gebhart/patrepeval huggingface dataset:
Molecular cloning of cDNA for the alpha, beta, and gamma chains of rat fibrinogen. A family of coordinately regulated genes. (1981)

Recently, we have found that defibrination of rats with Malayan pit viper venom induces a 10-38-fold increase in the levels of translatable fibrinogen mRNA in the liver. We have used this response to obtain cDNA clones for the three polypeptide chains of rat fibrinogen. A large cDNA library was created in pBR322 from induced rat liver polyadenylated RNA by the poly(dG, dC)-tailing method. Part of this library was screened using colony hybridization with [32P]cDNA prepared from induced and noninduced rat liver RNA. Colonies consistently giving a more intense signal with the induced [32P]cDNA were considered possible fibrinogen recombinants and were used for hybrid selection and translation of mRNA. In this way, cDNA clones for each of the three fibrinogen mRNA's were identified. Analysis of polyadenylated RNA by Northern blotting indicates that the three chains are synthesized from mRNA's of 2300, 2050, and 1950 nucleotides for the alpha, beta, and gamma chains, respectively. The fact tha each of the three chains has a separate mRNA indicates that the highly coordinated regulation of the three messages for rat fibrinogen does not occur by translation of a common cytoplasmic RNA.
Sink Metabolism in Tomato Fruit (1991)

Fruit of domesticated tomato (Lycopersicon esculentum) accumulate primarily glucose and fructose, whereas some wild tomato species, including Lycopersicon chmielewskii, accumulate sucrose. Genetic analysis of progeny resulting from a cross between L. chmielewskii and L. esculentum indicated that the sucrose-accumulating trait could be stably transferred and that the trait was controlled by the action of one or two recessive genes. Biochemical analysis of progeny resulting from this cross indicated that the sucrose-accumulating trait was associated with greatly reduced levels of acid invertase, but normal levels of sucrose synthase. Invertase from hexose-accumulating fruit was purified and could be resolved into three isoforms by chromatofocusing, each with isoelectric points between 5.1 and 5.5. The invertase isoforms showed identical polypeptide profiles on sodium dodecyl sulfate polyacrylamide gel electrophoresis, consisting of a primary 52 kilodalton polypeptide and two lower molecular mass polypeptides that appear to be degradation products of the 52 kilodalton polypeptide. The three invertase isoforms were indistinguishable based on pH, temperature, and substrate concentration dependence. Immunological detection of invertase indicated that the low level of invertase in sucrose-accumulating fruit was due to low levels of invertase protein rather than the presence of an invertase inhibitor. Based on comparison of genetic and biochemical data we speculate that a gene either encoding tomato fruit acid invertase or one required for its expression, plays an important role in determining sucrose accumulation.
Biodegradable Polycarbonate Synthesis by Copolymerization of Carbon Dioxide with Epoxides Using a Heterogeneous Zinc Complex (2005)

Abstract As a means for the chemical fixation of carbon dioxide and the synthesis of biodegradable polycarbonates, copolymerizations of carbon dioxide with various epoxides such as cyclohexene oxide (CHO), cyclopetene oxide, 4‐vinyl‐1‐cyclohexene‐1,2epoxide, phenyl glycidyl ether, allyl glycidyl ether, propylene oxide, butene oxide, hexene oxide, octene oxide, and 1‐chloro‐2,3‐epoxypropane were investigated in the presence of a double metal cyanide catalyst (DMC). The DMC catalyst was prepared by reacting K 3 Co(CN) 6 with ZnCl 2 , together with tertiary butyl alcohol and poly(tetramethylene ether glycol) as complexing reagents and was characterized by various spectroscopic methods. The DMC catalyst showed high activity (526.2 g‐polymer/g‐Zn atom) for CHO/CO 2 (P CO2 = 140 psi) copolymerization at 80 °C, to yield biodegradable aliphatic polycarbonates of narrow polydispersity (M w /M n = 1.67) and moderate molecular weight (M n = 8900). The DMC catalyst also showed high activities with different CO 2 reactivities for other epoxides to yield various aliphatic polycarbonates with narrow polydispersity.
Proteasome Inhibitors Block DNA Repair and Radiosensitize Non-Small Cell Lung Cancer (2013)

Despite optimal radiation therapy (RT), chemotherapy and/or surgery, a majority of patients with locally advanced non-small cell lung cancer (NSCLC) fail treatment. To identify novel gene targets for improved tumor control, we performed whole genome RNAi screens to identify knockdowns that most reproducibly increase NSCLC cytotoxicity. These screens identified several proteasome subunits among top hits, including the topmost hit PSMA1, a component of the core 20 S proteasome. Radiation and proteasome inhibition showed synergistic effects. Proteasome inhibition resulted in an 80-90% decrease in homologous recombination (HR), a 50% decrease in expression of NF-κB-inducible HR genes BRCA1 and FANCD2, and a reduction of BRCA1, FANCD2 and RAD51 ionizing radiation-induced foci. IκBα RNAi knockdown rescued NSCLC radioresistance. Irradiation of mice with NCI-H460 xenografts after inducible PSMA1 shRNA knockdown markedly increased murine survival compared to either treatment alone. Proteasome inhibition is a promising strategy for NSCLC radiosensitization via inhibition of NF-κB-mediated expression of Fanconi Anemia/HR DNA repair genes.
Enzyme activity assay for cholesterol 27-hydroxylase in mitochondria (2006)

Mitochondrial cholesterol 27-hydroxylase (CYP27A1) plays an important role in the maintenance of intracellular cholesterol homeostasis. Cholesterol delivery to the mitochondrial inner membrane is believed to be a rate-limiting step for the "acidic" pathway of bile acid synthesis. This work reports that proteinase K treatment of mitochondria markedly increases CYP27A1 specific activity. With endogenous mitochondrial cholesterol, treatment with proteinase K increased CYP27A1 specific activity by 5-fold. Moreover, the addition of the exogenous cholesterol in beta-cyclodextrin plus proteinase K treatment increased the specific activity by 7-fold. Kinetic studies showed that the increased activity was time-, proteinase K-, and substrate concentration-dependent. Proteinase K treatment decreased the apparent K(m) of CYP27A1 for cholesterol from 400 to 150 microM. Using this new assay, we found that during rat hepatocyte preparation and cell culture, mitochondria gradually lose CYP27A1 activity compared with mitochondria freshly isolated from rat liver tissue.
Dietary Agonists of TRPV1 Inhibit Gastric Acid Secretion in Mice (2012)

Capsaicin and 6-gingerol, pungent components of chilli pepper and ginger, are known as dietary agonists of transient receptor potential vanilloid-1. Transient receptor potential vanilloid-1 nerve fibers are recognized to play a role in gastric mucosal integrity in rats. In the present studies, we examined the acute effects of peroral administration of capsaicin and 6-gingerol on gastric acid secretion in conscious mice. These agents were given p. o. 30 min before the pylorus was ligated. Oral administration of capsaicin (1.0-100 mg/kg) or 6-gingerol (1.5-50 mg/kg) significantly and dose-dependently inhibited basal acid secretion. Pretreatment with BCTC, a transient receptor potential vanilloid-1 antagonist, significantly reversed the reduced basal acid secretion by capsaicin or 6-gingerol. The combination of the lowest doses of capsaicin and 6-gingerol markedly inhibited basal acid secretion in conscious mice and this was also significantly reversed by BCTC. Moreover, the combination of the maximal dose of capsaicin and 6-gingerol inhibited basal acid secretion only to the level of a single administration of the maximal dose of capsaicin. These results suggest that the combination of capsaicin and 6-gingerol has an additive effect on the inhibition of gastric acid secretion through activation of transient receptor potential vanilloid-1. In separate experiments, intraduodenal administration of either capsaicin (30 mg/kg) or 6-gingerol (15 mg/kg), whose doses were observed to have a significant inhibitory effect by oral administration, tended to inhibit basal acid secretion compared with the vehicle. These results suggest that the combination of capsaicin and 6-gingerol has an additive effect on inhibition of gastric acid secretion through activation of transient receptor potential vanilloid-1, and oral administration of transient receptor potential vanilloid-1 agonists directly stimulates transient receptor potential vanilloid-1 in the gastric lumen, resulting in a potent reduction of gastric acid secretion.
Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS (2003)

Ultrasensitive nanoscale proteomics approaches for characterizing proteins from complex proteomic samples of <50 ng of total mass are described. Protein identifications from 0.5 pg of whole proteome extracts were enabled by ultrahigh sensitivity (<75 zmol for individual proteins) achieved using high-efficiency (peak capacities of approximately 10(3)) 15-microm-i.d. capillary liquid chromatography separations (i.e., using nanoLC, approximately 20 nL/min mobile-phase flow rate at the optimal linear velocity of approximately 0.2 cm/s) coupled on-line with a micro-solid-phase sample extraction and a nanoscale electrospray ionization interface to a 11.4-T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer (MS). Proteome measurement coverage improved as sample size was increased from as little as 0.5 pg of sample. It was found that a 2.5-ng sample provided 14% coverage of all annotated open reading frames for the microorganism Deinococcus radiodurans, consistent with previous results for a specific culture condition. The estimated detection dynamic range for detected proteins was 10(5)-10(6). An improved accurate mass and LC elution time two-dimensional data analysis methodology, used to both speed and increase the confidence of peptide/protein identifications, enabled identification of 872 proteins/run from a single 3-h nanoLC/FTICR MS analysis. The low-zeptomole-level sensitivity provides a basis for extending proteomics studies to smaller cell populations and potentially to a single mammalian cell. Application with ion trap MS/MS instrumentation allowed protein identification from 50 pg (total mass) of proteomic samples (i.e., approximately 100 times larger than FTICR MS), corresponding to a sensitivity of approximately 7 amol for individual proteins. Compared with single-stage FTICR measurements, ion trap MS/MS provided a much lower proteome measurement coverage and dynamic range for a given analysis time and sample quantity.
The Bacillus subtilis division protein DivIC is a highly abundant membrane‐bound protein that localizes to the division site (1997)

The Bacillus subtilis divIC gene is involved in the initiation of cell division. It encodes a 14.7 kDa protein, with a potential transmembrane region near the N-terminus. In this paper, we show that DivIC is associated with the cell membrane and, in conjunction with previously published sequence data, conclude that it is oriented such that its small N-terminus is within the cytoplasm and its larger C-terminus is external to the cytoplasm. DivIC is shown to be a highly abundant division protein, present at approximately 50000 molecules per cell. Using immunofluorescence microscopy, DivIC was seen to localize at the division site of rapidly dividing cells between well-segregated nucleoids. Various DivIC immunostaining patterns were observed, and these correlated with different cell lengths, suggesting that the DivIC localization takes on various forms during the cell cycle. The DivIC immunolocalization patterns are very similar to those of another membrane-bound B. subtilis division protein, DivIB.
Long-Term Effect ofN-Acetyl-Seryl-Aspartyl-Lysyl-Proline on Left Ventricular Collagen Deposition in Rats With 2-Kidney, 1-Clip Hypertension (2001)

Ac-SDKP inhibited monocyte/macrophage infiltration, cell proliferation, and collagen deposition in the LV of hypertensive rats without affecting blood pressure or cardiac hypertrophy, suggesting that it may be partly responsible for the cardioprotective effect of angiotensin-converting enzyme inhibitors.
Recognition of a highly conserved region of human immunodeficiency virus type 1 gp120 by an HLA-Cw4-restricted cytotoxic T-lymphocyte clone (1993)

Human immunodeficiency virus type 1 (HIV-1) isolates exhibit extensive sequence variation, particularly in the gp120 subunit of the envelope glycoprotein, and the degree of this variation has raised questions as to whether conserved regions of the HIV-1 envelope can be recognized by the host immune response. A CD8+ cytotoxic T-lymphocyte (CTL) clone specific for the HIV-1 envelope was derived by culturing peripheral blood mononuclear cells from an HIV-1 seropositive subject in the presence of a CD3-specific monoclonal antibody, interleukin-2, and irradiated allogeneic peripheral blood mononuclear cells. Lysis of target cells was restricted by an HLA-C molecule, Cw4, which has not been previously shown to present viral antigen to CTL. Mapping of the specificity of this CTL clone by using synthetic HIV-1 peptides localized the epitope to an 8-amino-acid region of gp120 (amino acids 376 to 383) which is conserved among approximately 90% of sequenced viral isolates. Examination of the recognition of variant peptides by this CTL clone demonstrated that a single, nonconservative amino acid substitution within the 8-amino-acid minimal epitope could abrogate lysis of targets incubated with the variant peptide. The identification of a CTL epitope in a highly conserved region of gp120 documents the ability of cellular immune responses of infected persons to respond to relatively invariant portions of this highly variable envelope glycoprotein. However, the ability of even a single-amino-acid change in gp120 to abolish lysis by CTL supports the hypothesis that sequence variation in HIV-1 may serve as a mechanism of immune escape. In addition, the identification of an HLA-C molecule presenting viral antigen to CTL supports a functional role for these molecules.
Control of Granulocytes and Macrophages: Molecular, Cellular, and Clinical Aspects (1991)

The production and functional activity of two important white blood cells, the granulocytes and macrophages, are regulated mainly by a group of glycoprotein colony-stimulating factors. The colony-stimulating factors have been mass-produced with recombinant technology and are now proving of value in preventing or suppressing infections in a variety of individuals with subnormal or defective formation of blood cells.
One-Electron Oxidation of Electronically Diverse Manganese(III) and Nickel(II) Salen Complexes: Transition from Localized to Delocalized Mixed-Valence Ligand Radicals (2011)

Ligand radicals from salen complexes are unique mixed-valence compounds in which a phenoxyl radical is electronically linked to a remote phenolate via a neighboring redox-active metal ion, providing an opportunity to study electron transfer from a phenolate to a phenoxyl radical mediated by a redox-active metal ion as a bridge. We herein synthesize one-electron-oxidized products from electronically diverse manganese(III) salen complexes in which the locus of oxidation is shown to be ligand-centered, not metal-centered, affording manganese(III)-phenoxyl radical species. The key point in the present study is an unambiguous assignment of intervalence charge transfer bands by using nonsymmetrical salen complexes, which enables us to obtain otherwise inaccessible insight into the mixed-valence property. A d(4) high-spin manganese(III) ion forms a Robin-Day class II mixed-valence system, in which electron transfer is occurring between the localized phenoxyl radical and the phenolate. This is in clear contrast to a d(8) low-spin nickel(II) ion with the same salen ligand, which induces a delocalized radical (Robin-Day class III) over the two phenolate rings, as previously reported by others. The present findings point to a fascinating possibility that electron transfer could be drastically modulated by exchanging the metal ion that bridges the two redox centers.
Gellan-related polysaccharides and the genus Sphingomonas (1993)

SUMMARY: The biochemical and physiological characteristics of several different existing bacterial isolates which secrete gellan-related polysaccharides were compared. Although they were originally classified into diverse genera, these bacteria are shown here to be closely related to each other and to members of the genus Sphingomonas.
The protection of thymine and guanine residues in oligodeoxyribonucleotide synthesis (1984)

Thymidine is converted in four steps into its crystalline 4-O-phenyl derivative (14b) in 72% overall yield. 2′-Deoxyguanosine is converted in five steps into its 6-O-(2-nitrophenyl)-2-N-phenylacetyl and crystalline 6-O-(3,5-dichlorophenyl)-2-N-phenylacetyl derivatives [(19a) and (19b), respectively] in ca. 39 and 42% overall yields, respectively. Compounds (14b), (19a), and (19b) are converted into the corresponding crystalline 5′-O-(9-phenyl-9H-xanthen-9-yl) derivatives (15), (20a), and (20b), respectively. The actions of N1,N1,N3,N3-tetramethylguanidinium 2-nitrobenzaldehyde oximate, 80% acetic acid, potassium carbonate in aqueous dioxane, pyridine, and triethylammonium toluene-p-thiolate on (14b), (19a), and (19b) have been investigated.
Synthesis, Characterization, and Applications of Dendrimer-Encapsulated Nanoparticles (2004)

In this article we describe the synthesis, characterization, and applications of dendrimer-encapsulated nanoparticles (DENs). These materials are synthesized by a template approach in which metal ions are extracted into the interior of dendrimers and then subsequently chemically reduced to yield nearly size-monodisperse particles having dimensions of less than 3 nm. Monometallic, bimetallic (including core/shell), and semiconductor nanoparticles have been prepared by this route. The dendrimer component of these composites serves not only as a template for preparing the nanoparticle replica but also to stabilize the nanoparticle, makes it possible to tune solubility, and provides a means for immobilization of the nanoparticle on solid supports. These materials have a number of potential applications, but the focus here is on catalysis. Homogeneous catalytic reactions, including hydrogenations, Heck coupling, and Suzuki reactions, in water, organic solvents, biphasic fluorous/organic solvents, and liquid and supercritical CO2 are discussed. In many cases it is easy to recycle catalytic DENs. DENs can also be immobilized on supports, such as silica and titania, and used for heterogeneous catalysis. Bimetallic DENs are shown to have particularly interesting catalytic properties. In addition to a discussion of current progress in this field, a number of intriguing questions related to the properties and potential applications of these materials are examined.
The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia (2010)

Organotypic cultures of primary human airway epithelial cells have been used to investigate the morphology, ion and fluid transport, innate immunity, transcytosis, infection, inflammation, signaling, cilia, and repair functions of this complex tissue. However, we do not know how closely these cultures resemble the airway surface epithelium in vivo. In this study, we examined the genome-wide expression profile of tracheal and bronchial human airway epithelia in vivo and compared it with the expression profile of primary cultures of human airway epithelia grown at the air-liquid interface. For comparison, we also investigated the expression profile of Calu-3 cells grown at the air-liquid interface and primary cultures of human airway epithelia submerged in nutrient media. We found that the transcriptional profile of differentiated primary cultures grown at the air-liquid interface most closely resembles that of in vivo airway epithelia, suggesting that the use of primary cultures and the presence of an air-liquid interface are important to recapitulate airway epithelia biology. We describe a high level of similarity between cells of tracheal and bronchial origin within and between different human donors, which suggests a very robust expression profile that is specific to airway cells.
Expression of Epidermal Growth Factor-Related Proteins and Epidermal Growth Factor Receptor in Common Epithelial Ovarian Tumors (1997)

The biologic significance of epidermal growth factor (EGF)-related proteins and EGF receptor (EGFR) in the development and progression of human ovarian carcinoma was studied in 7 ovarian cystadenomas, 6 mucinous tumors of low malignant potential (LMP), and 25 invasive adenocarcinomas by immunohistochemistry. Results were correlated with clinicopathologic features. We also examined immunoreactivity in five serous adenocarcinomas both before and after cisplatin chemotherapy. Amphiregulin (AR) expression was observed only in mucinous tumors (4 of 8 cystadenomas, 2 of 6 tumors of LMP, and 6 of 10 cystadenocarcinomas), but was not detected in the serous tumors or clear cell adenocarcinomas. EGF, cripto, and EGFR expression was significantly higher in mucinous cystadenocarcinomas than in mucinous cystadenomas or mucinous tumors of LMP. Three of five specimens obtained at a second operation after chemotherapy had more intense or diffuse immunostaining for transforming growth factor alpha (TGF-alpha) than the initial specimens did. Coexpression of more than two of the EGF-related proteins or EGFR significantly correlated with increased surgical stage in serous and clear cell carcinoma. AR expression seems to correlate with mucinous differentiation rather than with advanced stages of ovarian tumors. Our results indicate that expression of some EGF-related proteins is greater in certain subtypes of ovarian carcinomas than in their benign counterparts and that coexpression of these proteins is associated with advanced stage in serous and clear cell carcinoma. Increased TGF-alpha expression may also be related to ovarian tumor resistance to cisplatin chemotherapy.
Noninvasively measuring blood glucose using saliva (1998)

Self-measurement of blood glucose level is a very important aspect in monitoring the health quality of diabetic patients who require insulin therapy. Typically, a blood sample for analysis is obtained via a finger stick or other such invasive procedure. Often, this blood collecting causes physical and mental stress to the patient. For this reason, it is desirable to establish a noninvasive bloodless procedure to monitor the blood glucose level (BGL). Here, the authors discuss the correlation between BGL and saliva glucose level and then present an approach that uses an enzyme-sensor system to noninvasively measure blood glucose using saliva.