gebhart/patrepeval huggingface dataset:
Cholesterol biosynthesis from lanosterol: development of a novel assay method and characterization of rat liver microsomal lanosterol Δ24-reductase (1997)

The membrane-bound sterol delta 24-reductase (24-reductase) catalyses anaerobic reduction of the 24(25)-enes of lanosterol and other obligatory intermediates of cholesterol biosynthesis from lanosterol. A novel assay method and properties of the 24-reductase are described. More than a 120-fold induction of the 24-reductase activity was achieved by feeding rats a diet containing 5% cholestyramine plus 0.1% lovastatin in chow and by modulating diurnal variation. With this enzyme induction condition, lanosterol was converted efficiently into dihydrolanosterol in both intact hepatic microsomes and freshly isolated hepatocytes only when either miconazole or CO was added to inhibit 14 alpha-demethylation of lanosterol. AR45 cells, which are deficient in 14 alpha-methyl demethylase (14 alpha-DM), exhibit lanosterol 24-reductase activity without addition of either CO or miconazole. Conversely, inhibition of the 24-reductase was not required for the expression of 14 alpha-DM activity. Studies on the substrate specificities for the 24-reductase using different 24(25)-enes showed that the most reactive substrate was 5 alpha-cholesta-7,24-dien-3 beta-ol, which exhibited a maximal 18-fold higher kcat than that of lanosterol without the aid of the 14 alpha-DM inhibitor. In addition, both the kinetic behaviour of lanosterol substrate in relation to the 24-reductase and a non-competitive inhibition mode of U18666A (Ki 0. 157 microM) as well as Triparanol (Ki 0.523 microM), two well-known 24-reductase inhibitors, were determined. On the basis of our new findings on the preferred substrate and on the negative effect of 14 alpha-DM on the 24-reductase, we suggest that C-24 reduction of sterols takes place straight after sterol delta 8-->7 isomerization of zymosterol, which occurs several steps after C-32 demethylation of lanosterol in the 19-step pathway of cholesterol biosynthesis from lanosterol.
Aggrecanases and cartilage matrix degradation. (2003)

The loss of extracellular matrix macromolecules from the cartilage results in serious impairment of joint function. Metalloproteinases called 'aggrecanases' that cleave the Glu373-Ala374 bond of the aggrecan core protein play a key role in the early stages of cartilage destruction in rheumatoid arthritis and in osteoarthritis. Three members of the ADAMTS family of proteinases, ADAMTS-1, ADAMTS-4 and ADAMTS-5, have been identified as aggrecanases. Matrix metalloproteinases, which are also found in arthritic joints, cleave aggrecans, but at a distinct site from the aggrecanases (i.e. Asn341-Phe342). The present review discuss the enzymatic properties of the three known aggrecanases, the regulation of their activities, and their role in cartilage matrix breakdown during the development of arthritis in relation to the action of matrix metalloproteinases.
Nuclear integration of JAK/STAT and Ras/AP-1 signaling by CBP and p300 (1997)

We report that interferon gamma (IFN-gamma) inhibits transcription of the macrophage scavenger receptor gene by antagonizing the Ras-dependent activities of AP-1 and cooperating ets domain transcription factors, apparently as a result of competition between AP-1/ets factors and activated STAT1 for limiting amounts of CBP and p300. Consistent with this model, STAT1 alpha interacts directly with CBP in cells, and microinjection of anti-CBP and anti-p300 antibodies blocks transcriptional responses to IFN-gamma. Cells lacking STAT1 fail to inhibit AP-1/ets activity, and overexpression of CBP both potentiates IFN-gamma-dependent transcription and relieves AP-1/ets repression. Thus, CBP and p300 integrate both positive and negative effects of IFN-gamma on gene expression by serving as essential coactivators of STAT1 alpha, modulating gene-specific responses to simultaneous activation of two or more signal transduction pathways.
Nitroxide-Stimulated H2O2Decomposition by Peroxidases and Pseudoperoxidases (1992)

Nitroxide free radicals interact with Hb/metHb, Mb/metMb and with peroxidases/phenols to induce a catalase-like conversion of H2O2 to O2 (catalatic activity), without being substantially consumed in the process. The mechanism of this reaction is postulated to involve a one-electron oxidation of the nitroxide to the immonium oxene, which then reacts further to release oxygen and the nitroxide. An involvement of the immonium oxene in the reaction mechanism is consistent with ferryl heme reduction by nitroxides and a detection of the reduced nitroxide when the reaction mixture is supplemented with the two-electron reductant sodium borohydride. The nitroxide-induced catalatic activity is completely inhibited when the reaction mixture is supplemented with glutathione. Nitroxides suppress free radical formation by hydroperoxide-activated heme proteins, as inferred from their inhibition of the spin-trapping of glutathionyl radicals. H2O2 decomposition and a suppression of reactive free radical formation by heme proteins appears to be an antioxidant activity of nitroxides, which is distinct from their previously reported superoxide dismutating activity and which may be a factor in their protective action in models of cardiac reperfusion injury.
Robustness Analysis of the Escherichia coli Metabolic Network (2000)

Genomic, biochemical, and strain-specific data can be assembled to define an in silico representation of the metabolic network for a select group of single cellular organisms. Flux-balance analysis and phenotypic phase planes derived therefrom have been developed and applied to analyze the metabolic capabilities and characteristics of Escherichia coli K-12. These analyses have shown the existence of seven essential reactions in the central metabolic pathways (glycolysis, pentose phosphate pathway, tricarboxylic acid cycle) for the growth in glucose minimal media. The corresponding seven gene products can be grouped into three categories: (1) pentose phosphate pathway genes, (2) three-carbon glycolytic genes, and (3) tricarboxylic acid cycle genes. Here we develop a procedure that calculates the sensitivity of optimal cellular growth to altered flux levels of these essential gene products. The results indicate that the E. coli metabolic network is robust with respect to the flux levels of these enzymes. The metabolic flux in the transketolase and the tricarboxylic acid cycle reactions can be reduced to 15% and 19%, respectively, of the optimal value without significantly influencing the optimal growth flux. The metabolic network also exhibited robustness with respect to the ribose-5-phosphate isomerase, and the ribose-5-phosephate isomerase flux was reduced to 28% of the optimal value without significantly effecting the optimal growth flux. The metabolic network exhibited limited robustness to the three-carbon glycolytic fluxes both increased and decreased. The development presented another dimension to the use of FBA to study the capabilities of metabolic networks.
Ribosomal RNA in Alzheimer Disease Is Oxidized by Bound Redox-active Iron (2005)

Oxidative modification of cytoplasmic RNA in vulnerable neurons is an important, well documented feature of the pathophysiology of Alzheimer disease. Here we report that RNA-bound iron plays a pivotal role for RNA oxidation in vulnerable neurons in Alzheimer disease brain. The cytoplasm of hippocampal neurons showed significantly higher redox activity and iron(II) staining than age-matched controls. Notably, both were susceptible to RNase, suggesting a physical association of iron(II) with RNA. Ultrastructural analysis further suggested an endoplasmic reticulum association. Both rRNA and mRNA showed twice the iron binding as tRNA. rRNA, extremely abundant in neurons, was considered to provide the greatest number of iron binding sites among cytoplasmic RNA species. Interestingly, the difference of iron binding capacity disappeared after denaturation of RNA, suggesting that the higher order structure may contribute to the greater iron binding of rRNA. Reflecting the difference of iron binding capacity, oxidation of rRNA by the Fenton reaction formed 13 times more 8-hydroxyguanosine than tRNA. Consistent with in situ findings, ribosomes purified from Alzheimer hippocampus contained significantly higher levels of RNase-sensitive iron(II) and redox activity than control. Furthermore, only Alzheimer rRNA contains 8-hydroxyguanosine in reverse transcriptase-PCR. Addressing the biological significance of ribosome oxidation by redox-active iron, in vitro translation with oxidized ribosomes from rabbit reticulocyte showed a significant reduction of protein synthesis. In conclusion these results suggest that rRNA provides a binding site for redox-active iron and serves as a redox center within the cytoplasm of vulnerable neurons in Alzheimer disease in advance of the appearance of morphological change indicating neurodegeneration.
Cell dispersal in biofilms: an extracellular DNA masks nature's strongest glue (2010)

Growth in biofilms provides bacterial species with many advantages over growth in suspension, e.g. colonization of nutrient-rich areas. In the α-proteobacterium Caulobacter crescentus biofilm formation is facilitated through its asymmetric cell division, where one daughter cell becomes a motile flagellated swarmer cell able to colonize new surfaces while the other remains as a stalked cell attached to the substrate through the adhesive holdfast. The Caulobacter biofilm consists of stalked cells arranged either in a monolayer or in a multicellular 'mushroom' structure. In this issue of Molecular Microbiology, Berne et al. demonstrate that extracellular DNA (eDNA) from lysed cells prevents biofilm maturation. eDNA masks the adhesive properties of newly synthesized holdfast to enable the escape of swarmer cells from the biofilm. By contrast, holdfasts on previously attached stalked cells remain unaffected by eDNA. Surprisingly, the inhibitory effect was genus-specific, as only DNA from Caulobacter, but not from other genera, could interfere with biofilm maturation. This study reveals a new role for DNA in biofilms, as a regulatory rather than a structural component, and a novel mechanism to facilitate the escape of cells from biofilms. A compelling case is made for the existence of a new type of genus-specific 'macromolecular language'.
Prostaglandins and the induction of food sensitive enteropathy (2000)

Intestinal inflammatory diseases are mediated by dysregulated immune responses to undefined luminal antigens. Feeding hen egg-white lysozyme to mice expressing a transgenic T-cell receptor that recognizes hen egg-white lysozyme peptide 46-61 resulted in no intestinal pathology; however, simultaneous administration of cyclooxygenase-2 inhibitors and dietary hen egg-white lysozyme resulted in increased proliferation of lamina propria mononuclear cells and crypt epithelial cells, crypt expansion and villus blunting. Lamina propria mononuclear cells produce high levels of cyclooxygenase-2-dependent arachidonic acid metabolites, which act as immunomodulators in the immune response to dietary antigen. These findings establish that cyclooxygenase-2dependent arachidonic acid metabolites are essential in the development and maintenance of intestinal immune homeostasis.
Confined lateral selective epitaxial growth of silicon for device fabrication (1990)

An epitaxy technique, confined lateral selective epitaxial growth (CLSEG), which produces wide, thin slabs of single-crystal silicon over insulator, using only conventional processing, is discussed. As-grown films of CLSEG 0.9 mu m thick, 8.0 mu m wide, and 500 mu m long were produced at 1000 degrees C at reduced pressure. Junction diodes fabricated in CLSEG material show ideality factors of 1.05 with reverse leakage currents comparable to those of diodes built in SEG homoepitaxial material. Metal-gate p-channel MOSFETs in CLSEG with channel dopings of 2*10/sup 16/ cm/sup -3/ exhibit average mobilities of 283 cm/sup 2//V-s and subthreshold slopes of 223 mV/decade.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of Hemangiogenesis and LymphangiogenesisafterNormal-Risk Corneal Transplantation by Neutralizing VEGF Promotes Graft Survival (2004)

There is concurrent, VEGF-A-dependent hem- and lymphangiogenesis after normal-risk keratoplasty within the preoperatively avascular recipient bed. Inhibition of hem- and lymphangiogenesis (afferent and efferent arm of an immune response) after normal-risk corneal transplantation improves long-term graft survival, establishing early postoperative hem- and lymphangiogenesis as novel risk factors for graft rejection even in low-risk eyes.
What forces keep the air spaces of the lung dry? (1982)

<h3>Abstract</h3> Recombinant AAV (rAAV) vectors have been developed for therapeutic treatment of genetic diseases. Nevertheless, current rAAV vectors administered to patients often contain non-vector related DNA contaminants. Here, we present a thorough molecular analysis of the configuration of non-standard AAV genomes generated during rAAV production. In addition to the sub-vector genomic size particles containing incomplete AAV genomes, our results found that rAAV preparations were contaminated with multiple categories of subgenomic particles with either snapback genomes or vector genomes with deletions in the mid regions. Through CRISPR and restriction enzyme-based in vivo and in vitro modeling, we identified that the main mechanism leading to the formation of non-canonical genome particles occurred through nonhomologous end joining of fragmented vector genomes caused by genome lesions or DNA breaks that were generated by the host cell/environment. The results of this study advance our understanding of AAV vectors and provide new clues on improving vector efficiency and safety profile for use in human gene therapy.
MHC class II tetramers identify peptide-specific human CD4+ T cells proliferating in response to influenza A antigen (1999)

Antigen-specific T helper cells present in peripheral blood at very low frequencies are capable of rapid clonal expansion during antigenic challenge. The exquisite specificity of this response provides for activation and expansion of a very select cohort of T cells, a feature we have used to directly identify and quantify human epitope-specific T helper cells from peripheral blood. Soluble tetramerized class II MHC molecules, loaded with an immunodominant peptide from hemagglutinin (HA) and labeled with fluorescent dyes, were constructed and used to directly identify antigen-specific T cells from influenza-immune individuals. After 7 days of proliferation in response to stimulation by HA peptide or whole influenza vaccine, cells staining positive with the HA tetramer had undergone between 6 and 9 divisions and were CD3(+), CD4(+), CD25(+), and CD8(-), characteristic of activated T helper cells responding to antigen. The HA epitope-specific component of the complex response to whole influenza vaccine represented a major subset of proliferating T helper cells. Soluble class II tetramers allow a direct approach for the analysis of immunodominant antigenic specificities. The identification of antigen-specific T helper cells in the peripheral blood provides a means for tracking the immune response against infectious agents and in autoimmune disease. This article may have been published online in advance of the print edition. The date of publication is available from the JCI website, http://www.jci.org.
Review on dry reforming of methane, a potentially more environmentally-friendly approach to the increasing natural gas exploitation (2014)

With the actual growth of the natural gas industry in the US as well as the potential and availability of this non-renewable carbon source worldwide, reforming of methane gas is getting increasing attention. Methane can be used for the production of heat or electricity, as well, it can be converted to syngas, a building block that could lead to the production of liquid fuels and chemicals, a very promising pathway in light of the increasing price of oil. Amongst the different reforming techniques, dry reforming could represent a very interesting approach both to valorize a cheap source or carbon (CO2) as well as to reduce the overall carbon footprint of the increasing worldwide fossil-based methane consumption. In this short review, attention will be given to the thermodynamics of dry reforming followed by an investigation on dry reforming using heterogeneous catalyst by focusing on the most popular elements used in literature for dry reforming. Attention will as well be given to other emerging techniques that may allow countering at one point the high thermodynamic penalties that accompanies conversion of methane using carbon dioxide.
BCL-6 expression during B-cell activation (1996)

Translocations involving the BCL-6 gene are common in the diffuse large cell subtype of non-Hodgkin's lymphoma. Invariably, the BCL-6 coding region is intact, but its 5' untranslated region is replaced with sequences from the translocation partner. The present study shows that BCL-6 expression is regulated in lymphocytes during mitogenic stimulation. Resting B and T lymphocytes contain high levels of BCL-6 mRNA. Stimulation of mouse B cells with anti-IgM or IgD antibodies, bacterial lipopolysaccharide, phorbol 12-myristate 13-acetate plus ionomycin, or CD40 ligand led to a five-fold to 35-fold decrease in BCL-6 mRNA levels. Similar downregulation of BCL-6 mRNA was seen in human B cells stimulated with Staphylococcus aureus plus interleukin-2 or anti-IgM antibodies and in human T lymphocytes stimulated with phytohemagglutinin. BCL-6 mRNA levels began to decrease 8 to 16 hours after stimulation, before cells entered S phase. Although polyclonal activation of B cells in vitro invariably decreased BCL-6 MRNA expression, activated B cells from human germinal centers expressed BCL-6 mRNA at levels comparable to the levels in resting B cells. Despite these similar mRNA levels, BCL-6 protein expression was threefold to 34-fold higher in germinal center B cells than in resting B cells, suggesting that BCL-6 protein levels are controlled by translational or posttranslational mechanisms. These observations suggest that the germinal center reaction provides unique activation signals to B cells that allow for continued, high-level BCL-6 expression.
Epithelial Cell Dysfunction in Cystic Fibrosis: Implications for Airways Disease (1989)

An important pathophysiologic factor in CF airways is the failure to clear poorly hydrated secretions. The water deficit in CF mucous secretions can now be ascribed to a fundamental defect of epithelial cell regulatory processes which promotes sodium reabsorption from surface liquids and interferes with chloride secretion onto the luminal surface. In addition, it is now known that CF airway epithelial cells oversulfate high molecular weight glycoconjugates, both secreted and cell surface-associated. Oversulfation of glycoconjugates may contribute to the altered clearance properties of CF airways mucus and in addition could favor colonization of airways by organisms such as P. aeruginosa.
Effects of hydrostatic pressure on matrix synthesis in different regions of the intervertebral disk (1996)

The intervertebral disk is routinely subjected to compressive loads that alter with posture and muscle activity and can produce pressures > 2 MPa in human lumbar disks in vivo (A. Nachemson and G. Elfstrom. Scand. J. Rehabil. Med. 2, Suppl. 1:1-40, 1979; A. Nachemson and J. M. Morris. J. Bone Jt. Surg. Am. Vol. 46A: 1077-1092, 1964). We measured the effect of load on hydrostatic pressures in bovine caudal disks. With increase in applied load, pressure increased linearly in the nucleus and inner annulus. The resting pressure measured after slaughter (0.19 +/- 0.05 MPa) and the pressure at failure (34 MPa, estimated from the vertebrae/disk segment failure load of 7,430 +/- 590 N) define the limits that can occur in vivo. Because hydrostatic pressure influences matrix synthesis in articular cartilage, we have examined the effects of pressures in the range 1-10 MPa applied for 20 s or 2 h on proteoglycan synthesis in bovine caudal and human lumbar intervertebral disks in vitro. In the nucleus pulposus and inner annulus of bovine disks, application of hydrostatic pressure in the range of 1-7.5 MPa for only 20 s stimulated matrix synthesis over the following 2 h at atmospheric pressure. The maximum stimulation in the bovine disks was seen in the inner annulus after application of 2.5 MPa, where proteoglycan synthesis rates doubled. Exposure to 2.5 MPa also stimulated synthesis in the nucleus pulposus of human disks taken at surgery, whereas 7.5 MPa inhibited synthesis in five out of six specimens. With 2-h continuous exposure to the same levels of pressure, no stimulation was seen in the nucleus of bovine disks, and significant stimulation was only observed at 5.0 MPa in the inner annulus. Exposure to 10 MPa for either 20 s or 2 h inhibited proteoglycan synthesis in these regions of the disks. In contrast, in the outer annulus, where loading does not lead to a rise in hydrostatic pressure in vivo, there was no significant response to hydrostatic pressure over the range of 1-10 MPa in bovine or human disks.
Atmospheric pressure glow discharge desorption mass spectrometry for rapid screening of pesticides in food (2008)

Flowing afterglow atmospheric pressure glow discharge tandem mass spectrometry (APGD-MS/MS) is used for the analysis of trace amounts of pesticides in fruit juices and on fruit peel. The APGD source was rebuilt after Andrade et al. (Andrade et al., Anal. Chem. 2008; 80: 2646-2653; 2654-2663) and mounted onto a hybrid quadrupole time-of-flight mass spectrometer. Apple, cranberry, grape and orange juices as well as fruit peel and salad leaves were spiked with aqueous solutions containing trace amounts of the pesticides alachlor, atrazine, carbendazim, carbofuran, dinoseb, isoproturon, metolachlor, metolcarb, propoxur and simazine. Best limits of determination (LODs) of pesticides in the fruit juices were achieved for metolcarb (1 microg/L in apple juice), carbofuran and dinoseb (2 microg/L in apple juice); for the analysis of apple skin best LODs were 10 pg/cm(2) of atrazine, metolcarb and propoxur which corresponds to an estimated concentration of 0.01 microg/kg apple, taking into account the surface area and the weight of the apple. The measured LODs were within or below the allowed maximum residue levels (MRLs) decreed by the European Union (1-500 microg/kg for pesticides in fruit juice and 0.01-5 microg/kg for apple skin). No sample pretreatment (extraction, pre-concentration, chromatographic separation) was necessary to analyze these pesticides by direct desorption/ionization using APGD-MS and to identify them using MS/MS. This makes APGD-MS a powerful high-throughput tool for the investigation of very low amounts of pesticides in fruit juices and on fruit peel/vegetable skin.