gebhart/patrepeval huggingface dataset:
The scrapie-associated form of PrP is made from a cell surface precursor that is both protease- and phospholipase-sensitive. (1991)

A common feature of scrapie and related transmissible spongiform encephalopathies is the accumulation of an abnormal protease-resistant form of PrP which may be the major component of the infectious agent. While it is known that both the normal (protease-sensitive) PrP and protease-resistant PrP are encoded by the same endogenous gene, the nature of the disease-associated modification of PrP is not understood. To study the cellular events leading to the formation of protease-resistant PrP, we have compared its biosynthesis to that of its normal isoform in scrapie-infected mouse neuroblastoma cells. In pulse-chase labeling experiments, the protease-resistant PrP was synthesized and degraded much more slowly than the normal PrP, suggesting that protease-resistant PrP is made from a protease-sensitive precursor. More significantly, we found that the precursor of protease-resistant PrP was eliminated from intact cells by treatments with phosphatidylinositol-specific phospholipase C and trypsin. This demonstrated that, unlike the protease-resistant PrP itself, the precursor is phospholipase- and protease-sensitive and at least transiently found on the cell surface. By these criteria, the precursor of protease-resistant PrP is indistinguishable from the normal PrP isoform. These results indicate that the conversion of PrP to the protease- and phospholipase-resistant state is a post-translational event that occurs after the precursor reaches the cell surface.
Architectural control of sugar-containing polymers by living polymerization: ring-opening polymerization of 2-oxazolines initiated with carbohydrate derivatives (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArchitectural control of sugar-containing polymers by living polymerization: ring-opening polymerization of 2-oxazolines initiated with carbohydrate derivativesKeigo Aoi, Hiroshi Suzuki, and Masahiko OkadaCite this: Macromolecules 1992, 25, 25, 7073–7075Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://pubs.acs.org/doi/10.1021/ma00051a056https://doi.org/10.1021/ma00051a056research-articleACS PublicationsRequest reuse permissionsArticle Views411Altmetric-Citations54LEARN 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
Toward Characterizing Seed Vigor in Alfalfa Through Proteomic Analysis of Germination and Priming (2011)

Alfalfa, the most widely grown leguminous crop in the world, is generally exposed to severe salinity stress in Tunisia, notably affecting its germination performance. Toward a better understanding of alfalfa seed vigor, we have used proteomics to characterize protein changes occurring during germination and osmopriming, a pretreatment that accelerates germination and improves seedling uniformity particularly under stress conditions. The data revealed that germination was accompanied by dynamic changes of 79 proteins, which are mainly involved in protein metabolism, cell structure, metabolism, and defense. Comparative proteomic analysis also revealed 63 proteins specific to osmopriming, 65 proteins preferentially varying during germination, and 14 proteins common to both conditions. Thus, the present study unveiled the unexpected finding that osmopriming cannot simply be considered as an advance of germination-related processes but involves other mechanisms improving germination such as the mounting of defense mechanisms enabling osmoprimed seeds to surmount environmental stresses potentially occurring during germination. The present results therefore provide novel avenues toward understanding the mechanisms of invigoration of low vigor seeds by priming treatments that are widely used both in commercial applications and in developing countries (on farm seed priming) to better control crop yields.
The Essential Function of Protein-disulfide Isomerase Is to Unscramble Non-native Disulfide Bonds (1995)

Protein-disulfide isomerase (PDI) is an abundant protein of the endoplasmic reticulum that catalyzes dithiol oxidation and disulfide bond reduction and isomerization using the active site CGHC. Haploid pdi1 delta Saccharomyces cerevisiae are inviable, but can be complemented with either a wild-type rat PDI gene or a mutant gene coding for CGHS PDI (shufflease). In contrast, pdi1 delta yeast cannot be complemented with a gene coding for SGHC PDI. In vitro, shufflease is an efficient catalyst for the isomerization of existing disulfide bonds but not for dithiol oxidation or disulfide bond reduction. SGHC PDI catalyzes none of these processes. These results indicate that in vivo protein folding pathways contain intermediates with non-native disulfide bonds, and that the essential role of PDI is to unscramble these intermediates.
Culture of Human Endothelial Cells Derived from Umbilical Veins. IDENTIFICATION BY MORPHOLOGIC AND IMMUNOLOGIC CRITERIA (1973)

Endothelial cells were isolated from freshly obtained human umbilical cords by collagenase digestion of the interior of the umbilical vein. The cells were grown in tissue culture as a homogeneous population for periods up to 5 mo and some lines were subcultured for 10 serial passages. During the logarithmic phase of cell growth, cell-doubling time was 92 h. Light, phase contrast, and scanning electron microscopy demonstrated that cultured human endothelial cells grew as monolayers of closely opposed, polygonal large cells whereas both cultured human fibroblasts and human smooth muscle cells grew as overlapping layers of parallel arrays of slender, spindle-shaped cells. By transmission electron microscopy, cultured endothelial cells were seen to contain cytoplasmic inclusions (Weibel-Palade bodies) characteristic of in situ endothelial cells. These inclusions were also found in endothelial cells lining umbilical veins but were not seen in smooth muscle cells or fibroblasts in culture or in situ. Cultured endothelial cells contained abundant quantities of smooth muscle actomyosin. Cultured endothelial cells also contained ABH antigens appropriate to the tissue donor's blood type; these antigens were not detectable on cultured smooth muscle cells or fibroblasts. These studies demonstrate that it is possible to culture morphologically and immunologically identifiable human endothelial cells for periods up to 5 mo.
Synthesis of Indole Phytoalexins Brassinin and Cyclobrassinin via [1-(tert-Butoxycarbonyl)indol-3-yl]-methyl Isothiocyanate as the Key Biomimetic Intermediate (1997)

A four-step synthesis of 1-protected indol-3-ylmethyl isothiocyanates from indole-3-carboxaldehyde has been elaborated. [1-(tert-Butoxycarbonyl)indol-3-yl]-methyl isothiocyanate appeared to be a suitable biomimetic intermediate for the synthesis of protected phytoalexins brassinin and cyclobrassinin. Removing of the tert-butoxycarbonyl protecting group under specific conditions afforded phytoalexins identical with previously described compounds.
Identification and characterization of a new Escherichia coli gene that is a dosage-dependent suppressor of a dnaK deletion mutation (1990)

We report the isolation and characterization of a previously unidentified Escherichia coli gene that suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant strain. Introduction of a multicopy plasmid carrying this wild-type gene into a dnaK deletion mutant strain rescued the temperature-sensitive growth of the dnaK deletion mutant strain at 40.5 degrees C and the filamentation, fully at 37 degrees C and partially at 40.5 degrees C. However, the inability of dnaK mutant cells to support bacteriophage lambda growth was not suppressed. This gene was also able to suppress the temperature-sensitive growth of a grpE280 mutant strain at 41 degrees C. Filamentation of the grpE280 mutant strain was suppressed at 37 degrees C but not at 41 degrees C. The dnaK suppressor gene, designated dksA, maps near the mrcB gene (3.7 min on the E. coli chromosome). DNA sequence analysis and in vivo experiments showed that dksA encodes a 17,500-Mr polypeptide. Gene disruption experiments indicated that dksA is not an essential gene.
Oligosaccharides related to tumor‐associate antigens. Part 3. Synthesis of the propyl glycosides of the trisaccharide β‐D‐Galp‐(1→3)‐β‐D‐GalpNAc‐(1→3)‐α‐D‐Galp and of the Tetrasaccharide α‐L‐Fucp‐(1→2)‐β‐D‐Galp‐(1→3)‐β‐D‐GalpNAc‐(1→3)‐α‐D‐Galp, components of a tumor antigen recognized by the antibody MBr1 (1995)

Abstract The synthesis of the trisaccharide β‐ D ‐Gal p ‐(1→3)‐β‐ D ‐Gal p NAc‐(1→3)‐α‐ D ‐Gal p ‐1‐OPr ( 2 ) and of the tetrasaccharide α‐ L ‐Fuc p ‐(1→2)‐β‐ D ‐Gal p NAc‐(1→3)‐β‐ D ‐Gal p ‐1‐OPr ( 3 ), starting from the disaccharidic dihydrooxazole donor 5 , is described. Glycosylation of 5 with 6 in the presence of Me 3 SiOTf gave the trisaccharide 7 which was deprotected with standard methods to give, via 8 , compound 2 ( Scheme 1 ). Alternatively, protection of 8 as the 4′,6′‐ O ‐benzylidene derivative 9 followed by glycosylation with 10 and by standard deprotection afforded the tetrasaccharide 3 ( Scheme 2 ). Biological testing showed that trisaccharide 2 is unable to inhibit the binding of the monoclonal antibody MBr1 to the target tumor cells MCF7, while tetrasaccharide 3 inhibits the binding in ca . 7‐fold extent with respect to the previously tested trisaccharide α‐ L ‐Fuc p ‐(1→2)‐β‐ D ‐Gal p ‐(1→3)‐β‐ D ‐Gal p NAc‐1‐OPr. These results indicate that the galactose corresponding to the unit D of compound 1 plays an important role in defining the MBr1‐recognized epitope and confirm the essential role of fucose for MAb recognition.
Blockade of the insulin‐like growth‐factor‐I receptor inhibits growth of human colorectal cancer cells: Evidence of a functional IGF‐II‐mediated autocrine loop (1994)

Insulin-like growth factors (IGFs) are potent proliferation stimulators for numerous tumor cells and often function as autocrine growth factors. We have previously shown that exogenous IGF-I and IGF-II enhance proliferation of colorectal carcinoma cells. The biological signal of both factors is transmitted through the IGF-I receptor (IGF-I-R). This receptor was expressed in 12/12 colorectal carcinoma cell lines tested. alpha IR3, a neutralizing monoclonal antibody (MAb) directed against the human IGF-I-R, inhibited proliferation in 7/12 lines (Caco-2, HT-29, LS411N, LS513, LS1034, WiDr and SW620), as reflected by a reduction of MTT conversion (19 to 42%), a decrease in cell number (39 to 72%) and an increase in doubling time (up to 2-fold). In addition, in 4 cell lines (Caco-2, LS513, LS1034, WiDr) alpha IR3 suppressed colony formation in methylcellulose (40 to 84%). Excess of exogenous IGF completely neutralized alpha IR3-mediated inhibitory effects. Northern blot analysis revealed abundant expression of 2 IGF-II transcripts of 5.0 and 4.3 kb in LS1034 cells. In addition, we observed that growth inhibition by alpha IR3 was correlated with a more differentiated phenotype. Our results suggest that growth of many colorectal carcinoma cell lines is regulated by autocrine IGF-II-mediated stimulation of the IGF-I-R.
The kinase insert domain receptor gene (KDR) has been relocated to chromosome 4q11→q12 (1995)

Through in situ hybridization of a genomic DNA probe to metaphase chromosomes, we have localized the KDR gene to 4q11-->q12. This is the same locus as that for two other receptor tyrosine kinases, PDGFRA and KIT. This location for KDR differs from that which we previously reported using a cDNA probe. Using cDNA probes for both KDR and KIT identifies a locus at 4q31-->q32 which may uncover another cluster of receptor tyrosine kinase genes.
Blood collection in cell-stabilizing tubes does not impact germline DNA quality for pediatric patients (2017)

Our study demonstrates that high-quality genomic studies may be performed from germline DNA obtained in Streck tubes. Therefore, these tubes may be used to simultaneously obtain samples for both liquid biopsy and germline studies in pediatric patients when the volume of blood available for research studies may be limited.
Nuclease mechanism of the avian retrovirus pp32 endonuclease (1986)

In vivo, the inferred circular retrovirus DNA precursor to the provirus contains two long terminal repeats (LTRs) in tandem. We studied the site-specific nicking of supercoiled DNA that contains tandem copies of avian retrovirus LTR DNA in vitro by using purified avian myeloblastosis virus pp32 endonuclease, Mg2+, and viral DNA substrates containing different LTR circle junction sequences. The results confirmed our previous observation that the pp32 protein generates two nicks, one in either viral DNA strand, each 2 nucleotides from the circle junction site. The specificity of nicking by pp32 was unchanged over an eight-fold range of protein concentration and with different avian retrovirus LTR circle junction substrates. These data are consistent with models which propose a role for the endonuclease in removal of two nucleotides from the LTR termini on integration of viral DNA in vivo.
Synthesis and characterization of PbSe quantum dots in phosphate glass (1997)

The controlled synthesis of PbSe nanocrystal quantum dots with narrow size distributions was achieved through phase decomposition of the PbSe solid solution in a phosphate glass host. Structural characterization by electron microscopy and x-ray diffraction shows that the dots have mean diameters between 2 and 15 nm. The exciton Bohr radius aB=46 nm in PbSe, so these quantum dots provide unusual and perhaps unique access to the regime of strong quantum confinement. The optical absorption spectra are compared to the predictions of a theoretical treatment of the electronic structure. The theory agrees well with experiment for dots larger than ∼7 nm, but for smaller dots there is some deviation from the theoretical predictions.
Molecular characterization of immune inhibitor A, a secreted virulence protease from Bacillus thuringiensis (1990)

The gene for the secreted neutral metalloprotease, immune inhibitor A (InA), from Bacillus thuringiensis var. alesti has been cloned and sequenced. The deduced amino acid sequence has been confirmed by partial amino acid sequencing. The central part of the amino acid sequence showed similarity to the active site in thermolysin. Southern and Western blots show that InA-related sequences are common among other B. thuringiensis subspecies. In Western blots, 17 out of 25 tested species gave a positive signal. Culture filtrates from subspecies expressing InA were toxic when injected in Trichoplusia ni larvae, whereas filtrate from a strain negative in Western blot had no effect when injected. The LD50 dose of purified InA protein injected in T. ni larvae was 12.5 +/- 2.5 ng per mg of larval body weight.
Soft Drugs (2012)

This chapter contains sections titled: Enzymatic Hydrolysis Soft Drug Approaches Inactive Metabolite–Based Soft Drugs Soft Analogs Active Metabolite–Based Soft Drugs Activated Soft Drugs Pro-Soft Drugs Computer-Aided Design Soft Drugs: Summary References
SEL-5, A Serine/Threonine Kinase That Facilitates lin-12 Activity in Caenorhabditis elegans (1999)

Ligands present on neighboring cells activate receptors of the LIN-12/Notch family by inducing a proteolytic cleavage event that releases the intracellular domain. Mutations that appear to eliminate sel-5 activity are able to suppress constitutive activity of lin-12(d) mutations that are point mutations in the extracellular domain of LIN-12, but cannot suppress lin-12(intra), the untethered intracellular domain. These results suggest that sel-5 acts prior to or during ligand-dependent release of the intracellular domain. In addition, sel-5 suppression of lin-12(d) mutations is tissue specific: loss of sel-5 activity can suppress defects in the anchor cell/ventral uterine precursor cell fate decision and a sex myoblast/coelomocyte decision, but cannot suppress defects in two different ventral hypodermal cell fate decisions in hermaphrodites and males. sel-5 encodes at least two proteins, from alternatively spliced mRNAs, that share an amino-terminal region and differ in the carboxy-terminal region. The amino-terminal region contains the hallmarks of a serine/threonine kinase domain, which is most similar to mammalian GAK1 and yeast Pak1p.
Hedgehog signaling pathway and gastrointestinal stem cell signaling network (Review) (2006)

Hedgehog, BMP/TGFbeta, FGF, WNT and Notch signaling pathways constitute the stem cell signaling network, which plays a key role in a variety of processes, such as embryogenesis, maintenance of adult tissue homeostasis, tissue repair during chronic persistent inflammation, and carcinogenesis. Sonic hedgehog (SHH), Indian hedgehog (IHH) and Desert hedgehog (DHH) bind to PTCH1/PTCH or PTCH2 receptor to release Smoothened (SMO) signal transducer from Patched-dependent suppression. SMO then activates STK36 serine/threonine kinase to stabilize GLI family members and to phosphorylate SUFU for nuclear accumulation of GLI. Hedgehog signaling activation leads to GLI-dependent transcriptional activation of target genes, such as GLI1, PTCH1, CCND2, FOXL1, JAG2 and SFRP1. GLI1-dependent positive feedback loop combined with PTCH1-dependent negative feedback loop gives rise to transient proliferation of Hedgehog target cells. Iguana homologs (DZIP1 and DZIP1L) and Costal-2 homologs (KIF7 and KIF27) are identified by comparative integromics. SHH-dependent parietal cell proliferation is implicated in gastric mucosal repair during chronic Helicobacter pylori infection. BMP-RUNX3 signaling induces IHH expression in surface differentiated epithelial cells of stomach and intestine. Hedgehog signals from epithelial cells then induces FOXL1-mediated BMP4 upregulation in mesenchymal cells. Hedgehog signaling is frequently activated in esophageal cancer, gastric cancer and pancreatic cancer due to transcriptional upregulation of Hedgehog ligands and epigenetic silencing of HHIP1/HHIP gene, encoding the Hedgehog inhibitor. However, Hedgehog signaling is rarely activated in colorectal cancer due to negative regulation by the canonical WNT signaling pathway. Hedgehog signaling molecules or targets, such as SHH, IHH, HHIP1, PTCH1 and GLI1, are applied as biomarkers for cancer diagnostics, prognostics and therapeutics. Small-molecule inhibitors for SMO or STK36 are suitable to be used for treatment of Hedgehog-dependent cancer.
Anticancer effect and immune induction by hyperthermia of malignant melanoma using magnetite cationic liposomes (2003)

The hyperthermic effect of magnetic particles was examined in an in vivo study of mouse B16 melanoma. Magnetite cationic liposomes (MCLs) have a positive surface charge and generate heat under an alternating magnetic field (AMF) by hysteresis loss. MCLs were injected into melanoma nodules, which were then subjected to an AMF. The mice were divided into four groups: group I (control), group II (hyperthermia at 43 degrees C for 30 min, once), group III (hyperthermia at 46 degrees C for 30 min, once) and group IV (hyperthermia at 46 degrees C for 30 min, twice). Complete tumour regression was observed in 90% of the mice in group IV, while no mice in groups I and II and only 40% in group III showed regression. To examine whether hyperthermia caused immune induction in B16 melanoma, in vitro cytotoxicity assays and rechallenge experiments were performed. Cytotoxic activity was observed in the spleen cells of the cured mice in group IV. In the rechallenge experiment, 66% of the cured mice rejected melanoma cells. These results suggest that hyperthermia using MCLs is an effective therapy for melanoma, since this treatment can kill the tumour cells not only by heat but also by inducing an immune response.
Kinase Inhibitors from Polygonum cuspidatum (1993)

Bioassay-directed fractionation of a medicinal plant, Polygonum cuspidatum (Polygonaceae), has led to the discovery of a hydroxystilbene, resveratrol [1], as an inhibitor of a protein-tyrosine kinase (p56lck) partially purified from bovine thymus. Both trans and cis isomers of resveratrol possess comparable protein-tyrosine kinase inhibitory activity. Comparison of the IC50 values of resveratrol for protein-tyrosine kinase inhibitory activity with those of piceid (resveratrol-O3-beta-glucoside) [2] and resveratrol-O4'-beta-glucoside [3] shows the requirement of free hydroxyl groups on both phenyl rings for the protein-tyrosine kinase inhibition. Protein kinase C inhibitory analysis suggests the requirements of two free hydroxyl groups on one phenyl ring only.
Gene therapy for haematopoietic and lymphoid disorders. (1997)

Gene transfer into haematopoietic stem cells (HSC) has been investigated for treatment of genetic disorders, conferral of chemotherapy resistance and insertion of genes to inhibit HIV-1 replication. Methods have been available for almost a decade to transduce murine HSC using high-titre retroviral vectors and stimulation of HSC proliferation with cytokines such as IL-3 and IL-6. Unfortunately, attempts to replicate the high efficiency of gene transfer using canine or simian gene transfer/bone marrow transplantation models have consistently shown that only a small fraction (0.1-1%) of reconstituting HSC are transduced using protocols similar to those which are successful in murine models. Initial clinical trials using retroviral-mediated gene transfer into human HSC also produced minimal transduction frequencies. The dicotomous results may reflect differences in the cell cycle kinetics of murine HSC versus those of larger mammals or the density of receptors for the retroviral vectors on the cells. Attempts to increase the fraction of HSC which are in active cell cycle, a prerequisite for retroviral-mediated transduction, have used either combinations of recombinant cytokines, culture on marrow stromal layers, or alternative sources for HSC, such as mobilized peripheral blood stem cells or umbilical cord blood. Other efforts have used retroviral vectors packaged with either the Gibbon Ape Leukemia virus envelope or the Vesicular Stomatitis Virus G protein. To date, none of these methods has produced a significantly increased frequency of long-term reconstituting HSC. Results using adeno-associated virus (AAV)-based vectors for HSC transduction have been conflicting, with the stable persistence of non-integrated virus particles making interpretation of results difficult using in vitro assays. Therefore, clinical trials may best be directed toward disorders that may benefit from a small fraction of genetically corrected HSC. These would include disorders where progeny of corrected HSC would be expected to have a selective survival advantage (e.g. SCID, WAS, HIV, chemoresistance) or where a small fraction of corrected cells can have a direct clinical benefit (e.g. CGD, MPS). Further basic research into HSC biology and gene delivery vectors must continue for wider application, such as haemoglobinopathies and some lysosomal storage diseases.