gebhart/patrepeval huggingface dataset:
Catalytic and Biophysical Properties of a Nitrogenase Apo-MoFe Protein Produced by a nifB-Deletion Mutant of Azotobacter vinelandii (1998)

A Zn-immobilized metal-affinity chromatography technique was used to purify a poly-histidine-tagged, FeMo-cofactorless MoFe protein (apo-MoFe protein) from a nifB-deletion mutant of Azotobacter vinelandii. Apo-MoFe protein prepared in this way was obtained in sufficient concentrations for detailed catalytic, kinetic, and spectroscopic analyses. Metal analysis and electron paramagnetic resonance spectroscopy (EPR) were used to show that the apo-MoFe protein does not contain FeMo-cofactor. The EPR of the as-isolated apo-MoFe protein is featureless except for a minor S = 1/2 signal probably arising from the presence of either a damaged P cluster or a P cluster precursor. The apo-MoFe protein has an alpha2beta2 subunit composition and can be activated to 80% of the theoretical MoFe protein value by the addition of isolated FeMo-cofactor. Oxidation of the as-isolated apo-MoFe protein by indigodisulfonate was used to elicit the parallel mode EPR signal indicative of the two-electron oxidized form of the P cluster (P2+). The midpoint potential of the PN/P2+ redox couple for the apo-MoFe protein was shown to be shifted by -63 mV when compared to the same redox couple for the intact MoFe protein. Although the apo-MoFe protein is not able to catalyze the reduction of substrates under turnover conditions, it does support the hydrolysis of MgATP at 60% of the rate supported by the MoFe protein when incubated in the presence of Fe protein. The ability of the apo-MoFe protein to specifically interact with the Fe protein was also shown by stopped-flow techniques and by formation of an apo-MoFe protein-Fe protein complex. Finally, the two-electron oxidized form of the apo-MoFe protein could be reduced to the one-electron oxidized form (P1+) in a reaction that required Fe protein and MgATP. These results are interpreted to indicate that the apo-MoFe protein produced in a nifB-deficient genetic background [corrected] contains intact P clusters and P cluster polypeptide environments. Small changes in the electronic properties of P clusters contained within the apo-MoFe protein are most likely caused by slight perturbations in their polypeptide environments.
Cassettes of theStreptoalloteichus hindustanus blegene for transformation of lower and higher eukaryotes to phleomycin resistance (1990)

Journal Article Cassettes of the Streptoalloteichus hindustanus ble gene for transformation of lower and higher eukaryotes to phleomycin resistance Get access Daniel Drocourt, Daniel Drocourt Search for other works by this author on: Oxford Academic PubMed Google Scholar Thierry Calmels, Thierry Calmels Search for other works by this author on: Oxford Academic PubMed Google Scholar Jean-Paul Reynes, Jean-Paul Reynes Search for other works by this author on: Oxford Academic PubMed Google Scholar Michel Baron, Michel Baron 1Centre de Recherche en Biochimie et Génétique Cellulaire, Université Paul Sabatier118 route de Narbonne, 31062 Toulouse Cedex, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Gérard Tiraby Gérard Tiraby 1Centre de Recherche en Biochimie et Génétique Cellulaire, Université Paul Sabatier118 route de Narbonne, 31062 Toulouse Cedex, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 13, 11 July 1990, Page 4009, https://doi.org/10.1093/nar/18.13.4009 Published: 11 July 1990
A Scalable and Accurate Method for Quantifying Vector Genomes of Recombinant Adeno-Associated Viruses in Crude Lysate (2017)

Increasing interest and application of recombinant adeno-associated viruses (rAAVs) in basic and clinical research have urged efforts to improve rAAV production quality and yield. Standard vector production workflows call for genome titration of purified vectors at the endpoint of production to assess yield. Unfortunately, quality control measures for preparations during mid-production steps and economical means to assess the fidelity of multiple batches of rAAV preparations are lacking. Here we describe a scalable and accurate method for the direct quantitative polymerase chain reaction (qPCR) titration of rAAV genomes in crude lysate. Lysate samples are pretreated with DNase I to remove vector and packaging plasmid DNAs, followed by proteinase K to release endonuclease-resistant packaged viral genomes and to proteolyze factors inherent to crude lysates that can impinge upon quantitative PCR efficiencies. We show that this method is precise, scalable, and applicable for vector genome titrations of both single-stranded and self-complementary AAV genomes irrespective of serotype differences-a major limitation for standard lysate transduction methods that indirectly screen for vector packaging efficiency. Our described method therefore represents a significant improvement to rAAV vector production in terms of alleviating time and cost burdens, in-process quality control assessment, batch/lot monitoring in large-scale preparations, and good manufacturing practices.
Aberrant methylation of SPARC in human lung cancers (2005)

SPARC (secreted protein acidic and rich in cysteine) is an extracellular Ca2+-binding matricellular glycoprotein associated with the regulation of cell adhesion and growth. We investigated loss of expression of SPARC gene and promoter methylation in lung cancers and correlated the data with clinicopathological features. We observed loss of SPARC expression in 12 of 20 (60%) lung cancer cell lines. Treatment of expression-negative cell lines with a demethylating agent restored expression in all cases. Methylation frequencies of SPARC gene were 55% in 20 lung cancer cell lines. Primary tumours had methylation at a rate of 69% (119 of 173), while nonmalignant lung tissues (n=60) had very low rates (3%). In lung adenocarcinomas, SPARC methylation correlated with a negative prognosis (P=0.0021; relative risk 4.65, 95% confidence interval 1.75-12.35, multivariate Cox's proportional-hazard model). Immunostaining revealed protein expression in bronchial epithelium (weak intensity) and in juxtatumoral stromal tissues (strong intensity) accompanied by frequent loss in cancer cells that correlated with the presence of methylation (P<0.001). Our findings are of biological interest and potentially of clinical importance in human lung cancers.
Susceptibility of AKXD recombinant inbred mouse strains to lymphomas (1993)

We analyzed the susceptibility of 10 AKXD recombinant inbred (RI) mouse strains to lymphomas. These strains were derived from crosses of AKR/J, a highly lymphomatous strain, and DBA/2J, a weakly lymphomatous strain. Of the 10 strains analyzed, nine showed a high incidence of lymphoma development. As with the other 13 AKXD strains analyzed previously (M. L. Mucenski, B. A. Taylor, N. A. Jenkins, and N. G. Copeland, Mol. Cell. Biol. 6:4236-4243, 1986), the mean age at onset of lymphomas and lymphoma types varied among the strains. Whereas some strains were susceptible to T-cell lymphomas, as was the AKR/J parent, other strains were susceptible to B-cell lymphomas or to a combination of T- and B-cell lymphomas. Somatic mink cell focus-forming proviruses appeared causally associated with T-cell lymphomas, whereas somatic ecotropic proviruses appeared causally associated with B-cell lymphomas. Mice with T-cell lymphomas died significantly earlier than mice with other lymphoma types (stem, pre-B, or B cell and myeloid). The numbers of effective loci influencing the mean age at onset of lymphomas, the presence or absence of mink cell focus-forming viruses in tumors, and the frequency of T-cell lymphomas were estimated to be 3.9, 1.8, and 2.7, respectively. Tests of association with marker loci already typed in the AKXD RI strains suggested that two loci, Rmcf and Pmv-25 (or a locus linked to Pmv-25), influence all three trait variables. Finally, D21S16h, a marker locus on distal chromosome 16, showed 50% probability of linkage to a locus that influences the mean age at onset of lymphomas. Additional studies in combination with classical genetic crosses should be helpful in confirming these linkages and in identifying other loci influencing tumor susceptibility in AKXD RI strains.
Evaluation of the Structure-Function Relationship in Glaucoma (2005)

A map relating regions of the ONH to SAP test locations has been produced. This map may be useful in elucidating the structure-function relationship, particularly for cases of localized glaucomatous loss.
Image Restoration Using Joint Statistical Modeling in a Space-Transform Domain (2014)

This paper presents a novel strategy for high-fidelity image restoration by characterizing both local smoothness and nonlocal self-similarity of natural images in a unified statistical manner. The main contributions are three-fold. First, from the perspective of image statistics, a joint statistical modeling (JSM) in an adaptive hybrid space-transform domain is established, which offers a powerful mechanism of combining local smoothness and nonlocal self-similarity simultaneously to ensure a more reliable and robust estimation. Second, a new form of minimization functional for solving the image inverse problem is formulated using JSM under a regularization-based framework. Finally, in order to make JSM tractable and robust, a new Split Bregman-based algorithm is developed to efficiently solve the above severely underdetermined inverse problem associated with theoretical proof of convergence. Extensive experiments on image inpainting, image deblurring, and mixed Gaussian plus salt-and-pepper noise removal applications verify the effectiveness of the proposed algorithm.
Parkin Binds to α/β Tubulin and Increases their Ubiquitination and Degradation (2003)

In addition to inhibiting the mitochondrial respiratory chain, toxins known to cause Parkinson9s disease (PD), such as 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and rotenone, also strongly depolymerize microtubules and increase tubulin degradation. Microtubules are polymers of tubulin α/β heterodimers, whose correct folding requires coordinated actions of cellular chaperonins and cofactors. Misfolded tubulin monomers are highly toxic and quickly degraded through a hitherto unknown mechanism. Here we report that parkin, a protein–ubiquitin E3 ligase linked to PD, was tightly bound to microtubules in taxol-mediated microtubule coassembly assays. In lysates from the rat brain or transfected human embryonic kidney (HEK) 293 cells, α-tubulin and β-tubulin were strongly coimmunoprecipitated with parkin at 4°C in the presence of colchicine, a condition in which tubulin exits as α/β heterodimers. At the subcellular level, parkin exhibited punctate immunostaining along microtubules in rat brain sections, cultured primary neurons, glial cells, and cell lines. This pattern of subcellular localization was abolished in cells treated with the microtubule-depolymerizing drug colchicine. The binding between parkin and tubulin apparently led to increased ubiquitination and accelerated degradation of α- and β-tubulins in HEK293 cells. Similarly ubiquitinated tubulins were also observed in rat brain lysates. Furthermore, parkin mutants found in PD patients did not ubiquitinate or degrade either tubulin. Taken together, our results show that parkin is a novel tubulin-binding protein, as well as a microtubule-associated protein. Its ability to enhance the ubiquitination and degradation of misfolded tubulins may play a significant role in protecting neurons from toxins that cause PD.
Stimulus-dependent Phosphorylation of MacMARCKS, a Protein Kinase C Substrate, in Nerve Termini and PC12 Cells (1996)

MacMARCKS (also known as myristoylated alanine-rich C kinase substrate (MARCKS)-related protein) is a member of the MARCKS family of protein kinase C substrates, which binds Ca2+/calmodulin in a phosphorylation-dependent manner. Immunoprecipitation demonstrated that MacMARCKS is present in both PC12 cells and in neurons. Upon depolarization of PC12 cells with 60 mM KCl, MacMARCKS phosphorylation increased 4-fold over basal levels in a Ca(2+)-dependent manner. By immunofluorescence microscopy, MacMARCKS was colocalized in PC12 cells to neurite tips with the synaptic vesicle membrane protein synaptophysin and to vesicles in the perinuclear region. Subcellular fractionation demonstrated that MacMARCKS associates tightly with membranes in PC12 cells. In Percoll-purified rat cerebrocortical synaptosomes, depolarization with 60 mM KCl in the presence of exogenous Ca2+ transiently increased MacMARCKS phosphorylation, whereas phorbol ester promoted a sustained increase in MacMARCKS phosphorylation. Subcellular fractionation of rat brain indicated that MacMARCKS was present in both soluble and particulate fractions; particulate MacMARCKS was associated with both small vesicles and highly purified synaptic vesicles. These results are consistent with a role for MacMARCKS in integrating Ca(2+)-calmodulin and protein kinase C-dependent signals in the regulation of neurosecretion.
Three dimensional reconstruction of trunk surface using structured light (2002)

A system using structured light images to reconstruct trunk surfaces is presented. The details of image feature extraction and three-dimensional reconstruction are described. The accuracy, efficiency and reliability of the image algorithms are investigated. The system was tested using solid models and human subjects. The results show that it has the potential of becoming a useful clinical tool.
Reconstitution of Diphtheria Toxin from Two Nontoxic Cross-Reacting Mutant Proteins (1972)

The isolation of a new type of mutant Corynephage beta, which carries a missense mutation in the structural gene for diphtheria toxin synthesis is described. The lysogenic C7(8)(beta(197))(tox-crm+) strain of Corynebacterium diphtheriae produces a nontoxic, extracellular protein of molecular weight 62,000. This protein is immunologically indistinguishable from toxin itself but inhibits the action of toxin on HeLa cells, probably by competing for attachment sites on the cell membrane. In contrast to fragment A derived from diphtheria toxin, fragment A(197) is unable to catalyze the inactivation of eucaryotic polypeptidyl-transfer RNA-transferase II. When mixtures of the two nontoxic mutant proteins, enzymically active crm(45) protein and enzymically inactive crm(197) protein, are subjected to mild treatment with trypsin in the presence of a thiol and then allowed to reoxidize after dialysis to remove excess thiol, "diphtheria toxin" is reconstituted in high yield.
Maximizing in vivo target clearance by design of pH-dependent target binding antibodies with altered affinity to FcRn (2017)

Antibodies with pH-dependent binding to both target antigens and neonatal Fc receptor (FcRn) provide an alternative tool to conventional neutralizing antibodies, particularly for therapies where reduction in antigen level is challenging due to high target burden. However, the requirements for optimal binding kinetic framework and extent of pH dependence for these antibodies to maximize target clearance from circulation are not well understood. We have identified a series of naturally-occurring high affinity antibodies with pH-dependent target binding properties. By in vivo studies in cynomolgus monkeys, we show that pH-dependent binding to the target alone is not sufficient for effective target removal from circulation, but requires Fc mutations that increase antibody binding to FcRn. Affinity-enhanced pH-dependent FcRn binding that is double-digit nM at pH 7.4 and single-digit nM at pH 6 achieved maximal target reduction when combined with similar target binding affinities in reverse pH directions. Sustained target clearance below the baseline level was achieved 3 weeks after single-dose administration at 1.5 mg/kg. Using the experimentally derived mechanistic model, we demonstrate the essential kinetic interplay between target turnover and antibody pH-dependent binding during the FcRn recycling, and identify the key components for achieving maximal target clearance. These results bridge the demand for improved patient dosing convenience with the "know-how" of therapeutic modality by design.
Quantitativein vitro kinase reaction as a guide for phosphoprotein analysis by mass spectrometry (2000)

A simple calculation using the radioactive decay of (32)P incorporated into a protein during in vitro kinase reactions is described that allows the overall stoichiometry of phosphorylation for the substrate protein or peptide to be calculated. Prior to using techniques such as diagnostic ion scanning to identify the molecular weight of an unknown phosphopeptide in a complex mixture followed by tandem mass spectrometry (MS/MS) to locate the phosphorylated residue within the phosphopeptide, such calculations are predictive of the chances for successful characterization by these methods. An example of estimating the stoichiometry of peptide phosphorylation will be presented along with calculations that predict when adequate phosphopeptide is present in any given spot on the thin-layer chromatography (TLC) plates used for two-dimensional phosphopeptide (2DPP) mapping to allow extraction and complete characterization by MS/MS.
Promise of radiosensitizers and radioprotectors in the treatment of human cancer. (1984)

Over the past 30 years, as an understanding of radiation chemistry has developed, it has been possible to develop compounds which modify the initial radiochemical event. In addition, certain physiologic means such as hyperbaric oxygen or blood flow restriction have also been developed as methods to modify radiation response through the radiochemical processes. Following the success of certain hyperbaric trials, a great effort was made to develop chemical agents which would mimic oxygen in their sensitization of hypoxic cells. A large series of compounds have now been identified with such properties and several of these have entered clinical trial. The first compound to receive widespread testing, misonidazole, has proven too toxic to be used in adequate doses for clinically relevant sensitization. Two new nitroimidazole analogs, which are excluded from the central nervous system, promise to allow much higher degrees of sensitization in planned clinical trials and new non-nitro drugs are under development. Radioprotection can be achieved through various methods, including restriction in blood flow and the use of sulfhydryl-containing compounds which again modify the initial radiochemical events. To be successful in tumor therapy, such agents must be selective in protecting the normal tissues. One class of compounds, the thiophosphates, show differential protection of normal tissue vis-à-vis tumor through several mechanisms. After extensive animal testing, one of these compounds, WR 2721, is now in phase I clinical testing, with phase II evaluation planned for the near future. Other potential sensitizers with varying degrees of differential activity in tumor versus normal tissue are also discussed.
Transformation of human embryo retinoblasts with simian virus 40, adenovirus and ras oncogenes. (1986)

Few human cell systems have been described in which a number of different genes induce transformation. The present investigation reports on our studies using primary human embryo retinoblasts as a model system to monitor transformation and the subsequent behaviour of individual transformants in terms of establishment, the frequency of immortalization and tumourigenic potential. SV40, Adenovirus E1 and E1A, and combinations of Adenovirus E1A and activated H-ras or N-ras were examined as transforming agents. Considerable differences were observed in the ability of these genes to transform human cells, to induce immortal lines and to produce cell lines with a tumourigenic phenotype. Activated ras genes were non-transforming in this system and the degree of complementation with adenovirus E1As in transformation experiments was dependent on both the adenovirus serotype and the ras gene used. The development of tumourigenic cell lines required the expression of more than one oncogene and additional genetic events were required in some in some instances before immortal cell lines were obtained. These findings contribute to the concept that the development of cancer is a multi-step process.
Colored 2D maps for robot navigation with 3D sensor data (2005)

This paper presents a navigation system for mobile service robots working in urban environments. The system combines a 3D laser sensor with 2D algorithms for path planning and simultaneous localization and mapping (SLAM). In contrast to other map representations the colored 2D map, first presented in this paper, is able to hold information adapted to both localization and path planning. The functionality of our approach is demonstrated by an experiment for online navigation with 3D data.
Expression of equine herpesvirus 1 glycoprotein D by using a recombinant baculovirus (1993)

Glycoprotein D (gD) of equine herpesvirus 1 (EHV-1) was expressed at the surface of insect cells infected by a recombinant baculovirus. EHV-1 gD was detected as multiple forms (56, 52, and 48 kDa) from 18 to 96 h postinfection. Laboratory animals inoculated with the recombinant EHV-1 gD developed neutralizing antibody responses against both EHV-1 and EHV-4.
Surface properties, more than size, limiting convective distribution of virus-sized particles and viruses in the central nervous system (2005)

These results indicate that convective distribution can be used to distribute therapeutic viral vectors in the CNS.
Expression of MUC4 and CerbB-2 protein in esophageal squamous cell carcinoma tissue (2007)

Aim:To explore the relationship between the expression of MUC4 and CerbB-2 protein and the occurrence, development,infiltration and metastasis of esophageal squamous cell carcinoma (ESCC).Methods:SP immunohistochemical method was used to detect the expression of MUC4 and CerbB-2 protein in 60 cases of ESCC, 30 cases of adjacent atypical hyperplasia epithelium and 60 cases of normal esophageal epithelium.Results: The expression rates of MUC4 protein in ESCC tissue,adjacent atypical hyperplasia epithelium and normal esophageal epithelium were 81.7%,56.7%,and 5.0%,respectively,and those for CerbB-2 protein were 73.3%,80.0%,and 36.7%,respectively. There were significant differences among the 3 groups in the 2 parameters(P0.05). The expressions of MUC4 and CerbB-2 protein were closely associated with the histological grade, infiltration depth, and lymphatic metastasis in ESCC tissue(P0.05). Conclusion: MUC4 and CerbB-2 play important roles in the infiltration, metastasis and carcinogenesis of esophageal carcinoma. United detection of MUC4 and CerbB-2 can be one of the molecular indexes in the early diagnosis and prognosis of ESCC.
Study of the heterocyclization of vic‐substituted hydrazides of acetylenylpyrazolecarboxylic acids into N‐amino pyrazolopyridinones (2002)

Abstract We report a new and efficient methodology to prepare N ‐amino pyrazolo[4,3‐ c ]pyridin‐4‐ones 4 and N ‐amino pyrazolo[3,4‐ c ]pyridin‐4‐ones 8 from vic ‐acetylenyl/hydrazido pyrazoles. The procedure involves the intermediate synthesis of methyl esters of acetylenyl‐pyrazole carboxylic acids and the subsequent cyclization under a variety of conditions.