Low-lying excited states of proteins revealed from nonlinear pressure shifts in 1H and 15N NMR.
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Animals↗
Biomedical subjects
H Li
Publications and source records attributed to H Li.
Identification of peptides from brain and pituitary of Cpe(fat)/Cpe(fat) mice.
Cpe(fat)/Cpe(fat) mice have a naturally occurring point mutation within the carboxypeptidase E gene that inactivates this enzyme, leading to an accumulation of many neuroendocrine peptides containing C-terminal basic residues. These processing intermediates can be readily purified on an anhydrotrypsin affinity resin. Using MS to obtain molecular mass and partial sequence information, more than 100 peptides have been identified. These peptides represent fragments of 16 known secretory pathway proteins, including proenkephalin, proopiomelanocortin, protachykinins A and B, chromogranin A and B, and secretogranin II. Many of the identified peptides represent previously uncharacterized fragments of the precursors. For example, 12 of the 13 chromogranin B-derived peptides found in the present study have not been previously reported. Of these 13 chromogranin B-derived peptides, only five contain consensus cleavage sites for prohormone convertases at both the C and N termini. Two distinct chromogranin B-derived peptides result from cleavage at Trp-Trp bonds, a site not typically associated with neuropeptide processing. An RIA was used to confirm that one of these peptides, designated WE-15, exists in wild-type mouse brain, thus validating the approach to identify peptides in Cpe(fat)/Cpe(fat) mice. These "orphan" peptides are candidate ligands for orphan G protein-coupled receptors. In addition, the general technique of using affinity chromatography to isolate endogenous substrates from a mutant organism lacking an enzyme should be applicable to a wide range of enzyme-substrate systems.
Amino Acid Sequence↗
Cluster-Rasch models for microarray gene expression data.
BACKGROUND: We propose two different formulations of the Rasch statistical models to the problem of relating gene expression profiles to the phenotypes. One formulation allows us to investigate whether a cluster of genes with similar expression profiles is related to the observed phenotypes; this model can also be used for future prediction. The other formulation provides an alternative way of identifying genes that are over- or underexpressed from their expression levels in tissue or cell samples of a given tissue or cell type. RESULTS: We illustrate the methods on available datasets of a classification of acute leukemias and of 60 cancer cell lines. For tumor classification, the results are comparable to those previously obtained. For the cancer cell lines dataset, we found four clusters of genes that are related to drug response for many of the 90 drugs that we considered. In addition, for each type of cell line, we identified genes that are over- or underexpressed relative to other genes. CONCLUSIONS: The cluster-Rasch model provides a probabilistic model for describing gene expression patterns across samples and can be used to relate gene expression profiles to phenotypes.
Acute Disease↗
Patterns of engraftment in different strains of immunodeficient mice reconstituted with human peripheral blood lymphocytes.
BACKGROUND: Models of immunodeficient mice reconstituted with a competent human immune system would represent an invaluable tool for the study of transplantation immunobiology allergy, autoimmunity, and infectious diseases. Severe combined immune deficiency (scid) mice can be successfully reconstituted with human peripheral blood lymphocytes (PBLs), but rates and levels of engraftment are poor. New strains of mice with diverse immunodeficiencies have been recently characterized or developed, which might prove to be advantageous for in vivo studies of human immune reactivity. METHODS: We have compared rates and patterns of human PBL engraftment in four available immunodeficient murine strains; scid-beige, nonobese diabetic (NOD)-scid, NOD-scid-beta2 m- and rag-. T- and B-lymphocyte engraftment, phenotype of engrafted cells, and occurrence of graft-versus-host disease (GVHD) were studied and compared. RESULTS: Successful engraftment of human PBL was readily obtained in the majority of scid-beige, NOD-scid, and NOD-scid-beta2 m- with a single i.p. administration of human PBLs, whereas it was seldom achieved in rag- animals. Human Ig levels were accordingly remarkably low in rag- recipients but, interestingly also in NOD-scid-beta2 m- mice. Engraftment was readily observed not only in peripheral blood but also in spleen and bone marrow of successfully reconstituted animals. Phenotypic analysis of engrafted human cells showed preserved CD4/CD8 ratios and a clear skewing toward an activated phenotype. GVHD was invariably observed in successfully reconstituted animals. CONCLUSIONS: Our data indicate that a high rate of reconstitution with human lymphocytes can be achieved in scid-beige, NOD-scid, and NOD-scid-beta2 m- mice. Human Ig are produced at high levels, except in NOD-scid-beta2 m-, including xenoreactive natural antibodies. Scid-beige and NOD-scid appear therefore better suited than NOD-scid-beta2 m- or rag- for analysis of human immunoreactivity in vivo. An important caveat is the invariable occurrence of GVHD that precludes long-term studies in this model system.
Animals↗
Clinical and molecular characterization of vancomycin-resistant Enterococcus faecium strains during establishment of endemicity.
To characterize the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREF) in Tennessee, VREF isolates that were recovered from patients during a 3-year period at a tertiary care center and throughout the state were typed by means of pulsed-field gel electrophoresis. Clinical characteristics and outcomes of patients colonized or infected with different strain types were also examined. A total of 34 different strain types were identified. A single VREF strain (type O) predominated (63 [61%] of 103 single-patient isolates (i.e., 1 isolate per patient) obtained from 7 different health care institutions). There were no significant differences between patients harboring type O strains and those harboring non-type O strains (P> or =.05). The rate of recovery of type O subtypes and strains other than type O increased over the 3-year study period. Establishment of VREF endemicity was initially characterized by clonal spread of type O strains. Subsequently, polyclonal dissemination may have been due to microevolutionary changes among type O strains.
Anti-Bacterial Agents↗
Modeling competitive cation exchange of aromatic amines in water-saturated soils.
Competitive association to several components of soil through ion exchange processes influences the fate of organic cations in the environment. To examine these processes, the distributions of aniline and 1-aminonaphthalene between aqueous 5 mM CaCl2 solutions and three different Indiana soils were evaluated. Solute ratios (Sr) of aniline to 1-aminonaphthalene of 0.4-4.7 were employed, and the soil solutions ranged in pH from 2.7 to 7.5, with all measurements made 24 h after the introduction of the chemicals to the soils. Two previously proposed equilibrium models--the two-site (TS) and distributed parameter (DP) models--were modified to predict competition. These models assume instantaneous equilibrium of the following reversible processes: (i) acid dissociation of the protonated organic base (BHaq+) in the aqueous phase; (ii) ion exchange on the soil between the protonated organic base and inorganic divalent cations (Daq2+ = Caaq2+ + Mgaq2+); and (iii) partitioning of the nonionic species of aniline (Baq) to soil organic carbon. The TS model is a general mass action model that does not take into consideration cation exchange site heterogeneity, whereas the DP model considers association constants to these sites to be distributed in a log-normal fashion. To describe competition for cation exchange sites within the DP model, it was necessary to add a correlation coefficient (rho) that relates the ion-exchange association constant (KBH) probability density distribution functions of the two compounds. The value of rho is characteristic of each soil. Results indicate that competition has a greater effect at low pH values, where ion exchange is the predominant process. For all cases, these models capture the general trends in the soil-water distribution data of both amines. The DP model also captures the nonlinearity of the 1-aminonaphthalene isotherms at low pH while at the same time capturing the nearly linear isotherms of aniline as a competing organic base.
1-Naphthylamine↗
Structural features of nonpeptide prenyl pyrophosphates that determine their antigenicity for human gamma delta T cells.
Human Vgamma2Vdelta2(+) T cells proliferate in vivo during many microbial infections. We have found that Vgamma2Vdelta2(+) T cells recognize nonpeptide prenyl pyrophosphates and alkylamines. We now have defined structural features that determine the antigenicity of prenyl pyrophosphates by testing synthetic analogs for bioactivity. We find that the carbon chain closest to the pyrophosphate moiety plays the major role in determining bioactivity. Changes in this area, such as the loss of a double bond, abrogated bioactivity. The loss of a phosphate from the pyrophosphate moiety also decreased antigenicity 100- to 200-fold. However, nucleotide monophosphates could be added with minimal changes in bioactivity. Longer prenyl pyrophosphates also retained bioactivity. Despite differences in CDR3 sequence, Vgamma2Vdelta2(+) clones and a transfectant responded similarly. Ag docking into a Vgamma2Vdelta2 TCR model reveals a potential binding site in germline regions of the Vgamma2Jgamma1.2 CDR3 and Vdelta2 CDR2 loops. Thus, Vgamma2Vdelta2(+) T cells recognize a core carbon chain and pyrophosphate moiety. This recognition is relatively unaffected by additions at distal positions to the core Ag unit.
Adult↗
Direct synthesis of beta-mannans. A hexameric [-->3)-beta-D-Man-(1](3) subunit of the antigenic polysaccharides from Leptospira biflexa and the octameric (1-->2)-linked beta-D-mannan of the Candida albicans phospholipomannan. X-ray crystal structure of a protected tetramer.
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Antigens, Bacterial↗
Lipopolysaccharide-induced switch between retinoid receptor (RXR) alpha and glucocorticoid attenuated response gene (GARG)-16 messenger RNAs in cultured rat microglia.
Glucocorticoid-attenuated response genes (GARG) belong to a recently described family of genes responsive to the action of dexamethasone. Full-length cDNA of one member of this family, GARG16, has been cloned from rat microglia and regulation of its mRNA expression has been studied. Moreover, regulation of retinoid/retinoic acid activated transcription factor (RXR/RAR) mRNAs in mixed astrocyte and in purified microglia cultures has been investigated. RARbeta mRNA was undetectable in microglia by RT-PCR, whereas clearly present in the mixed cultures. RXRalpha, RARgamma, and GARG16 mRNAs were found in both culture systems. RXRalpha mRNA was strongly expressed in control microglia but rapidly declined upon treatment with LPS. Conversely, GARG16 mRNA was almost untraceable in control microglia but rapidly increased by LPS. Time-course studies revealed an oscillating behavior of expression of both mRNAs during the first 6 hr, which receded to control levels (RXRalpha high, GARG16 low) at 72 hr of LPS-treatment. Additionally, p38 MAPK and SEK phosphorylations peaked at 1 hr followed by steady declines, whereas MEK and c-Jun showed double peaks at 1+4 hr and 1+6 hr, respectively, before subsiding to control levels. This behavior was not observed in comparative studies with TNF-alpha, interleukin-10 (IL-10), or interferon-gamma inducible protein 10 (IP-10). Finally, inhibitors of p38 MAPK, p42/p44 ERK, and PKCalpha as well as the use of dexamethasone revealed major influences of the p38 MAPK-c-Jun-AP-1 signaling pathway on RXRalpha and GARG16 mRNA expressions. The counter regulatory control of GARG16 and RXRalpha mRNA expression is believed to be an example of a fine-tuned cellular mechanism to react to inflammatory stimuli.
Animals↗
Apoptosis induction in cancer cells by a novel analogue of 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalenecarboxylic acid lacking retinoid receptor transcriptional activation activity.
The retinoid 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalenecarboxylic acid (AHPN) is reported to have anticancer activity in vivo. Induction of cell cycle arrest and apoptosis in cancer cell lines refractory to standard retinoids suggests a retinoid-independent mechanism of action for AHPN. Conformational studies suggested that binding of AHPN does not induce an unusual conformation in retinoic acid receptor (RAR) gamma. The 3-chloro AHPN analogue MM11453 inhibited the growth of both retinoid-resistant (HL-60R leukemia, MDA-MB-231 breast, and H292 lung) and retinoid-sensitive (MCF-7 breast, LNCaP prostate, and H460 lung) cancer cell lines by inducing apoptosis at similar concentrations. Before apoptosis, MM11453 induced transcription factor TR3 expression and loss of mitochondrial membrane potential characteristic of apoptosis. MM11453 lacked the ability to significantly activate RARs and retinoid X receptor alpha to initiate (TREpal)(2)-tk-CAT reporter transcription. These results, differential proteolysis-sensitivity assays, and glutathione S-transferase-pulldown experiments demonstrate that, unlike AHPN or the natural or standard synthetic retinoids, MM11453 does not behave as a RAR or retinoid X receptor alpha transcriptional agonist. These studies strongly suggest that AHPN exerts its cell cycle arrest and apoptotic activity by a signaling pathway independent of retinoid receptor activation.
Antineoplastic Agents↗
Structural and functional study of reconstituted peripheral benzodiazepine receptor.
Recombinant mouse 18 kDa peripheral-type benzodiazepine receptor (PBR) protein was overexpressed in Escherichia coli and isolated using a His. Bind metal chelation resin. Recombinant PBR protein was purified with sodium dodecyl sulfate and reincorporated into liposomes using Bio-Beads SM2 as a detergent removing agent. Negative staining of the reconstituted PBR samples, examined by electron microscopy, showed the formation of proteoliposomes. Freeze-fracture of these proteoliposomes revealed the presence of transmembranous particles of an average size of 3.5 +/- 0.25 nm, consistent with the presence of a monomeric form of the recombinant PBR protein. The reconstituted protein exhibited the ability to bind both the PBR drug ligand isoquinoline carboxamide PK 11195 and cholesterol with nanomolar affinities. These data suggest that a PBR monomer is the minimal functional unit, binding drug ligands and cholesterol.
Animals↗
Improved capillary electrophoresis conditions for the separation of kinase substrates by the laser micropipet system.
Phosphorylated and nonphosphorylated forms of peptide substrates for protein kinase C (PKC) and calcium-calmodulin activated kinase II (CamKII) were separated by capillary zone electrophoresis. Electrophoresis of the peptide substrates and products in biologic buffer solutions in uncoated capillaries yielded asymmetric analyte peaks with substantial peak tailing. Some of the peptides also exhibited broad peaks with unstable migration times. To improve the electrophoretic separation of the peptides, several strategies were implemented: extensive washing of the capillary with a base, adding betaine to the electrophoretic buffer, and coating the capillaries with polydimethylacrylamide (PDMA). Prolonged rinsing of the capillaries with a base substantially improved the migration time reproducibility and decreased peak tailing. Addition of betaine to the electrophoretic buffer enhanced both the migration time stability as well as the theoretical plate numbers of the peaks. Finally PDMA-coated capillaries brought about significant improvements in the resolving power of the separations. These modifications all utilized an electrophoretic buffer that was compatible with a living biologic cell. Consequently they should be adaptable for the new capillary electrophoresis-based methods to measure kinase activation in single cells.
Amino Acid Sequence↗
Conversion of phospholamban into a soluble pentameric helical bundle.
Although membrane proteins and soluble proteins may achieve their final folded states through different pathways, it has been suggested that the packing inside a membrane protein could maintain a similar fold if the lipid-exposed surface were redesigned for solubility in an aqueous environment. To test this idea, the surface of the transmembrane domain of phospholamban (PLB), a protein that forms a stable helical homopentamer within the sarcoplasmic reticulum membrane, has been redesigned by replacing its lipid-exposed hydrophobic residues with charged and polar residues. CD spectra indicate that the full-length soluble PLB is highly alpha-helical. Small-angle X-ray scattering and multiangle laser light scattering experiments reveal that this soluble variant of PLB associates as a pentamer, preserving the oligomeric state of the natural protein. Mutations that destabilize native PLB also disrupt the pentamer. However, NMR experiments suggest that the redesigned protein exhibits molten globule-like properties, possibly because the redesign of the surface of this membrane protein may have altered some native contacts at the core of the protein or possibly because the core is not rigidly packed in wild-type PLB. Nonetheless, our success in converting the membrane protein PLB into a specific soluble helical pentamer indicates that the interior of a membrane protein contains at least some of the determinants necessary to dictate folding in an aqueous environment. The design we successfully used was based on one of the two models in the literature; the alternative design did not give stable, soluble pentamers. This suggests that surface redesign can be employed in gaining insights into the structures of membrane proteins.
Amino Acid Sequence↗
Analysis of indications for surgical closure of subarterial ventricular septal defect without associated aortic cusp prolapse and aortic regurgitation.
Subarterial ventricular septal defect (VSD) is relatively common in Orientals. We reviewed the outcome of 214 patients (137 males) who were followed for 8.6 +/- 5.2 years (range 0.1 to 24.3) and addressed the issue regarding the necessity and optimum timing of closing subarterial defects before development of aortic valve deformities. Demographic data, transthoracic and transesophageal echocardiographic findings, cardiac catheterization results, and operative findings were reviewed. Kaplan-Meier actuarial analysis was performed to assess the development of aortic valve complications over time. Seventy-five patients with heart failure and pulmonary hypertension underwent surgical closure of VSD at the age of 2.4 +/- 2.9 years. No patient had aortic cusp prolapse before operation and none developed aortic cusp prolapse or aortic regurgitation (AR) on follow-up. In contrast, of the 139 asymptomatic patients managed conservatively, 102 (73%) developed aortic cusp prolapse, 78% of whom (80 of 102) developed AR. The prevalence of aortic cusp prolapse and AR at 1, 5, 10, and 15 years old was 8%, 30%, 64%, and 83%, and 3%, 24%, 45%, and 64%, respectively. Significant prolapse or AR prompted surgical closure of VSD with (n = 22) or without (n = 26) valvoplasty in 48 of 102 patients (47%). The size of the VSD was significantly larger in patients with heart failure (9.6 +/- 3.3 mm) or aortic cusp prolapse (11.7 +/- 4.1 mm) compared with those without heart failure (4.5 +/- 1.4 mm, p <0.001). All patients with aortic cusp prolapse and all but 1 with heart failure had a defect size of > or =5 mm. In conclusion, subarterial VSD of > or =5 mm should be closed as early as possible to prevent development of aortic cusp prolapse and AR. Asymptomatic patients with small defects <5 mm could be managed conservatively.
Adolescent↗
Pertussis toxin activates tyrosine kinase signaling cascade in myelomonocytic cells: a mechanism for cell adhesion.
Pertussis toxin (PTX) has recently been shown to specifically bind to CD14 to promote myelomonocytic cell adhesion to serum. The present study investigated the signaling mechanisms responsible for PTX-induced differentiated U937 cell adhesion. PTX-induced myelomonocytic cell adhesion was blocked by genistein or tyrphostin-47 (two protein tyrosine kinase inhibitors), LY294002 (a phosphatidylinositol 3-kinase (PI3K) inhibitor), or PD098059 (a mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) kinase (MEK) inhibitor). PTX induced a rapid tyrosine phosphorylation of several discrete cytoplasmic proteins, which could be inhibited by genistein or tyrphostin 47. In addition, PTX induced phosphorylation of Akt and of ERK2, which could be completely blocked by LY294002 and PD098059, respectively, and by genistein or tyrphostin 47 as well. All of these PTX-induced signaling events could be reproduced using purified PTX B-oligomer (PTX-B) alone. Our data show that PTX can activate tyrosine kinase signaling cascade, including the downstream PI3K and ERK/MAPK pathways, in myelomonocytic cells to induce cell adhesion to serum.
Cell Adhesion↗
20 A Cd4In16S35(14-) supertetrahedral T4 clusters as building units in decorated cristobalite frameworks.
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Journal Article↗
Release of hydrogen chloride from combustibles in municipal solid waste.
Study of the inorganic chlorides in municipal solid waste (MSW) shows that the main source of inorganic chlorides in MSW is food. The main organic source of HCl emission from MSW is plastic. But wood, textiles, and food also produce a large amount of HCl when they are combusted. Each combustible shows a different HCl releasing temperature range. At 973 K, there are 30-70% of the total chlorine left in the char of each combustibles in MSW.
Air Pollutants↗
Anti-CTLA-4 antibody treatment triggers determinant spreading and enhances murine myasthenia gravis.
CTLA-4 appears to be a negative regulator of T cell activation and is implicated in T cell-mediated autoimmune diseases. Experimental autoimmune myasthenia gravis (EAMG), induced by immunization of C57BL/6 mice with acetylcholine receptor (AChR) in adjuvant, is an autoantibody-mediated disease model for human myasthenia gravis (MG). The production of anti-AChR Abs in MG and EAMG is T cell dependent. In the present study, we demonstrate that anti-CTLA-4 Ab treatment enhances T cell responses to AChR, increases anti-AChR Ab production, and provokes a rapid onset and severe EAMG. To address possible mechanisms underlying the enhanced autoreactive T cell responses after anti-CTLA-4 Ab treatment, mice were immunized with the immunodominant peptide alpha(146-162) representing an extracellular sequence of the ACHR: Anti-CTLA-4 Ab, but not control Ab, treatment subsequent to peptide immunization results in clinical EAMG with diversification of the autoantibody repertoire as well as enhanced T cell proliferation against not only the immunizing alpha(146-162) peptide, but also against other subdominant epitopes. Thus, treatment with anti-CTLA-4 Ab appears to induce determinant spreading, diversify the autoantibody repertoire, and enhance B cell-mediated autoimmune disease in this murine model of MG.
Abatacept↗