gebhart/patrepeval huggingface dataset:
Identification of subunit I as the cytochrome b558 component of the cytochrome d terminal oxidase complex of Escherichia coli. (1984)

The cytochrome d terminal oxidase complex was recently purified from Escherichia coli membranes (Miller, M. J., and Gennis , R. B. (1983) J. Biol. Chem. 258, 9159-1965). The complex contains two polypeptides, subunits I and II, as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and three spectroscopically defined cytochromes, b558 , a1, and d. A mutant that failed to oxidize N,N,N',N'-tetramethyl-p-phenylenediamine was obtained which was lacking this terminal oxidase complex and was shown to map at a locus called cyd on the E. coli genome. In this paper, localized mutagenesis was used to generate a series of mutants in the cytochrome d terminal oxidase. These mutants were isolated by a newly developed selection procedure based on their sensitivity to azide. Two classes of mutants which map to the cyd locus were obtained, cydA and cydB . The cydA phenotype included the lack of all three spectroscopically detectable cytochromes as well as the absence of both polypeptides, determined by immunological criteria. Strains manifesting the cydB phenotype lacked cytochromes a1 and d, but had a normal amount of cytochrome b558 . Immunological analysis showed that subunit I (57,000 daltons) was present in the membranes, but that subunit II (43,000 daltons) was missing. These data justify the conclusion that subunit I of this two-subunit complex can be identified as the cytochrome b558 component of the cytochrome d terminal oxidase complex.
An immunoregulatory function for the CD8 molecule. (1989)

The molecular details of immunoregulatory phenomena associated with CD8+ T lymphocytes have not been clearly elucidated. We tested the hypothesis that the cell surface glycoprotein CD8 is itself essential in mediating the inhibitory effects associated with CD8+ T cells. For this purpose we utilized a T-cell clonal pair, consisting of a human CD8+ T-cell clone and a specific CD8- phenocopy of this clone obtained via antisense RNA mutagenesis, to modulate allogeneic responses in vitro. Our findings indicate that the expression of the CD8 molecule by the inhibitory cells is essential for down-regulation of both allogeneic proliferation and generation of cytotoxicity in mixed lymphocyte cultures. These results define an immunomodulatory function for the CD8 molecule and provide insights into the molecular basis of immunosuppression.
Selective Protection and Functionalization of Morphine:  Synthesis and Opioid Receptor Binding Properties of 3-Amino-3-desoxymorphine Derivatives,1 (2000)

As part of an effort to identify novel opioid receptor interactive agents, we recently prepared a series of 8-(substituted)amino analogues of cyclazocine. We found the chiral 8-phenylamino (NHC(6)H(5)) cyclazocine derivative to have subnanomolar affinity for kappa opioid receptors and a 2-fold lower affinity for mu, opioid receptors. To determine if the benefits of (substituted)amino groups could be extended to the morphine core structure, we have made five novel 3-amino-3-desoxymorphine derivatives of general structure 5 where RR'N = H(2)N, CH(3)NH, (CH(3))(2)N, C(6)H(5)NH, and C(6)H(5)CH(2)NH. Relative to morphine, these derivatives had 38-273-fold, 11-41-fold, and 10-141-fold lower affinity for mu, delta, and kappa opioid receptors, respectively. Target compounds were made via Pd-catalyzed amination of a morphine 3-trifluoromethylsulfonate substrate where the 6-OH group was protected with a tert-butyldiphenylsilyl group. To make 6-tert-butyldiphenylsilyloxymorphine selectively, a new high-yield method was developed whereby morphine was bis-silylated using normal conditions followed by selective removal of the 3-tert-butyldiphenylsilyl group with catalytic tetrabutylammonium fluoride.
Complement C3 Variant and the Risk of Age-Related Macular Degeneration (2007)

Complement C3 is important in the pathogenesis of age-related macular degeneration. This finding further underscores the influence of the complement pathway in the pathogenesis of this disease.
Residual Vibration Reduction Using Vector Diagrams to Generate Shaped Inputs (1994)

This paper describes a method for limiting vibration in flexible systems by shaping the input to the system. Unlike most previous input shaping strategies, this method does not require a precise system model or lengthy numerical computation; only estimates of the system natural frequency and damping ratio are required. The effectiveness of this method when there are errors in the system model is explored and quantified. Next, an algorithm is presented, which, given an upper bound on acceptable residual vibration amplitude, determines a shaping strategy that is insensitive to errors in the estimate of the natural frequency. Finally, performance predictions are compared to hardware experiments.
The superfamily of C3b/C4b-binding proteins. (1987)

The determination of primary structures by amino acid and nucleotide sequencing for the C3b-and/or C4b-binding proteins H, C4BP, CR1, B, and C2 has revealed the presence of a common structural element. This element is approximately 60 amino acids long and is repeated in a tandem fashion, commencing at the amino-terminal end of each molecule. Two other complement components, C1r and C1s, have two of these repeating units in the carboxy-terminal region of their noncatalytic A chains. Three noncomplement proteins, beta 2-glycoprotein I (beta 2I), the interleukin 2 receptor (IL 2 receptor), and the b chain of factor XIII, have 4, 2 and 10 of these repeating units, respectively. These proteins obviously belong to the above family, although there is no evidence that they interact with C3b and/or C4b. Human haptoglobin and rat leukocyte common antigen also contain two and three repeating units, respectively, which have more limited homology with the repetitive regions in this family. All available data indicate that multiple gene duplications and exon shuffling have been important features in the divergence of this family of proteins with the 60-amino-acid repeat.
A column gel electrophoresis‐coupled genomic DNA subtractive hybridization technique (2004)

We have developed a DNA subtractive hybridization technique especially designed for mammalian genome comparison. The core of this protocol is a newly devised denaturant-containing polyacrylamide gel formed in a glass-column. In this gel system, the following DNA manipulation steps are carried out sequentially: size separation by electrophoresis, heat-denaturation, renaturation, and recovery. In the first step, a mixture of tester and driver DNA fragments are segregated according to their size whilst keeping their double-stranded forms. This reduces the complexity of the original genomic DNA fragments and also segregates DNA fragments having closely related sequences. In the second step, fractionated DNA fragments are quickly denatured and subjected to successive subtractive hybridization in situ by controlling gel temperature in a water bath. In the third step, DNA fragments are recovered by electrophoresis towards the reverse-orientation and are adsorbed onto ion-exchange beads. Two lines of experiments show that our protocol is able to highly enrich or directly extract differences among genomic DNA samples.
Templated Self‐Assembly of Colloidal Nanoparticles Controlled by Electrostatic Nanopatterning on a Si3N4/SiO2/Si Electret (2006)

Controlled self-assembly of colloidal nanoparticles onto an electrically nanopatterned electret film is presented (see figure; EFM: electrostatic force microscopy). An unprecedented reolution of 30 nm is achieved for both charge patterning and nanoparticle assembly. Furthermore, only a close-packed monolayer of nanoparticles is assembled, allowing better structural control and the possibility of forming hierarchical nanoparticle structures. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2006/c1542_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Modular Synthesis of Salvileucalin B Structural Domains (2011)

A modular strategy leading to the salvileucalin B core structure has been accomplished. The developed synthetic strategy featured a bioinspired intramolecular Diels-Alder reaction to construct domain "A", REDOX chemistry to functionalize domain "B", and a palladium-mediated cross-coupling to install domain "C". This flexible approach should facilitate further chemical and biological investigations of this fascinating class of compounds.
Lignin Structural Variation in Hardwood Species (2012)

A comprehensive lignin structure analysis of ten industrially relevant hardwood species is presented. Milled wood lignin (MWL) was isolated from each species using a modified protocol and all milled wood lignin preparations were analyzed through quantitative (13)C NMR spectroscopy, elemental analysis, methoxyl analysis, sugar analysis, and nitrobenzene oxidation. Nitrobenzene oxidation and ozonation were carried out on extractive-free wood, alkali-extracted wood, milled wood lignin, and alkali-extracted lignin. Milled wood lignin isolated by the modified protocol was found to be representative of the total lignin in alkali-extracted wood. Significant variations in lignin structures, such as syringylpropane/guaiacylpropane ratio (S/G ratio), arylglycerol-β-aryl ether (β-O-4), degree of condensation, and elemental and methoxyl contents, were found among the hardwood species studied. These structural variations among species appear to be correlated to a single factor, the syringyl/guaiacyl ratio. A new method to predict the S/G ratio of total lignin in wood was developed, using a calibration line established by the syringaldehyde/vanillin (S/V) ratio (nitrobenzene oxidation) and the S/G ratio ((13)C NMR) of milled wood lignin (MWL).
Control of Anthrax Toxin Gene Expression by the Transition State Regulator abrB (2002)

Bacillus anthracis produces the anthrax toxin proteins protective antigen (PA), lethal factor (LF), and edema factor (EF) in a growth phase-dependent manner when cultured in liquid medium. Expression of the toxin genes pagA, lef, and cya peaks in late log phase, and steady-state levels of the toxin proteins are highest during the transition into stationary phase. Here we show that an apparent transition state regulator negatively regulates toxin gene expression. We identified two orthologues of the B. subtilis transition state regulator abrB in the B. anthracis genome: one on the chromosome and one on the 182-kb virulence plasmid pXO1. The orthologue located on the chromosome is predicted to encode a 94-amino-acid protein that is 85% identical to B. subtilis AbrB. The hypothetical protein encoded on pXO1 is 41% identical to B. subtilis AbrB but missing 27 amino acid residues from the amino terminus compared to the B. subtilis protein. Deletion of the pXO1-encoded abrB orthologue did not affect toxin gene expression under the conditions tested. However, a B. anthracis mutant in which the chromosomal abrB gene was deleted expressed pagA earlier and at a higher level than the parent strain. Expression of a transcriptional pagA-lacZ fusion in the abrB mutant was increased up to 20-fold during early exponential growth compared to the parent strain and peaked in mid-exponential rather than late exponential phase. In contrast to the strong effect of abrB on pagA expression, lef-lacZ and cya-lacZ expression during early-log-phase growth was increased only two- to threefold in the abrB null mutant. Western hybridization analysis showed increased PA, LF, and EF synthesis by the mutant. As is true in B. subtilis, the B. anthracis abrB gene is negatively regulated by spo0A. Our findings tie anthrax toxin gene expression to the complex network of postexponential phase adaptive responses that have been well studied in B. subtilis.
Structure and nature of the metal-support interface: characterization of iridium clusters on magnesium oxide by extended x-ray absorption fine structure spectroscopy (1993)

X-ray absorption spectroscopy was used to characterize the metal-support interface in catalysts consisting\nof very small Ir clusters of nearly uniform nuclearity on the surface of MgO powder. [Ir4(CO)12] on MgO was converted\nin high yield into [HIr4(CO)11]- and separately into [Ir6(CO)15l2-. Extended X-ray absorption fine structure (EXAFS)\ndata are consistent with the hypothesis that each cluster retained its nuclearity upon decarbonylation. The average\nIr-Ir coordination in Ir,/MgO is 2.6 neighbors at a distance of 2.72 A, and the structure is modeled as a mixture of\n40-50% tetrahedra and the remainder four-atom rafts on MgO. The average Ir-Ir coordination in Ir6/MgO is 2.7\nneighbors at a distance of 2.12 A, and the structure is modeled as a mixture of about 25% Ir6 octahedra and the\nremainder Ir rafts on MgO. Another sample was treated in H2 at 623 K to give a typical supported metal catalyst\nhaving a distribution of Ir clusters averaging 10 8, in diameter. The Ir-support interfaces in Ir4/MgO and Irb/MgO\nare characterized by single Ir-Mg coordinations at 1.6 A and fourfold Ir-O coordinations at 2.6 A; the interface It\natoms are suggested to be atop Mg ions in the (100) faces of MgO. However, this structural model is simplified, and\nthe Ir-Mg interactions are not fully understood. The results demonstrate that the structurally simple supported Ir\nclusters are among the simplest supported metals; the metal-oxygen distances of approximately 2.6 Aare quite generally\ncharacteristic of metal particles and clusters supported on metal oxides and zeolites; the long distance is attributed to\nmetal atoms interacting with oxygen of the support with hydrogen present at the interface.
The CD4 and CD8 antigens are coupled to a protein-tyrosine kinase (p56lck) that phosphorylates the CD3 complex. (1989)

Many mammalian receptors have been found to regulate cell growth by virtue of a protein-tyrosine kinase domain in their cytoplasmic tail. We recently described an association of the CD4 antigen with a T-cell-specific protein-tyrosine kinase (p56lck; formerly termed pp58lck; EC 2.7.1.112). This interaction represents a potential mechanism by which T-cell growth may be regulated and offers a model by which other members of the src family (products of c-src, c-yes, c-fgr, etc.) may interact with mammalian growth factor receptors. As in the case of the CD4 antigen, the CD8 antigen appears to serve as a receptor for nonpolymorphic regions of products of the major histocompatibility complex and has been implicated in the regulation of T-cell growth. In this study, we reveal that the human CD8 antigen is also associated with the T-cell-specific protein-tyrosine kinase (p56lck). The associated p56lck kinase was detected by use of both in vitro and in vivo labeling regimes using an antiserum to the C terminus of p56lck. Two-dimensional nonequilibrium pH-gradient gel electrophoresis and sodium dodecyl sulfate/polyacrylamide gel electrophoresis demonstrated the similarity of p56lck to the protein-tyrosine kinase associated with the CD4 antigen. The catalytic activity of p56lck was revealed by the autophosphorylation of the 55- to 60-kDa kinase and the occasional labeling of a 35-kDa protein. Last, we demonstrate directly that members of the CD3 complex, including the gamma, delta, and epsilon chains, as well as a putative zeta subunit, can be phosphorylated at tyrosine residues by the CD4/CD8.p56lck complex.
Conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates (1977)

The detailed conformational features and dynamics of heterodinucleoside monophosphates ApU, ApC, GpU, GpC, UpA, CpA, UpG, and CpG have been studied in aqueous solution by high field nuclear magnetic resonance (NMR) spectroscopy. Analysis of the resultant NMR parameters leads to a number of discernible trends throughout the series. Thus the ribose rings of the dimers exist as equilibrium mixtures of C(2')-endo(2E) in equilibrium C(3')-endo(3E) conformers with a proclivity for the 3E pucker in most cases; the C(4')-C(5') bonds of both nucleotidyl units show significant preference (74-96%) for a gg conformation and the dominant conformer (85-89%) about C(5')-O(5') is g'g'. Orientation about the C(3')-O(3') bond is coupled to the ribose conformational equilibrium and the system exists with a bias for the 3Eg- coupled conformation in which the H(3')-C(3')-O(3')-P dihedral angle occupies the narrow range of 33-35 degrees. Dimerization, on the average, causes about 10% increase in gg and g'g' populations and the g-domain becomes increasingly populated about the C(3')-O(3') bond. The ribose equilibrium 2E in equilibrium 3E shifts in favor of 3E upon dimerization, the effect being very conspicuous for the pu-py series (similar to 40 yields 60%) and less noticeable for the py-pu systems (similar to 47 yields 58%), clearly suggesting a correlation between sequence and ribose conformational equilibrium. The temperature and dimerization data for the heterodinucleoside monophosphates show that the transition 2E yields 3E is directly related to XCN changes induced by dimerization and stacking. Analysis of the ribose coupling data shows that the percentage populations of stacked species vary from dimer to dimer with GpC displaying a maximum of 45% stacked population and UpG about 10%. However, in general, the pu-py dimers show a higher preference (27-45%) for stacked conformations than py-pu dimers (10-25%). It is proposed that the pronounced deshielding of H(5') of the 5'-nucleotidyl units upon dimerization is associated with the presence of right-handed stacks (g-g-), whereas the chemical shift trends of H(5') and H(5') of 3'-nucleotidyl units are due to the presence of left-handed stacks (g+g+) in all the dimers. In pu-py dimers, the population of the g-g- species is found to be greater than that of g+g+. Also the population of g-g- stacks in pu-py dimers is generally greater than in their corresponding matched py-pu dimers. Thus the base sequence has not only an explicit effect on the overall populations of stacked species, but also on the handedness of the stacks. The present results further confirm the interdependence of conformational bonds throughout the nucleotidyl framework.
T-bet Controls Pathogenicity of CTLs in the Heart by Separable Effects on Migration and Effector Activity (2006)

CD8+ CTL contribute to the pathogenesis of myocarditis and cardiac allograft rejection. Using a transgenic model of myocarditis, we examined the role of the transcription factor T-bet in the differentiation of pathogenic cardiac Ag-specific CTL. We demonstrate that T-bet-deficient CTL are significantly impaired in their ability to cause disease, despite intact proliferation and activation phenotypes. In the absence of T-bet, there is markedly reduced expression of the chemokine receptor CXCR3, and CXCR3-gene knockout CTL are significantly less pathogenic than control CTL. Retroviral-mediated CXCR3 expression in T-bet-deficient CD8+ T cells reconstitutes their ability to infiltrate but not to damage the heart, establishing that CD8+ T cell pathogenicity is related to T-bet-dependent CXCR3 expression, reduced cytotoxicity, and enhanced regulation. These findings highlight the potential therapeutic benefit of targeting T-bet-regulated gene expression and CXCR3-dependent migration in immune-mediated heart disease.
Isolation and Expansion of Adult Cardiac Stem Cells From Human and Murine Heart (2004)

Cardiac myocytes have been traditionally regarded as terminally differentiated cells that adapt to increased work and compensate for disease exclusively through hypertrophy. However, in the past few years, compelling evidence has accumulated suggesting that the heart has regenerative potential. Recent studies have even surmised the existence of resident cardiac stem cells, endothelial cells generating cardiomyocytes by cell contact or extracardiac progenitors for cardiomyocytes, but these findings are still controversial. We describe the isolation of undifferentiated cells that grow as self-adherent clusters (that we have termed "cardiospheres") from subcultures of postnatal atrial or ventricular human biopsy specimens and from murine hearts. These cells are clonogenic, express stem and endothelial progenitor cell antigens/markers, and appear to have the properties of adult cardiac stem cells. They are capable of long-term self-renewal and can differentiate in vitro and after ectopic (dorsal subcutaneous connective tissue) or orthotopic (myocardial infarction) transplantation in SCID beige mouse to yield the major specialized cell types of the heart: myocytes (ie, cells demonstrating contractile activity and/or showing cardiomyocyte markers) and vascular cells (ie, cells with endothelial or smooth muscle markers).
Fungal ferritins: The ferritin from mycelia of Absidia spinosa is a bacterioferritin (1996)

Two distinct ferritin like iron containing proteins have been identified and isolated from the fungus Absidia spinosa; one from the spores and another from the mycelia. The mycelial protein has been purified and consists of two subunits of approx. 20 kDa. The N-terminal sequences of both subunits have been determined. The holoprotein as isolated contains approx. 750 iron atoms/molecule and exhibits a heme-like UV-Vis spectrum. Based on the heme spectrum and the high degree of sequence homology found, it has been established that the mycelial protein is a bacterioferritin. This is the first example demonstrating the presence of a bacterioferritin in a eukaryotic organism.
The nerve growth factor/tumor necrosis factor receptor family (1996)

Receptors in the nerve growth factor/tumor necrosis factor receptor family are characterized by the presence of cysteine-rich motifs of approximately 40 amino acids in the extracellular domain. The ligands are type II transmembrane proteins with beta-strands that form a jelly-roll beta-sandwich. The receptors recognize soluble or cell-surface-bound ligands and mediate diverse cellular responses. Activation of intracellular signals is mediated at least in part by the association of proteins with a RING finger motif or a death domain to the cytoplasmic domains of the receptors. In addition to cell-membrane-bound receptors soluble forms have been described for most of the receptors. Activation of intracellular signals not only occurs through ligand binding to the receptors but cross-linking of at least some members of the ligand family can regulate cell functions.
Effects of Probe Length, Probe Geometry, and Redox-Tag Placement on the Performance of the Electrochemical E-DNA Sensor (2009)

Previous work has described several reagentless, electrochemical DNA (E-DNA) sensing architectures comprised of an electrode-immobilized, redox-tagged probe oligonucleotide. Recent studies suggest that E-DNA signaling is predicated on hybridization-linked changes in probe flexibility, which will alter the efficiency with which the terminal redox tag strikes the electrode. This, in turn, suggests that probe length, probe geometry, and redox-tag placement will affect E-DNA signaling. To test this we have characterized E-DNA sensors comprised of linear or stem-loop probes of various lengths and with redox tags placed either distal to the electrode or internally within the probe sequence (proximal). We find that linear probes produce larger signal changes upon target binding than equivalent stem-loop probes. Likewise, long probes exhibit greater signal changes than short probes provided that the redox tag is placed proximal to the electrode surface. In contrast to their improved signaling, the specificity of long probes is poorer than that of short probes, suggesting that sensor optimization represents a trade off between sensitivity and specificity. Finally, we find that sensor response time and selectivity are only minimally affected by probe geometry or length. The results of this comparative study will help guide future designs and applications of these sensors.