacity of this 2D liquid-based FFE-IEF/RP-HPLC system is 6720.

Chromatography, High Pressure Liquid↗
PubMed2003

The characterization of protein post-translational modifications by mass spectrometry.

Most biological processes are regulated by post-translational modifications of proteins, and conditions that disrupt the regulation of such events can lead to disease. In the past decade, the identification and characterization of covalent modifications have been driven by advances in mass spectrometry. Here, we discuss current mass spectrometric and proteomic approaches for the identification of proteins and their covalent modifications, and we highlight high-throughput strategies for comprehensive analysis of cell proteomes.

Amino Acid Sequence↗
PubMed1994

Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions.

To characterize the role of water in protein-DNA interactions, we have studied the specificity of the EcoRI restriction endonuclease as a function of osmotic and hydrostatic pressure. The extent of cleavage by the enzyme at noncanonical ("star") sites is shown to depend uniquely upon the osmotic pressure in the reaction as controlled by the addition of a wide variety of neutral solutes. Alteration of cleavage specificity ("EcoRI* activity") is not uniformly correlated with any other colligative solvent property such as dielectric constant, viscosity, or water concentration. The application of hydrostatic pressure reverses the effects of osmotic pressure, restoring the natural selectivity of the enzyme for its canonical site GAATTC. This combination of observations provides compelling evidence that the site-specific recognition of canonical site DNA by EcoRI is mediated by discretely bound water molecules and that the release of these waters induces a fundamental change in the specificity of the interaction, leading to cleavage at alternative sites. This comprehensive analysis of solvent effects facilitates the unambiguous identification of structurally and functionally specific waters involved in macromolecular recognition events.

DNA↗
PubMed1994

Two-dimensional NMR characterization of the deoxymyoglobin heme pocket.

Traditionally, assigning the heme protein resonances has relied heavily on the comparison of spectra arising from protein reconstituted with specifically deuterated hemes and the native form. Such an approach can identify tentatively the broad, overlapping signals in the Fe(II) high-spin heme protein spectra. Although 2D NMR studies have reported alternative approaches to detect and assign paramagnetic signals, their effectiveness is limited primarily to Fe(III) low-spin systems and still depends upon isotopic labeling results to be definitive. For deoxymyoglobin, the reported 2D techniques have not produced any spin correlation maps. Nevertheless, our study demonstrates that the deoxymyoglobin spin correlations are indeed detectable and that a complete heme assignment, except for the meso protons, is achievable with only 2D NMR and saturation-transfer techniques. The 2D maps improve the spectral resolution dramatically and permit a comprehensive analysis of the deoxymyoglobin signals' temperature dependence, which supports the hypothesis that the electronic orbital ground state has contributions from both 5E and 5B2. The results also indicate a structural perturbation in the vicinity of the 2 vinyl group as the protein undergoes the transition from oxy- to deoxymyoglobin state and a significant contribution from zero field splitting. Moreover, saturation-transfer experiments show that NMR can observe directly oxygen binding kinetics.

Animals↗
PubMed2004

Characterization of peptides corresponding to the seven transmembrane domains of human adenosine A2a receptor.

Human adenosine A(2)a receptor is a member of the G-protein-coupled receptor (GPCR) superfamily of seven-helix transmembrane (TM) proteins. To test general models for membrane-protein folding and to identify specific features of folding and assembly for this representative member of an important and poorly understood class of proteins, we synthesized peptides corresponding to its seven TM domains. We assessed the ability of the peptides to insert into micelles and vesicles and measured secondary structure for each peptide in aqueous and membrane-mimetic environments. CD spectra indicate that each of the seven TM peptides form thermally stable, independent alpha-helical structures in both micelles and vesicles. The helical content of the peptides depends on the nature of the membrane-mimetic environment. Four of the peptides (TM3, TM4, TM5, and TM7) exhibit very high-helical structure, near the predicted maximum for their TM segments. The TM1 peptide also adopts relatively high alpha-helical structures. In contrast, two of peptides, TM2 and TM6, display low alpha helicity. Similarly, the ability of the peptides to insert into membrane-mimetic environments, assayed by intrinsic tryptophan fluorescence and fluorescence quenching, varied markedly. Most peptides exhibit higher alpha helicity in anionic sodium dodecyl sulfate than in neutral dodecyl-beta-D-maltoside micelles, and TM2 was disordered in zwiterionic DMPC but was alpha-helical in negatively charged DMPC/DMPG vesicles. These findings strongly suggest that electrostatic interactions between lipids and peptides control the insertion of the peptides and may be involved in membrane-protein-folding events. The measured helical content of these TM domains does not correlate with the predicted helicity based on amino acid sequence, pointing out that, while hydrophobic interactions can be a major determinant for folding of TM peptides, other factors, such as electrostatic interactions or helix-helix interactions, may play significant roles for specific TM domains. Our results represent a comprehensive analysis of helical propensities for a human GPCR and support models for membrane-protein folding in which interactions between TM domains are required for proper insertion and folding of some TM helix domains. The tendency of some peptides to self-associate, especially in aqueous environments, underscores the need to prevent improper interactions during folding and refolding of membrane proteins in vivo and in vitro.

Amino Acid Sequence↗
PubMed2005

Comprehensive identification of post-translational modifications of rat bone osteopontin by mass spectrometry.

Osteopontin (OPN) is a highly modified protein that is found in many tissues and has been associated with a variety of physiological and pathological processes. Bone OPN is a potent inhibitor of hydroxyapatite crystal formation and stimulates bone resorption by osteoclasts; these activities, as well as others, are dependent upon phosphorylation of the protein. We have used mass spectrometry (MS) to perform a comprehensive analysis of the post-translational modification of OPN purified from rat bone. Matrix-assisted laser desorption time-of-flight (MALDI-TOF) MS showed masses of 37.6 and 36.8 kDa before and after enzymatic dephosphorylation, respectively, corresponding to a content of approximately 10.4 phosphate groups. Using proteolytic digestion and tandem MS, we localized 29 sites of phosphorylation: S10, S11, S46, S47, T50, S60, S62, S65, S146, T154, S160, S164, S167, S193, S196, S203, S220, S223, S232, S241, S245, S257, S262, S267, S278, S290, S295, S296, and S297. In addition, Y150 was shown to be sulfated and T107, T110, T116, and T121 are O-glycosylated. No glycan was detected at the potential N-glycosylation site. Other modifications, including deamidation, oxidation, and carbamylation, are also present. A 36-amino acid sequence from residues 67-102 could not be analyzed in detail, even after sialidase treatment, presumably because of the presence of a large number of acidic residues. In comparison to the previously characterized cow milk isoform, rat bone OPN is sulfated and has an additional site of glycosylation, many different sites of phosphorylation, and a lower overall phosphate content.

Amino Acid Sequence↗
PubMed1998

Electrostatic effects in DNA bending by GCN4 mutants.

DNA architecture has been shown to be important for cellular processes such as activation of transcription, recombination, and replication. Many proteins reconfigure the shape of duplex DNA upon binding. Previous experiments have shown that some members of the eukaryotic bZIP family of DNA binding proteins appear to bend DNA, while others do not. We are exploring the role of electrostatic effects in DNA bending by bZIP proteins. The yeast bZIP transcription factor GCN4 does not induce DNA bending in vitro. Previously we substituted basic residues for three neutral amino acids in GCN4 to produce a GCN4 derivative that bends DNA by approximately 15 degrees. This result is consistent with a model of induced DNA bending wherein excess positive charge in proximity to one face of the double helix neutralizes local phosphate diester anions resulting in a laterally-asymmetric charge distribution along the DNA. Such an unbalanced charge distribution can result in collapse of the DNA toward the neutralized surface. We now present a more comprehensive analysis of electrostatic effects in DNA bending by GCN4 derivatives. It is shown that the direction and extent of DNA bending by these derivatives are a linear function of the charges of the amino acids adjacent to the basic domain of the protein. This relation holds over the charge range +6 (16 degrees bend toward the minor groove) to -6 (25 degrees bend toward the major groove).

Amino Acid Sequence↗
PubMed2000

Human mitochondrial DNA polymerase holoenzyme: reconstitution and characterization.

We have reconstituted the holoenzyme of the human mitochondrial DNA polymerase from cloned and overexpressed catalytic and accessory subunits. We have examined the polymerization activity of the catalytic subunit alone and of the holoenzyme to establish the function of the accessory subunit in this two subunit enzyme. The accessory subunit associates with the catalytic subunit with a dissociation constant of 35 +/- 16 nM as measured by the concentration dependence of its effect in stimulating maximal DNA binding and polymerization. At saturating concentrations, the accessory subunit contributes to every kinetic parameter examined to facilitate tighter binding of DNA and nucleotide and faster replication. The accessory protein makes the DNA binding 3.5-fold tighter (K(d) of 9.9 +/- 2.1 nM compared to 39 +/- 10 nM for the catalytic subunit alone) without significantly affecting the DNA dissociation rate (0.02 +/- 0.001 compared to 0.03 +/- 0.001 s(-)(1)). The ground-state nucleotide binding is improved from 4.7 +/- 2.0 to 0.78 +/- 0.065 microM, and the maximum DNA polymerization rate is increased from 8.7 +/- 1.1 to 45 +/- 1 s(-)(1) by the addition of the accessory protein. This leads to an increase in processivity from an estimated 290 +/- 46 to 2250 +/- 162. Although the accessory protein has been described as a "processivity factor" because of its effect on the ratio of rate constants defining processivity, this terminology falls short of adequately describing the profound effects of the small subunit on nucleotide-binding and incorporation catalyzed by the large subunit. By using the complete holoenzyme, we can now proceed with a comprehensive analysis of the structural and mechanistic determinants of enzyme specificity that govern toxicity of nucleoside analogues used in the treatment of viral infections such as AIDS.

Amino Acid Sequence↗
PubMed2002

A model to predict the adsorber thermal behavior during treatment of volatile organic compounds onto wet activated carbon.

A model for adsorption of volatile organic compounds (VOCs) onto a wet activated carbon bed was proposed in this study. This model accounts for temperature changes induced by the reversed and coupled mass-transfer processes of both organic species adsorption and water desorption. Indeed, it was experimentally pointed out that temperature rises, which result from the exothermal nature of the energetic interactions between the organic molecule and the activated carbon surface, are notably reduced when the adsorbent contains an initial moisture of approximately 10% in weight. Moreover, it was shown that water rate desorption was enhanced in the presence of organic vapor. This phenomenon may be explained by the displacement of sorbed water bythe organic molecules, owing to more intensive interactions with the activated carbon surface. The model proposed was elaborated from a previous comprehensive analysis of the diffusion mechanisms governing VOC adsorption at high concentrations onto a dry activated carbon bed. In a similar way, a theoretical approach was developed to model water desorption during drying of a wet activated carbon bed under pure flowing air. At last, a theoretical depiction of both competitive and reverse processes was outlined. The final model fits reasonably with experimental data relative to both breakthrough curves and thermal wave shape along the bed, even if local temperature change calculation may require some further improvement.

Adsorption↗