gebhart/patrepeval huggingface dataset:
Overexpression of L-Phenylalanine Ammonia-Lyase in Transgenic Tobacco Plants Reveals Control Points for Flux into Phenylpropanoid Biosynthesis (1996)

Transgenic tobacco (Nicotiana tabacum L.) plants overexpressing the enzyme L-phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) were grown from seeds of a primary transformant containing the bean PAL2 gene, which had shown homology-dependent silencing of the endogenous tobacco PAL genes. Analysis of endogenous and transgene-encoded PAL transcripts and protein in the primary transformant (T0) and first-generation (T1) overexpressor plants indicated that the transgene-encoded PAL is the cause of the greater than wild-type levels of PAL activity (up to 5- and 2-fold greater in leaf and stem tissue, respectively) in the T1 plants. Leaves of PAL-overexpressing plants contained increased levels of the hydroxycinnamic acid ester chlorogenic acid but not of the flavonoid rutin, indicating that PAL is the key control point for flux into chlorogenic acid. In addition, levels of the glucoside of 4-coumaric acid increased in the overexpressing plants, suggesting that the 4-coumarate:coenzyme A ligase or coumarate hydroxylase reactions might have become limiting. These results help to define the regulatory architecture of the phenylpropanoid pathway and indicate the possibility of engineering-selective changes in this complex metabolic pathway by overexpression of a single early pathway gene.
A Portable 2-Transistor Picowatt Temperature-Compensated Voltage Reference Operating at 0.5 V (2012)

Sensing systems such as biomedical implants, infrastructure monitoring systems, and military surveillance units are constrained to consume only picowatts to nanowatts in standby and active mode, respectively. This tight power budget places ultra-low power demands on all building blocks in the systems. This work proposes a voltage reference for use in such ultra-low power systems, referred to as the 2T voltage reference, which has been demonstrated in silicon across three CMOS technologies. Prototype chips in 0.13 μm show a temperature coefficient of 16.9 ppm/°C (best) and line sensitivity of 0.033%/V, while consuming 2.22 pW in 1350 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The lowest functional V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> 0.5 V. The proposed design improves energy efficiency by 2 to 3 orders of magnitude while exhibiting better line sensitivity and temperature coefficient in less area, compared to other nanowatt voltage references. For process spread analysis, 49 dies are measured across two runs, showing the design exhibits comparable spreads in TC and output voltage to existing voltage references in the literature. Digital trimming is demonstrated, and assisted one temperature point digital trimming, guided by initial samples with two temperature point trimming, enables TC <; 50 ppm/°C and ±0.35% output precision across all 25 dies. Ease of technology portability is demonstrated with silicon measurement results in 65 nm, 0.13 μm, and 0.18 μm CMOS technologies.
LOSS OF FIMBRIAL ADHESION WITH THE ADDITION OF VACCINUM MACROCARPON TO THE GROWTH MEDIUM OF P-FIMBRIATED ESCHERCHIA COLI (1998)

Cranberry juice irreversibly inhibits P-fimbriae. Electron micrographic evidence suggests that cranberry juice acts on the cell wall preventing proper attachment of the fimbrial subunits or as a genetic control preventing the expression of normal fimbrial subunits or both.
Recognition of substrates by tyrosylprotein sulfotransferase. Determination of affinity by acidic amino acids near the target sites. (1992)

The sulfation of proteins by tyrosylprotein sulfotransferase (TPST) is highly site-specific. In this study, we examined the sequence specificity of the target site for TPST by determining the kinetics of rat liver TPST with peptides related to the sequence of the C4 component of complement. The data obtained from this study demonstrate that selective elimination of negative charges from the -5 to +5 region of the acceptor tyrosine, either by removal or by isosteric substitution or the acidic amino acids in the region, produced a substantial change in the Km value, with relatively little effect on Vmax. Substitutions at -1 and +1 positions increase the Km value by 22- and 4-fold, respectively, whereas removal of the acidic amino acids from the -5, -4, or +4 positions increased the Km values by a factor of 2-4. The effect of elimination of an acidic amino acid on the Km value was constant and specific for its particular position in relation to tyrosine, and the effect of modification of more than one amino acid was multiplicative. This study provides evidence that: 1) acidic residues near tyrosines promote sulfation by increasing the affinity of enzyme-substrate binding and have little effect on catalytic rate; 2) the contribution of each acidic residue to affinity for TPST is independent and varies according to position relative to the acceptor tyrosine; and 3) the enzyme interacts with a segment of at least 4-5 residues on each side of the tyrosine, with the residues on the -1 and +1 positions being the most important determinants. In general, residues on the NH2-terminal side of the tyrosine have a greater effect on affinity for TPST.
Engineering yeast for efficient cellulose degradation (1998)

Saccharomyces cerevisiae produces several beta-1,3-glucanases, but lacks the multicomponent cellulase complexes that hydrolyse the beta-1,4-linked glucose polymers present in cellulose-rich biomass as well as in haze-forming glucans in certain wines and beers. We have introduced into S. cerevisiae a functional cellulase complex for efficient cellulose degradation by cloning the Endomyces fibuliger cellobiase (BGL1) gene and co-expressing it with the Butyrivibrio fibrisolvens endo-beta-1,4-glucanase (END1), the Phanerochaete chrysosporium cellobiohydrolase (CBH1) and the Ruminococcus flavefacies cellodextrinase (CEL1) gene constructs in this yeast. The END1, CBH1 and CEL1 genes were inserted into yeast expression/secretion cassettes. Expression of END1, CBH1 and CEL1 was directed by the promoter sequences derived from the alcohol dehydrogenase II (ADH2), the phosphoglycerate kinase I (PKG1) and the alcohol dehydrogenase I (ADH1) genes, respectively. In contrast, BGL1 was expressed under the control of its native promoter. Secretion of End1p and Cel1p was directed by the signal sequence of the yeast mating pheromone alpha-factor (MF alpha 1), whereas Cbh1p and Bgl1p were secreted using their authentic leader peptides. The construction of a fur1 ura3 S. cerevisiae strain allowed for the autoselection of this multicopy URA3-based plasmid in rich medium. S. cerevisiae transformants secreting biologically active endo-beta-1,4-glucanase, cellobiohydrolase, cellodextrinase and cellobiase were able to degrade various substrates including carboxymethylcellulose, hydroxyethylcellulose, laminarin, barley glucan, cellobiose, polypectate, birchwood xylan and methyl-beta-D-glucopyranoside. This study could lead to the development of industrial strains of S. cerevisiae capable of converting cellulose in a one-step process into commercially important commodities.
The Metastasis Cascade (2008)

Advances in the Biology, Detection Techniques, and Clinical Applications of Circulating Tumor Cells,
Preservation of Synaptic Structure by Rapid Freezing (1976)

It is becoming apparent that aldehyde fixatives cannot arrest many synaptic activities fast enough to reveal their structural basis in the electron microscope (Heuser et al. 1974). What is needed is a reliable technique to freeze synapses while they are active so that they can be examined directly in freeze-fracture replicas or can be fixed while still frozen and then examined in thin sections. Here we describe a machine that is potentially capable of freezing nerve and muscle tissues fast enough to capture the fleeting morphological changes that occur during synaptic transmission. Tissues frozen in this machine can be put directly into a Balzers freeze-fracture apparatus.
Synthesis of the Derivatives of 1,4,5,8-Tetrazanaphthano(2,3,-6,7)bisfurazan (2003)

Some derivatives of 1,4,5,8tetraazanaphthano(2,3,6,7) bisfurazan were synthesized by hydroxymethylation,acylation,nitration,azidation. The structures of these furazan energetic compounds were identified with 1HNMR,IR,MS and elemental analysis.
Does Lowering Glutamine Synthetase Activity in Nodules Modify Nitrogen Metabolism and Growth of Lotus japonicus? (2003)

A cDNA encoding cytosolic glutamine synthetase (GS) from Lotus japonicus was fused in the antisense orientation relative to the nodule-specific LBC3 promoter of soybean (Glycine max) and introduced into L. japonicus via transformation with Agrobacterium tumefaciens. Among the 12 independent transformed lines into which the construct was introduced, some of them showed diminished levels of GS1 mRNA and lower levels of GS activity. Three of these lines were selected and their T(1) progeny was further analyzed both for plant biomass production and carbon and nitrogen (N) metabolites content under symbiotic N-fixing conditions. Analysis of these plants revealed an increase in fresh weight in nodules, roots and shoots. The reduction in GS activity was found to correlate with an increase in amino acid content of the nodules, which was primarily due to an increase in asparagine content. Thus, this study supports the hypothesis that when GS becomes limiting, other enzymes (e.g. asparagine synthetase) that have the capacity to assimilate ammonium may be important in controlling the flux of reduced N in temperate legumes such as L. japonicus. Whether these alternative metabolic pathways are important in the control of plant biomass production still remains to be fully elucidated.
The Chaperone-Usher Pathway of Pilus Fiber Biogenesis (2014)

Many species of gram-negative bacteria employ a conserved protein secretion system termed the chaperone-usher pathway to assemble a diverse array of multisubunit protein fibers on their surfaces. Fibers assembled by the chaperone-usher pathway play critical roles in bacterially mediated disease: they mediate bacterial attachment to host tissues, often an essential early step in pathogenesis; they facilitate the evasion of host defenses; and they promote biofilm formation, a contributing factor both to the establishment of infection and to bacterial resistance to antibiotic treatment. Fibers assembled by the chaperone-usher pathway are typically encoded in individual gene clusters. The well-studied surface organelles, the capsular F1 antigen of Yersinia pestis and the hemagglutinating pilus of the human respiratory pathogen Haemophilus influenzae, highlight the structural diversity of fibers assembled by the chaperone-usher pathway. The periplasmic chaperones of the chaperone-usher pathway share conserved structural features first revealed in the crystal structure of PapD. Each chaperone consists of two domains that are oriented at an approximate right angle to each other to produce an L-shaped molecule. Donor strand exchange occurs very rapidly in vivo but only relatively slowly and inefficiently in vitro in the absence of the usher. This suggests that while the chaperone primes the subunit for donor strand exchange, additional interactions with the usher may facilitate subunit uncapping during fiber formation. The relative specificity of donor strand exchange determines, at least in part, the function of individual subunits and their order of incorporation into the fiber.
Transparent Nanocomposites with Ultrathin, Electrospun Nylon-4,6 Fiber Reinforcement (1999)

Transparent sheets of epoxy resin reinforced with nylon-4,6 nanofibers are described. The 30–200 nm diameter fibers, obtained by electrospinning from formic acid solutions, are reported to provide significant improvement in strength and stiffness to the epoxy film. The Figure is a scanning electron microscopy image of the electrospun nanofibers.
Experimental realization of order-finding with a quantum computer (2000)

Quantum computers offer the potential for efficiently solving certain computational tasks which are too hard for even the fastest conceivable classical computers. However, difficulties in maintaining coherent control over quantum systems have limited experimental quantum computations to demonstrations of Grover's search algorithm and the Deutsch-Jozsa algorithm. Shor's remarkable quantum factoring algorithm has remained beyond the reach of these small-scale realizations. Here we report the experimental implementation of a quantum algorithm which generalizes Shor's algorithm to find the order of a permutation in fewer steps than is possible using a deterministic or probabilistic classical computer. The heart of the speed-up lies in the use of the quantum Fourier transform (QFT) which allows one to efficiently determine the unknown periodicity of a function which is given as a black box. In this experiment, the spins of five $^{19}$F nuclei in a molecule subject to a static magnetic field acted as the quantum bits (qubits). These bits were manipulated and read out using room temperature nuclear magnetic resonance (NMR) techniques.
Transgenic rabbits with lymphocytic leukemia induced by the c-myc oncogene fused with the immunoglobulin heavy chain enhancer. (1988)

Transgenic rabbits with the rabbit c-myc oncogene fused with the rabbit immunoglobulin heavy chain enhancer region (E mu) DNA were developed by microinjecting pronuclei of single cell zygotes with the gene construct and implanting the microinjected eggs into pseudopregnant females. At age 17-20 days, 3 of 21 offspring born to seven females were found to have peripheral blood leukocyte counts of greater than 100,000 per mm3. Histology analyses showed extensive lymphocytic infiltration in the liver and kidney, indicating that these rabbits had a malignant lymphocytic leukemia. Genomic DNA analyses of thymus and peripheral blood lymphocytes revealed that the leukemic rabbits were transgenic and that both immunoglobulin heavy and kappa light chain genes were rearranged in the leukemic cells; thus, the leukemic cells are of B-cell lineage. One to four heavy and light chain gene rearrangements were observed, suggesting that the B-cell tumors were oligoclonal. Stable tissue culture cell lines from the bone marrow and peripheral blood of one of the transgenic rabbits have been developed. The development of B-cell leukemias in rabbits with the E mu-myc transgene contrasts with the development of B-cell lymphomas in mice carrying a similar transgene. The lymphomas in mice develop in adults and are monoclonal in origin. The leukemias in rabbits develop in juveniles, less than 3 weeks after birth, and appear oligoclonal in origin. The leukemias seem to develop in rabbit at a specific stage of development, and we suggest that a normal developmental signal may be involved in the oncogenesis.
Simultaneous Detection of Multiple Analytes Using Copalis Technology: A Reduction to Practice (1998)

Coupled Particle Light Scattering (Copalis) is a homogeneous immunoassay technology that enables the simultaneous determination of multiple analytes in serum, plasma, or whole blood (1) . The Copalis system measures changes in light-scattering properties of particles when they form antibody-mediated complexes. The system can measure two types of events: polystyrene microparticle coagglutination and polystyrene-gold colloid microparticle coupling. In the first format, polystyrene microparticles are differentiated from their complexed aggregates as a function of antigen concentration or serological response. The second format measures the broadening of the microparticle light scatter histogram as gold particles are attached. In both cases, light scattering analysis is performed as particles flow singly through a finely focused laser beam.

The ability to differentiate various sizes of polystyrene microparticles allows the system to measure multiple analytes or serological responses simultaneously. This capability has been demonstrated by the ToRC assay (toxoplasma, rubella, cytomegalovirus), in which antibodies to three different infectious agents are detected simultaneously (2) . In the present work, we demonstrate the application of Copalis technology to a variety of areas of diagnostic medicine in which the simultaneous measurement of multiple analytes or variables may be advantageous, including infectious disease, autoimmunity, and reproductive endocrinology.

This format is useful for detecting the presence of antibodies to infectious agents or autoantigens, which are coated onto latex microparticles. By using only forward-scatter measurement, Copalis instrumentation …
Impaired Immunogenicity of a Meningococcal Factor H-Binding Protein Vaccine Engineered To Eliminate Factor H Binding (2010)

Meningococcal factor H-binding protein (fHbp) is a promising antigen that is part of two vaccines in clinical development. The protein specifically binds human complement factor H (fH), which downregulates complement activation on the bacterial surface and enables the organism to evade host defenses. In humans, the vaccine antigen forms a complex with fH, which may affect anti-fHbp antibody repertoire and decrease serum bactericidal activity by covering important fHbp epitopes. In a recent study, fHbp residues in contact with fH were identified from a crystal structure. Two fHbp glutamate residues that mediated ion-pair interactions with fH were replaced with alanine, and the resulting E218A/E239A mutant no longer bound the fH fragment. In the present study, we generated the E218A/E239A mutant recombinant protein and confirmed the lack of fH binding. By enzyme-linked immunosorbent assay (ELISA), the mutant fHbp showed similar respective concentration-dependent inhibition of binding of four bactericidal anti-fHbp monoclonal antibodies (MAbs) to fHbp, compared with inhibition by the soluble wild-type protein. In two mouse strains, the mutant fHbp elicited up to 4-fold-lower IgG anti-fHbp antibody titers and up to 20-fold-lower serum bactericidal titers than those elicited by the wild-type fHbp vaccine. Thus, although introduction of the two alanine substitutions to eliminate fH binding did not appear to destabilize the molecule globally, the mutations resulted in decreased immunogenicity in mouse models in which neither the mutant nor the wild-type control vaccine bound fH. These results cast doubt on the vaccine potential in humans of this mutant fHbp.
The Biphasic Nature of Nitric Oxide Responses in Tumor Biology (2006)

The dual or biphasic responses of cancer to nitric oxide (NO) arise from its concentration dependent ability to regulate tumor growth, migration, invasion, survival, angiogenesis, and metastasis. The outcome of these various NO-dependent processes is dictated by several factors including NO flux, the chemical redox environment, and the duration of NO exposure. Further, it was recently discovered that an NO-induced redox flux in vascular endothelial cells hypersensitizes these cells to the antiangiogenic effects of thrombospondin-1. This suggests a novel treatment paradigm for targeting tumor-driven angiogenesis that combines redox modulation with mimetic derivatives of thrombospondin-1. This article discusses the biphasic nature of NO in cancer biology and the implications of NO-driven redox flux for modulation of tumor-stimulated angiogenesis, growth, and metastasis.
In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases (2012)

The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites). The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position-, cell type-, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM) to calculate the relative contribution of DNA methyltransferases (Dnmts) for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs.
Microcalorimetric study of the acidity and basicity of metal oxide surfaces (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicrocalorimetric study of the acidity and basicity of metal oxide surfacesAline. Auroux and Antonella. GervasiniCite this: J. Phys. Chem. 1990, 94, 16, 6371–6379Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/j100379a041https://doi.org/10.1021/j100379a041research-articleACS PublicationsRequest reuse permissionsArticle Views2936Altmetric-Citations414LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
FUNGAL ENDOPHYTES: A Continuum of Interactions with Host Plants (1998)

▪ Abstract Endophytic fungi living asymptomatically within plant tissues have been found in virtually all plant species. Endophytes are considered plant mutualists: They receive nutrition and protection from the host plant while the host plant may benefit from enhanced competitive abilities and increased resistance to herbivores, pathogens, and various abiotic stresses. Limited evidence also indicates that endophytes may influence population dynamics, plant community diversity, and ecosystem function. However, most of the empirical evidence for this mutualism and its ecological consequences has been based on a few agronomic grass endophytes. More recent studies suggest that endophyte-host plant interactions are variable and range from antagonistic to mutualistic. A more comprehensive view of the ecology and evolution of endophytes and host plants is needed. This article discusses how life history traits—such as fungal reproduction and pattern of infections and genotypic variation and ecological factors—influence the direction and strength of the endophyte-host plant interaction.