gebhart/patrepeval huggingface dataset:
Preparation and evaluation of novel derivatives of geldanamycin (2006)

1121 Background: Geldanamycin (GA) is a potent inhibitor of Hsp90. Its derivative, 17-AAG is in Phase II clinical trials for the treatment of several cancers. However, due to its hydrophobicity, 17-AAG is administered in cremophor. Both GA and 17-AAG contain a quinone group that is well known to have redox-active properties that may be linked to potential toxicity. Herein we describe the preparation and biological evaluation of novel geldanamycin derivatives. Methods: The new derivatives of GA were prepared from GA or 17-substituted GA Purity and authenticity of new compounds were confirmed with NMR, MS and HPLC. The new derivatives of GA were evaluated for invitro cytotoxicity against MX-1 (human mammary carcinoma), HT29 (colon), HepG2 (hepatoma), HCT116 (colon), and 3T3 (fibroblast). Hsp90 binding affinity of the new GA derivatives was evaluated using a competitive Hsp90α fluorescence polarization binding assay. Nanoparticle albumin bound (nab) forms of 17AAG and the novel compounds were prepared for further invivo studies. Results: More than forty new derivatives of GA were prepared from either GA or 17-substituted GA in 50-80% yield. All of derivatives were obtained in single E isomers. Some of the prepared derivatives showed significantly increased cytotoxicity compared to 17-AAG. For example, ABI328 (IC50 = 0.11 μM and 0.13 μM) exhibited more potent activity than 17-AAG (IC50 = 1.7 μM and 9.4 μM ) on MX-1 and HCT116 respectively; ABI287 (IC50=1.66 μM) was more active than 17-AAG (IC50 = 142 μM) against HT29. Some of the new derivatives of GA retained similar binding affinities to Hsp90 in comparison to 17-AAG. Nanoparticle nab-17AAG and nab-ABI328 were successfully prepared. . Conclusion: We have successfully prepared a series of geldanamycin derivatives, some of which exhibit higher cytotoxic activities and comparable Hsp90 affinities in comparison to 17-AAG. Nanoparticle (nab) versions of 17AAG and the novel compounds were successfully prepared. The evaluation of antitumor activity of ABI328 and ABI287 in xenograft models is in progress.
Folding of Firefly (Photinus pyralis) Luciferase:  Aggregation and Reactivation of Unfolding Intermediates (1998)

The guanidine-induced unfolding of firefly (Photinus pyralis) luciferase involves two inactive equilibrium intermediates and is freely reversible at low protein concentration and low temperature. However, reactivation is exceedingly slow so that the equilibrium is attained only after several days of incubation and reactivation yields decrease strongly with increasing protein concentration, suggesting that aggregation is a competing side reaction [Herbst et al. (1997) J. Biol. Chem. 272, 7099-7105]. We investigated the role of the equilibrium intermediates in the aggregation process using size-exclusion chromatography and dynamic light scattering to monitor their association state. Although the more unfolded intermediate aggregated much more rapidly, both intermediates associated irreversibly without a conformational change visible by fluorescence or circular dichroism, forming small oligomers which remained soluble in the presence of the denaturant. The association kinetics are compatible with a nucleated polymerization mechanism. Unfolding kinetics at 1 M denaturant indicated the presence of a further inactive intermediate capable to reactivate rapidly with kinetics similar to those observed for luciferase reactivation in the presence of cell extracts. The data suggest a kinetic trap in luciferase refolding that is accessible from both equilibrium intermediate conformations and is avoided in the presence of molecular chaperones.
Crystal and Molecular Structures of Asymmetric cis- and trans-Platinum(II/IV) Compounds and Their Reactions with DNA Fragments (1997)

The asymmetrically substituted platinum(II) complexes cis-Pt(NH3)(c-C6H11NH2)Cl2 and trans-Pt(NH3)(c-C6H11NH2)Cl2 have been synthesized and their crystal structures have been determined. Crystals of cis-Pt(NH3)(c-C6H11NH2)Cl2 (1) are orthorhombic, space group Pbca (no. 61) with a = 10.1994(12), b = 10.494(2), c = 18.826(2) Å, Z = 8. The structure refinement converged to R1 = 0.0518 and wR2 = 0.1143. Crystals of trans-Pt(NH3)(c-C6H11NH2)Cl2 (2) are monoclinic, space group P21/c (no. 14) with a = 12.141(3), b = 6.0965(9), c = 19.864(3) Å, β = 118.71(2)°, Z = 4. The structure refinement converged to R1 = 0.0711 and wR2 = 0.1846. In addition, the Pt(IV) analogues with axial hydroxide ligands have been synthesized. Also the corresponding bis(carboxylato)platinum(IV) compound of formula trans,cis,cis-Pt(NH3)(c-C6H11NH2)Cl2(OOCCH3)2 has been obtained by conversion of the hydroxide with acetic anhydride. Reactions of these platinum complexes with 9-methylhypoxanthine and guanosine-5‘-monophosphate (5‘-GMP) have been studied in significant detail. The course of the reactions was followed by NMR spectroscopy, and 1H and 195Pt techniques were used to identify the formation of the products. It was found that the Pt(II) compounds easily react with the bases at the N7 position, whereas the Pt(IV) compounds react very slowly (for trans,cis,cis-Pt(NH3)(c-C6H11NH2)Cl2(OOCCH3)2) or not at all (for trans,trans,trans-Pt(NH3)(c-C6H11NH2)Cl2(OH)2). Only in the presence of glutathione does a reaction of the latter with 5‘-GMP takes place. In this case a major product was found to be the reduced trans-Pt(II) complex with one molecule of 5‘-GMP and one molecule of S-bonded glutathione.
Spodoptera littoralis (Lepidoptera: Noctuidae) Resistance to CryIC and Cross-Resistance to Other Bacillus thuringiensis Crystal Toxins (1996)

International audience
Functional characterization of the EMCV IRES in plants (2000)

The translation of eukaryotic messenger RNA is typically dependent upon the presence of an m7GpppN cap structure at the 5' end of the transcript. However, several animal viruses, including the Picorna viruses, have been shown to exhibit cap-independent translation through the presence of an internal ribosome entry site or IRES. This IRES-mediated cap-independent internal translation initiation has been exploited to generate bicistronic transcripts that function in animal cells. Recently IRES elements have also been identified in a small number of vertebrate, insect and yeast cellular messenger RNAs although no such sequences have been identified in endogenous plant genes and there are no reports of animal virus derived IRES activity in plant cells. Here we have constructed a bicistronic gene containing both green fluorescent protein and luciferase open-reading frames separated by the encephalomyocarditis IRES element under the control of the CaMV 35S promoter. Northern analysis reveals expression of the bicistronic transcript and in vivo imaging of GFP and luciferase activities demonstrates the functional presence of both proteins. Western blot analysis confirms the independent translation of both reporter proteins. These data suggest that insertion of the encephalomyocarditis virus (EMCV) IRES element between two open-reading frames of a plant bicistronic transcript can mediate translation of the second open-reading frame. This activity is more apparent in the leaves, than in the roots, of transgenic seedlings carrying the bicistronic reporter gene construct.
Kallikrein Gene Delivery Improves Serum Glucose and Lipid Profiles and Cardiac Function in Streptozotocin-Induced Diabetic Rats (2005)

We investigated the role of the kallikrein-kinin system in cardiac function and glucose utilization in the streptozotocin (STZ)-induced diabetic rat model using a gene transfer approach. Adenovirus harboring the human tissue kallikrein gene was administered to rats by intravenous injection at 1 week after STZ treatment. Human kallikrein transgene expression was detected in the serum and urine of STZ-induced diabetic rats after gene transfer. Kallikrein gene delivery significantly reduced blood glucose levels and cardiac glycogen accumulation in STZ-induced diabetic rats. Kallikrein gene transfer also significantly attenuated elevated plasma triglyceride and cholesterol levels, food and water intake, and loss of body weight gain, epididymal fat pad, and gastrocnemius muscle weight in STZ-induced diabetic rats. However, these effects were blocked by icatibant, a kinin B2 receptor antagonist. Cardiac function was significantly improved after kallikrein gene transfer as evidenced by increased cardiac output and +/-delta P/delta t (maximum speed of contraction/relaxation), along with elevated cardiac sarco(endo)plasmic reticulum (Ca2+ + Mg2+)-ATPase (SERCA)-2a, phosphorylated phospholamban, NOx and cAMP levels, and GLUT4 translocation into plasma membranes of cardiac and skeletal muscle. Kallikrein gene delivery also increased Akt and glycogen synthase kinase (GSK)-3beta phosphorylation, resulting in decreased GSK-3beta activity in the heart. These results indicate that kallikrein through kinin formation protects against diabetic cardiomyopathy by improving cardiac function and promoting glucose utilization and lipid metabolism.
Altered activities of anti-atherogenic enzymes LCAT, paraoxonase, and platelet-activating factor acetylhydrolase in atherosclerosis-susceptible mice (2002)

We examined whether the putative anti-atherogenic enzymes LCAT, paraoxonase (PON), and platelet-activating factor acetylhydrolase (PAF-AH) are impaired in 8 week old atherosclerosis susceptible apolipoprotein E (apoE)(-/-) and LDL receptor (LDLr)(-/-) mice and whether plasma concentrations of bioactive oxidized phospholipids accumulate in plasma. ApoE(-/-) mice had reduced (28%) LCAT activity and elevated lysophosphatidylcholine and bioactive oxidized phospholipids (1-palmitoyl-2-oxovaleryl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine) compared with controls on the chow diet. Elevated oxidized phospholipids and reduced LCAT activity may, in part, contribute to spontaneous lesions in these mice on a chow diet. A Western diet decreased LCAT activity further (50% of controls) and PON activity was decreased 38%. The LDLr(-/-) mice showed normal LCAT activity on chow diet and little accumulation of oxidized phospholipids. On a Western diet, LDLr(-/-) mice had reduced LCAT activity (21%), but no change in PON activity. All genotypes had reduced PAF-AH activity on the Western diet. ApoE(-/-) and LDLr(-/-) mice, but not controls, had elevated plasma bioactive oxidized phospholipids on the Western diet. We conclude that impairment of LCAT activity and accumulation of oxidized phospholipids are part of an early atherogenic phenotype in these models.
A modeling analysis of monoclonal antibody percolation through tumors: a binding-site barrier. (1990)

For successful use of radiolabeled monoclonal antibodies (MAbs) for diagnosis and therapy, it is helpful to understand both global and microscopic aspects of antibody biodistribution. In this study, antibody distribution in a tumor is simulated by splicing together information on global pharmacokinetics: transport across the capillary wall, diffusive penetration through the tumor interstitial space, and antigen-antibody interaction. The geometry simulated corresponds to spherical nodules of densely packed tumor cells. This modeling analysis demonstrates that: 1) antigen-antibody binding in tumors can retard antibody percolation; 2) high antibody affinity at a given dose tends to decrease antibody percolation because there are fewer free antibody molecules. The result is a more heterogeneous distribution; 3) the average antibody concentration in the tumor does not increase linearly with affinity; and 4) increasing antibody dose leads to better percolation and more uniform distribution. This mathematical model and the general principles developed here can be applied as well to other biologic ligands.
Inflammation of the brain in Alzheimer's disease: implications for therapy (1999)

Abstract We briefly describe the similarities and differences between a systemic and a local immune reaction and review the evidence that the latter occurs in Alzheimer's disease (AD) brains. The evidence comes mainly from studies on the complement system, microglia, and cytokines, all of which are important actors in the inflammatory process. The evidence is now overwhelming that the complement proteins and many of the mediators of inflammation are produced locally by brain cells. We will mention briefly the many epidemiological studies indicating that the use of anti-inflammatory drugs reduces the incidence and slows the progress of AD. Mention will also be made of some recent work on animal models of possible relevance to AD and inflammation. J. Leukoc. Biol. 65: 409–415; 1999.
Calmodulin Point Mutations Affect Drosophila Development and Behavior (1997)

Calmodulin (CAM) is recognized as a major intermediary in intracellular calcium signaling, but as yet little is known of its role in developmental and behavioral processes. We have generated and studied mutations to the endogenous Cam gene of Drosophila melanogaster that change single amino acids within the protein coding region. One of these mutations produces a striking pupal lethal phenotype involving failure of head eversion. Various mutant combinations produce specific patterns of ectopic wing vein formation or melanotic scabs on the cuticle. Anaphase chromosome bridging is also seen as a maternal effect during the early embryonic nuclear divisions. In addition, specific behavioral defects such as poor climbing and flightlessness are detected among these mutants. Comparisons with other Drosophila mutant phenotypes suggests potential CAM targets that may mediate these developmental and behavioral effects, and analysis of the CAM crystal structure suggests the structural consequences of the individual mutations.
Morphological response of cultured cells to Naegleria amoeba cytopathogenic material (1985)

Naegleria amoebae contain cytopathogenic material (NACM). The morphological response of cultured cells to this material follows a number of characteristics in common with those resulting from infectious agents. The cytopathologic changes varied depending on the strain of the cultured cells. Among those from 17 different vertebrate sources, both primary and continuous cell lines, some were destroyed completely by dilutions of NACM up to 10(-8) while others appeared unaffected by NACM at any concentration. The response had no apparent relationship to species, organ source, or passage level of the cells. The reaction was typified by a long latent period (4-10 days) during which the number of cells in the culture increased up to 10-fold, followed abruptly by a short period (less than 24 h) during which all of the cells were destroyed. The latent period was prolonged when the culture conditions were adverse, or when the amount of NACM in the inoculum was minimal. A high multiplicity of NACM in the inoculum lysed the entire culture, while dilutions near the end-point caused generalized or only focal changes of rounded cytopathic cells. The cytopathic effect could be maintained in cultured cells by serial passage, such that the total activity greatly exceeded what could be attributed to the original inoculum. These findings are consistent with the concept that NACM has properties of an infectious agent and that its quantity is enhanced and spread through the culture by cell-to-cell contact and by cell division.
A two-stage poly(ethylenimine)-mediated cytotoxicity: implications for gene transfer/therapy (2005)

Poly(ethylenimine) (PEI) is a cationic macromolecule commonly used in gene transfer/therapy protocols with high transfection efficiency both in vitro and in vivo. PEI is also cytotoxic, but the molecular basis of its cytotoxicity is poorly understood. Here, we have demonstrated that branched (25 kDa) and linear (750 kDa) PEI can both induce membrane damage and initiate apoptosis in three clinically relevant human cell lines (Jurkat T cells, umbilical vein endothelial cells, and THLE3 hepatocyte-like cells). We have defined Phase I toxicity as early necrotic-like changes (30 min) resulting from compromised membrane integrity, assessed by considerable lactate dehydrogenase release and phosphatidylserine translocation from the inner plasma membrane to the outer cell surface. Phase II cytotoxicity (24 h) was due to activation of a "mitochondrially mediated apoptotic program," resulting from PEI-induced channel formation in the outer mitochondrial membrane. This led to the release of proapoptotic cytochrome c, subsequent activation of caspase 3, and alteration in mitochondrial membrane potential as a result of caspase translocation into the mitochondria. The reported observations have important implications for the design and execution of gene therapy protocols as well for controlling intracellular distribution of drugs with cationic-based polymer-delivery systems.
Transdifferentiation of mouse aortic smooth muscle cells to a macrophage-like state after cholesterol loading (2003)

Mouse aortic smooth muscle cells (SMCs) were loaded for 72 h with cholesterol by using cholesterol:methyl-beta-cyclodextrin complexes, leading to approximately 2-fold and approximately 10-fold increases in the contents of total cholesterol and cholesteryl ester, respectively. Foam-cell formation was demonstrated by accumulation of intracellular, Oil Red O-stained lipid droplets. Immunostaining showed decreased protein levels of smooth muscle alpha-actin and alpha-tropomyosin and increased levels of macrophage markers CD68 and Mac-2 antigen. Quantitative real-time RT-PCR revealed that after cholesterol loading, the expression of SMC-related genes alpha-actin, alpha-tropomyosin, myosin heavy chain, and calponin H1 decreased (to 11.5 +/- 0.5%, 29.3 +/- 1.4%, 23.8 +/- 1.4%, and 3.8 +/- 0.5% of unloaded cells, respectively; P < 0.05 for all), whereas expression of macrophage-related genes CD68, Mac-2, and ABCA1 mRNA increased (to 709 +/- 84%, 330 +/- 11%, and 207 +/- 13% of unloaded cells, respectively; P < 0.05 for all), thereby demonstrating that the protein changes were regulated at the mRNA level. Furthermore, these changes were accompanied by a gain in macrophage-like function as assessed by phagocytotic activity. Expression of vascular cell adhesion molecule 1 and monocyte chemoattractant protein 1, known responders to inflammation, were not changed. In conclusion, cholesterol loading of SMC causes phenotypic changes regulated at the mRNA level that result in a transdifferentiation to a macrophage-like state. This finding suggests that not all foam cells in lesions may have a macrophage origin, despite what is indicated by immunostaining for macrophage-related markers. Furthermore, inflammatory changes in foam cells observed in vivo may not be simple consequences of cholesterol accumulation.
Endogenous γ‐Hydroxybutyrate in Rat Brain Areas: Postmortem Changes and Effects of Drugs Interfering with γ‐Aminobutyric Acid Metabolism (1983)

The possibility that gamma-hydroxybutyrate (GHB), a metabolite of gamma-aminobutyric acid (GABA), may play a role in the CNS has recently come to attention. We describe here a sensitive and specific mass fragmentographic technique that allows the measurement of picomole amounts of GHB in single rat brain areas. Moreover, we show that GHB can accumulate postmortem, an effect that is blocked by the use of microwave irradiation to kill the animals. To understand further the relationship between GABA and GHB formation, we treated rats with drugs known to interfere with GABA metabolism at different levels and concomitantly measured GABA and GHB in cerebral cortex and cerebellum. Isoniazide, which blocks the formation of GABA, also decreases GHB. Blockers of the catabolism of GABA, such as aminooxyacetic acid and gamma-acetylenic GABA, increase GABA levels and decrease those of GHB. Sodium dipropylacetate increases both GABA and GHB, supporting the hypothesis that this effective antiepileptic drug also blocks in vivo the enzyme that converts succinic semialdehyde to succinic acid.
Photonics at Sandia National Laboratories: From research to applications (1994)

Photonics activities at Sandia National Laboratories (SNL) are founded on a strong materials research program. The advent of the Compound Semiconductor Research Laboratory (CSRL) in 1988, accelerated device and materials research and development. Recently, industrial competitiveness has been added as a major mission of the labs. Photonics projects have expanded towards applications-driven programs requiring device and subsystem prototype deliveries and demonstrations. This evolution has resulted in a full range of photonics programs from materials synthesis and device fabrication to subsystem packaging and test.
X-ray excited optical luminescence, photoluminescence, photostimulated luminescence and x-ray photoemission spectroscopy studies on BaFBr:Eu (1997)

The results of x-ray excited optical luminescence (XEOL), photoluminescence (PL), photostimulated luminescence (PSL) and x-ray photoemission spectroscopy (XPS) studies on the x-ray storage phosphor BaFBr:Eu are presented in this paper. Analyses of XEOL, PL and PSL spectra reveal features corresponding to the transitions from to configurations in different site symmetries of . Increasing x-ray dose is seen to lead to a red shift in the maximum of the PL excitation spectrum for the 391 nm emission. The XEOL and XPS spectra do not show any signature of in the samples studied by us, directly raising doubts about the model of Takahashi et al in which is expected to ionize to upon x-ray irradiation and remain stable until photostimulation. XEOL and PSL experiments with simultaneous x-ray irradiation and He - Ne laser excitation as well as those with sequential x-ray irradiation and laser stimulation bring out the competition between the F centre population and depopulation rates. A time scale - 2 s, possibly related to the process of production of the electron/hole traps themselves, during x-ray irradiation, is observed. Relaxation of these traps upon photostimulation is also seen.
Detection of Coxsackie B Virus RNA sequences in whole blood samples from adult patients at the onset of type I diabetes mellitus (1997)

Enteroviruses may be linked to insulin-dependent diabetes mellitus (IDDM). The prevalence of enteroviral (EV) infection at onset of adult IDDM was investigated by detection of specific EV sequences in peripheral blood using a reverse transcription and a seminested polymerase chain reaction (seminested RT-PCR). EDTA-treated whole blood samples taken from 12 newly diagnosed IDDM patients with ketosis or ketoacidosis were examined. The comparison groups were 12 adult patients suffering from metabolic decompensation in the course of IDDM, 12 adult patients with decompensated non-IDDM, and 15 healthy adults without any presumed EV infection or metabolic disease. EV genome was detected in five of 12 (42%) newly diagnosed IDDM patients and in one of 12 (8%) patients in the course of IDDM. By contrast, none of the 12 non-IDDM patients and none of the 15 healthy adults had EV sequences in whole blood. Subsequent sequencing of the EV PCR products from the six positive patients showed a significant homology with Coxsackie B3 or B4 viruses, and some common patterns were observed among the sequences. The present study demonstrates that Coxsackie B virus RNA sequences can be detected in peripheral blood from patients at the onset or in the course of IDDM and provides evidence for a role for enteroviruses in adult type I diabetes.