gebhart/patrepeval huggingface dataset:
AlgR-binding sites within the algD promoter make up a set of inverted repeats separated by a large intervening segment of DNA (1992)

Activation of algD by AlgR is essential for mucoidy, a virulence factor expressed by Pseudomonas aeruginosa in cystic fibrosis. Two AlgR-binding sites, RB1 and RB2, located far upstream from the algD mRNA start site, are essential for the high-level activity of algD. However, the removal of RB1 and RB2 does not completely abolish inducibility of algD in response to environmental signals. In this work, a third binding site for AlgR, termed RB3, near the algD mRNA start site was characterized. Deletion of RB3 abrogated both the AlgR-binding ability and the residual inducibility of the algD promoter. DNase I footprinting analysis of RB3 resulted in a protection pattern spanning nucleotides -50 to -30. Eight of 10 residues encompassing a continuous region of protection within RB3 (positions -45 to -36) matched in the inverted orientation the conserved core sequence (ACCGTTCGTC) of RB1 and RB2. Quantitative binding measurements of AlgR association with RB1, RB2, and RB3 indicated that AlgR had significantly lower affinity for RB3 than for RB1 and RB2, with differences in the free energy of binding of 1.05 and 0.93 kcal/mol (4.39 and 3.89 kJ/mmol), respectively. Altering the core of RB2 to match the core of RB3 significantly reduced AlgR binding. Conversely, changing the core of RB3 to perfectly match the core of RB2 (mutant site termed RB3*) improved AlgR binding, approximating the affinity of RB2. RB3*, in the absence of the far upstream sites, showed an increase in activity, approaching the levels observed with the full-size algD promoter. Changing 4 nucleotides in two different combinations within the core of RB3 abolished the binding of AlgR to this site and resulted in a significant reduction of promoter activity in the presence of the far upstream sites. Thus, (i) the core sequence is essential for AlgR binding; (ii) the three binding sites, RB1, RB2, and RB3, are organized as an uneven palindrome with symmetrical sequences separated by 341 and 417 bp; and (iii) all three sites participate in algD activation.
Flavivirus Entry Receptors: An Update (2013)

Flaviviruses enter host cells by endocytosis initiated when the virus particles interact with cell surface receptors. The current model suggests that flaviviruses use at least two different sets of molecules for infectious entry: attachment factors that concentrate and/or recruit viruses on the cell surface and primary receptor(s) that bind to virions and direct them to the endocytic pathway. Here, we present the currently available knowledge regarding the flavivirus receptors described so far with specific attention to C-type lectin receptors and the phosphatidylserine receptors, T-cell immunoglobulin and mucin domain (TIM) and TYRO3, AXL and MER (TAM). Their role in flavivirus attachment and entry as well as their implication in the virus biology will be discussed in depth.
Genetic Control of Yeast Mannan Structure (1973)

Abstract The yeast Saccharomyces cerevisiae X2180, the strain most commonly used for genetic studies on yeasts, was treated with the mutagen ethyl methanesulfonate, and mutants defective in the synthesis of cell wall mannan were isolated. The initial selection of mutants was made on the basis of their failure to agglutinate with antiserum that was specific for the mannotetraose side chain of the mannan, the immuno-dominant group of this yeast strain, which has the structure αMan(1→3)αMan(1→2)αMan(1→2)Man. Nonagglutinating cells were assumed to have modified mannan structures, and this was confirmed by chemical analysis of the isolated mutant mannans. Two classes of mutants were obtained. One was apparently defective in the formation of the α-1→3-mannosyl-transferase (mnn1) which is presumed to be involved in the addition of the terminal α-1→3-linked mannose unit to form the mannotetraose side chain. The other class was defective in one of two α-1→2-mannosyltransferases that must be involved in adding the two α-1→2-linked mannose units, one of them (mnn2) directly to the α-1→6-linked mannose units in the backbone of the polysaccharide and the other (mnn3) to this first side chain mannose unit. No mutant was obtained that was defective in forming the backbone. Since such a mutation would yield a cell completely lacking mannan, it might be lethal. Complementation studies on diploid crosses of representatives of the different mutant classes gave results that were consistent with the interpretations based on chemical analysis of the mutant mannans. Thus, diploids obtained from crosses between mnn1 x mnn2, mnn2 x mnn3, or mnn1 x mnn3 mutants all made mannan of the X2180 chemotype. We conclude that all of the mutations involve structural genes for the various mannosyltransferases that are required for mannan synthesis and not regulatory genes that control expression of a particular mannan chemotype.
High serum YKL‐40 concentration is associated with severe bone disease in newly diagnosed multiple myeloma patients (2007)

Newly diagnosed MM patients with elevated serum concentrations of YKL-40 have more severe bone destruction including increased bone resorptive activity and shorter time to progression of bone disease. At this point, a potential role for YKL-40 in myeloma-related bone disease must be considered.
Adenovirus-mediated introduction of DNA into pig sperm and offspring (1999)

The ability of adenoviral vectors to transfer DNA into boar spermatozoa and to offspring was tested. Exposure of spermatozoa to adenovirus bearing the E. coli lacZ gene resulted in the transfer of the gene to the head of the spermatozoa. Treatment did not affect either viability or acrosomal integrity of boar sperm. Of the 2-to 8-cell embryos obtained after in vitro fertilization with adenovirus-exposed sperm, 21.7% expressed the LacZ product. Four out of 56 piglets (about 7%) obtained after artificial insemination with adenovirus-exposed spermatozoa were positive in PCR analyses, even though none of the piglets showed the LacZ gene after southern blot analysis. RT-PCR analysis performed in tissues from two positive stillborn piglets showed the presence of the LacZ mRNA in all of the tissues tested. The offspring obtained after mating two positive animals did not show LacZ gene presence. Our results indicate that adenovirus could be a feasible mechanism for the delivery of DNA into spermatozoa, even though the transfer of the transgene may be limited to the first generation.
Recovery of an arenavirus entirely from RNA polymerase I/II-driven cDNA (2006)

The prototypic arenavirus lymphocytic choriomeningitis virus has been a primary workhorse of viral immunologists for almost a century, and it has served as an important model for studying basic principles of arenavirus molecular biology. Its negative-stranded bisegmented RNA genome has, however, posed a major obstacle to attempts at manipulating the infectious virus by reverse genetic techniques. Here, we report the recovery of infectious lymphocytic choriomeningitis virus (the immunosuppressive strain clone 13) entirely from cDNA. Intracellular transcription of the short and the long viral genome segment from polymerase (pol) I-driven vectors and coexpression of the minimal viral-transacting factors NP and L from pol II-driven plasmids resulted in the efficient formation of infectious virus with genetic tags in both genome segments. The cDNA-derived viruses behaved identically to wild-type virus in both cell culture and infected mice. Importantly, they caused a chronic infection and suppressed the adaptive immune response to an unrelated third-party virus. This technology provides an important basis for investigating viral determinants of persistent infection and immunosuppression. In addition, our findings demonstrate that pol I/II-based vector systems may represent an efficient alternative strategy for the recovery of cytoplasmic negative-strand RNA viruses from cDNA.
Monitoring disulfide bond formation in the eukaryotic cytosol (2004)

Glutathione is the most abundant low molecular weight thiol in the eukaryotic cytosol. The compartment-specific ratio and absolute concentrations of reduced and oxidized glutathione (GSH and GSSG, respectively) are, however, not easily determined. Here, we present a glutathione-specific green fluorescent protein-based redox probe termed redox sensitive YFP (rxYFP). Using yeast with genetically manipulated GSSG levels, we find that rxYFP equilibrates with the cytosolic glutathione redox buffer. Furthermore, in vivo and in vitro data show the equilibration to be catalyzed by glutaredoxins and that conditions of high intracellular GSSG confer to these a new role as dithiol oxidases. For the first time a genetically encoded probe is used to determine the redox potential specifically of cytosolic glutathione. We find it to be -289 mV, indicating that the glutathione redox status is highly reducing and corresponds to a cytosolic GSSG level in the low micromolar range. Even under these conditions a significant fraction of rxYFP is oxidized.
Coexpression of erbB2 and erbB3 proteins reconstitutes a high affinity receptor for heregulin. (1994)

The heregulin/neu differentiation factor gene products were purified and cloned based on their ability to stimulate the phosphorylation of a 185-kDa protein in human breast carcinoma cell lines known to express erbB2. However, not all cells that express erbB2 respond to heregulin, indicating that other components besides erbB2 may be required for heregulin binding. Cells that are transfected with the closely related receptor, erbB3, display a single class of lower affinity heregulin binding sites than has been previously observed on breast carcinoma cell lines. Little or no stimulation of tyrosine phosphorylation in response to heregulin occurs in cells that are transfected with erbB3 alone. Transfection of cells with erbB3 and erbB2 reconstitutes a higher affinity binding receptor, which is also capable of generating a tyrosine phosphorylation signal in response to heregulin. A monoclonal antibody to erbB2 will inhibit heregulin activation of tyrosine phosphorylation and binding in cells transfected with both receptors but not with erbB3 alone. In cells expressing erbB2 and erbB3, both proteins become tyrosine-phosphorylated upon interaction with heregulin. Direct interaction between heregulin and the two proteins was demonstrated by chemical cross-linking experiments using 125I-heregulin followed by immunoprecipitation with antibodies specific for erbB2 or erbB3.
The free solution mobility of DNA (1997)

The free solution mobility of DNA has been measured by capillary electrophoresis in the two buffers most commonly used for DNA gel electrophoresis, Tris-borate-EDTA (TBE) and Tris-acetate-EDTA (TAE). The capillaries were coated with polymers of either of two novel acrylamide monomers, N-acryloylaminoethoxyethanol or N-acryloylaminopropanol, both of which are stable at basic pH and effectively eliminate the electroendosmotic mobility due to the capillary walls. The free solution mobility of DNA in TAE buffer was found to be (3.75 +/- 0.04) x 10(-4) cm2 V-1 s-1 at 25 degrees C, independent of DNA concentration, sample size, electric field strength, and capillary coating, and in good agreement with other values in the literature. The free solution mobility was independent of DNA molecular weight from approximately 400 base pairs to 48.5 kilobase pairs, but decreased monotonically with decreasing molecular weight for smaller fragments. Surprisingly, the free solution mobility of DNA in TBE buffer was found to be (4.5 +/- 0.1) x 10(-4) cm2 V-1 s-1, about 20% larger than observed in TAE buffer, presumably because of the formation of nonspecific borate-deoxyribose complexes.
Seeding Growth for Size Control of 5−40 nm Diameter Gold Nanoparticles (2001)

Following a seeding growth approach, gold nanoparticles of diameters 5−40 nm were prepared with 10−15% standard deviation in diameter from 3.5 ± 0.7 nm gold particle seeds. Particle size can be controlled by varying the ratio of seed to metal salt, and thus any size in the range 5−40 nm can be prepared. The method can also be scaled up to produce 10−100 mg of gold nanoparticles.
PtCl2-Catalyzed Cycloisomerizations of 5-En-1-yn-3-ol Systems (2004)

5-En-1-yn-3-ol substrates bearing a free hydroxyl group or an acyl group are highly versatile partners for PtCl2-catalyzed cycloisomerizations. Electrophilic activation of the alkyne moiety triggers at wish a hydride or an O-acyl migration yielding at the end to regioisomeric keto derivatives. The efficient preparation of Sabina ketone, an important monoterpene precursor, has been worked out.
Phosphorylation-dependent Regulation of Kv2.1 Channel Activity at Tyrosine 124 by Src and by Protein-tyrosine Phosphatase ε (2003)

Voltage-gated potassium (Kv) channels are a complex and heterogeneous family of proteins that play major roles in brain and cardiac excitability. Although Kv channels are activated by changes in cell membrane potential, tyrosine phosphorylation of channel subunits can modulate the extent of channel activation by depolarization. We have previously shown that dephosphorylation of Kv2.1 by the nonreceptor-type tyrosine phosphatase PTPepsilon (cyt-PTPepsilon) down-regulates channel activity and counters its phosphorylation and up-regulation by Src or Fyn. In the present study, we identify tyrosine 124 within the T1 cytosolic domain of Kv2.1 as a target site for the activities of Src and cyt-PTPepsilon. Tyr(124) is phosphorylated by Src in vitro; in whole cells, Y124F Kv2.1 is significantly less phosphorylated by Src and loses most of its ability to bind the D245A substrate-trapping mutant of cyt-PTPepsilon. Phosphorylation of Tyr(124) is critical for Src-mediated up-regulation of Kv2.1 channel activity, since Y124F Kv2.1-mediated K(+) currents are only marginally up-regulated by Src, in contrast with a 3-fold up-regulation of wild-type Kv2.1 channels by the kinase. Other properties of Kv2.1, such as expression levels, subcellular localization, and voltage dependence of channel activation, are unchanged in Y124F Kv2.1, indicating that the effects of the Y124F mutation are specific. Together, these results indicate that Tyr(124) is a significant site at which the mutually antagonistic activities of Src and cyt-PTPepsilon affect Kv2.1 phosphorylation and activity.
Peptide-Modified Surfaces for Enzyme Immobilization (2011)

A simple method for immobilizing enzymes through specific interactions with peptides anchored on surfaces has been developed. This approach will be applicable to the immobilization of a wide variety of enzymes on surfaces with optimized orientation, location and performance, and provides a potential mechanism for the patterned self-assembly of multiple enzymes on surfaces.
RESEARCH PAPERS : Syntheses of Novel Macrocyclic Ethers Containing Nitro Groups (1998)

The macrocyclic polyether, 1,30; 6,11; 13,18; 23,28-tetrabenzo-9,15,26,32-tetra-nitro-2,5,19,22tetraoxacyclotetratriacontane 1 and 1,36; 9,14; 16,21; 29,34-tetra-benzo-12,18,32,38-tetranitro-2,5,8,22,25, 28-hexaoxacyclotetracontane 2 have been synthesized by the reaction of 2,2`-methylenebis(4,4`-nitrophenol) 3 with 1,2-dichloro-ethane and bis(2-chloroethyl)ether respectively in the presence of NaOBu-t and t-BuOH. The macrocyclic polyethers were purified by chromatography and recrystallization.
A new synthesis of benzoporphyrins using 4,7-dihydro-4,7-ethano-2H-isoindole as a synthon of isoindole (1998)

Heating 4,7-dihydro-4,7-ethano-2H-isoindole at 200 °C induces the retro-Diels–Alder reaction to give isoindole in essentially quantitative yield, which can be applied to a new synthesis of tetrabenzoporphyrins and monobenzoporphyrins.
Stain etching of silicon pillars and macropores (2005)

Abstract We used a XeCl excimer laser (308 nm, ∼3 J cm –2 ) and chemically enhanced laser ablation in the presence of SF 6 to create arrays of silicon pillars. Etching of these pillars with KOH leads to arrays of macropores whose morphology depends on surface crystallography. Several new stain etchants – containing some combination of HF, NH 4 HF 2 , HCl, HNO 3 , Fe(III), Mn(VII) and water – have been used to cover these structures with a layer of microporous silicon. Both pillars and macropores are black, i.e., exhibit low reflectivity across the visible spectrum. When porosified, pillars exhibit visible photoluminescence whose angular distribution differs from that of planar porous silicon with significantly more intensity at high angles. The peak photoluminescence wavelength depends on the stain etchant composition and exposure to air. The use of metal ions in place of HNO 3 in the stain etchant ameliorates the production of gas bubbles and leads to more uniform films. (© 2005 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Characterization of mutations in <em>PRNP</em> (prion) gene and their possible roles in neurodegenerative diseases (2018)

Abnormal prion proteins are responsible for several fatal neurodegenerative diseases in humans and in animals, including Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker disease, and fatal familial insomnia. Genetics is important in prion diseases, but in the most cases, cause of diseases remained unknown. Several mutations were found to be causative for prion disorders, and the effect of mutations may be heterogeneous. In addition, different prion mutations were suggested to play a possible role in additional phenotypes, such as Alzheimer's type pathology, spongiform encephalopathy, or frontotemporal dementia. Pathogenic nature of several prion mutations remained unclear, such as M129V and E219K. These two polymorphic sites were suggested as either risk factors for different disorders, such as Alzheimer's disease (AD), variant CJD, or protease-sensitive prionopathy, and they can also be disease-modifying factors. Pathological overlap may also be possible with AD or progressive dementia, and several patients with prion mutations were initially diagnosed with AD. This review also introduces briefly the diagnosis of prion diseases and the issues with their diagnosis. Since prion diseases have quite heterogeneous phenotypes, a complex analysis, a combination of genetic screening, cerebrospinal fluid biomarker analysis and imaging technologies could improve the early disease diagnosis.
Radioimmunoassay for Proparathyroid Hormone (1974)

A sensitive radioimmunoassay has been developed to bovine proparathyroid hormone which employs an antiserurm produced by immunization of rabbits with a synthetic 18-amino acid peptide fragment of the bovine prohormone. The synthetic prohormone fragment was prepared by solid-phase synthesis and consists of the amino-terminal 12 residues of bovine parathyroid hormone plus the hexapeptide sequence of the bovine prohormone. The antiserum is uniquely specific to detection of the prohormone or synthetic fragments that preserve the peptide linkage between the prohormone region and amino-terminal hormonal sequences. Bovine proparathyroid hormone of natural origin, as well as synthetic fragments incorporating the prohormone hexapeptide sequence and amino-terminal sequences of bovine parathyroid hormone, are bound by the antiserum, but the hexapeptide, intact bovine or human hormone and amino-terminal hormonal fragments alone are not detected. The assay readily measures prohormone in extracts of bovine but not human parathyroids, a finding that may be explained by the fact that human proparathyroid hormone differs from bovine by a substitution of serine for alanine at position number one and leucine for phenylalanine at position seven of the prohormone sequence. Thus, the assay should be particularly useful in studies of the intracellular localization of bovine proparathyroid hormone and the mechanism of intracellular transport and conversion of proparathyroid hormone to parathyroid hormone. In preliminary studies, it was found that proparathyroid hormone was undetectable in peripheral or parathyroid effluent blood from calves, a finding which reflects either a low rate of prohormone secretion or a rapid cleavage of the prohormone in blood once secreted.
Enhanced Antitumor Effect of the Combination of Tumstatin Gene Therapy and Gemcitabine in Murine Models (2005)

Targeting tumor endothelium is an important strategy for cancer therapy. We evaluated the effectiveness of gene therapy, that is, intramuscular delivery of plasmid DNA encoding tumstatin (pSecTag2B-tum), combined with gemcitabine administration in vitro and in vivo, using colon carcinoma (CT26) and Lewis lung carcinoma (LLC) murine models. The in vitro growth-inhibitory and proapoptotic effects of gemcitabine and/or tumstatin on human umbilical vein endothelial cells (HUVECs) and mouse endothelial cells (SVEC4-10), respectively, were assessed. in vitro, conditioned medium from pSecTag2B-tum-transfected COS cells inhibited the growth of endothelial cells but not of CT26 or LLC cells, whereas gemcitabine inhibited the growth of both endothelial cells and CT26 and LLC cells. Mice bearing subcutaneously established CT26 or LLC tumors received pSecTag2B-tum alone or in combination with gemcitabine to assess tumor growth inhibition. in vivo, combined treatment with pSecTag2B-tum and gemcitabine significantly decreased tumor growth through increased inhibition of tumor angiogenesis and increased tumor cell apoptosis compared with either agent alone. Enhanced antiproliferative and proapoptotic activity of the combination therapy on tumor-associated endothelial cells was calculated to be significant. This study suggests that combined treatment by the intramuscular delivery of plasmid DNA encoding tumstatin and gemcitabine augments tumor growth inhibition by suppressing angiogenesis and enhancing apoptosis in murine models. A combination of these agents could be used in future studies and translated into the clinical setting.
Serum concentrations of salicylate and naproxen during concurrent therapy in patients with rheumatoid arthritis (1987)

The kinetic interaction between salicylate and naproxen was investigated in 25 rheumatoid arthritis patients. Kinetic interactions were tested in serum after patients had been on each drug regimen for 1 month. Salicylate decreased serum naproxen concentration from 89.5 mg/liter to 65.9 mg/liter (P less than 0.001) and increased serum naproxen clearance by 56%. Naproxen had minimal effect on serum salicylate concentrations.
Identification of a Germ Line Transcript from the Unrearranged Kappa Gene in Human B Cells (1989)

A novel kappa immunoglobulin-hybridizing mRNA in cell lines derived from human B cells arrested at several stages of development has been identified. Hybridization studies demonstrate that this 1.5-kilobase mRNA species is the spliced product of a precursor germ line transcript initiating upstream of the unrearranged JKappa locus.
Inhibition of Human CD4+CD25+high Regulatory T Cell Function (2002)

CD4(+)CD25(+high) T cells are potent regulators of autoreactive T cells. However, it is unclear how regulatory CD4(+)CD25(+high) cells discriminate between desirable inflammatory immune responses to microbial Ags and potentially pathologic responses by autoreactive T cells. In this study, an in vitro model was created that allowed differential activation of regulatory CD4(+)CD25(+high) and responder CD4(+) T cells. If CD4(+)CD25(+high) regulatory cells were strongly activated, they maintained suppressive effector function for only 15 h, while stimulation with weaker TCR stimuli produced regulatory cells that were suppressive until 60 h after activation. In contrast, strongly activated CD4(+) responder T cells were resistant to regulation at all time points, while weakly stimulated CD4(+) cells were sensitive to suppression until 38 or 60 h after activation depending upon the strength of the stimulus. The extent of suppression mediated by CD4(+)CD25(+high) cells also depended on the strength of stimulation in an Ag-specific system. Thus, the stronger the TCR signal, the more rapidly and more completely the responder cells become refractory to suppression.