gebhart/patrepeval huggingface dataset:
Proteins Specified by Herpes Simplex Virus V. Purification and Structural Proteins of the Herpesvirion (1972)

We are reporting a procedure for the purification of herpes simplex enveloped nucleocapsids (virions), an evaluation of the purification procedure and the results of analyses of the virion proteins by high-resolution acrylamide gel electrophoresis. The data may be summarized as follows. (i) The procedure for the purification of virions consists of careful extraction of cytoplasm to prevent nuclear breakage, separation of enveloped nucleocapsids from soluble proteins and membrane vesicles by rate zonal centrifugation of cytoplasmic extracts through dextran 10 gradients, treatment with urea to dissociate virus-debris aggregates, and, lastly, separation of virions from naked nucleocapsids and free membranes by isopycnic flotation in discontinuous sucrose gradients. (ii) Purity was evaluated in three ways, i.e., electron microscopic examination, analysis of purified virions produced in cells labeled with amino acids before infection, and analysis of purified virions from artificial mixtures of infected and labeled, uninfected cells. The extent of purification was 120-to 200-fold with respect to host proteins. Residual contaminants were identified as host and viral constituents of membrane vesicles. Residual host proteins are very likely contaminants and not structural components of the virion. (iii) Analyses by staining and autoradiography of structural proteins of purified virions in 6, 7, 8.5, 9, and 14% acrylamide gels revealed 24 bands of proteins and glycoproteins made and labeled after infection. Co-electrophoresis of viral proteins with six known standards ranging from 25,700 to 220,000 daltons in molecular weight in 6, 7, 8.5, and 9% acrylamide gels indicate that viral proteins range from 25,000 to 275,000 daltons. The sum of the molecular weights of viral proteins is 2,580,000 daltons. Assuming that messenger transcription is asymmetric and noncomplementary, this corresponds to 47% of the genetic information of the virus. (iv) The nonionic detergent NP-40 removes from purified virions some nonglycosylated proteins and a large fraction of the glycosylated proteins. It leaves behind traces of the envelope visible in the electron microscope as well as some glycoproteins thought to be in the envelope.
Cyclical quantum memory for photonic qubits (2002)

We have performed a proof-of-principle experiment in which qubits encoded in the polarization states of single photons from a parametric down-conversion source were coherently stored and read out from a quantum memory device. The memory device utilized a simple free-space storage loop, providing a cyclical readout that could be synchronized with the cycle time of a quantum computer. The coherence of the photonic qubits was maintained during switching operations by using a high-speed polarizing Sagnac interferometer switch.
Display of peptides and proteins on the surface of bacteriophage lambda. (1995)

The display of peptides or proteins on the surface of viruses is an important technology for studying peptides or proteins and their interaction with other molecules. Here we describe a display vehicle based on bacteriophage lambda that incorporates a number of features distinct from other currently used display systems. Fusions of peptides or protein domains have been made to the amino terminus of the 11-kDa D protein of the lambda capsid. These fusions assemble onto the viral capsid and appear to be accessible to ligand interactions, based on the ability of a monoclonal antibody to recognize an epitope fused to the D protein on phage heads. To produce large D fusion display libraries and yet avoid the cumbersome task of cloning many fragments into lambda DNA, we have used the Cre-loxP site-specific recombination system in vivo to incorporate plasmids encoding the D fusions into the phage genome. Finally, we show that D fusion proteins can be added in vitro to phage lacking D protein and be assembled onto the viral capsid.
Complementary functions of E1a conserved region 1 cooperate with conserved region 3 to activate adenovirus serotype 5 early promoters (1994)

The amino-terminal region of the adenovirus type 5 E1a protein including conserved regions (CRs) 1 and 2 binds the 105-kDa retinoblastoma protein and a second, 300-kDa, cellular protein. We show that mutant viruses with deletions of CR1 which release the binding of either p105 or p300 still activate early promoters and infect cells productively. However, mutations which disrupt binding of both proteins disrupt early promoter activity and block the viral life cycle. Ela CR3, which has an established role in early promoter activation, can act in trans to the amino-terminal functions. This suggests that the amino terminus provides distinct, redundant functions related to p300 and Rb binding that synergize with CR3 to transactivate early genes.
Effect of atropine on proximal gastric motor and sensory function in normal subjects (2000)

In humans, fasting and postprandial proximal gastric motor function is under cholinergic control. Atropine induced inhibition of transient LOS relaxations is unlikely to be caused by its effect on the proximal stomach, but rather by a central action on the integrating mechanisms in the brain stem.
High-NA achromatic metalenses by inverse design (2020)

We use inverse design to discover metalens structures that exhibit broadband, achromatic focusing across low, moderate, and high numerical apertures. We show that standard unit-cell approaches cannot achieve high-efficiency high-NA focusing, even at a single frequency, due to the incompleteness of the unit-cell basis, and we provide computational upper bounds on their maximum efficiencies. At low NA, our devices exhibit the highest theoretical efficiencies to date. At high NA-of 0.9 with translation-invariant films and of 0.99 with "freeform" structures-our designs are the first to exhibit achromatic high-NA focusing.
Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication† (2005)

To develop synthetic short interfering RNA (siRNA) molecules as therapeutic agents for systemic administration in vivo, chemical modifications were introduced into siRNAs targeted to conserved sites in hepatitis B virus (HBV) RNA. These modifications conferred significantly prolonged stability in human serum compared with unmodified siRNAs. Cell culture studies revealed a high degree of gene silencing after treatment with the chemically modified siRNAs. To assess activity of the stabilized siRNAs in vivo initially, an HBV vector-based model was used in which the siRNA and the HBV vector were codelivered via high-volume tail vein injection. More than a 3 log10 decrease in levels of serum HBV DNA and hepatitis B surface antigen, as well as liver HBV RNA, were observed in the siRNA-treated groups compared with the control siRNA-treated and saline groups. Furthermore, the observed decrease in serum HBV DNA was 1.5 log10 more with stabilized siRNA compared with unmodified siRNA, indicating the value of chemical modification in therapeutic applications of siRNA. In subsequent experiments, standard systemic intravenous dosing of stabilized siRNA 72 hours after injection of the HBV vector resulted a 0.9 log10 reduction of serum HBV DNA levels after 2 days of dosing. In conclusion, these experiments establish the strong impact that siRNAs can have on the extent of HBV infection and underscore the importance of stabilization of siRNA against nuclease degradation.
Polynucleotide: adenosine glycosidase activity of saporin-L1: effect on DNA, RNA and poly(A) (1996)

The ribosome-inactivating proteins (RIPs) are a family of plant enzymes for which a unique activity has been determined: rRNA N-glycosidase, which removes adenine at a specific universally conserved position (A4324 in the case of rat ribosomes). Here we report that saporin-L1, a RIP from the leaves of Saponaria officinalis, recognizes other substrates, including RNAs from different sources, DNA and poly(A). Saporin-L1 depurinated DNA extensively and released adenine from all adenine-containing polynucleotides tested. Adenine was the only base released from DNA or artificial polynucleotides. The characteristics of the reactions catalysed by saporin-L1 have been determined: optimal pH and temperature, ionic requirements, and the kinetic parameters Km and kcat. The reaction proceeded without cofactors, at low ionic strength, in the absence of Mg2+ and K+. Saporin-L1 had no activity towards various adenine-containing non-polynucleotide compounds (cytokinins, cofactors, nucleotides). This plant protein may now be classified as a polynucleotide: adenosine glycosidase.
Photodynamic therapy can kill Cryptococcus neoformans in in vitro and in vivo models (2009)

Cryptococcosis is an infection caused by the encapsulated yeast Cryptococcus neoformans and the most afflicted sites are lung, skin and central nervous system. A range of studies had reported that photodynamic therapy (PDT) can inactivate yeast cells; however, the in vivo experimental models of cryptococcosis photoinactivation are not commonly reported. The aim of this study was to investigate the ability of methylene blue (MB) combined with a low-power red laser to inactivate Cryptococcus neoformans in in vitro and in vivo experimental models. To perform the in vitro study, suspension of Cryptococcus neoformans ATCC-90112 (106cfu/mL) was used. The light source was a laser (Photon Lase III, DMC, São Carlos, Brazil) emitting at &lambda;660nm with output power of 90mW for 6 and 9min of irradiation, resulting fluences at 108 and 162J/cm². As photosensitizer, 100&mu;M MB was used. For the in vivo study, 10 BALB/c mice had the left paw inoculated with C. neoformans ATCC-90112 (107cfu). Twenty-four hours after inoculation, PDT was performed using 150&mu;M MB and 100mW red laser with fluence at 180J/cm2. PDT was efficient in vitro against C. neoformans in both parameters used: 3 log reduction with 108J/cm² and 6 log reduction with 162J/cm². In the in vivo experiment, PDT was also effective; however, its effect was less expressive than in the in vitro study (about 1 log reduction). In conclusion, PDT seems to be a helpful alternative to treat dermal cryptococcosis; however, more effective parameters must be found in in vivo studies.
Methods for mitigating surface damage growth in NIF final optics (2002)

We report a summary of the surface damage, growth mitigation effort at 3(omega) for fused silica optics at LLNL. The objective was to experimentally validate selected methods that could be applied to pre-initiated or retrieved-from- service optics, to stop further damage growth. A specific goal was to obtain sufficient data and information of successful methods for fused silica optics to select a single approach for processing NIF optics. This paper includes the test results and the evaluation thereof, for several mitigation methods for fused silica. The mitigation methods tested in this study are wet chemical etching, cold plasma etching, CO<SUB>2</SUB> laser processing, and micro-flame torch processing. We found that CO<SUB>2</SUB> laser processing produces the most significant and consistent results to halt laser-induced surface damage growth on fused silica. We recorded successful mitigation of the growth of laser-induced surface damage sites as large as 0.5-mm diameter, for 1000 shots at fluences in the range of 8 to 13 J/cm<SUP>2</SUP>. We obtained sufficient data for elimination of damage growth using CO<SUB>2</SUB> laser processing on sub-aperture representative optics, to proceed with application to full- scale NIF optics.
Recombinant human growth hormone stimulates B cell immunoglobulin synthesis and proliferation in serum-free medium (1992)

In order to investigate the effects of growth hormone on human B cells, we studied immunoglobulin synthesis and [ 3 H]-thymidine uptake by B cell lines, IM-9, GM-1056 and CBL, and purified tonsil B cells. Cells were cultured in a serum- and albumin-free medium, Cosmedium-001 to exclude interaction between a certain growth-promoting substance and any unknown substances that serum may contain. GH enhanced IgG synthesis and [3H]-thymidine uptake by IM-9 cells, IgA synthesis by GM-1056 cells and IgM synthesis by CBL cells in a dose-dependent fashion. This was not a non-specific effect of protein in GH, since equivalent or higher concentrations of proteins such as bovine serum albumin, interleuki-2, interleukin-5, granulocyte/macrophage colony-stimulating factor, or erythropoietin did not stimulate B cell lines. Moreover, the rabbit anti-GH antibody blocked the enhancing effect of GH, while normal rabbit antibody failed to do so. GH also enhanced immunoglobulin synthesis (IgG and IgM) and thymidine uptake by Staphylococcus aureus Cowan strain I-activated tonsil B cells. These results indicate that GH has a direct stimulating effect on B cells, and, in addition to its endocrinological function, GH may also act as an immunoregulatory cytokine.
Bradykinin receptor antagonists (1990)

Bradykinin and its active metabolites are produced at the sites of their actions by kallikreins. They potently elicit a variety of biological effects: hypotension, bronchoconstriction, gut and uterine contraction, epithelial secretion in airway, gut, and exocrine glands, vascular permeability, pain, connective tissue proliferation, and eicosanoid formation. These effects are mediated by at least two broad classes of receptors. The most common is the B2 subtype. The Stewart and Vavrek peptides characterized by a DPhe7 substitution have provided powerful tools for study of bradykinin's actions by competitively and specifically blocking bradykinin B2 receptors. The significance of kinins in certain human diseases is being explored using these new tools and potential therapeutic agents. At present, human clinical trials are underway to test the usefulness of bradykinin receptor antagonists in the symptoms of the common cold and in the pain associated with severe burns. Trials for use in asthma will be initiated in 1990.
High-Density Lipoproteins Inhibit Cytokine-Induced Expression of Endothelial Cell Adhesion Molecules (1995)

While an elevated plasma concentration of HDLs is protective against the development of atherosclerosis and ensuing coronary heart disease (CHD), the mechanism of this protection is unknown. One early cellular event in atherogenesis is the adhesion of mononuclear leukocytes to the endothelium. This event is mediated principally by vascular cell adhesion molecule-1 (VCAM-1) but also involves other molecules, such as intercellular adhesion molecule-1 (ICAM-1) and E-selectin. We have investigated the effect of isolated plasma HDLs and reconstituted HDLs on the expression of these molecules by endothelial cells. We show that physiological concentrations of HDLs inhibit tumor necrosis factor-alpha (TNF-alpha) or interleukin-1 (IL-1) induction of these leukocyte adhesion molecules in a concentration-dependent manner. Steady state mRNA levels of TNF-alpha-induced VCAM-1 and E-selectin are significantly reduced by physiological concentrations of HDLs. An an HDL concentration of 1 mg/mL apolipoprotein A-I, the protein expressions of VCAM-1, ICAM-1, and E-selectin were inhibited by 89.6 +/- 0.4% (mean +/-SD, n=4), 64.8 +/- 1.0%, and 79.2 +/- 0.4%, respectively. In contrast, HDLs have no effect on the expression of platelet endothelial cell adhesion molecule (PECAM) or on the expression of the p55 and p75 subunits of the TNF-alpha receptor. HDLs were effective when added from 16 hours before to 5 minutes after cytokine stimulation. HDLs had no effect on TNF-alpha-induced expression of ICAM-1 by human foreskin fibroblasts, suggesting that the effect is cell-type restricted.(ABSTRACT TRUNCATED AT 250 WORDS)
A bivalent single-chain antibody-toxin specific for ErbB-2 and the EGF receptor (1996)

ErbB-2 and EGF receptors are often co-expressed in human tumors and have been shown to synergize in the transformation of cells in experimental model systems. Transactivation of ErbB-2 can occur via ligand-induced heterodimerization with EGF receptor or other members of the ErbB family of receptor tyrosine kinases. We have previously described the potent anti-tumoral activity of the monospecific single-chain antibody-toxins scFv(FRP5)-ETA and scFv(225)-ETA binding to, respectively, ErbB-2 and the EGF receptor. Here we report the construction and functional characterization of a novel bivalent, bispecific single-chain antibody-toxin, scFv2(FRP5/225)-ETA. The fusion protein consists of 2 scFv domains specific for ErbB-2 and the EGF receptor linked to a modified Pseudomonas exotoxin A. ScFv2(FRP5/225)-ETA displayed in vitro cell killing activity on tumor cells overexpressing either ErbB-2 or the EGF receptor similar to that of the monospecific toxins. It was more potent in vitro and in vivo in inhibiting the growth of tumor cells expressing both receptors. Treatment of A431 cells with scFv2(FRP5/225)-ETA led to an increase in EGF receptor and ErbB-2 phosphotyrosine content, most likely via the induction of receptor heterodimers. This may explain the enhanced toxicity of the bispecific antibody-toxin.
Structural Basis for Chk1 Inhibition by UCN-01 (2002)

Chk1 is a serine-threonine kinase that plays an important role in the DNA damage response, including G(2)/M cell cycle control. UCN-01 (7-hydroxystaurosporine), currently in clinical trials, has recently been shown to be a potent Chk1 inhibitor that abrogates the G(2)/M checkpoint induced by DNA-damaging agents. To understand the structural basis of Chk1 inhibition by UCN-01, we determined the crystal structure of the Chk1 kinase domain in complex with UCN-01. Chk1 structures with staurosporine and its analog SB-218078 were also determined. All three compounds bind in the ATP-binding pocket of Chk1, producing only slight changes in the protein conformation. Selectivity of UCN-01 toward Chk1 over cyclin-dependent kinases can be explained by the presence of a hydroxyl group in the lactam moiety interacting with the ATP-binding pocket. Hydrophobic interactions and hydrogen-bonding interactions were observed in the structures between UCN-01 and the Chk1 kinase domain. The high structural complementarity of these interactions is consistent with the potency and selectivity of UCN-01.
Molecular Cloning and Characterization of the Helicobacter pylori fliD Gene, an Essential Factor in Flagellar Structure and Motility (1999)

ABSTRACT Helicobacter pylori colonizes the human stomach and can cause gastroduodenal disease. Flagellar motility is regarded as a major factor in the colonizing ability of H. pylori . The functional roles of flagellar structural proteins other than FlaA, FlaB, and FlgE are not well understood. The fliD operon of H. pylori consists of flaG , fliD , and fliS genes, in the order stated, under the control of a ς 28 -dependent promoter. In an effort to elucidate the function of the FliD protein, a hook-associated protein 2 homologue, in flagellar morphogenesis and motility, the fliD gene (2,058 bp) was cloned and isogenic mutants were constructed by disruption of the fliD gene with a kanamycin resistance cassette and electroporation-mediated allelic-exchange mutagenesis. In the fliD mutant, morphologically abnormal flagellar appendages in which very little filament elongation was apparent were observed. The fliD mutant strain was completely nonmotile, indicating that these abnormal flagella were functionally defective. Furthermore, the isogenic fliD mutant of H. pylori SS1, a mouse-adapted strain, was not able to colonize the gastric mucosae of host mice. These results suggest that H. pylori FliD is an essential element in the assembly of the functional flagella that are required for colonization of the gastric mucosa.
Substrate Specificities and Identification of Putative Substrates of ATM Kinase Family Members (1999)

Ataxia telangiectasia mutated (ATM) phosphorylates p53 protein in response to ionizing radiation, but the complex phenotype of AT cells suggests that it must have other cellular substrates as well. To identify substrates for ATM and the related kinases ATR and DNA-PK, we optimized in vitro kinase assays and developed a rapid peptide screening method to determine general phosphorylation consensus sequences. ATM and ATR require Mn(2+), but not DNA ends or Ku proteins, for optimal in vitro activity while DNA-PKCs requires Mg(2+), DNA ends, and Ku proteins. From p53 peptide mutagenesis analysis, we found that the sequence S/TQ is a minimal essential requirement for all three kinases. In addition, hydrophobic amino acids and negatively charged amino acids immediately NH(2)-terminal to serine or threonine are positive determinants and positively charged amino acids in the region are negative determinants for substrate phosphorylation. We determined a general phosphorylation consensus sequence for ATM and identified putative in vitro targets by using glutathione S-transferase peptides as substrates. Putative ATM in vitro targets include p95/nibrin, Mre11, Brca1, Rad17, PTS, WRN, and ATM (S440) itself. Brca2, phosphatidylinositol 3-kinase, and DNA-5B peptides were phosphorylated specifically by ATR, and DNA Ligase IV is a specific in vitro substrate of DNA-PK.
Novel mutations in the inhibitory adaptor protein LNK drive JAK-STAT signaling in patients with myeloproliferative neoplasms (2010)

Dysregulated Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling due to activation of tyrosine kinases is a common feature of myeloid malignancies. Here we report the first human disease-related mutations in the adaptor protein LNK, a negative regulator of JAK-STAT signaling, in 2 patients with JAK2 V617F-negative myeloproliferative neoplasms (MPNs). One patient exhibited a 5 base-pair deletion and missense mutation leading to a premature stop codon and loss of the pleckstrin homology (PH) and Src homology 2 (SH2) domains. A second patient had a missense mutation (E208Q) in the PH domain. BaF3-MPL cells transduced with these LNK mutants displayed augmented and sustained thrombopoietin-dependent growth and signaling. Primary samples from MPN patients bearing LNK mutations exhibited aberrant JAK-STAT activation, and cytokine-responsive CD34(+) early progenitors were abnormally abundant in both patients. These findings indicate that JAK-STAT activation due to loss of LNK negative feedback regulation is a novel mechanism of MPN pathogenesis.
The Role of AHA Motifs in the Activator Function of Tomato Heat Stress Transcription Factors HsfA1 and HsfA2 (2000)

Using reporter assays in tobacco protoplasts and yeast, we investigated the function of the acidic C-terminal activation domains of tomato heat stress transcription factors HsfA1 and HsfA2. Both transcription factors contain short, essential peptide motifs with a characteristic pattern of aromatic and large hydrophobic amino acid residues embedded in an acidic context (AHA motifs). The prototype is the AHA1 motif of HsfA2, which has the sequence DDIWEELL. Our mutational analysis supports the important role of the aromatic and large hydrophobic amino acid residues in the core positions of the AHA motifs. The pattern suggests the formation of an amphipathic, negatively charged helix as the putative contact region with components of the basal transcription complex. In support of this concept, proline or positively charged residues in or adjacent to the AHA motifs markedly reduce or abolish their activity. Both AHA motifs of HsfA1 and HsfA2 contribute to activator potential, and they can substitute for each other; however, there is evidence for sequence and positional specificity.