gebhart/patrepeval huggingface dataset:
p16 (CDKN2/cyclin-dependent kinase-4 inhibitor/multiple tumor suppressor-1) gene is not altered in uterine cervical carcinomas or cell lines. (1996)

The p16 (CDKN2/cyclin-dependent kinase-4 inhibitor/multiple tumor suppressor-1) gene is frequently altered in cell lines and some types of cancers. To assess whether alterations of this gene are important in the pathogenesis of cervical cancer, we examined 41 primary tumors and 8 cell lines, using Southern blot and polymerase chain reaction-single strand conformation polymorphism analyses. We did not detect any deletions or mutations, which indicates that inactivation of the p16CDKN2 gene is not critical in the tumorigenesis of cervical cancer or in establishment of cervical cancer cell lines.
Cloning and characterization of a cDNA encoding a cellobiose dehydrogenase from the white rot fungus Phanerochaete chrysosporium (1995)

The cDNA of cellobiose dehydrogenase (CDH) from Phanerochaete chrysosporium has been cloned and sequenced. The 5' end was obtained by PCR amplification. The cDNA contains 2310 translated bases excluding the poly(A) tail. The deduced mature protein contains 770 amino acid residues and is preceded by a 18 residue long signal peptide. The regions of the amino acid sequence corresponding to the heme and FAD domains of CDH were identified as well as the nucleotide-binding motif, the disulfide pairing and a methionine residue chelating the heme iron. No homologous sequences were found for the heme domain, however, the FAD domain appears to be distantly related to the GMC oxidoreductase family.
Geldanamycin and 17-allylamino-17-demethoxygeldanamycin potentiate the in vitro and in vivo radiation response of cervical tumor cells via the heat shock protein 90-mediated intracellular signaling and cytotoxicity. (2003)

Ansamycin antibiotics inhibit function of the heat shock protein (HSP) 90, causing selective degradation of several intracellular proteins regulating such processes as proliferation, cell cycle regulation, and prosurvival signaling cascades. HSP90 has been identified previously as a molecular target for anticancer agents, including ionizing radiation (IR). Therefore, we hypothesized that the ansamycin geldanamycin and its 17-allylamino-17-demethoxy analog (17-AAG), which inhibit HSP90, would enhance tumor cell susceptibility to the cytotoxicity of IR. Treatment of two human cervical carcinoma cell lines (HeLa and SiHa) with geldanamycin and 17-AAG resulted in cytotoxicity and, when combined with IR, enhanced the radiation response, each effect with a temporal range from 6 to 48 h after drug exposure. In addition, mouse in vivo models using 17-AAG at clinically achievable concentrations yielded results that paralleled the in vitro radiosensitization studies of both single and fractioned courses of irradiation. The increase in IR-induced cell death appears to be attributable to a combination of both programmed and nonprogrammed cell death. We also measured total levels of several prosurvival and apoptotic signaling proteins. Akt1, extracellular signal-regulated kinase-1, Glut-1, HER-2/neu, Lyn, cAMP-dependent protein kinase, Raf-1, and vascular endothelial growth factor expression were down-regulated in 17-AAG-treated cells, identifying these factors as molecular markers and potential therapeutic targets. Finally, a series of immortalized and human papillomavirus-transformed cell lines were used to demonstrate that the radiosensitizing effects of 17-AAG were limited to transformed cells, suggesting a possible differential cytotoxic effect. This work shows that altered HSP90 function induces significant tumor cytotoxicity and radiosensitization, suggesting a potential therapeutic utility.
Molecular Signatures of Proliferation and Quiescence in Hematopoietic Stem Cells (2004)

Stem cells resident in adult tissues are principally quiescent, yet harbor enormous capacity for proliferation to achieve self renewal and to replenish their tissue constituents. Although a single hematopoietic stem cell (HSC) can generate sufficient primitive progeny to repopulate many recipients, little is known about the molecular mechanisms that maintain their potency or regulate their self renewal. Here we have examined the gene expression changes that occur over a time course when HSCs are induced to proliferate and return to quiescence in vivo. These data were compared to data representing differences between naturally proliferating fetal HSCs and their quiescent adult counterparts. Bioinformatic strategies were used to group time-ordered gene expression profiles generated from microarrays into signatures of quiescent and dividing stem cells. A novel method for calculating statistically significant enrichments in Gene Ontology groupings for our gene lists revealed elemental subgroups within the signatures that underlie HSC behavior, and allowed us to build a molecular model of the HSC activation cycle. Initially, quiescent HSCs evince a state of readiness. The proliferative signal induces a preparative state, which is followed by active proliferation divisible into early and late phases. Re-induction of quiescence involves changes in migratory molecule expression, prior to reestablishment of homeostasis. We also identified two genes that increase in both gene and protein expression during activation, and potentially represent new markers for proliferating stem cells. These data will be of use in attempts to recapitulate the HSC self renewal process for therapeutic expansion of stem cells, and our model may correlate with acquisition of self renewal characteristics by cancer stem cells.
Designing Ago2-specific siRNA/shRNA to Avoid Competition with Endogenous miRNAs (2014)

Relatively large amounts of transfected siRNA can compete for Ago proteins and thus compromise endogenous miRNA function, potentially leading to toxicities. Here, we show that shRNA can also perturb endogenous miRNA function similarly. More importantly, we also show that the problem can be solved by designing shRNAs in the context of pre-miR-451 structure with completely complementary stem, which significantly improves the Ago2 specificity. This shRNA was shown to be Ago2-specific, and maintain target-silencing ability while avoiding competition with endogenous miRNAs by not competing for Agos 1, 3, and 4. We conclude that modified pre-miR-451 structure provides a general platform to design shRNAs that significantly reduce perturbation of miRNA function.
The Biochemical and Cellular Basis of Cell Proliferation Assays That Use Tetrazolium Salts (1996)

The MTT assay is widely used in cell proliferation and cytotoxicity assays. Most cellular bioreduction of MTT is associated with enzymes of the endoplasmic reticulum and involves the reduced pyridine nucleotides NADH and, to a lesser extent, NADPH. Succinate is a weak electron donor for mitochondrial MTT reduction. Recently, new tetrazolium salt assays that use intermediate electron acceptors to facilitate reduction have been introduced. In this article, we compare the biochemical basis of reduction of MTT, XTT, and WST-1. Unlike MTT, XTT and WST-1 are efficiently reduced by NADH and NADPH in the absence of cells or enzymes, and their reduction involves superoxide. Cellular reduction of WST-1 occurs at the cell surface and also involves superoxide.
Treatment of Murine Colitis by Lactococcus lactis Secreting Interleukin-10 (2000)

The cytokine interleukin-10 (IL-10) has shown promise in clinical trials for treatment of inflammatory bowel disease (IBD). Using two mouse models, we show that the therapeutic dose of IL-10 can be reduced by localized delivery of a bacterium genetically engineered to secrete the cytokine. Intragastric administration of IL-10-secreting Lactococcus lactis caused a 50% reduction in colitis in mice treated with dextran sulfate sodium and prevented the onset of colitis in IL-10(-/-) mice. This approach may lead to better methods for cost-effective and long-term management of IBD in humans.
Sendai virus, an RNA virus with no risk of genomic integration, delivers CRISPR/Cas9 for efficient gene editing (2016)

The advent of RNA-guided endonuclease (RGEN)-mediated gene editing, specifically via CRISPR/Cas9, has spurred intensive efforts to improve the efficiency of both RGEN delivery and targeted mutagenesis. The major viral vectors in use for delivery of Cas9 and its associated guide RNA, lentiviral and adeno-associated viral systems, have the potential for undesired random integration into the host genome. Here, we repurpose Sendai virus, an RNA virus with no viral DNA phase and that replicates solely in the cytoplasm, as a delivery system for efficient Cas9-mediated gene editing. The high efficiency of Sendai virus infection resulted in high rates of on-target mutagenesis in cell lines (75-98% at various endogenous and transgenic loci) and primary human monocytes (88% at the ccr5 locus) in the absence of any selection. In conjunction with extensive former work on Sendai virus as a promising gene therapy vector that can infect a wide range of cell types including hematopoietic stem cells, this proof-of-concept study opens the door to using Sendai virus as well as other related paramyxoviruses as versatile and efficient tools for gene editing.
Diethylstilboestrol: the binding and effects of diethylstilboestrol upon the polymerisation and depolymerisation of purified microtubule protein in vitro (1985)

Diethylstilboestrol (DES) was shown to bind to purified microtubule (MT) protein and inhibit the binding of colchicine. The polymerisation and depolymerisation characteristics of MT protein in vitro were examined using spectrophotometry and electron microscopy. At high doses of DES the polymerisation of intact microtubules was inhibited, whilst at lower doses enhanced microtubule formation was observed. The lower doses of DES inhibit the depolymerisation of intact microtubules.
The 93-kilodalton protein of Borrelia burgdorferi: an immunodominant protoplasmic cylinder antigen (1992)

Using immunoblots, we identified proteins of Borrelia burgdorferi recognized by sera from 62 patients with either acute or chronic Lyme disease. In all groups studied, the 41-kDa flagellar protein and a relatively minor 93-kDa protein (p93) were the most commonly recognized antigens in patients with acute and chronic disease due to B. burgdorferi. A murine monoclonal antibody (MAb 181.1) was developed against p93, and the antigen was detected by immunoblot analysis in four European and American strains of B. burgdorferi. On two-dimensional gel electrophoresis, p93 had an apparent pI of 6.8. Immunoelectronmicroscopy with MAb 181.1 demonstrated that p93 is located within the protoplasmic cylinder compartment of the organism. The gene encoding p93 was retrieved from a phage expression library. The derived amino acid sequence of p93 confirmed chemical characterization of the antigen, including its amino-terminal peptide sequence. The derived amino acid sequence predicted it to be predominantly alpha helical. A prominent antigenic domain located at the carboxy portion of the protein was recognized by human and rabbit polyclonal antisera and human (MAb D4) and mouse (MAb 181.1) MAbs.
Effect of Patterned Surfaces of Adhesive Islands on the Shape, Cytoskeleton, Adhesion and Behaviour of Swiss Mouse 3T3 Fibroblasts (1987)

A pattern of circular islands of adhesive substratum can be used to control cell shape and behaviour. We have shown previously that the proportion of Swiss 3T3 cells that synthesize DNA varies with the area of the island to which they are attached, within the range 500-5000 microns2. In this paper we investigate the cytoskeleton and adhesions of cells on islands using a variety of techniques including phalloidin staining and interference reflection microscopy. Islands of area 2000 microns2 or less constrain cell shape, and cause focal contacts and actin microfilament bundles to accumulate in a circle at the margin. These changes are most obvious in islands of about 1000 microns2, in which a complete ring of adhesion is sometimes formed in the periphery of the cell. This peripheral distribution is less common in cells on even smaller islands, and the focal contacts become smaller and less numerous. It is not yet clear whether any of these structural changes are associated directly with the proliferative stimulus due to contact with the substratum. However, we expect that the use of patterned substrata will contribute to the study of how cell shape and structure regulate many cell functions.
Vaccinia Virus G9 Protein Is an Essential Component of the Poxvirus Entry-Fusion Complex (2006)

ABSTRACT The vaccinia virus G9R gene (VACWR087) encodes a protein of 340 amino acids with the following structural features that are conserved in all poxviruses: a site for N-terminal myristoylation, 14 cysteines, and a C-terminal transmembrane domain. Previous studies showed that G9 is one of eight proteins associated in a putative entry-fusion complex. Our attempt to isolate a mutant without the G9R gene was unsuccessful, suggesting that it is essential for virus replication. To further investigate its role, we constructed a recombinant vaccinia virus in which G9R is regulated by addition of an inducer. Induced G9 protein was associated with mature infectious virions and could be labeled with a membrane-impermeant biotinylation reagent, indicating surface exposure. Omission of inducer reduced the infectious-virus yield by about 1.5 logs; nevertheless, all stages of virus morphogenesis appeared normal and extracellular virions were present on the cell surface. Purified virions assembled without inducer had a specific infectivity of less than 5% of the normal level and a comparably small amount of G9, whereas their overall polypeptide composition, including other components of the entry-fusion complex, was similar to that of virions made in the presence of inducer or of wild-type virions. G9-deficient virions bound to cells, but penetration of cores into the cytoplasm and early viral RNA synthesis were barely detected, and cell-cell fusion was not triggered by low pH. Of the identified components of the multiprotein complex, G9 is the sixth that has been shown to be required for entry and membrane fusion.
G2 checkpoint abrogators as anticancer drugs (2004)

Many conventional anticancer treatments kill cells irrespective of whether they are normal or cancerous, so patients suffer from adverse side effects due to the loss of healthy cells. Anticancer insights derived from cell cycle research has given birth to the idea of cell cycle G2 checkpoint abrogation as a cancer cell specific therapy, based on the discovery that many cancer cells have a defective G1 checkpoint resulting in a dependence on the G2 checkpoint during cell replication. Damaged DNA in humans is detected by sensor proteins (such as hHUS1, hRAD1, hRAD9, hRAD17, and hRAD26) that transmit a signal via ATR to CHK1, or by another sensor complex (that may include gammaH2AX, 53BP1, BRCA1, NBS1, hMRE11, and hRAD50), the signal of which is relayed by ATM to CHK2. Most of the damage signals originated by the sensor complexes for the G2 checkpoint are conducted to CDC25C, the activity of which is modulated by 14-3-3. There are also less extensively explored pathways involving p53, p38, PCNA, HDAC, PP2A, PLK1, WEE1, CDC25B, and CDC25A. This review will examine the available inhibitors of CHK1 (Staurosporin, UCN-01, Go6976, SB-218078, ICP-1, and CEP-3891), both CHK1 and CHK2 (TAT-S216A and debromohymenialdisine), CHK2 (CEP-6367), WEE1 (PD0166285), and PP2A (okadaic acid and fostriecin), as well as the unknown checkpoint inhibitors 13-hydroxy-15-ozoapathin and the isogranulatimides. Among these targets, CHK1 seems to be the most suitable target for therapeutic G2 abrogation to date, although an unexplored target such as 14-3-3 or the strategy of targeting multiple proteins at once may be of interest in the future.
A case of Aeromonas hydrophila sepsis with generalized gas-formation and intravascular hemolysis. (1987)

患者は75才,男性.再生不良性貧血および胃癌の治療経過中,発熱,意識障害,高度の血管内溶血をきたし,発熱後約18時間で死亡した.剖検所見では広範な皮下気腫に加え,心,肝,腎,脾等の臓器に気泡形成と無数の桿菌の増殖を認め,心室からの血液培養によってAeromonas hydrophilaが同定された.本症例はAeromonas hydrophila敗血症としてはきわめてまれな病像を呈したと考えられ,文献的考察を加えて報告した.
Recombinant Antibody Technology (1995)

36:801-803. Smith, D.B., and K.S. Johnson. 1988. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene 67:31-40. Snapper, CM., and J.J. Mond. 1993. Towards a comprehensive view of immunoglobulin class switching. Immunol. Today 14:15-17. Snorasse, T., B. Flamand, G. De Becker, H. Bazin, F. Tielemans, K. Thielemans, J. Urbain, O. Leo, and M. Moser. 1992. Antigen-pulsed dendritic cells can efficiently induce an antibody response in vivo. J. Exp. Med. 175:15-21. Spira, G., A. Bargellesi, J.-L. Teillaud, and M.D. Scharff. 1984. The identification of monoclonal class switch variants by sib selection and an ELISA assay. J. Immunol. Methods 74:307-315. Spira, G., P. Gregor, H.L. Aguila, and M.D. Scharff. 1994. Clonal variants of hybridoma cells that switch isotype at a high frequency. Proc. Natl. Acad. Sci. USA 91:3423-3427. Spira, G., P.D. Gregor, and M.D. Scharff. 1993. The use of chemiluminescence and the ELISA spot assay to identify and enumerate rare immunoglobulin switch variants. J. Immunol. Methods 165:263-268. Stauber, N., U. Kihm, and K.C. McCullough. 1993. Rapid generation of monoclonal antibody-secreting hybridomas against African horse sickness virus by in vitro immunization and the fusion/cloning technique. J. Immunol. Methods 161:157-168. Steinmetz, I., F. Albrecht, S. Haubler, and B. Brenneke. 1994. Monoclonal IgA class-switch variants against bacterial surface antigens: Molecular forms and transport into murine respiratory secretions. Eur. J. Immunol. 24:2855-2862. Tarn, J.P. 1988. Synthetic peptide vaccine design: Synthesis and properties of a high-density multiple antigenic peptide system. Proc. Natl. Acad. Sci. USA 85:5409-5413. Tonegawa, S. 1983. Somatic generation of antibody diversity. Nature 302:575-581. Townsend, A., and H. Bodmer. 1989. Antigen recognition by class I-restricted T lymphoctyes. Annu. Rev. Immunol. 7:601-624. Unanue, E.R. 1984. Antigen-presenting function of the macrophage. Annu. Rev. Immunol. 2:395-428. Vahlsing, H.L., M.A. Yankauckas, M. Sawdey, S.H. Gromkowski, and M. Manthorpe. 1994. Immunization with plasmid DNA using a pneumatic gun. J. Immunol. Methods 175:11-22. Weigert, M.G., I.M. Cesari, and SJ. Yondovich. 1970. Variability in the lambda light chain sequences of mouse antibody. Nature 228:10451047. Williams, C.V., C.L. Stechmann, and S.C. McLoon. 1992. Subtractive immunization techniques for the production of monoclonal antibodies to rare antigens. BioTechniques 12:842-847. Wilson, I.A., J.B. Ghiara, and R.L. Stanfield. 1994. Structure of anti-peptide antibody complexes. Res. Immunol. 145:73-78.
Cloning and functional expression of a human eosinophil CC chemokine receptor. (1995)

Vol. 270, p. 16491 Page 16493, Figs. 3 and 4: The cells whose properties were described in these figures were not transfected with the CC CKR3 cDNA that we reported, but were inadvertently transfected instead with another CC chemokine receptor cDNA designated CC CKR5. Thus, the agonists for CC CKR5 are MIP-1α, MIP-1β, and RANTES (C. Combadiere, S. K. Ahuja, H. L. Tiffany, and P. M. Murphy, submitted for publication). We have confirmed the DNA and deduced protein sequences, genomic restriction fragments, and RNA distribution originally assigned to CC CKR3. When calcium mobilization was measured in transfected human embryonic kidney 293 cells, human eotaxin, an eosinophil-selective CC chemokine, was a potent agonist for CC CKR3, whereas MIP-1α, MIP-1β, and RANTES were inactive (M. Kitaura, T. Nakajima, T. Imai, S. Harada, C. Combadiere, H. L. Tiffany, P. M. Murphy, and O. Yoshie, submitted for publication). We regret the confusion caused by this error.
All-Atom Model for Stabilization of α-Helical Structure in Peptides by Hydrocarbon Staples (2009)

Recent work has shown that the incorporation of an all-hydrocarbon "staple" into peptides can greatly increase their alpha-helix propensity, leading to an improvement in pharmaceutical properties such as proteolytic stability, receptor affinity, and cell permeability. Stapled peptides thus show promise as a new class of drugs capable of accessing intractable targets such as those that engage in intracellular protein-protein interactions. The extent of alpha-helix stabilization provided by stapling has proven to be substantially context dependent, requiring cumbersome screening to identify the optimal site for staple incorporation. In certain cases, a staple encompassing one turn of the helix (attached at residues i and i+4) furnishes greater helix stabilization than one encompassing two turns (i,i+7 staple), which runs counter to expectation based on polymer theory. These findings highlight the need for a more thorough understanding of the forces that underlie helix stabilization by hydrocarbon staples. Here we report all-atom Monte Carlo folding simulations comparing unmodified peptides derived from RNase A and BID BH3 with various i,i+4 and i,i+7 stapled versions thereof. The results of these simulations were found to be in quantitative agreement with experimentally determined helix propensities. We also discovered that staples can stabilize quasi-stable decoy conformations, and that the removal of these states plays a major role in determining the helix stability of stapled peptides. Finally, we critically investigate why our method works, exposing the underlying physical forces that stabilize stapled peptides.
Contrast-based assist feature optimization (2002)

By defining contrast as the maximum image-log-slope (ILS), we propose a novel method to optimize assist feature sites and locations. We present results that indicate that an ILS optimization at best focus provides enough information to arrive at a solution that improves the depth of focus of the design. Sub-resolution assist features (SRAF) are inserted using a rule-based approach that depends on the equivalent contrast of the original design. Later, an optical rule check (ORC) is performed to identify the regions in which the contrast of the main features is below a certain threshold. After such regions have been properly identified and selected, the neighboring edges are subjected to a sensitivity analysis that returns a contrast matrix which can be later compressed in a global contrast cost function. New positions of the assist feature edges are later evaluated and the assist features are modified accordingly. By following these steps, it is possible to alter: location, width and shape of the assist features in such a way that there is an overall improvement of the main feature contrast. A complete and integrated approach should be able to accept restrictions in the printability of assist features. In order to eliminate errors coming from the cross interactions between the globally optimized assist features and the original design, we incorporate a local clean up procedure that preserves the global validity of the current assist feature rule while improving the local behavior of the original edges. In this fashion, killer defects due to inter-rule dependencies are avoided.
Dual-target Inhibition of HIV-1 in Vitro by Means of an Adeno-Associated Virus Antisense Vector (1992)

An adeno-associated virus vector encoding an antisense RNA was used to transduce stable intracellular resistance to human immunodeficiency virus-1 (HIV-1) in human hemopoietic and non-hemopoietic cell lines. The antisense targets are present in all HIV-1 transcripts and include the TAR sequence, which is critical for transcription and virus replication, and the polyadenylation signal. Cell lines expressing antisense RNA showed up to 95 percent inhibition of gene expression directed by the HIV-1 long terminal repeat and greater than 99 percent reduction in infectious HIV-1 production, with no detectable cellular toxicity. Because of their efficient transcription and inability to recombine with HIV-1, adeno-associated virus vectors represent a promising form of anti-retroviral gene therapy.