gebhart/patrepeval huggingface dataset:
A simple and rapid method for the preparation of plant genomic DNA for PCR analysis (1991)

Journal Article A simple and rapid method for the preparation of plant genomic DNA for PCR analysis Get access K. Edwards, K. Edwards Plant Biotechnology Section, ICI Seeds, Jealott's Hill Research StationBracknell, Berks, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Johnstone, C. Johnstone Plant Biotechnology Section, ICI Seeds, Jealott's Hill Research StationBracknell, Berks, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Thompson C. Thompson Plant Biotechnology Section, ICI Seeds, Jealott's Hill Research StationBracknell, Berks, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 6, 25 March 1991, Page 1349, https://doi.org/10.1093/nar/19.6.1349 Published: 25 March 1991 Article history Accepted: 02 January 1991 Published: 25 March 1991
Infrared spectroscopic study of SiOx films produced by plasma enhanced chemical vapor deposition (1986)

We have studied the local atomic structure of silicon suboxide (SiOx, x&amp;lt;2) thin films using infrared (IR) spectroscopy. The films were prepared by plasma enhanced chemical vapor deposition (PECVD) of silane (SiH4) and nitrous oxide (N2O) mixtures, which were then diluted with He. The IR spectra were found to vary significantly with the degree of He dilution. Films grown with no He showed SiN, NH, and SiH bonding groups in addition to the three characteristic vibrations of the Si–O–Si linkage. The addition of He reduced the strength of the SiN, NH, and SiH absorption bands, and resulted in systematic increases in the frequency of the Si–O–Si asymmetric stretching vibration. The frequency of this Si–O–Si stretching vibration scales linearly with the oxygen concentration from approximately 940 cm−1 in oxygen doped amorphous silicon to 1075 cm−1 in stoichiometric noncrystalline SiO2. A deposition temperature of 350 °C and a He dilution of 50% gave a film composition close to SiO1.9. We propose a model for the deposition process that emphasizes the role of the He dilution.
Identification with monoclonal antibodies of hemolysin produced by clinical isolates of Escherichia coli (1987)

Murine monoclonal antibodies were generated against the 107,000-dalton hemolysin encoded by the hemolytic determinant from Escherichia coli LE 2001, and colony blotting was used to assay for production of the hemolysin by 35 hemolytic strains of E. coli and other hemolytic members of the family Enterobacteriaceae of clinical origin. All hemolytic E. coli strains gave positive reactions with two monoclonal antibodies. In contrast, none of the hemolytic, non-E. coli isolates yielded positive colony blots. In addition, Western blotting showed that the hemolysins produced by all clinical E. coli isolates had a similar molecular weight of about 107,000. Discrete antigenic variation may occur in the molecule, since a third monoclonal antibody did not react with the hemolysin from a number of wild-type E. coli strains. Western blot analysis was used to assess the presence of immunoglobulin G (IgG), IgA, and IgM antibodies to E. coli hemolysin in human sera. All 20 of the tested sera from healthy adults contained antibodies to the toxin, with various constellations among the antibody classes. In contrast, sera from five of eight infants aged 8 to 36 months contained no antihemolysin antibodies. We conclude that the 107,000-dalton hemolysin of E. coli is a widespread immunogen that is produced by most or all hemolytic E. coli strains in the human host.
Molecular behavior adapts to context: heparanase functions as an extracellular matrix-degrading enzyme or as a T cell adhesion molecule, depending on the local pH. (1995)

Migration of lymphocytes into inflammatory sites requires their adhesion to the vascular endothelium and subendothelial extracellular matrix (ECM). The ensuing penetration of the ECM is associated with the expression of ECM-degrading enzymes, such as endo-beta-D glucuronidase (heparanase), which cleaves heparan sulfate (HS) proteoglycans. We now report that, depending on the local pH, a mammalian heparanase can function either as an enzyme or as an adhesion molecule. At relatively acidified pH conditions, heparanase performs as an enzyme, degrading HS. In contrast, at the hydrogen ion concentration of a quiescent tissue, heparanase binds specifically to HS molecules without degrading them, and thereby anchors CD4+ human T lymphocytes. Thus, the local state of a tissue can regulate the activities of heparanase and can determine whether the molecule will function as an enzyme or as a proadhesive molecule.
Intracellular Glycation of Nuclear DNA, Mitochondrial DNA, and Cytosolic Proteins During Senescence-like Growth Arrest (2011)

To investigate the accumulation of intracellular advanced glycation end products (AGEs), a method was established for the simultaneous analysis of glycation products of cytosolic proteins, nuclear DNA, and mitochondrial DNA (mtDNA). Nuclear DNA, mtDNA, and cytosolic proteins were simultaneously isolated from one cell lysate by differential centrifugation and combined mechanical and chemical cell disruption methods. The major DNA-AGE N(2)-carboxyethyl-2'-deoxyguanosine (CEdG) was quantified in nuclear DNA and mtDNA by ELISA, whereas the protein-AGEs N(ɛ)-(carboxymethyl)lysine (CML) and N(ɛ)-(carboxyethyl)lysine (CEL) were determined by western blot. The method was used to analyze NIH3T3 fibroblasts. In untreated cells, CEdG levels of mtDNA (14.84 ± 3.07 pg CEdG/μg mtDNA) were significantly higher compared with nuclear DNA (4.40 ± 0.64 pg CEdG/μg DNA; p < 0.001). Then, fibroblasts were analyzed after 7 days of senescence-like growth arrest. In senescent fibroblasts, the CEdG content of nuclear DNA significantly increased by 25%. However, the CEdG level of mtDNA significantly decreased to 52%; in parallel, an increase in mitochondrial mass and mtDNA was observed. Senescence did not lead to general accumulation of protein-AGEs, but two protein bands at 32 and 34 kDa showed a significant increase in the CML/CEL modification rate (208%, p < 0.001; 196%, p = 0.0016) in senescent fibroblasts compared with control cells.
A mechanism for inhibition of E-cadherin-mediated cell-cell adhesion by the membrane-associated mucin episialin/MUC1. (1996)

Episialin (MUC1, PEM, EMA, CA15-3 antigen) is a sialylated, membrane-associated glycoprotein with an extended mucin-like ectodomain. This domain mainly consists of 30-90 homologous 20-amino acid repeats that are rich in O-glycosylation sites (serines and threonines). It is likely that this part forms a polyproline beta-turn helix. As a result, the ectodomain can protrude more than 200 nm above the cell surface, whereas most cell surface molecules do not exceed a length of 35 nm. Normally, episialin is present at the apical side of glandular epithelial cells. On carcinoma cells, however, it can be strongly overexpressed and it is often present over the entire cell surface. We have previously shown that episialin, if it is interspersed between adhesion molecules, nonspecifically reduces cell-cell and cell-extracellular matrix interactions in vitro and in vivo, presumably by steric hindrance caused by the extreme length and high density of the episialin molecules at the cell surface. To analyze the molecular mechanism for this anti-adhesion effect in more detail, we have now deleted an increasing number of repeats in the episialin cDNA and transfected the resulting mutants into murine L929 cells expressing the homophilic adhesion molecule E-cadherin. Here we show that the length of episialin is the dominant factor that determines the inhibition of E-cadherin-mediated cell-cell interactions. For the anti-adhesive effect mediated by the full length episialin, charge repulsion by negatively charged sialylated O-linked glycans is far less important.
Acid-induced transformation of palladium(0)-benzoquinone complexes to palladium(II) and hydroquinone (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcid-induced transformation of palladium(0)-benzoquinone complexes to palladium(II) and hydroquinoneHelena Grennberg, Adolf Gogoll, and Jan E. BaeckvallCite this: Organometallics 1993, 12, 5, 1790–1793Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/om00029a040https://doi.org/10.1021/om00029a040research-articleACS PublicationsRequest reuse permissionsArticle Views2028Altmetric-Citations177LEARN 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-Alertsclose Get e-Alerts
Endogenous Brain-Derived Neurotrophic Factor Triggers Fast Calcium Transients at Synapses in Developing Dendrites (2007)

Brain-derived neurotrophic factor (BDNF) is involved in many aspects of the formation of functional neuronal networks. BDNF signaling regulates neuronal development not only globally, at the level of entire neurons or networks, but also at a subcellular level and with high temporal specificity; however, the spatiotemporal characteristics of intrinsic BDNF signaling are essentially unknown. Here, we used calcium imaging to directly observe intrinsic BDNF signaling in developing hippocampal neurons. We found that blocking intrinsic BDNF signaling with function-blocking BDNF antibodies (alphaBDNF) or K252-a reduced the frequency of spontaneously occurring fast and localized calcium rises in dendrites. Conversely, focal application of BDNF evoked fast and local dendritic calcium transients, which required activation of TrkB (tropomyosin-related kinase B) receptors as well as activation of voltage-gated sodium and calcium channels. Virus-mediated expression of PSD-95:CFP (postsynaptic density-95 tagged with cyan fluorescent protein) revealed that spontaneous local calcium transients occurred frequently at postsynaptic sites along the dendrite. The frequency of synaptically localized calcium transients was specifically reduced by blocking intrinsic BDNF signaling, whereas nonsynaptic calcium rises were not affected. Furthermore, focal BDNF delivery evoked localized and fast calcium elevations specifically at postsynaptic sites. Together, our results demonstrate that BDNF-dependent calcium signaling in developing hippocampal neurons is fast and occurs at synapses. These temporal and spatial characteristics of intrinsic BDNF signaling as well as its relative abundance renders BDNF an ideal signaling molecule in the establishment of specific synaptic connectivity and functional neuronal networks.
Club cells surviving influenza A virus infection induce temporary nonspecific antiviral immunity (2016)

A brief window of antigen-nonspecific protection has been observed after influenza A virus (IAV) infection. Although this temporary immunity has been assumed to be the result of residual nonspecific inflammation, this period of induced immunity has not been fully studied. Because IAV has long been characterized as a cytopathic virus (based on its ability to rapidly lyse most cell types in culture), it has been a forgone conclusion that directly infected cells could not be contributing to this effect. Using a Cre recombinase-expressing IAV, we have previously shown that club cells can survive direct viral infection. We show here not only that these cells can eliminate all traces of the virus and survive but also that they acquire a heightened antiviral response phenotype after surviving. Moreover, we experimentally demonstrate temporary nonspecific viral immunity after IAV infection and show that surviving cells are required for this phenotype. This work characterizes a virally induced modulation of the innate immune response that may represent a new mechanism to prevent viral diseases.
Isolation and Identification of N,N- and N,N' -Dimethylarginine, Nε-Mono-, Di-, and Trimethyllysine, and Glucosylgalactosyl- and Galactosyl-δ-hydroxylysine from Human Urine (1970)

Abstract 1. Eight different substances were isolated in crystalline forms by ion exchange chromatography of the aliphatic basic amino acid fraction of human urine. 2. Structures of guanidino-N,N-dimethylarginine and guanidino-N,N'-dimethylarginine were assigned for two substances by analyses of the degradation products, elemental compositions, and nuclear magnetic resonance spectra. The identities of the compounds were confirmed by synthesis followed by comparison of infrared and nuclear magnetic resonance spectra and of chromatographic properties with those of the isolated compounds. The concentrations of these two compounds in human urine are higher than that of arginine. Their natural occurrence has not been reported previously. 3. Three compounds, Ne-methyl-, Ne,Ne-dimethyl-, and Ne,Ne,Ne-trimethyllysine, were identified by elementary analyses and syntheses. Occurrence of the last two compounds in free state in nature has not been reported previously. 4. Two compounds, glucosylgalactosyl- and galactosyl-δ-hydroxylysine, whose occurrence in human urine has been reported previously, were isolated as crystals for the first time. 5. The concentrations of these N-methyl derivatives of lysine and arginine in the urine were not changed by oral loading of either lysine or arginine. Protein-free diet did not affect the amounts of these compounds in urine. The possibility that these compounds are derived from tissue proteins in which lysine and arginine residues are methylated was discussed.
Identification and Analysis of Staphylococcus aureus Components Expressed by a Model System of Growth in Serum (2001)

A model system mimicking Staphylococcus aureus bacteremia was developed by growth in serum under microaerobic conditions. Eight genes induced by growth in serum were identified, including an antimicrobial peptide biosynthesis locus, amino acid biosynthetic loci, and genes encoding putative surface proteins. Nine independent insertions were found in the major lysine biosynthesis operon, which encodes eight genes, is repressed by lysine in vitro, and is expressed in vivo.
Solution Structure of a Functional Biomimetic and Mechanistic Implications for Nickel Superoxide Dismutases (2008)

The nickel complex of a synthetic nonapeptide (HCDLPCFVY-NH2) is capable of catalytically disproportionating O2(.-) and is thus a functional biomimetic for nickel superoxide dismutases. This represents a simplification as compared to a NiSOD "maquette" that is based on a dodecapeptide that was recently reported [Inorg. Chem. 2006, 45, 2358]. The 3D solution structure reveals that the first six residues form a stable macrocyclic structure with a preformed binding site for Ni(II). Proline 5 exhibits a trans peptide linkage in the biomimetic and a cis conformation in NiSOD enzymes. DFT calculations reveal the source of this preference. Mechanistic consequences for the mode of action (identity of the fifth ligand) are discussed. The SOD activity is compared to enzymatic systems, and selected modifications allowed the biomimetic to be reduced to a functional minimal motif of only six amino acids (ACAAPC-NH2).
cDNA clones coding for the pro-alpha1(IV) chain of human type IV procollagen reveal an unusual homology of amino acid sequences in two halves of the carboxyl-terminal domain. (1985)

We report the isolation and characterization of cDNA clones coding for part of the pro-alpha1(IV) chain of human type IV procollagen. A cDNA library was prepared from total RNA isolated from a cultured human tumor cell line, HT-1080, and screened with a cloned mouse cDNA coding for the pro-alpha1(IV) chain. The largest cDNA clone encoded for 185 amino acid residues of the -Gly-X-Y-sequence of the human pro-alpha1(IV) chain, all of the globular carboxyl-terminal domain, and the 3' noncoding region. The results provide the first complete sequence for the carboxyl-terminal globular portion of a type IV procollagen chain. A striking feature of the carboxyl-terminal globular domain was a homology between the first and second half of the structure. The homology involved all 12 cysteine residues, the spacing between the cysteine residues, and many adjacent amino acids. The results raised the possibility that evolution of the globular domain involved duplication of an ancestral sequence coding for about 100 amino acids, 6 of which were cysteine. The homology, however, was more apparent in the amino acid sequence than in the nucleotide sequence, and, therefore, the results suggested that the homology reflects selective pressure on the function of the protein more than conservation of the nucleotide sequences in the gene. The nucleotide sequences of the 3' noncoding region of the cDNAs contained four polyadenylation signals of AATAAA. Three or four of the polyadenylation signals were probably used in transcription, since one major and two minor smaller RNA species from human skin fibroblasts hydridized with the cDNAs. In further studies, sorted human chromosomes were used to locate the gene for the pro-alpha1(IV) chain on chromosome 13.
Absolute distance measurement system using a femtosecond laser as a modulator (2010)

The generation of broadband microwave frequency comb from a femtosecond pulse train by direct photodetection opens the possibility for high-accuracy length measurements of long distances. We demonstrate a relatively simple realization of this measurement principle: an electronic distance measurement system based on a time-of-flight approach, driven by a femtosecond fibre laser source as a modulator. By the evaluation of the phase shifts of two distinct comb frequencies, a coarse and a fine measurement of the absolute distance can be performed. The range of the measurement system is demonstrated up to a length of 100 m. The experimental comparison of the femtosecond laser system with a conventional reference counting interferometer shows a precision better than ±10 µm at 100 m, corresponding to a relative measurement uncertainty of 1 × 10−7 L. The limiting factors for the measurement uncertainty of the system are theoretically investigated and shown to be of the same order of magnitude.
Epiblast Stem Cell-Based System Reveals Reprogramming Synergy of Germline Factors (2012)

Epigenetic reprogramming in early germ cells is critical toward the establishment of totipotency, but investigations of the germline events are intractable. An objective cell culture-based system could provide mechanistic insight on how the key determinants of primordial germ cells (PGCs), including Prdm14, induce reprogramming in germ cells to an epigenetic ground state. Here we show a Prdm14-Klf2 synergistic effect that can accelerate and enhance reversion of mouse epiblast stem cells (epiSCs) to a naive pluripotent state, including X reactivation and DNA demethylation. Notably, Prdm14 alone has little effect on epiSC reversion, but it enhances the competence for reprogramming and potentially PGC specification. Reprogramming of epiSCs by the combinatorial effect of Prdm14-Klf2 involves key epigenetic changes, which might have an analogous role in PGCs. Our study provides a paradigm toward a systematic analysis of how other key genes contribute to complex and dynamic events of reprogramming in the germline.
A Review of the Most Important Classes of Serine Protease Inhibitors in Insects and Leeches (2005)

The constant increase of life expectancy is associated with major aging of developed populations. This indicates that the new century will have one of most epidemic progressions of cardiovascular, cancer and inflammatory diseases. The high challenge for medical research is to compress such morbidity. Invertebrates have demonstrated to be truly useful models in drug discovery for such aging diseases. The last decade, drug discovery in leeches has opened the gate for new molecules to treat emphysema, coagulation, inflammation, dermatitis and cancer. Also other invertebrates, such as insects, harvest potential interesting molecules, such as serine protease inhibitors that can be exploited by the medical industry. In this review we discuss the most important classes of serine protease inhibitors in insects and leeches. Keywords: hirudin, leech, locust, pacifastin, serine protease inhibitor
HLA Typing by Restriction Fragment Length Polymorphism Analysis (2003)

As a practical method for the identification of human leukocyte antigen (HLA) class I or II alleles, the restriction fragment length polymorphism (RFLP) approach has almost entirely been superceded by other DNA-based methods, in particular those based on polymerase chain reaction (PCR). Historically, RFLP identification of HLA class II polymorphism was important at a time when class II antisera were relatively poorly defined and B cell separation for serological typing from peripheral blood was sometimes problematic. The close correlation found between serology and RFLP pointed to the conserved organization of introns within the major histocompatibility complex (MHC), and the RFLP method quickly established that HLA and disease associations were not due to gross genomic reorganizations (insertions or deletions) in the areas examined. Some relatively recent publications have used RFLP for the identification of HLA class II polymorphism in large population studies (1). In this chapter, the basic method for Southern blot and the identification of RFLP will be outlined. This approach may also find application for the identification of polymorphism in new genes within the MHC and perhaps for the nonclassical HLA genes.
Lack of Antibody Production Following Immunization in Old Age: Association with CD8+CD28− T Cell Clonal Expansions and an Imbalance in the Production of Th1 and Th2 Cytokines (2002)

Although it is generally recognized that the function of the immune system declines with age, the nature of the underlying defects is still poorly understood. We now demonstrate the predominance of CD8(+)CD28(-) T cell clonal expansions in elderly persons who fail to produce specific Abs following influenza vaccination. These clones express effector cell markers and are mostly CD45RA(+). When isolated and put into culture, they are unable to proliferate, but produce IFN-gamma (but no IL-5) upon stimulation with anti-CD3 or autoantigen. These autoreactive CD8(+) type 1 effector cells seem to trigger a Th1 polarization, as CD4(+) T cells from elderly persons without in vivo Ab production produce Th1, but only low amounts of Th2 cytokines upon in vitro stimulation with PHA. Therefore, the increased occurrence of CD8(+)CD28(-) clonal expansions may be decisive for the development of immune deficiency in the elderly.