gebhart/patrepeval huggingface dataset:
Reaction Mechanisms of Homodimeric Plant Polyketide Synthases (Stilbene and Chalcone Synthase) (1995)

Stilbene (STS) and chalcone (CHS) synthases are homodimeric, related plant-specific polyketide synthases. Both perform a sequential condensation of three acetate units to a starter residue to form a tetraketide intermediate that is folded to the ring systems specific to the different products. Protein cross-linking and site-directed mutagenesis identified a subunit contact site in position 158, close to the active site (Cys169). This suggested that the active site pockets may be neighboring, possibly alternating in the condensing reactions rather than acting independently. This was investigated by co-expression of active site mutants with differently mutated, inactive proteins. With both STS and CHS, the heterodimers synthesized the end products, indicating that each subunit performed all three condensations. In co-action with a monomeric reductase, CHS also synthesizes 6′-deoxychalcone, but with the chalcone as second product when using plant preparations. The two enzymes expressed as single species in Escherichia coli synthesized both products, and both were also obtained with a CHS heterodimer containing a single active site. The results showed that 6′-deoxychalcone synthesis required no other plant factor and that the formation of two products may be an intrinsic property of the interaction between dimeric CHS and monomeric reductase. Stilbene (STS) and chalcone (CHS) synthases are homodimeric, related plant-specific polyketide synthases. Both perform a sequential condensation of three acetate units to a starter residue to form a tetraketide intermediate that is folded to the ring systems specific to the different products. Protein cross-linking and site-directed mutagenesis identified a subunit contact site in position 158, close to the active site (Cys169). This suggested that the active site pockets may be neighboring, possibly alternating in the condensing reactions rather than acting independently. This was investigated by co-expression of active site mutants with differently mutated, inactive proteins. With both STS and CHS, the heterodimers synthesized the end products, indicating that each subunit performed all three condensations. In co-action with a monomeric reductase, CHS also synthesizes 6′-deoxychalcone, but with the chalcone as second product when using plant preparations. The two enzymes expressed as single species in Escherichia coli synthesized both products, and both were also obtained with a CHS heterodimer containing a single active site. The results showed that 6′-deoxychalcone synthesis required no other plant factor and that the formation of two products may be an intrinsic property of the interaction between dimeric CHS and monomeric reductase.
Stress response of yeast (1993)

Research Article| February 15 1993 Stress response of yeast W H Mager; W H Mager *Department of Biochemistry and Molecular Biology, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar P M Ferreira P M Ferreira †Departamento de Biologia Molecular, Instituto de Ciencias Biomedicas Abel Salazar, Universidade do Porto, 4000 Porto, Portugal Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1993) 290 (1): 1–13. https://doi.org/10.1042/bj2900001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation W H Mager, P M Ferreira; Stress response of yeast. Biochem J 15 February 1993; 290 (1): 1–13. doi: https://doi.org/10.1042/bj2900001 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1993 The Biochemical Society, London1993 Article PDF first page preview Close Modal You do not currently have access to this content.
FDC-SP, a Novel Secreted Protein Expressed by Follicular Dendritic Cells (2002)

To define better the molecular basis for follicular dendritic cell (FDC) function, we used PCR-based cDNA subtraction to identify genes specifically expressed in primary FDC isolated from human tonsils. In this work we report the discovery of a novel gene encoding a small secreted protein, which we term FDC-SP (FDC secreted protein). The FDC-SP gene lies on chromosome 4q13 adjacent to clusters of proline-rich salivary peptides and C-X-C chemokines. Human and mouse FDC-SP proteins are structurally unique and contain a conserved N-terminal charged region adjacent to the leader peptide. FDC-SP has a very restricted tissue distribution and is expressed by activated FDCs from tonsils and TNF-alpha-activated FDC-like cell lines, but not by B cell lines, primary germinal center B cells, or anti-CD40 plus IL-4-activated B cells. Strikingly, FDC-SP is highly expressed in germinal center light zone, a pattern consistent with expression by FDC. In addition, FDC-SP is expressed in leukocyte-infiltrated tonsil crypts and by LPS- or Staphylococcus aureus Cowan strain 1-activated leukocytes, suggesting that FDC-SP can also be produced in response to innate immunity signals. We provide evidence that FDC-SP is posttranslationally modified and secreted and can bind to the surface of B lymphoma cells, but not T lymphoma cells, consistent with a function as a secreted mediator acting upon B cells. Furthermore, we find that binding of FDC-SP to primary human B cells is markedly enhanced upon activation with the T-dependent activation signals such as anti-CD40 plus IL-4. Together our data identify FDC-SP as a unique secreted peptide with a distinctive expression pattern within the immune system and the ability to specifically bind to activated B cells.
Extending a relational DBMS to support complex objects (2003)

The definition and manipulation of complex objects in an extended relational database management system are discussed. Complex object types are defined as relation domains encapsulated within methods written in LISP or C. Objects are structured using the set, array and list constructors concepts. Structured objects are manipulated using built-in functions. For a given application, the database administrator introduces the complex domains with the encapsulating methods within the DBMS meta-base using a specific command. Complex domains can be described using an hierarchy which makes possible the inheritance of methods along domains. The domain methods are directly used in the external data manipulation language, which is an extended version of SQL with object-oriented features. Graphical interface procedures are available to input and display nonstandard data. A fully running version of the system is commercially available for Sun Unix workstations. Only the list constructor is available in the current version.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Time to Take Myocardial Reperfusion Injury Seriously (2008)

Every year, 500,000 people in the United States have an ST-elevation myocardial infarction.1 Timely and effective reperfusion with the use of either primary percutaneous coronary intervention (PCI) or thrombolytic therapy remains the most effective treatment strategy for limiting the size of the myocardial infarct, preserving left ventricular ejection fraction, and improving the clinical outcomes in such patients. However, despite optimal reperfusion therapy, morbidity and mortality remain substantial, with about 5 to 6% of patients having a subsequent cardiovascular event by 30 days.2 One treatment strategy that might reduce the size of the infarct and improve the clinical outcomes in these . . .
Scaling-up from nutrient physiology to the size-structure of phytoplankton communities (2006)

In many community assemblages, the abundance of organisms is a power-law function of organism size. In phytoplankton communities, changes in size structure associated with increases in resource availability and total biomass have often been interpreted as a release from grazer control. A metapopulation-like approach is used to scale up from the individual physiological responses to environmental conditions to community size structure assuming the community taxonomic composition reflects the species pool. We show that the size scaling of cellular nutrient requirements and growth can cause (1) the power-law relationship between cell size and abundance, (2) dominance of small phytoplankton cells under oligotrophic conditions, and (3) relative increase in abundance of larger phytoplankton cells under eutrophic conditions. If physiological differences associated with the taxonomic composition of different community size fractions are considered, then the model can replicate detailed field observations such as the absence of small, slow-growing Prochlorococcus spp. and the relative dominance of large diatom species in nutrient-rich, upwelling regions of the ocean.
Synthesis and central nervous system activities of certain fluorine-containing 3-substituted indol-2-ones. (1984)

Several fluorine-containing 3- aroylmethyl -3-hydroxyindol-2-ones (4a-g), 3- aroylmethyleneindol -2-ones (5a-g) and 3- aroylmethylindol -2-ones (6a-g) were synthesized from the corresponding fluorine-containing indole-2,3-diones and appropriate ketones. The compounds were characterized by spectral studies. Representative compounds of each series were tested on mice for CNS activities, viz. analgesic and anticonvulsant and the effects were also observed against amphetamine-induced stereotypy, on conditioned avoidance response and on potentiation of pentobarbitone sodium hypnosis. Of the compounds examined, the greatest degree of activity was observed in 3- aroyl - methyleneindol -2-ones with a pronounced unsaturation in the system.
Positron emission tomography radioligands for in vivo imaging of Aβ plaques (2013)

The development of positron emission tomography (PET) radioligands for the non-invasive imaging of amyloid-β plaque burden has been the focus of intense research efforts over the last decade. A variety of structural backbones have been investigated and several radiolabeled molecules have been evaluated in phase I (and later) clinical studies. These efforts have been driven by the desire not only to develop a suitable diagnostic imaging agent but also to develop a means to evaluate potential therapies for Alzheimer's disease. This review focuses on the development of these ligands, as well as the radiochemistry and current regulatory status of these PET radioligands. Particular attention is given to those ligands that have progressed to the later stages of drug development (phase II/III clinical trial studies) or approved New Drug Application status.
A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment (2003)

The targeting of molecular repertoires to complex systems rather than biochemically pure entities is an accessible approach that can identify proteins of biological interest. We have probed antigens presented by a monolayer of tumor cells for their ability to interact with a pool of aptamers. A glioblastoma-derived cell line, U251, was used as the target for systematic evolution of ligands by exponential enrichment by using a single-stranded DNA library. We isolated specifically interacting oligonucleotides, and biochemical strategies were used to identify the protein target for one of the aptamers. Here we characterize the interaction of the DNA aptamer, GBI-10, with tenascin-C, an extracellular protein found in the tumor matrix. Tenascin-C is believed to be involved in both embryogenesis and oncogenesis pathways. Systematic evolution of ligands by exponential enrichment appears to be a successful strategy for the a priori identification of targets of biological interest within complex systems.
Supramolecular assemblies of carotenoids (2001)

Carotenoid self-assemblies were formed by aqueous dilution of ethanolic solutions. The four 3',6'-epimers of capsanthol ((all-E,3R,5'R)-3,3',6'-trihydroxy-beta,kappa-carotene) give rise to right- and left-handed card-pack and head-to-tail types of self-assemblies detected by exciton couplets appearing in the CD spectra. Slow kinetics of formation followed for some of the aggregates indicate the complexity of the process. The exciton signals do not appear from equimolar mixtures of related compounds that produce identical type of aggregates of opposite sense on their own. Transformation of self-assembly may reflect the population of kappa-ring rotamers.
A β-Peptide Reverse Turn that Promotes Hairpin Formation (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA β-Peptide Reverse Turn that Promotes Hairpin FormationYong Jun Chung, Laurie A. Christianson, Heather E. Stanger, Douglas R. Powell, and Samuel H. GellmanView Author Information Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706 Cite this: J. Am. Chem. Soc. 1998, 120, 40, 10555–10556Publication Date (Web):September 29, 1998Publication History Received29 June 1998Published online29 September 1998Published inissue 1 October 1998https://pubs.acs.org/doi/10.1021/ja982249ahttps://doi.org/10.1021/ja982249arapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views812Altmetric-Citations128LEARN 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:Amides,Conformation,Hydrogen,Noncovalent interactions,Nucleic acid structure Get e-Alerts
Identification of an HLA‐DR‐restricted peptide epitope with a promiscuous binding pattern derived from the cancer testis antigen HOM‐MEL‐40/SSX2 (2004)

The SSX2 gene encodes the tumor-specific antigen HOM-MEL-40/SSX2 expressed in a broad spectrum of tumors of different origin, against which humoral and CD8+ T-cell-mediated MHC-I-restricted responses have been demonstrated. Searching for promiscuous MHC-II-restricted peptides that might be suitable as a CD4+ stimulating vaccine for many patients, we used the SYFPEITHI algorithm and identified a HOM-MEL-40/SSX2-derived pentadecamer epitope (p45-59) that induced specific CD4+ T-cell responses restricted by the HLA-DRB1 subtypes *0701, *1101 and *1302 that have a cumulative prevalence of approximately 25% in the Caucasian population. The CD4+-mediated response against p45-59 and its DR restriction was demonstrated by inhibition with anti-CD4 and HLA-DR antibodies, respectively, and by blocking experiments using HLA-specific antibodies. The natural processing and presentation of p45-59 was demonstrated by recognition of the SSX2+ melanoma cell line Me 275 as well as autologous and allogeneic dendritic cells pulsed with whole-protein SSX2 by T cells with specificity for p45-59. p45-59 was able to induce responses in 3/6 breast cancer patients and 1/5 healthy controls. No correlation was found between CD4+ T-cell responses against p45-59 reactivity and anti-SSX2 antibody titers in the serum of patients, suggesting that CD4+ and B-cell responses are regulated independently. p45-59 holds promise as a broadly applicable peptide vaccine for patients with SSX2-positive neoplasms.
Liquid Crystalline Cholestanyl and Cholesteryl Ether Lipids (1994)

Abstract A homologous series of 3ß-alkyl cholestanyl ethers was prepared and their liquid crystalline properties were studied. The compounds with alkyl groups consisting of n = 3 to n = 20 carbon atoms exhibit a cholesteric phase. In addition, the ethers with alkyl groups consisting of n = 9 to n = 18 carbon atoms show a SA phase. Ordered or tilted smectic phases or blue phases are not observed. The SA phase shows unusual textures several tenths of a degree below the transition to the cholesteric phase. The results obtained are compared with those of 3ß-alkyl cholesteryl ethers and other homologous series of cholestanyl derivatives such as cholestanyl esters and cholestanyl carbonates.
Hierarchical faceted metadata in site search interfaces (2002)

One of the most pressing usability issues in the design of large web sites is that of the organization of search results. A previous study on a moderate-sized web site indicated that users understood and preferred dynamically organized faceted metadata over standard search. We are now examining how to scale this approach to very large collections, since it is difficult to present hierarchical faceted metadata in a manner appealing and understandable to general users. We have iteratively designed and tested interfaces that address these design challenges; the most recent version is receiving enthusiastic responses in ongoing usability studies.
Protein expression and secretion in the yeastYarrowia lipolytica (2002)

Strains and vectors for protein expression and secretion have been developed in the yeast Yarrowia lipolytica. Host strains were constructed with non-reverting auxotrophic markers, deletions of protease-encoding genes, and carrying a docking platform. To drive transcription, either the synthetic hp4d or the inducible POX2 promoter were used. Protein secretion is either directed by the targeting sequence of the alkaline extracellular protease or the extracellular lipase (LIP2p) signal sequence. We describe a set of vectors based on these promoters, targeting sequences and two URA3 alleles as selection markers. The wild-type URA3 allele, ura3d1, was used for single-copy integration and a mutant URA3 allele, ura3d4, was used to select for multi-copy integration into the genome. These vectors were used to express the Y. lipolytica extracellular lipase LIP2p and the Aspergillus oryzae leucine amino peptidase II. Lipase production under the control of the hp4d promoter by a strain containing a single copy reached 1000 U ml−1 in shake flasks, while a strain containing multiple integrations reached 2000 U ml−1 in shake flasks, 11 500 U ml−1 in batch and 90 500 U ml−1 in fed batch. Leucine amino peptidase production under the control of the hp4d promoter reached 320 mU ml−1 in batch with a mono-copy lapA integrant and 28 000 mU ml−1 in fed batch with a multi-copy transformant.
Determination of pyrophosphorylated forms of lipid A in Gram-negative bacteria using a multivaried mass spectrometric approach (2008)

Lipid A isolated from several bacteria (Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, and various strains of Yersinia) showed abundant formation of pyrophosphate anions upon ion dissociation. Pyrophosphate [H(3)P(2)O(7)](-) and/or [HP(2)O(6)](-) anions were observed as dominant fragments from diphosphorylated lipid A anions regardless of the ionization mode (matrix-assisted laser desorption ionization or electrospray ionization), excitation mode (collisional activation or infrared photoexcitation), or mass analyzer (time-of-flight/time-of-flight, tandem quadrupole, Fourier transform-ion cyclotron resonance mass spectrometry). Dissociations of anions from model lipid phosphate, pyrophosphate, and hexose diphosphates confirmed that pyrophosphate fragments were formed abundantly only in the presence of an intact pyrophosphate group in the analyte molecule and were not due to intramolecular rearrangement upon ionization, ion-molecule reactions, or rearrangement following activation. This indicated that pyrophosphate groups are present in diphosphorylated lipid A from a variety of Gram-negative bacteria.
Plasticity of nonneuronal brain tissue: Roles in developmental disorders (2004)

Neuronal and nonneuronal plasticity are both affected by environmental and experiential factors. Remodeling of existing neurons induced by such factors has been observed throughout the brain, and includes alterations in dendritic field dimensions, synaptogenesis, and synaptic morphology. The brain loci affected by these plastic neuronal changes are dependent on the type of experience and learning. Increased neurogenesis in the hippocampal dentate gyrus is a well-documented response to environmental complexity ("enrichment") and learning. Exposure to challenging experiences and learning opportunities also alters existing glial cells (i.e., astrocytes and oligodendrocytes), and up-regulates gliogenesis, in the cerebral cortex and cerebellum. Such glial plasticity often parallels neuronal remodeling in both time and place, and this enhanced morphological synergism may be important for optimizing the functional interaction between glial cells and neurons. Aberrant structural plasticity of nonneuronal elements is a contributing factor, as is aberrant neuron plasticity, to neurological and developmental disorders such as epilepsy, autism, and mental retardation (i.e., fragile X syndrome). Some of these nonneuronal pathologies include abnormal cerebral and cerebellar white matter and myelin-related proteins in autism; abnormal myelin basic protein in fragile X syndrome (FXS); and abnormal astrocytes in autism, FXS, and epilepsy. A number of recent studies demonstrate the possibility of using environmental and experiential intervention to reduce or ameliorate some of the neuronal and nonneuronal abnormalities, as well as behavioral deficits, present in these neurological and developmental disorders.
Fabrication of Miniature PO2 and pH Sensors Using Microelectronic Techniques (1982)

Miniature PO2 and pH sensors can be used in combination with enzymatic catalysts such as glucose oxidase and glucose dehydrogenase as the basis for the development of a small glucose sensor. The applications of microelectronic techniques such as photolithography techniques and thick- and thin-film metallization are novel approaches in fabricating highly uniform and reproducible sensors that are relatively simple to calibrate and operate.
Brain Metabolism during Fasting* (1967)

Catheterization of cerebral vessels in three obese patients undergoing 5-6 wk of starvation demonstrated that beta-hydroxybutyrate and acetoacetate replaced glucose as the predominant fuel for brain metabolism. A strikingly low respiratory quotient was also observed, suggesting a carboxylation mechanism as a means of disposing of some of the carbon of the consumed substrates.
Hydrodynamic Focusing for a Micromachined Flow Cytometer (2001)

This paper describes hydrodynamic focusing inside a micromachined flow cytometer. Flow cytometry is a process whereby cells are analyzed and sorted based on hydrodynamic focusing phenomenon and specific cellular characteristics. In this study, the hydrodynamic focusing phenomenon is first modeled by employing potential flow theory. Then the flow field inside the flow cytometer is numerically simulated. The effect of the device geometry and relative sheath and sample flow rate on the focusing of the center flow is explored systematically. At last, a micromachine-based flow chamber is designed and fabricated on plastic substrates as a micro flow cytometer. Hydrodynamic focusing is verified with the use of microscopic visualization of water sheath flows and dye-containing sample flow. Experimental data indicate that the size of focused sample stream can be reduced to about 3 μm, which is applicable to cell sorting and counting.