gebhart/patrepeval huggingface dataset:
Spontaneous mutagenesis associated with nucleotide excision repair in Escherichia coli (2008)

The vast majority of spontaneous mutations occurring in Escherichia coli are thought to be derived from spontaneous DNA lesions, which include oxidative base damage. Systems for removing intrinsic mutagens and repairing DNA lesions contribute to the suppression of spontaneous mutations. Nucleotide excision repair (NER) is a general DNA repair system that eliminates various kinds of lesions from DNA. We therefore predicted that NER might be involved in suppression of spontaneous mutations, and analyzed base substitutions occurring spontaneously within the rpoB gene in NER-proficient (wild-type), -deficient and -overproducing E. coli strains. Surprisingly, the mutation frequency was lower in NER-deficient strains, and higher in NER-overproducing strains, than in the NER-proficient strain. These results suggest, paradoxically, that NER contributes to the generation of spontaneous mutation rather than to its suppression under normal growth conditions, and that transcription-coupled repair also participates in this process. Using E. coli strains that carried an editing exonuclease-deficient polA mutation, we further obtained data suggesting that unnecessary NER might account for these findings, so that errors introduced during repair DNA synthesis by DNA polymerase I would result in unwanted base substitutions. The repair system itself may thus be an important generator of spontaneous mutation.
Rapid isolation of DNA from complex biological samples ustng a novel capture reagent—methidium spermine-sepharose (1989)

We have synthesized and analyzed the functional properties of a novel DNA capture reagent containing a methidium moiety attached to a sepharose bead by a spermine linker. DNA present in a biological fluid or other complex sample binds to the reagent. The DNA-capture reagent complex is then separated from the sample by centrifugation and the DNA is released from the reagent by brief incubation in 0.1 to 0.5 N NaOH or KOH. Capture of DNA from complex samples is independent of the salt concentration of the sample, and occurs in the presence of high concentrations of EDTA, proteinase K and detergents. Many samples can be processed simultaneously. The following specific applications, in which denatured DNA is quantitated or characterized, are demonstrated: 1). Isolation of hepatitis B virus DNA from serum and quantitation by dot-blot hybridization, 2). Isolation and quantitation of DNA from urine, 3). Isolation of human genomic DNA from one microliter of blood or 100 HeLa cells followed by amplification of a specific gene sequence using the Polymerase Chain Reaction, 4). Isolation of single stranded phage M13 sequencing templates from bacterial cultures. These investigations suggest that a capture reagent containing an intercalating moiety bound to a solid support may be useful for many applications in molecular biology and molecular diagnostics.
Polymer-supported half-titanocene catalysts for the syndiospecific polymerization of styrene (2000)

Monocyclopendienyltitanium trichloride (CpTiCl3) was supported on polymer carriers with different hydroxyl contents, and the supported catalysts were used for styrene polymerization. The supported catalysts exhibited high activity even at low Al/Ti ratios and increased the molecular weight of the products, indicating that polymer carriers could stabilize the active sites. The polymers prepared with unsupported and supported catalysts were extracted with boiling n-butanone and characterized by carbon nuclear magnetic resonance (13C NMR) and differential scanning calorimetry. The polymers obtained by supported catalysts had a high fraction of boiling n-butanone-insoluble part and high melting temperatures, but 13C NMR results showed that syndiotacticity decreased compared with that of polymers prepared with an unsupported catalyst. ESR study on the supported catalysts confirmed that the active sites supported on the carrier dropped into the solution and formed active sites the same as those in the unsupported system when they reacted with methylaluminoxane. 13C NMR analysis showed that the polymerization mechanism of the supported active sites was an active-site controlled mechanism instead of a chain-end controlled mechanism of the unsupported active sites. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 127–135, 2000
Penetration, Adhesion, and Fusion in Mammalian Sperm-Egg Interaction (2002)

Fertilization is the sum of the cellular mechanisms that pass the genome from one generation to the next and initiate development of a new organism. A typical, ovulated mammalian egg is enclosed by two layers: an outer layer of approximately 5000 cumulus cells and an inner, thick extracellular matrix, the zona pellucida. To reach the egg plasma membrane, sperm must penetrate both layers in steps requiring sperm motility, sperm surface enzymes, and probably sperm-secreted enzymes. Sperm also bind transiently to the egg zona pellucida and the egg plasma membrane and then fuse. Signaling in the sperm is induced by sperm adhesion to the zona pellucida, and signaling in the egg by gamete fusion. The gamete molecules and molecular interactions with essential roles in these events are gradually being discovered.
Interleukin 13 and interleukin 13 receptor are frequently expressed by Hodgkin and Reed-Sternberg cells of Hodgkin lymphoma (2001)

Hodgkin lymphoma (HL) is characterized by the abnormal expression of multiple cytokines, accounting for its unique clinicopathologic features. We have previously shown that interleukin-13 (IL-13) is secreted by HL cell lines and may serve as an autocrine growth factor. To determine the frequency of IL-13 expression in lymphoma patients, tissue sections from 36 patients with classical HL, 5 patients with nodular lymphocyte predominance HL (NLPHL), and 23 patients with non-Hodgkin lymphoma (NHL) were subjected to in situ hybridization. In 31 of 36 cases (86%) of classical HL patients of all histologic subtypes, between 25% to almost 100% of Hodgkin and Reed Sternberg (HRS) cells were positive for IL-13 expression. In contrast, in no case of NLPHL and in only 4 of 23 NHL cases (1 of 5 T-cell-rich B-cell lymphomas, 2 of 5 anaplastic large cell lymphomas, and 1 of 5 peripheral T-cell lymphomas) did the neoplastic cells express IL-13. The expression of the IL-13 receptor chain alpha1 (IL-13Ralpha1) was also analyzed by in situ hybridization. In 24 of 27 (89%) cases of classical HL, between 25% to 75% of HRS cells, as well as a high frequency of lymphocytes and histiocytes, were positive for IL-13Ralpha1 expression. These results were confirmed by the construction of complementary DNA libraries from single HRS cells, followed by polymerase chain reaction analysis, in which IL-13Ralpha1 transcripts were found to be present in all 6 cases of HL. These data indicate that expression of IL-13 and IL-13Ralpha1 is a common feature of HRS cells in HL, consistent with the hypothesis that IL-13 may play a role in autocrine growth in classical HL.
Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase (1990)

High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.
Identification of a Stat‐6‐responsive element in the promoter of the human interleukin‐4 gene (1997)

Interleukin (IL)-4 is an immunomodulatory cytokine produced by a number of cell types including T cells, basophils, and mast cells. This pleiotropic cytokine has a number of immunoregulatory functions; however, the molecular mechanisms controlling the transcription of this gene are not yet completely understood. Several studies have implicated a possible autoregulatory mechanism for its own expression. Here, we have identified a Stat-6-responsive element (Stat-6RE) in the promoter of the human IL-4 gene. Utilizing electrophoretic mobility shift analysis, we have demonstrated the presence of two specific IL-4-responsive DNA-protein complexes in nuclear extracts of both human Th1 and Th2 clones. Phytohemagglutinin-blasted peripheral blood T cells also generated an inducible complex in response to stimulation with IL-4 and the IL-4-like cytokine IL-13. Transient transfection of the murine pre-B cell line BA/F3 stably transfected with the full-length human IL-4 receptor alpha chain demonstrated the ability of multicopy Stat-6RE to initiate transcription from a heterologous promoter upon IL-4 or IL-13 stimulation. These results indicate a possible autocrine mechanism for the regulation of IL-4 gene transcription through the Stat-6RE as well as a possible mechanism for IL-13 regulation of the human IL-4 promoter.
Genome-wide analysis of gene expression in synovial sarcomas using a cDNA microarray. (2002)

Among a histologically heterogeneous group of soft tissue sarcomas, synovial sarcoma (SS) is regarded as a "miscellaneous" entity of uncertain origin. Although recent molecular analysis has disclosed involvement of a specific chromosomal translocation in the pathogenesis of SS, its genetic features remain largely unclear. In the work reported here we examined genome-wide gene expression profiles of 13 SS cases and 34 other spindle-cell sarcoma cases by cDNA microarray consisting of 23,040 genes. A hierarchical clustering analysis grouped SS and malignant peripheral nerve sheath tumor into the same category, and these two types of tumor shared expression patterns of numerous genes relating to neural differentiation. Several genes were up-regulated in almost all SS cases, and the presumed functions of known genes among them were related to migration or differentiation of neural crest cells, suggesting the possibility of neuroectodermal origin of SS. Moreover, we identified a set of genes that divided SS cases into two putative subclasses, a feature that may shed light on novel biological aspects of SS in addition to those having to do with epithelial differentiation. These data have provided clues for understanding the origin and tumorigenesis of SS.
Extending Interval from Seventeen to Nineteen Days in the Melengestrol Acetate - Prostaglandin Estrous Synchronization Program for Heifers (2000)

Two experiments were conducted to determine whether extending the interval between removal of melengestrol acetate (MGA) from feed and injection of prostaglandin F2α (PGF) from 17 to 19 d would affect synchronization of estrus, conception, and pregnancy rates of beef heifers. In both experiments, heifers were fed MGA for 14 d, and PGF was given at either 17 or 19 d after cessation of MGA feeding. Heifers were observed for estrus and artificially inseminated for 5 d after PGF injection. In Exp. 1, 240 yearling heifers were randomly assigned to either a 17- or a 19-d treatment group according to estrous status and day of the estrous cycle. In Exp. 2, 1409 yearling heifers on a cooperating ranch were randomly assigned to the same two treatment groups without knowledge of estrous status. The PGF injection at 19 d (Exp. 1) caused a higher (P<0.05) percentage of heifers to exhibit estrus by 72 h after the injection compared with heifers receiving the injection at 17 d. A greater percentage (P<0.01) of heifers in the 19-d group were in the late luteal phase of the estrous cycle at the time of PGF injection compared with the heifers in the 17-d group, and pregnancy rates were higher for the heifers in the late luteal phase. In Exp. 2, heifers injected with PGF at 19 d after MGA had a greater (P<0.05) percentage in estrus (10%) during the 5-d breeding period, and had higher (P<0.05) pregnancy rates in 5 d (7.6%) and 50 d of breeding (5.5%), compared with heifers injected with PGF 17 d after withdrawal of MGA. These results indicate that the PGF injection given at 19 d after removal of MGA from the diet increases synchronized estrous response and results in higher pregnancy rates in heifers compared with the 17-d injection treatment.
Mutations in the 2-microns circle site-specific recombinase that abolish recombination without affecting substrate recognition. (1987)

The site-specific recombinase encoded by the yeast plasmid 2-microns circle (FLP) forms a transient covalent linkage with its substrate DNA via a tyrosine residue, which appears to be located near its COOH terminus. The homology of the COOH terminus of FLP with that of the Int family of recombinases suggests that tyrosine-343 of FLP could be involved in forming the DNA-protein bridge. We have mutated tyrosine-343 to a phenylalanine or serine. We demonstrate that the binding of each of the two mutant proteins to its substrate is indistinguishable from that of wild-type FLP. However, both mutant proteins are incapable of catalyzing strand cleavage and recombination.
Danazol Therapy for Chronic Immune-Mediated Thrombocytopenic Purpura in a Patient with Common Variable Immunodeficiency (1991)

We describe a patient with common variable immunodeficiency (CVI) and chronic immune-mediated thrombocytopenic purpura (ITP), refractory to treatment with corticosteroids, splenectomy, and intravenous immunoglobulin. He had a prompt response to danazol, and the platelet counts have been maintained in the normal range with low-dose, alternate-day, danazol therapy. This case provides evidence that danazol is effective in the treatment of chronic ITP in patients with immunodeficiency and indicates that some patients can be maintained on an alternate-day regimen.
Reversible Wettability of Photoresponsive Pyrimidine-Coated Surfaces (1999)

Thin coatings of photoresponsive, pyrimidine-terminated molecules, attached to gold or quartz substrates in contact with water, undergo dimerization and wettability changes when irradiated with UV light at 280 and 240 nm. Self-assembled monolayers of long chain thymine-terminated thiols give the largest, reversible photoinduced contact angle changes. The latter are caused by a decrease in surface charge as the thymine monomer dimerizes upon irradiation, a process which is accompanied by an increase in the acidity constant of the dimer. Uracil self-assembled monolayers photodimerize but do not photocleave; there is an irreversible change in contact angle. Spin-cast films of thymines give smaller contact angle changes, the maximum values corresponding to films which are composed of a mixture of crystalline and amorphous states.
eIF2B activator prevents neurological defects caused by a chronic integrated stress response (2019)

The integrated stress response (ISR) attenuates the rate of protein synthesis while inducing expression of stress proteins in cells. Various insults activate kinases that phosphorylate the GTPase eIF2 leading to inhibition of its exchange factor eIF2B. Vanishing White Matter (VWM) is a neurological disease caused by eIF2B mutations that, like phosphorylated eIF2, reduce its activity. We show that introduction of a human VWM mutation into mice leads to persistent ISR induction in the central nervous system. ISR activation precedes myelin loss and development of motor deficits. Remarkably, long-term treatment with a small molecule eIF2B activator, 2BAct, prevents all measures of pathology and normalizes the transcriptome and proteome of VWM mice. 2BAct stimulates the remaining activity of mutant eIF2B complex in vivo, abrogating the maladaptive stress response. Thus, 2BAct-like molecules may provide a promising therapeutic approach for VWM and provide relief from chronic ISR induction in a variety of disease contexts.
Combinatorial efficacy of anti-CS1 monoclonal antibody elotuzumab (HuLuc63) and bortezomib against multiple myeloma (2009)

Monoclonal antibody (mAb) therapy for multiple myeloma, a malignancy of plasma cells, has not been clinically efficacious in part due to a lack of appropriate targets. We recently reported that the cell surface glycoprotein CS1 (CD2 subset 1, CRACC, SLAMF7, CD319) was highly and universally expressed on myeloma cells while having restricted expression in normal tissues. Elotuzumab (formerly known as HuLuc63), a humanized mAb targeting CS1, is currently in a phase I clinical trial in relapsed/refractory myeloma. In this report we investigated whether the activity of elotuzumab could be enhanced by bortezomib, a reversible proteasome inhibitor with significant activity in myeloma. We first showed that elotuzumab could induce patient-derived myeloma cell killing within the bone marrow microenvironment using a SCID-hu mouse model. We next showed that CS1 gene and cell surface protein expression persisted on myeloma patient-derived plasma cells collected after bortezomib administration. In vitro bortezomib pretreatment of myeloma targets significantly enhanced elotuzumab-mediated antibody-dependent cell-mediated cytotoxicity, both for OPM2 myeloma cells using natural killer or peripheral blood mononuclear cells from healthy donors and for primary myeloma cells using autologous natural killer effector cells. In an OPM2 myeloma xenograft model, elotuzumab in combination with bortezomib exhibited significantly enhanced in vivo antitumor activity. These findings provide the rationale for a clinical trial combining elotuzumab and bortezomib, which will test the hypothesis that combining both drugs would result in enhanced immune lysis of myeloma by elotuzumab and direct targeting of myeloma by bortezomib.
Roles of globotriosyl- and galabiosylceramide in verotoxin binding and high affinity interferon receptor. (1987)

The cellular specificity of the Escherichia coli-derived verotoxin is of particular interest because of its extreme toxicity and high selectivity toward certain primate cells. The human Burkitt lymphoma cell line (Daudi) is highly susceptible to the cytotoxicity of verotoxin and contains large amounts of the verotoxin-binding glycolipids on its surface. A mutant selected from Daudi cells for verotoxin resistance was found to be deficient in the verotoxin-binding glycolipids, globotriosylceramide and galabiosylceramide, and failed to bind verotoxin to its surface; interestingly, these mutant cells were found to be cross-resistant to inhibition of growth by alpha-interferon. Mutant cells also lack the high affinity component of alpha-interferon binding. These observations suggest that, in addition to providing the functional cell-surface receptor for verotoxin, these glycolipids may also play a role in the modulation of the affinity of alpha-interferon for its membrane protein receptors.
Systemic cancer therapy with a tumor-selective vaccinia virus mutant lacking thymidine kinase and vaccinia growth factor genes. (2001)

We have demonstrated previously the oncolytic effects of a systemically delivered, replicating vaccinia virus. To enhance the tumor specificity of this vector, we have developed a combined thymidine kinase-deleted (TK-) and vaccinia growth factor-deleted (VGF-) vaccinia virus and investigated its properties in vitro and in vivo. The gene for enhanced green fluorescent protein (EGFP) was inserted into the TK locus of a VGF- vaccinia virus by homologous recombination creating a double-deleted mutant vaccinia virus (vvDD-GFP). Infection of resting and dividing NIH3T3 cells with vvDD-GFP yielded reduced viral recovery compared with wild-type (WT), TK-, or VGF- viruses from resting cultures but equivalent virus recovery from dividing cultures. Eight days after nude mice were injected i.p. with 10(7) plaque-forming units (pfu) of WT, TK-, VGF-, or vvDD-GFP vaccinia virus, tissues and tumor were harvested for viral titer determination. No virus was recovered from the brains of mice injected with vvDD-GFP compared with the other viruses, which ranged from 130 to 28,000 pfu/mg protein; however, equivalent amounts were recovered from tumor. There was no toxicity from vvDD-GFP because nude mice receiving 10(8) pfu of IP vvDD-GFP lived >100 days, whereas mice receiving WT, VGF-, or TK- virus had median survivals of only 6, 17, and 29 days, respectively. Similar results were seen when 10(9) pfu of vvDD-GFP were given. Nude mice bearing s.c. murine colon adenocarcinoma (MC38) had significant tumor regression after treatment with 10(9) pfu of systemic (i.p.) vvDD-GFP compared with control (mean tumor size, 180.71 +/- 35.26 mm(3) versus 2796.79 +/- 573.20 mm(3) 12 days after injection of virus). Our data demonstrate that a TK- and VGF- mutant vaccinia virus is significantly attenuated in resting cells in vitro and demonstrates tumor-specific replication in vivo. It is a promising vector for use in tumor-directed gene therapy, given its enhanced safety profile, tumor selectivity, and the oncolytic effects after systemic delivery.
The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies (2015)

The SWI/SNF multisubunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF-mutant tumors, including SMARCA4-deficient lung cancer; however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstruct the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic, and pharmacologic tools. We evaluate a selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterize its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF complex (e.g., lung, synovial sarcoma, leukemia, and rhabdoid tumors). We demonstrate that PFI-3 is a potent, cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor fails to display an antiproliferative phenotype. Mechanistically, the lack of pharmacologic efficacy is reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation, and target gene expression studies. Furthermore, using inducible RNAi and cDNA complementation (bromodomain- and ATPase-dead constructs), we unequivocally identify the ATPase domain, and not the bromodomain of SMARCA2, as the relevant therapeutic target with the catalytic activity suppressing defined transcriptional programs. Taken together, our complementary genetic and pharmacologic studies exemplify a general strategy for multidomain protein drug-target validation and in case of SMARCA2/4 highlight the potential for drugging the more challenging helicase/ATPase domain to deliver on the promise of synthetic-lethality therapy.
Improved queueing analysis of shared buffer switching networks (1993)

The authors describe several methods for analyzing the queueing behavior of switching networks with flow control and shared buffer switches. They compare the various methods on the basis of accuracy and computation speed, where the performance metric of most concern is the maximum throughput. The best of the methods accurately predicts throughput for multistage networks constructed from large switches (>or=8 ports).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>