gebhart/patrepeval huggingface dataset:
Transcription and Regulation of the Bidirectional Hydrogenase in the Cyanobacterium Nostoc sp. Strain PCC 7120 (2007)

The filamentous, heterocystous cyanobacterium Nostoc sp. strain PCC 7120 (Anabaena sp. strain PCC 7120) possesses an uptake hydrogenase and a bidirectional enzyme, the latter being capable of catalyzing both H2 production and evolution. The completely sequenced genome of Nostoc sp. strain PCC 7120 reveals that the five structural genes encoding the bidirectional hydrogenase (hoxEFUYH) are separated in two clusters at a distance of approximately 8.8 kb. The transcription of the hox genes was examined under nitrogen-fixing conditions, and the results demonstrate that the cluster containing hoxE and hoxF can be transcribed as one polycistronic unit together with the open reading frame alr0750. The second cluster, containing hoxU, hoxY, and hoxH, is transcribed together with alr0763 and alr0765, located between the hox genes. Moreover, alr0760 and alr0761 form an additional larger operon. Nevertheless, Northern blot hybridizations revealed a rather complex transcription pattern in which the different hox genes are expressed differently. Transcriptional start points (TSPs) were identified 66 and 57 bp upstream from the start codon of alr0750 and hoxU, respectively. The transcriptions of the two clusters containing the hox genes are both induced under anaerobic conditions concomitantly with the induction of a higher level of hydrogenase activity. An additional TSP, within the annotated alr0760, 244 bp downstream from the suggested translation start codon, was identified. Electrophoretic mobility shift assays with purified LexA from Nostoc sp. strain PCC 7120 demonstrated specific interactions between the transcriptional regulator and both hox promoter regions. However, when LexA from Synechocystis sp. strain PCC 6803 was used, the purified protein interacted only with the promoter region of the alr0750-hoxE-hoxF operon. A search of the whole Nostoc sp. strain PCC 7120 genome demonstrated the presence of 216 putative LexA binding sites in total, including recA and recF. This indicates that, in addition to the bidirectional hydrogenase gene, a number of other genes, including open reading frames connected to DNA replication, recombination, and repair, may be part of the LexA regulatory network in Nostoc sp. strain PCC 7120.
Physical Association of Gi2α with Interleukin-8 Receptors (1996)

Interleukin-8 (IL-8), one of the major mediators of the inflammatory response, belongs to a family of chemokines that includes NAP-2 (neutrophil-activating peptide-2) and Gro-alpha and whose biological activities are directed to a great extent toward neutrophils. Two distinct receptors have been described with overlapping, but not identical, binding affinities for IL-8, NAP-2, and Gro-alpha. This study was designed to examine the intracellular pathways activated upon the occupation of each of the IL-8 receptors (IL-8R). The formation of a physical coupling between IL-8 receptors and the alpha-subunit of heterotrimeric G proteins was tested in neutrophils by examining the presence of the former in anti-Galpha immune precipitates. The addition of IL-8 to a suspension of human neutrophils led to a time-dependent detection of IL-8 in anti-Gi2alpha (raised against amino acids 159-168 (LERIAQSDYI) of Gi2alpha) and anti-Gtalpha (raised against the COOH-terminal 10 amino acids (KENLKDCGLF) of Gtalpha), but not anti-Gq, immunoprecipitates. Similar results were obtained in human 293 cells stably transfected with IL-8RA or IL-8RB. The peptide derived from the COOH-terminal sequence of Gt inhibited the co-immunoprecipitation of IL-8R and Gi observed in response to the anti-Gtalpha and anti-Gi2alpha antibodies. On the other hand, the Gi2alpha peptide only inhibited the immunoprecipitation induced by the anti-Gi2alpha antibody. Peptides derived from Gi1alpha or Gi3alpha had no effect in this assay. The introduction of the anti-Gi2alpha or anti-Gtalpha antibodies or their neutralizing peptides, but not the Gi1alpha or Gi3alpha peptides, into 293 IL-8RA or 293 IL-8RB cells completely blocked the calcium responses obtained upon stimulation with IL-8. These results demonstrate that the occupation of either type of IL-8 receptor leads to a physical coupling to the alpha-subunit of Gi2. In addition, the use of the subunit-specific peptides identified two functionally important but distinct regions of Gialpha, one involved in receptor/Gialpha interaction (KENLKDCGLF) and the other mediating downstream signal transmission (LERIAQSDYI). Finally, the results of this study also validate the use of the transfected 293 cell line as a model for the study of the signal transduction pathway(s) initiated by IL-8.
Separation of DNA Binding from the Transcription-Activating Function of a Eukaryotic Regulatory Protein (1986)

The yeast GAL4 protein (881 amino acids) binds to specific DNA sites upstream of target genes and activates transcription. Derivatives of this protein bearing as few as 74 amino terminal residues bind to these sites but fail to activate transcription. When appropriately positioned in front of a gene these derivatives act as repressors. These and related findings support the idea that GAL4 activates transcription by touching other DNA-bound proteins.
Strand-invasion of duplex DNA by peptide nucleic acid oligomers. (1993)

Polyamide oligomers, termed peptide nucleic acids (PNAs), bind with high affinity to both DNA and RNA and offer both antisense and antigene approaches for regulating gene expression. When a PNA binds to a complementary sequence in a double-stranded DNA, one strand of the duplex is displaced, and a stable D-loop is formed. Unlike oligodeoxynucleotides for which binding polarity is determined by the deoxyribose sugar, the unrestrained polyamide backbone of the PNA could permit binding to a DNA target in an orientation-independent manner. We now provide evidence that PNAs can, in fact, bind to their complementary sequence in DNA independent of the DNA-strand polarity--that is, a PNA binds to DNA in both "parallel" and "antiparallel" fashion. With a mixed-sequence 15-mer PNA, kinetic studies of PNA.DNA interactions revealed that D-loop formation was rapid and the complex was stable for several hours. However, when measured either by gel-mobility-shift analysis or RNA polymerase II-elongation termination, D-loop formation was salt dependent, but PNA-strand dissociation was not salt dependent. We observed that D-loop-containing DNA fragments had anomalous gel mobilities that varied as a function of the position of the D-loop relative to the DNA termini. On the basis of permutation analysis, the decreased mobility of the PNA.DNA complex was attributed to a bend in the DNA at or near the D-loop.
Generation of anti-peptide monoclonal antibodies which recognize mature CSF-2 alpha (IL 3) protein. (1985)

The colony-stimulating factor CSF-2 alpha (IL 3) has been purified to homogeneity, the protein sequenced, and the gene encoding this lymphokine cloned. Knowledge of the protein sequence permitted the synthesis of peptides corresponding to the amino terminus of the molecule. These peptides, after conjugation to palmitic acid, were used to immunize mice. Spleen cells from mice immunized with one of these peptides (CSF-2 alpha 1-14) were fused with the myeloma cell line NS-1. The fusion resulted in the isolation of two hybridoma cell lines, designated 6A5 and 4D4, that secreted antibodies that were specific for the immunizing peptide. The antibodies did not react with a closely related peptide CSF-2 alpha 7-16. The antibodies were capable, however, of recognized CSF-2 alpha protein as judged by the ability of the antibodies to remove CSF-2 alpha activity from culture medium of PHA-stimulated LBRM-33-5A4 cells, to immunoprecipitate radiolabeled CSF-2 alpha protein, and to detect CSF-2 alpha protein bound to nitrocellulose membranes.
Adrenoceptor genes in human obesity (1999)

The genes causing obesity in rodent models have been characterized, but do not seem to be important for human obesity. Recently the putative association between obesity and polymorphism in human beta-adrenergic receptor genes have been studied intensely in the light of the important role of these receptors in the regulation of energy mobilization and utilization. A polymorphism (Trp64Arg) in the beta3-adrenergic receptor gene is associated with obesity (relative risk approximately 2) in some but not all investigations on Caucasian and Japanese populations. When expressed in artificial cell systems, the polymorphism is associated with alterations of the beta -adrenoceptor. The genetic allele variance influences also the native receptor function when measured in isolated human fat cells. The human beta2-adrenoceptor gene shows a high degree of polymorphism. The role of beta2-receptor gene polymorphism for obesity has so far only been investigaed in women. A Gln27Glu variant is markedly associated with obesity with a relative risk for obesity of approximately 7 and odds ratio of approximately 10. Women who are homozygous for 27Glu have approximately 20 kg higher fat mass than controls. Thus, polymorphism in genes coding for different beta-adrenoceptor subtypes may be important for the development of human obesity.
Neuromuscular fatigue after low‐ and medium‐frequency electrical stimulation in healthy adults (2018)

Both currents induced similar neuromuscular fatigue. Clinicians can choose either PC or MF and expect similar treatment effects when the goal is to generate gains in muscle strength. Muscle Nerve 58: 293-299, 2018.
Role of Carbon Monoxide and Biliverdin in Renal Ischemia/Reperfusion Injury (2006)

Heme oxygenase (HO) isoforms catalyze the conversion of heme to carbon monoxide (CO) and biliverdin/bilirubin with a concurrent release of iron. There is strong evidence that HO activity and products play a major role in renoprotection, however the exact molecular mechanisms underlying the beneficial effects exerted by this pathway are not fully understood. This review is aimed at illustrating the possible mechanism/s by which HO is renoprotective in the context of ischemia/reperfusion. We will first analyze the effects of exogenous administration of bilirubin/biliverdin and CO and then describe their biological activities once generated endogenously following stimulation of the HO pathway by either pharmacological means or gene targeting-mediated approaches.
Cardiac Tissue Enriched Factors Serum Response Factor and GATA-4 Are Mutual Coregulators (2000)

Combinatorial interaction among cardiac tissue-restricted enriched transcription factors may facilitate the expression of cardiac tissue-restricted genes. Here we show that the MADS box factor serum response factor (SRF) cooperates with the zinc finger protein GATA-4 to synergistically activate numerous myogenic and nonmyogenic serum response element (SRE)-dependent promoters in CV1 fibroblasts. In the absence of GATA binding sites, synergistic activation depends on binding of SRF to the proximal CArG box sequence in the cardiac and skeletal alpha-actin promoter. GATA-4's C-terminal activation domain is obligatory for synergistic coactivation with SRF, and its N-terminal domain and first zinc finger are inhibitory. SRF and GATA-4 physically associate both in vivo and in vitro through their MADS box and the second zinc finger domains as determined by protein A pullout assays and by in vivo one-hybrid transfection assays using Gal4 fusion proteins. Other cardiovascular tissue-restricted GATA factors, such as GATA-5 and GATA-6, were equivalent to GATA-4 in coactivating SRE-dependent targets. Thus, interaction between the MADS box and C4 zinc finger proteins, a novel regulatory paradigm, mediates activation of SRF-dependent gene expression.
The porphyrias: advances in diagnosis and treatment (2012)

The inborn errors of heme biosynthesis, the porphyrias, are 8 genetically distinct metabolic disorders that can be classified as "acute hepatic," "hepatic cutaneous," and "erythropoietic cutaneous" diseases. Recent advances in understanding their pathogenesis and molecular genetic heterogeneity have led to improved diagnosis and treatment. These advances include DNA-based diagnoses for all the porphyrias, new understanding of the pathogenesis of the acute hepatic porphyrias, identification of the iron overload-induced inhibitor of hepatic uroporphyrin decarboxylase activity that causes the most common porphyria, porphyria cutanea tarda, the identification of an X-linked form of erythropoietic protoporphyria due to gain-of-function mutations in erythroid-specific 5-aminolevulinate synthase (ALAS2), and new and experimental treatments for the erythropoietic porphyrias. Knowledge of these advances is relevant for hematologists because they administer the hematin infusions to treat the acute attacks in patients with the acute hepatic porphyrias, perform the chronic phlebotomies to reduce the iron overload and clear the dermatologic lesions in porphyria cutanea tarda, and diagnose and treat the erythropoietic porphyrias, including chronic erythrocyte transfusions, bone marrow or hematopoietic stem cell transplants, and experimental pharmacologic chaperone and stem cell gene therapies for congenital erythropoietic protoporphyria. These developments are reviewed to update hematologists on the latest advances in these diverse disorders.
[Genetic analysis of the UGT1A1 gene mutation sites in a Chinese family suffered from Gilbert's syndrome]. (2006)

To learn the variation in the gene for UGT1A1 enzyme, the genetic mechanism in a Chinese Han nationality family suffered from Gilbert's syndrome was studied. At first, genomic DNA from peripheral blood of the sufferer in this family was used for amplifying all of the five exons of the UGT1A1 gene by PCR, and then direct sequencing of the PCR product was applied to analyze gene mutation. The results showed that there existed a G-->A homozygous transition at nucleotide 211 leading the substitution of arginine for glycine at position 71 of corresponding protein product (G71R) and a T-->G homozygous transition at nucleotide 1456 leading the substitution of aspartic acid for tyrosine at position 486 of corresponding protein product (Y486D). No mutation was detected in promoter region and the splicing junction sites. The relevant mutation sites of the other family members were sequenced and identified to be heterozygous in the two above-mentioned mutation sites and in the TA repeat mutation in the promoter region. Furthermore, fresh blood samples were collected from all of the members to detect the serum bilirubin levels to determine the sufferer. The result was consistent with the mutation analysis. It could thus be inferred that this family was caused by mutation in the open reading frame of the gene UGT1A1.
Homoepitaxial growth of GaN under Ga-stable and N-stable conditions by plasma-assisted molecular beam epitaxy (1997)

The structure, morphology, and optical properties of homoepitaxial GaN layers grown by molecular beam epitaxy on metalorganic chemical vapor deposition (MOCVD)-grown GaN “template” layers were investigated as a function of the group III/group V flux ratio during growth. GaN layers grown with a low III/V ratio (N-stable growth) displayed a faceted surface morphology and a tilted columnar structure with a high density of stacking faults. In contrast, films grown with a high III/V ratio (Ga-stable growth) displayed comparable structure to the underlying MOCVD-grown template. The transition from N-stable to Ga-stable growth modes was found to occur over a narrow range of Ga fluxes at a growth temperature of 650 °C. Evidence of Ga accumulation and step-flow growth was observed for films grown under Ga-stable conditions, leading to the formation of spiral growth features at the surface termination of mixed edge/screw dislocations. Photoluminescence measurements indicate that the deep-level (∼550 nm) emission is increased relative to the near-band edge emission for films grown under N-stable conditions.
Orientation and rupture of fractal colloidal gels during start-up of steady shear flow (2005)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Ali Mohraz, Michael J. Solomon; Orientation and rupture of fractal colloidal gels during start-up of steady shear flow. J. Rheol. 1 May 2005; 49 (3): 657–681. https://doi.org/10.1122/1.1895799 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Society of RheologyJournal of Rheology Search Advanced Search |Citation Search
Carbopols as factors buffering triethanolamine interacting with artificial skin sebum. (2004)

Triethanolamine is an ethanolamine applied as counter-ion for fatty acid soaps. Interaction between triethanolamine and free fatty acids is suggested to be useful for cleansing sebaceous follicles in acne prevention. Considering relatively high pH of aqueous triethanolamine solutions we investigated influence of different concentrations of anionic polymers--Carbopol 934P, Carbopol 974P and Carbopol 980 on pH, rheological behavior and, most of them, intensity of triethanolamine interaction with artificial skin sebum components. Triethanolamine buffered using Carbopols influenced artificial skin sebum. Intensity of this interaction was measured applying specific optical method. Penetration of triethanolamine into artificial sebum and its uplift induced by above mentioned interaction were measured. Respective penetration rates and uplift rates were calculated. We found significant differences between Carbopols. The values of the penetration rates amounted 2.94 x 10(-04) h(-1) to 4.12 x 10(-03) h(-1), whereas rates for the uplift process were from 1.97 x 10(-04) h(-1) to 3.28 x 10(-03) h(-1). The value of pH is reduced from 10.06 for pure 0.1 M aqueous triethanolamine solution to 7.67 with the increase of polymer to triethanolamine molar ratio in the preparations. It is considered that triethanolamin buffered with acrylic acid polymers--Carbopols could influence cleansing of pilosebaceous unit follicles and contribute to acne prevention.
Chemical aminoacylation of tRNAs with fluorinated amino acids for in vitro protein mutagenesis (2010)

This article describes the chemical aminoacylation of the yeast phenylalanine suppressor tRNA with a series of amino acids bearing fluorinated side chains via the hybrid dinucleotide pdCpA and ligation to the corresponding truncated tRNA species. Aminoacyl-tRNAs can be used to synthesize biologically relevant proteins which contain fluorinated amino acids at specific sites by means of a cell-free translation system. Such engineered proteins are expected to contribute to our understanding of discrete fluorines' interaction with canonical amino acids in a native protein environment and to enable the design of fluorinated proteins with arbitrary desired properties.
RFID enhances visitors' museum experience at the Exploratorium (2005)

Interactive RFID-enhanced museum exhibits let visitors continue their scientific exploration beyond the museum's walls. But museums must still help them understand the technology and address their data privacy concerns.
Reduction of 12-oxo derivatives of some bile acids (1985)

Methyl ester of 3α-acetoxy-12-oxo-9 (11)-cholenic acid and some other analogous compounds were reduced to the corresponding 9(11)-unsaturated 12-hydroxy derivatives by the action of sodium borohydride in the presence of cerium(III) chloride. A part of our work, viz. preparation of steroid hormones from bile acids, was the reduction of 9(11)-unsaturated 12-oxo derivatives of some bile acids, with the view of obtaining the corresponding 9(11)-unsaturated 12-hydroxy derivatives. Hitherto, the only safe route has been hydrogenation of the starting 9(11)-unsaturated 12-oxo derivatives on platinum at elevated pressures, which, preserving the allyl double bond, yields a mixture of the two isomeric 12-hydroxy derivatives.
Susceptibilities of Mycoplasma hominis, Mycoplasma pneumoniae, and Ureaplasma urealyticum to new glycylcyclines in comparison with those to older tetracyclines (1994)

The glycylcyclines are new tetracycline derivatives that include the N,N-dimethylglycylamido derivative of minocycline (DMG-MINO) and the N,N-dimethylglycylamido derivative of 6-demethyl-6-deoxytetracycline (DMG-DMDOT). The susceptibilities of Mycoplasma pneumoniae, Mycoplasma hominis, and Ureaplasma urealyticum to DMG-MINO, DMG-DMDOT, tetracycline, doxycycline, and minocycline were determined by the agar dilution method. The glycylcyclines with MICs at which 50% of the isolates are inhibited of 0.25 to 0.5 micrograms/ml for M. pneumoniae were two- to fourfold more active than tetracycline and had the same activity as minocycline and doxycycline. Tetracycline-susceptible M. hominis strains were four- to eightfold more susceptible to the glycylcyclines (0.12 to 0.25 micrograms/ml) than to tetracycline. Strains of M. hominis known to be resistant to tetracycline, doxycycline, and minocycline because of the tet(M) determinant were as susceptible to the glycylcyclines as the tetracycline-susceptible strains. For tetracycline-susceptible U. urealyticum strains, the glycylcyclines showed the same activity as tetracycline (MICs at which 50% of the isolates are inhibited of 1 to 2 micrograms/ml). Tetracycline-resistant strains of U. urealyticum were resistant to doxycycline and minocycline and showed variable susceptibility to the glycylcyclines (range, 0.5 to 32 micrograms/ml). In view of the increasing resistance of M. hominis and U. urealyticum strains to tetracyclines, the glycylcyclines have promise, pending assessment of their pharmacokinetic and safety profiles.
HMG-CoA Reductase Inhibitors for Treatment of Hypercholesterolemia (1988)

THE recent introduction of a unique class of cholesterol-lowering drugs offers new promise for the treatment of hypercholesterolemia. These drugs are inhibitors of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, the rate-limiting enzyme in the synthesis of cholesterol. Relatively low doses of these agents will reduce plasma cholesterol levels markedly, and in short-term studies, they have not been found to produce serious side effects. Thus, in 1987 the Food and Drug Administration approved one HMG-CoA reductase inhibitor — lovastatin. If reductase inhibitors prove to be free of long-term adverse effects, they will undoubtedly be used widely for treating hypercholesterolemia. This review will examine . . .
Bacteriorhodopsin Mutants of Halobacterium sp. GRB (1989)

The bacterioopsin genes of Halobacterium sp. GRB (Ebert, K., Goebel, W., and Pfeifer, F. (1984) Mol. & Gen. Genet. 194, 91-97) wild type and 10 independent mutants of different phenotypes have been cloned and sequenced. The wild type gene has two conservative changes compared to the gene of Halobacterium halobium, so that the proteins of the two species are identical. Six different mutations at five different codons have been found, leading to the following amino acid changes compared to the wild type: Trp10----Cys (three cases), Tyr57----Asn, Asp85----Glu, Asp06----Asn (three cases), Asp96----Gly, Trp138----Arg. A first characterization of the mutant proteins is given, and their implications for models of bacteriorhodopsin structure and function are discussed.