gebhart/patrepeval huggingface dataset:
Primary human astrocytes functionally express RIG-I, a member of the retinoic acid-inducible gene-I family of viral pattern recognition receptors (133.48) (2009)

Abstract Astrocytes are ideally positioned to detect and respond to invading pathogens of the CNS and previous studies have demonstrated the ability of these cells to produce key inflammatory mediators following exposure to members of the Mononegavirales order of viruses that are the causative agents of lethal human CNS diseases including rabies. However, the mechanisms by which resident cells of the CNS perceive such viral challenges have not been defined. Recently, several cytosolic DExD/H box RNA helicases have been described that can bind early viral replicative intermediates leading to the realization that retinoic acid-inducible gene I (RIG-I)-like helicases, such as RIG-I, function as intracellular receptors for RNA viruses. In the present study, we demonstrate that cultured primary human astrocytes constitutively express RIG-I receptor protein. Interestingly, such expression is rapidly elevated following exposure to vesicular stomatitis virus (VSV), a neurotropic rhabdovirus that closely resembles rabies virus. Evidence for the functional nature of RIG-I expression in human glial cells comes from the observation that this molecule associates with its downstream effector molecule, interferon promoter stimulator-1 (IPS-1), following VSV infection as assessed by co-immunoprecipitation techniques. Furthermore, we have confirmed that this molecule functions as an intracellular pattern recognition receptor in astrocytes by demonstrating that a putative ligand for RIG-I can elicit inflammatory cytokine production by this cell type. These findings raise the exciting possibility that RIG-I plays an important role in the detection of viral CNS pathogens and the initiation of protective immune responses or, alternatively, the progression of damaging inflammation within the brain.
Collisional focusing effects in radio frequency quadrupoles (1992)

The transmission of ions through a conventional two-dimensional radiofrequency-only (rf) quadrupole has been studied for comparatively high operating pressures between 5 × 10(-4) and 1 × 10(-2) torr. Measurements of signals from mass-resolved analyte ions and total ion currents show that, provided the initial injection ion energy is low (1-30 eV), the ion transmission observed through a small aperture at the exit of the rf quadrupole first increases as the gas pressure increases, reaching a maximum at - 8 × 10(-3) torr before decreasing at higher pressures. This is in direct contrast to the expectations of classical scattering. This "collisional focusing" appears to be analogous to effects seen in three-dimensional ion traps. The collisional focusing increases with the mass of the ion (not mass-to-charge ratio) for masses up to at least 16,950 u. The collisional focusing of the ions is found to be accompanied by significant losses of axial kinetic energy. A Monte Carlo simulation of the energy loss process is reported that can provide agreement with the observed losses for reasonable collision cross-sections. The results suggest that operation of rf quadrupoles at relatively high pressure may find practical application in sampling ions from high (e.g., atmospheric) pressure ion sources.
Loss of Tumor Suppressor p53 Decreases PTEN Expression and Enhances Signaling Pathways Leading to Activation of Activator Protein 1 and Nuclear Factor κB Induced by UV Radiation (2005)

Transcription factor p53 and phosphatase PTEN are two tumor suppressors that play essential roles in suppression of carcinogenesis. However, the mechanisms by which p53 mediates anticancer activity and the relationship between p53 and PTEN are not well understood. In the present study, we found that pretreatment of mouse epidermal Cl41 cells with pifithrin-alpha, an inhibitor for p53-dependent transcriptional activation, resulted in a marked increase in UV-induced activation of activator protein 1 (AP-1) and nuclear factor kappaB (NF-kappaB). Consistent with activation of AP-1 and NF-kappaB, pifithrin-alpha was also able to enhance the UV-induced phosphorylation of c-Jun-NH2-kinases (JNK) and p38 kinase, whereas it did not show any effect on phosphorylation of extracellular signal-regulated kinases. Furthermore, the UV-induced signal activation, including phosphorylation of JNK, p38 kinase, Akt, and p70S6K, was significantly enhanced in p53-deficient cells (p53-/-), which can be reversed by p53 reconstitution. In addition, knockdown of p53 expression by its small interfering RNA also caused the elevation of AP-1 activation and Akt phosphorylation induced by UV radiation. These results show that p53 has a suppressive activity on the cell signaling pathways leading to activation of AP-1 and NF-kappaB in cell response to UV radiation. More importantly, deficiency of p53 expression resulted in a decrease in PTEN protein expression, suggesting that p53 plays a critical role in the regulation of PTEN expression. In addition, overexpression of wild-type PTEN resulted in inhibition of UV-induced AP-1 activity. Because PTEN is a well-known phosphatase involved in the regulation of phosphatidylinositol 3-kinase (PI-3K)/Akt signaling pathway, taken together with the evidence that PI-3K/Akt plays an important role in the activation of AP-1 and NF-kappaB during tumor development, we anticipate that inhibition of AP-1 and NF-kappaB by tumor suppressor p53 seems to be mediated via PTEN, which may be a novel mechanism involved in anticancer activity of p53 protein.
Folate: In Vitro and in Vivo Effects on VLDL and LDL Oxidation (2007)

Raised total homocysteine (tHcy) levels may be involved in the etiology of cardiovascular disease and can lead to damage of vascular endothelial cells and arterial wall matrix. Folic acid supplementation can help negate these detrimental effects by reducing tHcy. Recent evidence has suggested an additional anti-atherogenic property of folate in protecting lipoproteins against oxidation. This study utilized both an in vitro and in vivo approach. In vitro: Very-low-density lipoprotein (VLDL) and low density lipoprotein (LDL) were isolated by rapid ultracentrifugation and then oxidized in the presence of increasing concentrations (0-->10 micromol/L) of either folic acid or 5-methyltetrahydrofolate (5-MTHF). In vivo: Twelve female subjects were supplemented with folic acid (1 mg/day), and the pre- and post-VLDL and LDL isolates subjected to oxidation. In vitro: 5-MTHF, but not folic acid, significantly increased the resistance of VLDL and LDL to oxidation. In vivo: Following folic acid supplementation, tHcy decreased, serum folate increased, and both VLDL and LDL displayed a significant increase in their resistance to oxidation. These results indicated that in vitro, only the active form of folate, 5-MTHF, had antioxidant properties. In vivo results demonstrated that folic acid supplementation reduced tHcy and protected both VLDL and LDL against oxidation. These findings provide further support for the use of folic acid supplements to aid in the prevention of atherosclerosis.
Zinc Finger Structures in the Human Immunodeficiency Virus Type 1 Nucleocapsid Protein Facilitate Efficient Minus- and Plus-Strand Transfer (2000)

The nucleocapsid protein (NC) of human immunodeficiency virus type 1 (HIV-1) has two zinc fingers, each containing the invariant metal ion binding residues CCHC. Recent reports indicate that mutations in the CCHC motifs are deleterious for reverse transcription in vivo. To identify reverse transcriptase (RT) reactions affected by such changes, we have probed zinc finger functions in NC-dependent RT-catalyzed HIV-1 minus- and plus-strand transfer model systems. Our approach was to examine the activities of wild-type NC and a mutant in which all six cysteine residues were replaced by serine (SSHS NC); this mutation severely disrupts zinc coordination. We find that the zinc fingers contribute to the role of NC in complete tRNA primer removal from minus-strand DNA during plus-strand transfer. Annealing of the primer binding site sequences in plus-strand strong-stop DNA [(+) SSDNA] to its complement in minus-strand acceptor DNA is not dependent on NC zinc fingers. In contrast, the rate of annealing of the complementary R regions in (-) SSDNA and 3' viral RNA during minus-strand transfer is approximately eightfold lower when SSHS NC is used in place of wild-type NC. Moreover, unlike wild-type NC, SSHS NC has only a small stimulatory effect on minus-strand transfer and is essentially unable to block TAR-induced self-priming from (-) SSDNA. Our results strongly suggest that NC zinc finger structures are needed to unfold highly structured RNA and DNA strand transfer intermediates. Thus, it appears that in these cases, zinc finger interactions are important components of NC nucleic acid chaperone activity.
Interdigitated array microelectrodes for the determination of enzyme activities (1994)

An array of closely spaced interdigitated microelectrodes was applied to the sensitive detection of reversible redox couples. The measurement is based on the redox cyclization between the adjacent microband electrodes of the interdigitated array (IDA), when both the respective oxidation and reduction potential are applied at the electrode pairs. The multiple oxidation and reduction result in an increased generation of current. The steady-state current of mediators, such as phenazine methosulfate, hexacyanoferrate(II), pyrocatechol, benzoquinone and p-aminophenol, was amplified by a factor of 10–20 compared with the current of single electrodes. The high collection efficiency enabled this signal amplification rate to be obtained. The detection limit for p-aminophenol was 100 nmol l–1. The IDA sensor was applied to the determination of alkaline phosphatase and β-galactosidase activity by detecting enzymatically generated p-aminophenol.
Direct Interaction with Contactin Targets Voltage-gated Sodium Channel Nav1.9/NaN to the Cell Membrane (2001)

The mechanisms that target various sodium channels within different regions of the neuronal membrane, which they endow with different physiological properties, are not yet understood. To examine this issue we studied the voltage-gated sodium channel Na(v)1.9/NaN, which is preferentially expressed in small sensory neurons of dorsal root ganglia and trigeminal ganglia and the nonmyelinated axons that arise from them. Our results show that the cell adhesion molecule contactin binds directly to Na(v)1.9/NaN and recruits tenascin to the protein complex in vitro. Na(v)1.9/NaN and contactin co-immunoprecipitate from dorsal root ganglia and transfected Chinese hamster ovary cell line, and co-localize in the C-type neuron soma and along nonmyelinated C-fibers and at nerve endings in the skin. Co-transfection of Chinese hamster ovary cells with Na(v)1.9/NaN and contactin enhances the surface expression of the sodium channel over that of Na(v)1.9/NaN alone. Thus contactin binds directly to Na(v)1.9/NaN and participates in the surface localization of this channel along nonmyelinated axons.
Metalloproteases and intracranial vascular lesions (1999)

Recent studies have suggested that metalloproteinases (MMP) might be involved in the pathogenesis of cerebral aneurysm formation and rupture and that elevated serum levels of MMP may effectively be considered as possible markers of cerebrovascular malformations. The present study was planned in order to verify if serum levels of MMPs may be the mirror of the MMP activity in the wall of intracranial aneurysms, reflecting the predisposition to aneurysm development and/or rupture. A series of 84 patients operated for intracranial cerebrovascular lesions (63 aneurysms and 21 arterovenous malformations (AVM)) and 20 controls entered the study. Among the 63 cases of intracranial aneurysms, nine were discovered before rupture, while 54 patients were included after subarachnoid hemorrhage (SAH). Using radioimmunoassay, plasma elastase levels were measured in all cases, while in 25 cases, when aneurysmectomy was possible, the activity of elastase and collagenase were measured in aneurysm samples. Mean plasma elastase level in patients bearing both an intracranial aneurysm or an intracranial AVM was significantly higher than in controls, while there was no significant difference between plasmatic level of elastase in patients with aneurysms when compared with patients bearing an intracranial AVM; there was no significant difference between mean elastase level in patients who suffered SAH and patients bearing an intracranial unruptured aneurysm. The activity of elastase and collagenase measured in the aneurysm wall were significantly higher in cases of ruptured than in unruptured aneurysms. The present results show that plasmatic level of elastase does not reflect the activity of MMP as measured in the aneurysm wall and that the patterns of MMP activities measured in the aneurysm wall differ considerably at different stages of SAH. This suggests that local rather than systemic changes in metalloproteases activity might be involved in cerebral aneurysm formation and rupture.
Biological activities and chemical composition of purified tracheal cytotoxin of Bordetella pertussis (1989)

Specific destruction of ciliated epithelial cells lining the large airways is the primary respiratory tract cytopathology associated with human Bordetella pertussis infections. We have purified a single low-molecular-weight glycopeptide, tracheal cytotoxin (TCT), that appears to cause this pathology. By using a combination of solid-phase extraction and reversed-phase high-pressure liquid chromatography, about 700 nmol of biologically active peptide can be isolated from 1 liter of B. pertussis culture supernatant (approximately 60% yield). TCT at concentrations of 1 microM destroyed the ciliated cell population when incubated with respiratory epithelium in vitro. This concentration of TCT is similar to the concentrations found in the culture supernatant of growing B. pertussis. Purified TCT also inhibited DNA synthesis of hamster trachea epithelial cells in a quantitative, dose-dependent fashion. Endotoxin was not detected in the purified material, and neither B. pertussis nor Escherichia coli endotoxin could duplicate the biological activities of TCT. Amino acid and amino sugar analyses of purified TCT revealed the presence of glucosamine, muramic acid, alanine, glutamic acid, and diaminopimelic acid in molar ratios of 1:1:2:1:1. This suggests that TCT, the released ciliostatic principle of B. pertussis, is a disaccharide tetrapeptide subunit of peptidoglycan.
Allele-Specific RNA Silencing of Mutant Ataxin-3 Mediates Neuroprotection in a Rat Model of Machado-Joseph Disease (2008)

Recent studies have demonstrated that RNAi is a promising approach for treating autosomal dominant disorders. However, discrimination between wild-type and mutant transcripts is essential, to preserve wild-type expression and function. A single nucleotide polymorphism (SNP) is present in more than 70% of patients with Machado-Joseph disease (MJD). We investigated whether this SNP could be used to inactivate mutant ataxin-3 selectively. Lentiviral-mediated silencing of mutant human ataxin-3 was demonstrated in vitro and in a rat model of MJD in vivo. The allele-specific silencing of ataxin-3 significantly decreased the severity of the neuropathological abnormalities associated with MJD. These data demonstrate that RNAi has potential for use in MJD treatment and constitute the first proof-of-principle for allele-specific silencing in the central nervous system.
Transformation system for prototrophic industrial yeasts using the AUR1 gene as a dominant selection marker (1998)

We show a new transformation system for prototrophic yeast strains including those of Saccharomyces cerevisiae, Kluyveromyces lactis, K. marxianus, and Candida glabrata. This system is composed of an antibiotic, aureobasidin A (AbA), and its resistance gene AUR1-C as a selection marker. Southern analysis of genomic DNAs of the transformants indicated that the copy number of the plasmid increased from one to more than four, depending on the concentration of AbA used for selection of the transformants. The AUR1-C gene was also effective as a selection marker for gene disruption, and was able to disrupt both copies of the gene on homologous chromosomes of diploid cells by a single round of transformation. This system has a broad application in the transformation and gene disruption of prototrophic strains of a variety of yeast species.
Delta-Like 4 Induces Notch Signaling in Macrophages (2007)

Dll4-triggered Notch signaling may mediate inflammatory responses in macrophages and promote inflammation.
Factors governing selective formation of specific disulfides in synthetic variants of .alpha.-conotoxin (1991)

alpha-Conotoxin GI is a snail toxin protein consisting of 13 amino acids cross-linked by 2 intramolecular disulfide bridges. This toxin is an antagonist of acetylcholine receptors. The native sequence has been synthesized, along with nine additional variants in which non-cysteine residues are replaced by alanine or the cysteine positions are altered. Each reduced peptide has been oxidized by reaction with oxygen or glutathione both in a folding buffer and in 6 M guanidine hydrochloride. Purified products of oxidation have been characterized with respect to molecular weights and the positions of disulfides. The four cysteines in conotoxin can form two intramolecular disulfides in three different combinations. Relative yields of each of the three isomers have been determined, thereby permitting evaluation of the roles of non-cysteine residues and cysteine placements in the folding of conotoxin. Cysteine positions dominate factors directing formation of the nativelike isomer in a manner that may be predicted from equilibrium constants for loop formation in model peptides containing two cysteines. Alanine substitutions at several positions which are conserved in naturally occurring conotoxins affect the discrimination between the two most favored disulfide arrangements. Substitutions at three nonconserved positions have no structural effect on isomer yields. It therefore is possible to vary these latter three positions in a manner which might help to generate a functional binding surface which is complementary to receptors in the specific prey of a particular species of snail, without affecting the toxin's folding.
Molecular cloning of a mink prion protein gene (1992)

Transmissible mink encephalopathy (TME) is a rare disease which is presumably transmitted to ranch-raised mink from scrapie-infected sheep offal or bovine spongiform encephalopathy-infected cattle products. Although the infectious agent of TME has not been isolated, there is circumstantial evidence that TME is caused by prions. The experimental host range of TME includes sheep, cattle, monkeys and hamsters. However, TME has never been transmitted to mice. Since experiments in transgenic animals have shown that the prion protein (PrP) gene modulates the susceptibility, incubation time and neuropathology of prion-induced disease, we have started to analyse the mink PrP gene. PrP, as deduced from a genomic DNA sequence, consists of 257 amino acids and overall shows similarity of 84 to 90% with the sequences of the PrPs of other mammalian species. It remains to be determined whether these differences in the primary structure of PrP will explain the peculiar host range of TME.
Measurement of 18 Perfluorinated Organic Acids and Amides in Human Serum Using On-Line Solid-Phase Extraction (2005)

We have developed an on-line solid-phase extraction (SPE) method coupled to high-performance liquid chromatography (HPLC)-tandem mass spectrometry (MS/MS) for measuring trace levels of 18 perfluorinated chemicals (3 perfluorosulfonates, 8 perfluorocarboxylates, 7 perfluorosulfonamides) in serum. Without protein precipitation, only dilution with 0.1 M formic acid, one aliquot of 100 microL of serum was injected into a commercial column switching system that allowed for concurrent SPE and HPLC-MS/MS acquisition. First, the analytes were concentrated on a C18 SPE column. Then, this column was placed automatically in front of a C8 analytic HPLC column for chromatographic separation of the analytes. Detection and quantification were done using negative-ion TurboIonSpray ionization, a variant of electrospray ionization, MS/MS. Excellent recovery was achieved for all analytes including the volatile sulfonamide derivatives that could not be determined before using traditional off-line SPE methods. The high throughput and low limits of detection (0.05-0.8 ng/mL) using a small sample volume (100 microL of serum) and isotope dilution quantification make this method suitable for large-scale epidemiologic studies.
Arginine metabolism in benign and malignant disease of breast and colon: evidence for possible inhibition of tumor-infiltrating macrophages. (1992)

L-Arginine concentrations have been measured in benign and malignant breast and colonic neoplasms and compared with the macrophage content and arginase activity within these tumors. Our study confirmed previous findings of elevated plasma arginine concentrations in malignancy and demonstrated that tissue free-arginine concentrations are substantially higher in malignant (mean 9.8 mumol/g protein) than benign (2.8 mumol/g protein) breast disease. Similarly, malignant colonic neoplasms had a higher free-arginine concentration than benign colonic polyps (14.0 vs. 7.0 mumol/g protein). The macrophage content of the malignant tumors was also significantly higher than in the benign conditions (278 vs 29/high power field in breast disease), but despite this, there was no detectable difference in the arginase activity. These findings suggest that tumor-infiltrating macrophages are not able to produce this enzyme, and/or its activity is inhibited within the tumor cell milieu. The differences observed in the arginine concentrations within these lesions has potentially important implications for the pathway of arginine metabolism and local host antitumor responses.
Engineered biosynthesis of novel polyketides: Stereochemical course of two reactions catalyzed by a polyketide synthase (1994)

A genetically engineered strain expressing the essential components of the tetracenomycin polyketide synthase (tcm PKS) along with the actinorhodin ketoreductase (act KR) was found to produce two new (diastereomeric) aromatic polyketides, designated RM20b and RM20c, in addition to RM20, whose structure was reported earlier [McDaniel, R., Ebert-Khosla, S., Hopwood, D. A., & Khosla, C. (1993) Science 262, 1546-1550]. Spectroscopic and in vivo isotopic labeling analysis of RM20b and RM20c revealed that their polyketide backbones were identical to that of RM20 with respect to chain length, regiospecificity of ketoreduction, and regiospecificity of the first intramolecular aldol condensation. This is consistent with earlier predictions that the essential components of the PKS--a bifunctional ketosynthase/acyltransferase, a chain length determining factor, and an acyl carrier protein--are responsible for controlling each of these features of the polyketide backbone [McDaniel, R., Ebert-Khosla, S., Hopwood, D. A., & Khosla, C. (1993) Science 262, 1546-1550; McDaniel, R., Ebert-Khosla, S., Hopwood, D. A., & Khosla, C. (1993) J. Am. Chem. Soc. 115, 11671-11675; Fu, H., Ebert-Khosla, S., Hopwood, D. A., & Khosla, C. (1994) J. Am. Chem. Soc. 116, 4166-4170]. In addition, however, RM20b and RM20c possess two unusual features. In both molecules the hydroxyls on sp3 C-9 and C-7 of the first six-membered ring, which arise as a result of ketoreduction and aldol condensation, respectively, are intact, rather than being lost via dehydration. Furthermore, the relative yield of RM20b (in which these hydroxyls are syn) is 7-fold greater than that of RM20c (in which they are anti).(ABSTRACT TRUNCATED AT 250 WORDS)