gebhart/patrepeval huggingface dataset:
4-Coumarate:Coenzyme A Ligase in Hybrid Poplar1 (1998)

The enzyme 4-coumarate:coenzyme A ligase (4CL) is important in providing activated thioester substrates for phenylpropanoid natural product biosynthesis. We tested different hybrid poplar (Populus trichocarpa x Populus deltoides) tissues for the presence of 4CL isoforms by fast-protein liquid chromatography and detected a minimum of three 4CL isoforms. These isoforms shared similar hydroxycinnamic acid substrate-utilization profiles and were all inactive against sinapic acid, but instability of the native forms precluded extensive further analysis. 4CL cDNA clones were isolated and grouped into two major classes, the predicted amino acid sequences of which were 86% identical. Genomic Southern blots showed that the cDNA classes represent two poplar 4CL genes, and northern blots provided evidence for their differential expression. Recombinant enzymes corresponding to the two genes were expressed using a baculovirus system. The two recombinant proteins had substrate utilization profiles similar to each other and to the native poplar 4CL isoforms (4-coumaric acid > ferulic acid > caffeic acid; there was no conversion of sinapic acid), except that both had relatively high activity toward cinnamic acid. These results are discussed with respect to the role of 4CL in the partitioning of carbon in phenylpropanoid metabolism.
Ionic Polysaccharide Hydrogels via the Passerini and Ugi Multicomponent Condensations:  Synthesis, Behavior and Solid-State NMR Characterization (2000)

Original data are provided demonstrating that the title condensations are simple and versatile methods for the synthesis of hydrogels based on a variety of carboxylated polysaccharides. In this work, the biopolymers considered are sodium hyaluronate and sodium alginate. Nonnatural carboxylated polysaccharides were commercial (carboxymethyl)cellulose or were obtained by carboxymethylation or selective oxidation of primary alcohol groups of scleroglucan and dextran. Hydrogels prepared via the Passerini reaction were transparent, alkali labile materials whereas the transparency of the Ugi gels depended on the polysaccharide, the cross-linker, and the degree of cross-linking. The Ugi gels were stable for several months at a pH ranging from 1.3 to 11 and up to temperatures over 90 degrees C. The structure of the networks was studied by means of 13C CP-MAS and 15N CP-MAS NMR spectroscopy. A quantitative NMR analysis and elemental analysis of the dry gels allowed us to estimate the efficiency of the reactions, i.e., the actual degree of cross-linking, which appeared to be about 80% of theoretical. The influence of added salt and pH on the swelling of several Ugi gels with different degrees of cross-linking was studied in a qualitative manner.
Human and avian influenza viruses target different cell types in cultures of human airway epithelium (2004)

The recent human infections caused by H5N1, H9N2, and H7N7 avian influenza viruses highlighted the continuous threat of new pathogenic influenza viruses emerging from a natural reservoir in birds. It is generally believed that replication of avian influenza viruses in humans is restricted by a poor fit of these viruses to cellular receptors and extracellular inhibitors in the human respiratory tract. However, detailed mechanisms of this restriction remain obscure. Here, using cultures of differentiated human airway epithelial cells, we demonstrated that influenza viruses enter the airway epithelium through specific target cells and that there were striking differences in this respect between human and avian viruses. During the course of a single-cycle infection, human viruses preferentially infected nonciliated cells, whereas avian viruses as well as the egg-adapted human virus variant with an avian virus-like receptor specificity mainly infected ciliated cells. This pattern correlated with the predominant localization of receptors for human viruses (2-6-linked sialic acids) on nonciliated cells and of receptors for avian viruses (2-3-linked sialic acids) on ciliated cells. These findings suggest that although avian influenza viruses can infect human airway epithelium, their replication may be limited by a nonoptimal cellular tropism. Our data throw light on the mechanisms of generation of pandemic viruses from their avian progenitors and open avenues for cell level-oriented studies on the replication and pathogenicity of influenza virus in humans.
DNA and RNA Modification Promoted by [Co(H2O)6]Cl2 and KHSO5:  Guanine Selectivity, Temperature Dependence, and Mechanism (1996)

Reaction of a single-stranded oligodeoxynucleotide or a 17-base hairpin-forming oligodeoxynucleotide with CoCl2 and KHSO5 produced guanine-specific cleavage after piperidine treatment. The observed reactivity is shown to be nearly twice that obtained for NiCR (CR = 2,12-dimethyl-3,7,11,17-tetraazabicyclo[11.3.1]heptadeca-1(17),2,11,13,15-pentaene) under equivalent conditions, although NiCR displays a slightly higher degree of selectivity for unpaired guanine residues. Cobalt-induced DNA modification was catalytic with respect to the metal complex and was observed at temperatures up to 80 °C, conditions under which NiCR was ineffective. Mechanistic studies of the cobalt-mediated reaction suggest that SO4•- is responsible for guanine oxidation. Reaction with tRNAPhe induced aniline·HOAc-labile (pH 4.5) lesions also at accessible guanine sites. The high reactivities of G20 and G34 are consistent with attack of SO4•- on the π face of the guanine heterocycle as opposed to recognition of G N7 as proposed for NiCR. CoCl2 should become an extremely attractive probe of nucleic acid structure since it induces base-specific and conformation-specific cleavage of DNA under a much wider variety of experimental conditions than NiCR, acts with a different mode of guanine selectivity than do nickel complexes, and is commercially available.
Nucleotide sequences of cDNAs for human papillomavirus type 18 transcripts in HeLa cells (1988)

HeLa cells expressed 3.4- and 1.6-kilobase (kb) transcripts of the integrated human papillomavirus (HPV) type 18 genome. Two types of cDNA clones representing each size of HPV type 18 transcript were isolated. Sequence analysis of these two types of cDNA clones revealed that the 3.4-kb transcript contained E6, E7, the 5' portion of E1, and human sequence and that the 1.6-kb transcript contained spliced and frameshifted E6 (E6*), E7, and human sequence. There was a common human sequence containing a poly(A) addition signal in the 3' end portions of both transcripts, indicating that they were transcribed from the HPV genome at the same integration site with different splicing. Furthermore, the 1.6-kb transcript contained both of the two viral TATA boxes upstream of E6, strongly indicating that a cellular promoter was used for its transcription.
Pathogenic Potential of Canine Parvovirus Types 2a and 2c in Domestic Cats (2001)

The in vivo pathogenicity of canine parvovirus (CPV) type 2c (strain V203) and of CPV type 2a (strain V154) against cats was investigated. Our results indicate that both types of CPV have the potential to induce disease in cats.
Acetyl Coenzyme A:Salutaridinol-7-O-Acetyltransferase from Papaver somniferum Plant Cell Cultures: (1995)

Acetyl coenzyme A:salutaridinol-7-O-acetyltransferase, a highly substrate-specific enzyme, has been purified nearly 3,000-fold to homogeneity from Papaver somniferum plant cell suspension cultures. Purification was achieved by fractionated ammonium sulfate precipitation, dye-ligand affinity chromatography on matrex red A, gel filtration, ion exchange chromatography on Mono Q and a second dye-ligand affinity chromatography on fractogel TSK AF Blue. The purified enzyme was a single polypeptide with an M(r) = 50,000 displaying an isoelectric point of 4.8, a pH optimum between pH 6 and 9 and a temperature optimum at 47 degrees C. The Km values for the substrate salutaridinol and the co-substrate acetyl co-enzyme A were 7 and 46 microM, respectively. Salutaridinol-7-O-acetyltransferase catalyzes the stoichiometric transfer of the acetyl group from acetyl coenzyme A to the 7-OH group of salutaridinol yielding salutaridinol-7-O-acetate, which is a new intermediate in morphine biosynthesis. Salutaridinol-7-O-acetate undergoes a subsequent spontaneous allylic elimination at pH 8-9, leading to the formation of thebaine (1), the first morphinan alkaloid with the complete pentacyclic ring system, or at pH 7 leading to dibenz[d,f]azonine alkaloids that contain a nine-membered ring. Acetylation and subsequent allylic elimination is a new enzymic mechanism in alkaloid biosynthesis, which in the poppy plant can transform one precursor into alkaloids possessing markedly different ring systems, depending on the reaction pH.
Physical Properties of the Aminoazobenzene Dyes. IX. Absorption Spectra in Alcohol and Acid Solution of Disazobenzene Dyes1 (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhysical Properties of the Aminoazobenzene Dyes. IX. Absorption Spectra in Alcohol and Acid Solution of Disazobenzene Dyes1EUGENE SAWICKICite this: J. Org. Chem. 1958, 23, 4, 532–535Publication Date (Print):April 1, 1958Publication History Published online1 May 2002Published inissue 1 April 1958https://pubs.acs.org/doi/10.1021/jo01098a008https://doi.org/10.1021/jo01098a008research-articleACS PublicationsRequest reuse permissionsArticle Views214Altmetric-Citations11LEARN 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
Entertainment Video-On-Demand At T1 Transmission Speeds (1.5 Mb/S ) (1988)

With the emergence of high speed packet networks as proposed in CCITT Study Group XVIII, metropolitan area networks as defined in IEEE 802.6, and multimedia, high capacity storage such as CDROMs, there is renewed interest among image processing specialists in achieving high bit rate compressions without severe compromises in image quality. Advances in signal processing techniques and their implementation in VLSI have lead to the point where it is now possible to digitally encode full motion video sequences at less than 1.5 Mbps with a spatial and temporal resolution comparable to that commonly viewed on a standard VHS video tape recorder. Work at the David Sarnoff Labs on DVI encoding for CD-ROMs has demonstrated impressive image quality for scenes compressed to an average of l.SMbps. Lippman and his colleagues at MIT Media Lab, also are making significant progress in improving the image quality while maintaining the same 1.5 Mbps rate (important because it is the transfer rate of CD-ROMs). Recently, work at Bellcore analyzed a broad spectrum of video material and determined the feasibility of achieving 1.5Mbps while maintaining near VCR quality.
Loss of glucose-induced insulin secretion and GLUT2 expression in transplanted beta-cells (1995)

Either 200 or 400 syngeneic islets were transplanted under the kidney capsule of normal or streptozocin-induced diabetic B6/AF1 mice. The diabetic mice with 400 islets became normoglycemic, but those with 200 islets, an insufficient number, were still diabetic after the transplantation (Tx). Two weeks after Tx, GLUT2 expression in the islet grafts was evaluated by immunofluorescence and Western blots, and graft function was examined by perfusion of the graft-bearing kidney. Immunofluorescence for GLUT2 was dramatically reduced in the beta-cells of grafts with 200 islets exposed to hyperglycemia. However, it was plentiful in grafts with 400 islets in a normoglycemic environment. Densitometric analysis of Western blots on graft homogenates demonstrated that GLUT2 protein levels in the islets, when exposed to chronic hyperglycemia for 2 weeks, were decreased to 16% of those of normal recipients. Moreover, these grafts had defective glucose-induced insulin secretion, while the effects of arginine were preserved. We conclude that GLUT2 expression in normal beta-cells is promptly down-regulated during exposure to hyperglycemia and may contribute to the loss of glucose-induced secretion of diabetes.
Mapping the Functional Domains of Nucleolar Protein B23 (2000)

Protein B23 is a multifunctional nucleolar protein whose cellular location and characteristics strongly suggest that it is a ribosome assembly factor. The protein has nucleic acid binding, ribonuclease, and molecular chaperone activities. To determine the contributions of unique polypeptide segments enriched in certain classes of amino acid residues to the respective activities, several constructs that produced N- and C-terminal deletion mutant proteins were prepared. The C-terminal quarter of the protein was shown to be necessary and sufficient for nucleic acid binding. Basic and aromatic segments at the N- and C-terminal ends, respectively, of the nucleic acid binding region were required for activity. The molecular chaperone activity was contained in the N-terminal half of the molecule, with important contributions from both nonpolar and acidic regions. The chaperone activity also correlated with the ability of the protein to form oligomers. The central portion of the molecule was required for ribonuclease activity and possibly contains the catalytic site; this region overlapped with the chaperone-containing segment of the molecule. The C-terminal, nucleic acid-binding region enhanced the ribonuclease activity but was not essential for it. These data suggest that the three activities reside in mainly separate but partially overlapping segments of the polypeptide chain.
Suppression of TGF-ß signaling in both normal conjunctival fibroblasts and pterygial body fibroblasts by amniotic membrane (2000)

Amniotic membrane matrix uniquely suppresses TGF- beta signaling in both types of fibroblasts. It may also suppress signaling via CD44, b1 integrin and FGFR1/flg. As a result, the phenotype may become less mitogenic, contractile and fibrogenic. These data support in part why amniotic membrane transplantation has an anti-scarring effect for conjunctival surface reconstruction.
Cloning of the murine c-fgr proto-oncogene cDNA and induction of c-fgr expression by proliferation and activation factors in normal bone marrow-derived monocytic cells. (1989)

Normal murine bone marrow-derived monocytic cells were found to contain transcripts for c-fgr and hck, two members of the src family of proto-oncogene tyrosine kinases. While hck transcripts were increased only in response to bacterial lipopolysaccaride (LPS), expression of c-fgr was transiently induced both by the monocyte/macrophage proliferative stimulus CSF-1 as well as by signals which activate monocytic cells to functional states (granulocyte-macrophage colony stimulating factor (GM-CSF), LPS, and gamma interferon). These data suggest that these highly related tyrosine kinases may differentially mediate the effects of distinct monocyte/macrophage stimuli; and, that the c-fgr proto-oncogene in particular, which in normal cells is selectively expressed in monocytes, may play a pivotal functional role in these cells. A 2.2 kb cDNA clone, containing a 1551 base pair open reading frame encoding a protein with all of the hallmarks of a protein-tyrosine kinase, was isolated from a cDNA library made from RNA of CSF-1-stimulated bone marrow-derived monocytic cells. This clone had the highest homology to v-fgr and likely encodes the murine c-fgr transcript expressed by normal monocytes. However, when compared to sequences previously reported for human c-fgr derived from EBV-transformed B cells and heterogeneous peripheral blood cells, the c-fgr cDNA derived from normal murine monocytic cells differed significantly in sequence from amino acids 12-62 in the amino terminal domain of the protein which may mediate the substrate specificity and subcellular location of the src family of protein-tyrosine kinases.
Mutational and expressional analysis of SMC2 gene in gastric and colorectal cancers with microsatellite instability (2014)

Structural maintenance of chromosomes 2 (SMC2) gene encodes condensin complexes that are required for proper chromosome segregation and maintenance of chromosomal stability. Although cells with defective chromosome segregation become aneuploid and are prone to harbor chromosome instability, pathologic implications of SMC2 gene alterations are largely unknown. In a public database, we found that SMC2 gene had mononucleotide repeats that could be mutated in cancers with microsatellite instability (MSI). In this study, we analyzed these repeats in 32 gastric cancers (GC) with high MSI (MSI-H), 59 GC with low MSI (MSI-L)/stable MSI (MSS), 43 colorectal cancers (CRC) with MSI-H and 60 CRC with MSI-L/MSS by single-strand conformation polymorphism (SSCP) and DNA sequencing. We also analyzed SMC2 protein expression in GC and CRC tissues using immunohistochemistry. We found SMC2 frameshift mutations in two GC and two CRC that would result in truncation of SMC2. The mutations were detected exclusively in MSI-H cancers, but not in MSI-L/MSS cancers. Loss of SMC2 expression was observed in 22% of GC and 25% of CRC. Of note, all of the cancers with SMC2 frameshift mutations displayed loss of SMC2 expression. Also, both GC and CRC with MSI-H had significantly higher incidences in SMC2 frameshift mutations and loss of SMC2 expression than those with MSI-L/MSS. Our data indicate that SMC2 gene is altered by both frameshift mutation and loss of expression in GC and CRC with MSI-H, and suggest that SMC2 gene alterations might be involved in pathogenesis of these cancers.
A Closer Look at the Active Site of γ-Class Carbonic Anhydrases:  High-Resolution Crystallographic Studies of the Carbonic Anhydrase from Methanosarcina thermophila, (2000)

The prototype of the gamma-class of carbonic anhydrase has been characterized from the methanogenic archaeon Methanosarcina thermophila. Previously reported kinetic studies of the gamma-class carbonic anhydrase are consistent with this enzyme having a reaction mechanism similar to that of the mammalian alpha-class carbonic anhydrase. However, the overall folds of these two enzymes are dissimilar, and apart from the zinc-coordinating histidines, the active site residues bear little resemblance to one another. The crystal structures of zinc-containing and cobalt-substituted gamma-class carbonic anhydrases from M. thermophila are reported here between 1.46 and 1.95 A resolution in the unbound form and cocrystallized with either SO(4)(2)(-) or HCO(3)(-). Relative to the tetrahedral coordination geometry seen at the active site in the alpha-class of carbonic anhydrases, the active site of the gamma-class enzyme contains additional metal-bound water ligands, so the overall coordination geometry is trigonal bipyramidal for the zinc-containing enzyme and octahedral for the cobalt-substituted enzyme. Ligands bound to the active site all make contacts with the side chain of Glu 62 in manners that suggest the side chain is likely protonated. In the uncomplexed zinc-containing enzyme, the side chains of Glu 62 and Glu 84 appear to share a proton; additionally, Glu 84 exhibits multiple conformations. This suggests that Glu 84 may act as a proton shuttle, which is an important aspect of the reaction mechanism of alpha-class carbonic anhydrases. A hydrophobic pocket on the surface of the enzyme may participate in the trapping of CO(2) at the active site. On the basis of the coordination geometry at the active site, ligand binding modes, the behavior of the side chains of Glu 62 and Glu 84, and analogies to the well-characterized alpha-class of carbonic anhydrases, a more-defined reaction mechanism is proposed for the gamma-class of carbonic anhydrases.
Expression and characterization of recombinant human eosinophil-derived neurotoxin and eosinophil-derived neurotoxin-anti-transferrin receptor sFv. (1994)

The gene for the human recombinant eosinophil-derived neurotoxin (rEDN) was synthesized and fused to the gene encoding a single chain antibody (sFv) to the human transferrin receptor (EDNsFv). Both rEDN and EDNsFv were expressed as insoluble proteins in inclusion bodies in Escherichia coli BL21(DE3). Following denaturation and renaturation, EDN and EDNsFv were partially purified by chromatography on heparin-Sepharose. Final purification of EDN was achieved by Sephadex G-100, whereas EDNsFv which contained a 6-histidyl residue carboxyl terminus was highly purified using the metal chelate resin, Ni(2+)-nitriloacetic acid. Whereas the recombinant EDN had ribonuclease activity that was similar to the native protein, the fusion protein had enzymatic activity that was 6-13% that of native EDN. The fusion protein was able to bind to the human transferrin receptor. In contrast to rEDN that had no inherent cytotoxicity to human tumor cells, the EDNsFv fusion protein was cytotoxic to human leukemia cells that express the human transferrin receptor with an IC50, 0.2-1 nM. At 1.3 nM EDNsFv, no cytotoxicity was observed on cells that lack the human transferrin receptor. Free antibody to the human transferrin receptor, E6, inhibited the cytotoxicity of the EDNsFv. Human enzymes may be engineered to acquire cytotoxic properties by fusing them to antibodies. Thus, they may be candidates for the construction of immunofusion proteins that may be less immunogenic than immunotoxins containing bacterial- or plant-derived toxin moieties.
New attachment formation in the human periodontium by guided tissue regeneration Case reports (1986)

The aim of the present study was to evaluate whether a regenerative surgical procedure, based on guided tissue regeneration, could predictably result in the formation of a new attachment in human teeth. The material included 12 teeth in 10 patients with advanced periodontal disease. Following flap elevation, scaling, root planing and removal of granulation tissue, a teflon membrane was placed over the denuded root surface in such a way that the epithelium and the gingival connective tissue were prevented from reaching contact with the root during healing. The flap was replaced on the outer surface of the membrane and secured with interdental sutures. This design of wound preparation gives preference to the cells originating from the periodontal ligament (PDL-cells) to repopulate the wound area adjacent to the root. Histologic analysis of the result of treatment was made in 5 of the 12 teeth scheduled for extraction. In the remaining 7 teeth, the result was evaluated using clinical measurements. The result of healing disclosed that in all teeth treated, substantial amounts of new attachment had formed. This suggests that predictable restitution of the attachment apparatus can be accomplished by using a method of treatment which is based on the principle of guided tissue regeneration.