gebhart/patrepeval huggingface dataset:
Synthesis of a troponin C cDNA and expression of wild-type and mutant proteins in Escherichia coli. (1988)

An avian fast striated muscle troponin C cDNA was designed and synthesized from six oligonucleotides using the overlap-fill in method and overproduced in Escherichia coli for the purpose of developing recombinant DNA approaches to study structure-function relationships in this calcium-binding regulatory protein. The recombinant protein isolated from E. coli functions as a bona fide troponin C in all properties that were assayed: calcium binding, calcium-dependent conformational change, calcium-dependent interaction with troponin I, and formation of a functional ternary complex with troponin I and troponin T that can confer calcium sensitivity on the actomyosin MgATPase. The initiating methionine was removed by E. coli leaving alanine as the first amino acid, as in the muscle troponin C. The first amino acid was not acetylated, but this difference from the muscle protein has no apparent effect on the function. The presence of Glu at position 99, as in turkey, versus Ala in chicken resulted in no detectable difference in comparing recombinant with chicken troponin C. A mutant in which residues 91-93 (Lys-Gly-Lys) in the D/E helical linker were deleted differs in function from wild-type troponin C in the conformational change that takes place upon calcium binding and its interaction with troponin I. Also, the mutant troponin C is impaired in its ability to form a functional complex with troponin I and troponin T that will confer calcium sensitivity on the actomyosin MgATPase.
STUDIES ON HYPERSENSITIVITY (1961)

In earlier observations with the picryl system, it was concluded that contact sensitivity was a form of delayed (cellular) hypersensitivity to conjugates of sensitizer with autologous proteins indistinguishable in its immunological mechanism from other classical forms of delayed hypersensitivity to proteins. This conclusion has been confirmed and extended with the picryl and chlorbenzoyl chloride systems. 1. It is shown that to induce a state of contact sensitivity, the minimal necessary amounts of hapten are of the same order of magnitude, whether this hapten is conjugated with protein or the free reactive chemical itself. From this, it is evident that contamination of conjugates with small amounts of unreacted sensitizer plays no part in the induction of contact reactivity by the conjugate. With the dinitrophenyl system, no contact sensitivity could be induced by the conjugates used; possible reasons for this discrepancy are discussed. 2. Animals sensitized to contact by homologous conjugate can be completely desensitized by injections of such a conjugate in large amount; a similar injection schedule has no effect on the contact sensitivity of animals sensitized with the free reactive sensitizer. 3. The capacity of heterologous (ovalbumin) conjugates to evoke anti-hapten antibodies is shown to be greater than that of homologous (guinea pig seralbumin) conjugates: the reverse is true of their capacity to induce delayed reactivity. 4. Evidence is brought forward to suggest that in animals sensitized with homologous albumin conjugates, the specificity of the delayed reaction involves more than the hapten alone, even though the carrier protein is non-antigenic on its own. The contrast with the apparent lesser specificity of the antibodies later produced is discussed.
The Potential of the ESAT-6 Antigen Secreted by Virulent Mycobacteria for Specific Diagnosis of Tuberculosis (1997)

Tuberculosis (TB) remains a global health problem in humans and animals, and improved diagnostic methods are needed urgently. This study examined the potential of an interferon-gamma blood test based on a recently identified low-molecular-mass secreted protein antigen, ESAT-6, for early detection of bovine TB. It was found that field cases of bovine TB and experimentally infected cattle exhibited strong in vitro interferon-y responses directed toward this antigen. Of importance, ESAT-6 reactivity was found to discriminate between cattle infected with TB and cattle sensitized by environmental mycobacteria, and the gene encoding this molecule was demonstrated to be absent from >90% of the nontuberculous mycobacterial strains isolated from healthy sensitized cattle. These results demonstrate the feasibility of using single defined antigens for the highly specific diagnosis of TB.
Proton Transport by Proteorhodopsin Requires that the Retinal Schiff Base Counterion Asp-97 Be Anionic (2003)

At pH >7, proteorhodopsin functions as an outward-directed proton pump in cell membranes, and Asp-97 and Glu-108, the homologues of the Asp-85 and Asp-96 in bacteriorhodopsin, are the proton acceptor and donor to the retinal Schiff base, respectively. It was reported, however [Friedrich, T. et al. (2002) J. Mol. Biol., 321, 821-838], that proteorhodopsin transports protons also at pH <7 where Asp-97 is protonated and in the direction reverse from that at higher pH. To explore the roles of Asp-97 and Glu-108 in the proposed pumping with variable vectoriality, we compared the photocycles of D97N and E108Q mutants, and the effects of azide on the photocycle of the E108Q mutant, at low and high pH. Unlike at high pH, at a pH low enough to protonate Asp-97 neither the mutations nor the effects of azide revealed evidence for the participation of the acidic residues in proton transfer, and as in the photocycle of the wild-type protein, no intermediate with unprotonated Schiff base accumulated. In view of these findings, and the doubts raised by absence of charge transfer after flash excitation at low pH, we revisited the question whether transport occurs at all under these conditions. In both oriented membrane fragments and liposomes reconstituted with proteorhodopsin, we found transport at high pH but not at low pH. Instead, proton transport activity followed the titration curve for Asp-97, with an apparent pK(a) of 7.1, and became zero at the pH where Asp-97 is fully protonated.
Bone matrix to growth factors: location, location, location (2010)

The demonstration that fibrillin-1 mutations perturb transforming growth factor (TGF)-β bioavailability/signaling in Marfan syndrome (MFS) changed the view of the extracellular matrix as a passive structural support to a dynamic modulator of cell behavior. In this issue, Nistala et al. (2010. J. Cell Biol. doi: 10.1083/jcb.201003089) advance this concept by demonstrating how fibrillin-1 and -2 regulate TGF-β and bone morphogenetic protein (BMP) action during osteoblast maturation.
A Role for Diacylglycerol Acyltransferase during Leaf Senescence (2002)

Lipid analysis of rosette leaves from Arabidopsis has revealed an accumulation of triacylglycerol (TAG) with advancing leaf senescence coincident with an increase in the abundance and size of plastoglobuli. The terminal step in the biosynthesis of TAG in Arabidopsis is catalyzed by diacylglycerol acyltransferase 1 (DGAT1; EC 2.3.1.20). When gel blots of RNA isolated from rosette leaves at various stages of development were probed with the Arabidopsis expressed sequence tag clone, E6B2T7, which has been annotated as DGAT1, a steep increase in DGAT1 transcript levels was evident in the senescing leaves coincident with the accumulation of TAG. The increase in DGAT1 transcript correlated temporally with enhanced levels of DGAT1 protein detected immunologically. Two lines of evidence indicated that the TAG of senescing leaves is synthesized in chloroplasts and sequesters fatty acids released from the catabolism of thylakoid galactolipids. First, TAG isolated from senescing leaves proved to be enriched in hexadecatrienoic acid (16:3) and linolenic acid (18:3), which are normally present in thylakoid galactolipids. Second, DGAT1 protein in senescing leaves was found to be associated with chloroplast membranes. These findings collectively indicate that diacylglycerol acyltransferase plays a role in senescence by sequestering fatty acids de-esterified from galactolipids into TAG. This would appear to be an intermediate step in the conversion of thylakoid fatty acids to phloem-mobile sucrose during leaf senescence.
Direct evidence that polypyrimidine tract binding protein (PTB) is essential for internal initiation of translation of encephalomyocarditis virus RNA. (1995)

The requirement of PTB, polypyrimidine tract binding protein, for internal initiation of translation has been tested using an RNA affinity column to deplete rabbit reticulocyte lysates of PTB. The affinity column was prepared by coupling CNBr-activated Sepharose with the segment of the 5'-untranslated region of encephalomyocarditis virus (EMCV) RNA previously shown to bind PTB. Lysates passed through this column were devoid of PTB, and were incapable of internal initiation of translation dependent on the EMCV 5'-untranslated region, while retaining the capacity for translation dependent on ribosome scanning. Full activity for internal initiation was restored by the addition of recombinant PTB at the physiologically relevant concentration of about 5 micrograms/mL. When various PTB deletion mutants were tested, it was found that this activity required virtually the full-length protein. Thus, PTB is an essential protein for internal initiation promoted by the EMCV 5'-untranslated region. However, the PTB-depleted lysate retained the capacity for internal initiation promoted by the 5'-untranslated regions of another cardiovirus, Theiler's murine encephalomyelitis virus, and of the unrelated hepatitis C virus, and in neither case did addition of recombinant PTB stimulate internal initiation. Therefore, PTB is not a universal internal initiation factor that is indispensable in every case of internal ribosome entry.
Expression of the Evi-1 gene in myelodysplastic syndromes. (1995)

Increased expression of the proto-oncogene Evi-1 has been shown to block the in vitro granulocytic differentiation of myeloid cells in response to granulocytic colony-stimulating factor and to interfere with the proliferation of erythroid cells in response to erythropoietin. We determined the frequency of Evi-1 expression in myelodysplastic syndromes (MDS), a disorder with altered proliferation and differentiation in the erythroid and myeloid lineages. Twenty-one patients were studied. Abnormal expression was found in 1/9 patients with refractory anemia and in 7/12 patients with refractory anemia with excess of blasts (RAEB) or in transformation (RAEBt). No correlation could be found between expression of Evi-1 and age, sex, hemoglobin level and percentage of bone marrow blasts or erythroblasts. This result suggests that the high incidence of Evi-1 expression which remains at low levels in RAEB and RAEBt is not a major determinant of ineffective erythropoiesis and myelopoiesis in MDS.
Characterization of InGaN/GaN multi-quantum-well blue-light-emitting diodes grown by metal organic chemical vapor deposition (2004)

The structural, surface morphology, and the temperature dependence photoluminescence of InGaN(3 nm)/GaN(7 nm) 5 period multi-quantum-well blue-light-emitting diode (LED) structures grown by metal organic chemical vapor deposition (MOCVD) have been studied. Quantum dot-like structures and strain contrast evident by black lumps were observed in the quantum wells using high-resolution transmission electron microscopy (HRTEM) analysis. Double-crystal high-resolution x-ray diffraction (HRXRD) spectra of blue LED were simulated using kinematical theory method, to obtain composition, and period thickness of well and barrier. The “S” shape character shift as red–blue–redshift of the quantum-well emission line, i.e., blue emission peak 2.667 eV at 10 K, was observed with variation of temperature in the photoluminescence (PL) spectra. The shift is assigned to the potential fluctuations due to alloy inhomogeneous distribution in the quantum wells. The In composition in the quantum wells obtained by two independent techniques, namely HRXRD and PL, was 8% and 19%, respectively. The reason for this large difference in composition is explained in this letter.
Engineered nanoporous and nanostructured films (2009)

Nanoporous and nanostructured films have become increasingly important to the microelectronics and photonics industries. They provide a route to low dielectric constant materials that will enable future generations of powerful microprocessors. They are the only route to achieving materials with refractive indices less than 1.2, a key feature for the future development of photonic crystal devices, enhanced omni-directional reflectors, enhanced anti-reflection coatings and black-body absorbers. In addition, these films exhibit tremendous potential for separations, catalytic, biomedical and heat transfer applications. This article will review two primary techniques for manufacturing these films, evaporation induced self-assembly and oblique or glancing angle deposition, and will discuss some of the film properties critical to their use in the microelectronics and photonics industries.
Phylogenetic conservation of the molecular and immunological properties of the chaperones gp96 and hsp70 (2001)

The heat shock proteins (HSP) gp96 and hsp70 have been shown to have a critical role in eliciting adaptive immune responses to cancers and viruses. This role derives from (i) their ability to chaperone antigenic peptides generated in the cells from which the HSP are isolated, and (ii) their capacity to interact with antigen presenting cells (APC) which re-present the HSP-chaperoned peptides in context of MHC I molecules. We have asked whether the immunological properties of HSP extend beyond the mammals to other phyla. We report here the serological, biochemical, genetic, and immunological characterization of the Xenopus gp96. Like mammalian gp96, Xenopus gp96 forms non-covalent complexes with peptides. Immunization with gp96 and hsp70 purified from Xenopus tumors, elicits potent and specific anti-tumor immunity, which is dependent on their ability to chaperone peptides in vivo. An immunogenic peptide chaperoned by the Xenopus gp96 can be processed and presented by mouse APC, to antigen-specific CD8+ T cells of mice. The remarkable conservation of these essential immunological properties of gp96 and hsp70 between amphibians and mammals suggests the importance of HSP in the evolution of the vertebrate immune system.
Utility of liquid-based cytology for cervical carcinoma screening (1999)

In a population-based study of high risk women, ThinPrep cytology demonstrated significantly increased sensitivity for detecting HSIL and carcinoma, with a concurrent significant increase in colposcopy referrals.
A New and Practical Synthesis of α-Amino Acids from Alkenyl Boronic Acids (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA New and Practical Synthesis of α-Amino Acids from Alkenyl Boronic AcidsNicos A. Petasis and Ilia A. ZavialovView Author Information Department of Chemistry and Loker Hydrocarbon Research Institute University of Southern California Los Angeles, California 90089-1661 Cite this: J. Am. Chem. Soc. 1997, 119, 2, 445–446Publication Date (Web):January 15, 1997Publication History Received10 September 1996Published online15 January 1997Published inissue 1 January 1997https://pubs.acs.org/doi/10.1021/ja963178nhttps://doi.org/10.1021/ja963178nrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views7858Altmetric-Citations406LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Monomers,Peptides and proteins,Reaction products,Separation science Get e-Alerts
Rapid Melting and Regrowth Velocities in Silicon Heated by Ultraviolet Picosecond Laser Pulses (1984)

Direct measurements of the silicon liquid/solid interface velocity have been made during both melt-in and regrowth for crystalline silicon irradiated with a pulsed (15 psec) ultraviolet laser. The liquid films produced were up to 40 nm thick and were fully amorphized upon resolidification. Above threshold, the regrowth velocity was 25 m/sec, independent of laser fluence. The results imply a nonlinear relationship between supercooling and interface velocity.
Functional Role of High-Affinity Anandamide Transport, as Revealed by Selective Inhibition (1997)

Anandamide, an endogenous ligand for central cannabinoid receptors, is released from neurons on depolarization and rapidly inactivated. Anandamide inactivation is not completely understood, but it may occur by transport into cells or by enzymatic hydrolysis. The compound N-(4-hydroxyphenyl)arachidonylamide (AM404) was shown to inhibit high-affinity anandamide accumulation in rat neurons and astrocytes in vitro, an indication that this accumulation resulted from carrier-mediated transport. Although AM404 did not activate cannabinoid receptors or inhibit anandamide hydrolysis, it enhanced receptor-mediated anandamide responses in vitro and in vivo. The data indicate that carrier-mediated transport may be essential for termination of the biological effects of anandamide, and may represent a potential drug target.
International consensus for a definition of disease flare in lupus (2010)

The Lupus Foundation of America (LFA) convened an international working group to obtain a consensus definition of disease flare in lupus. With help from the Paediatric Rheumatology International Trials Organization (PRINTO), two web-based Delphi surveys of physicians were conducted. Subsequently, the LFA held a second consensus conference followed by a third Delphi survey to reach a community-wide agreement for flare definition. Sixty-nine of the 120 (57.5%) polled physicians responded to the first survey. Fifty-nine of the responses were available to draft 12 preliminary statements, which were circulated in the second survey. Eighty-seven of 118 (74%) physicians completed the second survey, with an agreement of 70% for 9/12 (75%) statements. During the second conference, three alternative flare definitions were consolidated and sent back to the international community. One hundred and sixteen of 146 (79.5%) responded, with agreement by 71/116 (61%) for the following definition: "A flare is a measurable increase in disease activity in one or more organ systems involving new or worse clinical signs and symptoms and/or laboratory measurements. It must be considered clinically significant by the assessor and usually there would be at least consideration of a change or an increase in treatment." The LFA proposes this definition for lupus flare on the basis of its high face validity.
Two‐dimensional gel‐based approaches for the assessment of N‐Linked and O‐GlcNAc glycosylation in human and simian immunodeficiency viruses (2008)

The glycosylation state of envelope glycoproteins in human and simian immunodeficiency viruses (HIV/SIV) is critical to viral infectivity and tropism, viral protein processing, and in virus evasion of the immune system. Using a rapid fluorescent 2-D gel-based method coupled with enzymatic pre-treatment of virus with PNGase F (Peptide: N-Glycosidase F) and fluorescent 2-D gels or 2-D gel Western blotting, we show significant differences in the glycosylation patterns of two SIV strains widely used in animal models of HIV disease and vaccine studies. We also demonstrate the modification of a host protein important in HIV biology (HLA-DR) by O-GlcNAc. Further, this experimental pipeline allows for the identification of the modified protein and the site of N-linked glycosylation by fluorescent 2-DE coupled with MS and the qualitative and semi-quantitative assessment of viral glycosylation. The method is fully compatible with downstream glycomics analysis. This approach will permit correlation of virus glycosylation status with pathological severity and may serve as a rapid screen of viruses from physiological samples for further study by more advanced MS methodology.
Sinapine as a Supply of Choline for the Biosynthesis of Phosphatidylcholine in Raphanus sativus Seedlings (1981)

Biosynthesis of phosphatidylcholine in young seedlings of Raphanus sativus is supplied with choline from degradation of the seed constituent sinapine (sinapoylcholine). This conclusion has been deduced from the following results: (1) Raphanus sativus seedlings accumulate approx. 70 nmol phosphatidylcholine which may be relevant for the consumption of choline, liberated during hydrolysis of approx. 130 nmol sinapine. (2) [ 14 C]choline and [ 14 C]ethanolamine, taken up by germinating Raphanus seeds, are exclusively consumed in the biosynthesis of phosphatidylcholine and phosphatidylethanolamine, respectively. (3) Pulse-chase experiments with seedlings at different germination stages show a reduced [ 14 C]choline incorporation into phosphatidylcholine at the time when degradation of sinapine occurs, obviously as a result of an isotope dilution by an increase of the endogenous choline pool. (4) After [ 14 C]choline pulse to immature seeds, during the process of seed maturation most of the activity taken up is incorporated into accumulating sinapine and approx. 50% compared to this into phosphatidylcholine. During seedling development the quantity of labelled sinapine rapidly decreases as a result of sinapine degradation with a concomitant label increase in free choline, phosphorylcholine, and phosphatidylcholine. Approx. 50% of the choline liberated from sinapine, is consumed in the biosynthesis of phosphatidylcholine. High performance liquid chromatographic analyses of phosphatidylcholine during Raphanus germination revealed that this phospholipid might be a metabolically active compound. Changes in the absorptivity of this compound at 210 nm indicate changes in the degree of unsaturation in the fatty acyl groups
Triptolide modulates T‐cell inflammatory responses and ameliorates experimental autoimmune encephalomyelitis (2008)

Triptolide (TPT), a diterpenoid triepoxide, is the major component isolated from the Chinese herb Tripterygium wilfordii Hook. f. Previous studies have shown that TPT has immunosuppressive properties and is effective in prolonging graft survival and suppressing autoimmune responses. The aim of this study was to investigate the protective effect of TPT in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Treatment of C57BL/6 mice with TPT from the date of EAE induction significantly delayed EAE onset and suppressed disease severity, accompanied with reduced inflammation and demyelination in the central nervous system. TPT treatment lead to a significant inhibition of the mRNA expression of both Th1/Th(IL-17) and Th2 cytokines in spleen mononuclear cells (MNC) as well as in spinal cord tissues. In addition, the expression of Forkhead box p3 (Foxp3) was up-regulated in spleen MNC after TPT treatment. Furthermore, we detected apparent inhibition of nuclear factor-kappa B (NF-kappaB)-DNA binding activity, increased expression of the inhibitor of nuclear factor-kappa Balpha (IkappaBalpha) and decreased expression of pIkappaBalpha in spleen MNC in TPT-treated EAE mice. Taken together, these findings indicate that TPT has profound immunoregulatory functions and potential protective values for the treatment of autoimmune inflammatory disorders.