gebhart/patrepeval huggingface dataset:
Maintenance on extracellular matrix and expression of heparanase activity by human ovarian carcinoma cells from biopsy specimens (1990)

A routine procedure has been developed for the isolation and maintenance in culture of human ovarian carcinoma cells derived from biopsy specimens. Cell attachment, plating efficiency and initial outgrowth were greatly improved by seeding the cells on a basement-membrane-like extracellular matrix (ECM) deposited by cultured corneal endothelial cells. These effects were most significant in serum-free conditions which markedly reduced the rate of cell attachment and growth on regular tissue culture plastic. In 60-80% of the cases and regardless of the patient's age, cells cultured on ECM in the absence of serum divided actively and formed a tightly packed epithelial cell monolayer. Fibroblast overgrowth and cell detachment often occurred on ECM in the presence of serum. Incubation of the human ovarian carcinoma cells with sulfate-labelled ECM, resulted in the release of heparan sulfate degradation fragments, 4- to 7-fold smaller than intact heparan sulfate side chains. This degradation was brought about by endoglycosidase (heparanase) activity expressed to a higher extent by cells that were first maintained in primary cultures as compared with cell aggregates taken directly from the biopsy specimen. In most cases, cells derived from metastatic tumors expressed a higher heparanase activity than cells from the primary ovarian tumor. This result corroborates previous studies, performed with cell lines, on the possible involvement of heparanase in tumor cell invasion and metastasis.
Human influenza virus hemagglutinin is expressed in monkey cells using simian virus 40 vectors. (1982)

We have cloned and expressed the hemagglutinin (HA) gene of a human influenza virus (A/WSN/33) in monkey kidney cells by linking it to deleted simian virus 40 (SV40) genomes that contain the entire early gene region, the origin of replication, and late leader sequences. The HA gene (1775 base pairs long) was originally inserted by the dG . dC tailing technique into the multicopy plasmid of Escherichia coli, pBR322, using cDNA made from viral RNA. The cloned gene was further modified by treatment with nuclease Bal 31 to remove the dG . dC tails and some of the untranslated sequences and recloned in E. coli after addition of BamHI restriction endonuclease linkers. A number of SV40 and HA recombinants (SV--HA) were constructed by inserting recloned HA DNA into the late gene region of SV40. The SV--HA recombinants, when complemented in a lytic infection of monkey cells by the helper function of SV40 early deletion mutants expressed influenza HA as detected by immunofluorescence and immunoprecipitation of in vivo-labeled proteins using either heterogeneous anti-influenza rabbit antibodies or monoclonal antibodies against HA. Furthermore, the WSN HA expressed by the SV--HA recombinants was also glycosylated and possessed the same molecular weight (approximately 70,000) as the uncleaved HA of WSN virus in monkey cells.
[Immunotherapy and cancer: the role of monoclonal antibodies]. (1989)

Monoclonal antibodies, produced in vitro from hybridoma supernatants, may be administered to cancer patients either directly or after coupling to an anticancer agent (immunoconjugates). Monoclonal antibodies concentrate in tumor site, where they initiate an anti-tumor effect, either by activation of the patient's immune system or by the cytotoxic agent which is present at high concentration within the tumor, while systemic concentrations of this agent remain low. Monoclonal antibodies which are radiolabelled also allow the immunoscintigraphic study of the immunoconjugates' diffusion within the body. Given certain precautions of administration, the clinical and biological tolerance of this type of treatment is satisfactory, most of the side effects correspond to an allergic response to the murine antibodies used. Clinical studies performed in patients with leukemias have demonstrated a significant antitumor effect although this effect is transitory. Studies performed on small series of patients with solid tumors (gastrointestinal neoplasms, melanoma, leptomeningeal localizations, ovarian peritoneal carcinosis) have shown a few cases of major responses and/or complete remissions having lasted up to periods of many months. These studies as well as the perspectives for the development of this type of therapy are presented and discussed.
Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM‐3 by molecular dynamics simulations (1995)

Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3. Each simulation was 200 ps in length and included a 10 A layer of explicit solvent. The simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-averaged structures are to each other. In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations. The mouth of the substrate binding pocket is significantly more mobile in the simulation of molecule 2 than in the simulation of molecule 1. For molecule 1, the width of the mouth is only slightly larger than its X-ray value of 8.7 A and undergoes fluctuations of about 1 A. However, in molecule 2, the mouth of the substrate binding pocket is dramatically more open in the time-average molecular dynamics structure (14.7 A) than in the X-ray structure (10.9 A). Furthermore, this region of the protein undergoes large amplitude motions during the trajectory that are not seen in the trajectory of molecule 1, repeatedly opening and closing up to 7 A. Presumably, the binding of different substrates will induce the mouth region to adopt different conformations from within the wide range of structures that are accessible.
Differential responsiveness of myc- and ras-transfected cells to growth factors: selective stimulation of myc-transfected cells by epidermal growth factor. (1986)

To identify functional relationships between oncogenes and growth factors, we compared the effects of transfected myc and ras oncogenes on the responsiveness of Fischer rat 3T3 cells to three growth factors: epidermal growth factor (EGF), platelet-derived growth factor (PDGF), and transforming growth factor-beta (TGF-beta). Control cells did not grow in soft agar under any conditions. ras-Transfected cells grew in soft agar under all conditions tested and were insensitive to the stimulatory effects of exogenous growth factors. These cells secreted elevated levels of both EGF-like factors and TGF-beta, suggesting that the lack of responsiveness of these cells to exogenous growth factors arose from autocrine stimulation. myc-Transfected cells displayed conditional anchorage-independent growth: they formed numerous colonies in soft agar in the presence of EGF but relatively few colonies in the presence of PDGF or TGF-beta. Secretion of EGF-like factors and TGF-beta by these cells was not elevated above that of control cells. These results suggest a model for the mechanism of cooperation between myc and ras oncogenes in which ras-like genes induce growth factor production, while myc-like genes increase the responsiveness of cells to these factors.
Characterization of the tre Locus and Analysis of Trehalose Cryoprotection in Lactobacillus acidophilus NCFM (2006)

Freezing and lyophilization are common methods used for preservation and storage of microorganisms during the production of concentrated starter cultures destined for industrial fermentations or product formulations. The compatible solute trehalose has been widely reported to protect bacterial, yeast and animal cells against a variety of environmental stresses, particularly freezing and dehydration. Analysis of the Lactobacillus acidophilus NCFM genome revealed a putative trehalose utilization locus consisting of a transcriptional regulator, treR; a trehalose phosphoenolpyruvate transferase system (PTS) transporter, treB; and a trehalose-6-phosphate hydrolase, treC. The objective of this study was to characterize the tre locus in L. acidophilus and determine whether or not intracellular uptake of trehalose contributes to cryoprotection. Cells subjected to repeated freezing and thawing cycles were monitored for survival in the presence of various concentrations of trehalose. At 20% trehalose a 2-log increase in survival was observed. The trehalose PTS transporter and trehalose hydrolase were disrupted by targeted plasmid insertions. The resulting mutants were unable to grow on trehalose, indicating that both trehalose transport into the cell via a PTS and hydrolysis via a trehalose-6-phosphate hydrolase were necessary for trehalose fermentation. Trehalose uptake was found to be significantly reduced in the transporter mutant but unaffected in the hydrolase mutant. Additionally, the cryoprotective effect of trehalose was reduced in these mutants, suggesting that intracellular transport and hydrolysis contribute significantly to cryoprotection.
Characterization of sites for tyrosine phosphorylation in the transforming protein of Rous sarcoma virus (pp60v-src) and its normal cellular homologue (pp60c-src). (1981)

The transforming protein of Rous sarcoma virus (pp60v-src) and its normal cellular homologue (pp60c-src) appear to be protein kinases that phosphorylate tyrosine in a variety of protein substrates. In addition, pp60v-src and pp60-c-src are themselves phosphorylated on serine and tyrosine. It is likely that these phosphorylations serve to regulate the function(s) of pp60v-src and pp60c-src. We have therefore characterized the sites of tyrosine phosphorylation in the two proteins. Tyrosine phosphorylation of pp60v-src in infected cells occurs mainly (if not entirely) at residue 419 in the deduced amino acid sequence of the protein. Surrounding this residue is the sequence Leu-Ile-Glu-Asp-Asn-Glu-Tyr(P)-Thr-Ala-Arg. This peptide is distinguished by the fact that three out of the four amino acids that precede the phosphorylated tyrosine are acidic in nature. These results define what may prove to be a widely used site for tyrosine phosphorylation in the regulation of cellular function. The same site was phosphorylated when partially purified pp60v-src was used in a phosphotransfer reaction in vitro. The results with pp60c-src were more complex. The site of tyrosine phosphorylation in vitro appeared to be the same as that found in pp60v-src. By contrast, phosphorylation of pp60c-src in vivo apparently occurred at a different, and currently unidentified, tyrosine residue. It is therefore possible that pp60v-src and pp60c-src respond differently to regulatory influences in the intact cell.
Healable thermoset polymer composite embedded with stimuli-responsive fibres (2012)

Severe wounds in biological systems such as human skin cannot heal themselves, unless they are first stitched together. Healing of macroscopic damage in thermoset polymer composites faces a similar challenge. Stimuli-responsive shape-changing polymeric fibres with outstanding mechanical properties embedded in polymers may be able to close macro-cracks automatically upon stimulation such as heating. Here, a stimuli-responsive fibre (SRF) with outstanding mechanical properties and supercontraction capability was fabricated for the purpose of healing macroscopic damage. The SRFs and thermoplastic particles (TPs) were incorporated into regular thermosetting epoxy for repeatedly healing macroscopic damages. The system works by mimicking self-healing of biological systems such as human skin, close (stitch) then heal, i.e. close the macroscopic crack through the thermal-induced supercontraction of the SRFs, and bond the closed crack through melting and diffusing of TPs at the crack interface. The healing efficiency determined using tapered double-cantilever beam specimens was 94 per cent. The self-healing process was reasonably repeatable.
Aromatic vs Aliphatic C−H Bond Activation by Rhodium(I) as a Function of Agostic Interactions:  Catalytic H/D Exchange between Olefins and Methanol or Water (2003)

The aryl-PC type ligand 3, benzyl(di-tert-butyl)phosphane, reacts with [Rh(coe)(2)(solv)(n)()]BF(4) (coe = cyclooctene, solv = solvent), producing the C-H activated complexes 4a-c (solv = (a). acetone, (b). THF, (c). methanol). Complexes 4a-c undergo reversible arene C-H activation (observed by NMR spin saturation transfer experiments, SST) and H/D exchange into the hydride and aryl ortho-H with ROD (R = D, Me). They also promote catalytic H/D exchange into the vinylic C-H bond of olefins, with deuterated methanol or water utilized as D-donors. Unexpectedly, complex 2, based on the benzyl-PC type ligand 1 (analogous to 3), di-tert-butyl(2,4,6-trimethylbenzyl)phosphane, shows a very different reversible C-H activation pattern as observed by SST. It is not active in H/D exchange with ROD and in catalytic H/D exchange with olefins. To clarify our observations regarding C-H activation/reductive elimination in both PC-Rh systems, density functional theory (DFT) calculations were performed. Both nucleophilic (oxidative addition) and electrophilic (H/D exchange) C-H activation proceed through eta(2)-C,H agostic intermediates. In the aryl-PC system the agostic interaction causes C-H bond acidity sufficient for the H/D exchange with water or methanol, which is not the case in the benzyl PC-Rh system. In the latter system the C-H coordination pattern of the methyl controls the reversible C-H oxidative addition leading to energetically different C-H activation processes, in accordance with the experimental observations.
Identification ofListeria monocytogenesGenes Contributing to Intracellular Replication by Expression Profiling and Mutant Screening (2005)

A successful transition of Listeria monocytogenes from the extracellular to the intracellular environment requires a precise adaptation response to conditions encountered in the host milieu. Although many key steps in the intracellular lifestyle of this gram-positive pathogen are well characterized, our knowledge about the factors required for cytosolic proliferation is still rather limited. We used DNA microarray and real-time reverse transcriptase PCR analyses to investigate the transcriptional profile of intracellular L. monocytogenes following epithelial cell infection. Approximately 19% of the genes were differentially expressed by at least 1.6-fold relative to their level of transcription when grown in brain heart infusion medium, including genes encoding transporter proteins essential for the uptake of carbon and nitrogen sources, factors involved in anabolic pathways, stress proteins, transcriptional regulators, and proteins of unknown function. To validate the biological relevance of the intracellular gene expression profile, a random mutant library of L. monocytogenes was constructed by insertion-duplication mutagenesis and screened for intracellular-growth-deficient strains. By interfacing the results of both approaches, we provide evidence that L. monocytogenes can use alternative carbon sources like phosphorylated glucose and glycerol and nitrogen sources like ethanolamine during replication in epithelial cells and that the pentose phosphate cycle, but not glycolysis, is the predominant pathway of sugar metabolism in the host environment. Additionally, we show that the synthesis of arginine, isoleucine, leucine, and valine, as well as a species-specific phosphoenolpyruvate-dependent phosphotransferase system, play a major role in the intracellular growth of L. monocytogenes.
The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA (1985)

M13 RF IV DNA may be prepared in vitro to contain phosphorothioate-modified internucleotidic linkages in the (-)strand only. Certain restriction enzymes react with this modified DNA to hydrolyze the (+)strand exclusively when a phosphorothioate linkage occurs at the normal cleavage point in the (-)strand. The reaction of Pvu I with M13mp2 RF IV DNA containing dCMPS residues in the (-)strand is of this type, and is exploited to allow subsequent digestion with exonuclease III of a portion of the (+)strand opposite different mutagenic mismatched oligonucleotide primers. Two methods are described by which this approach has been used to produce mutations in M13mp2 phage DNA with high efficiency as a result of simple and rapid in vitro manipulations. Plaques containing mutant phage in a genetically-pure form are obtained at a frequency of 40-66%, allowing their characterisation directly by sequence analysis without prior screening and plaque purification. The wide applicability of this approach is discussed.
Limiting dilution analysis of lymphokine-activated killer cell precursor frequencies in peripheral blood lymphocytes of cancer patients receiving interleukin-2 therapy. (1990)

Eleven patients receiving weekly cycles of therapy with recombinant interleukin-2 (IL-2) were evaluated with a sensitive limiting dilution analysis to determine lymphokine-activated killer (LAK) cell precursor frequencies in peripheral blood lymphocytes. An increase in LAK precursor frequency above baseline was suggested by day 6 of this protocol and was clearly significant by day 20, indicating an expansion of the circulating precursor pool results from in vivo IL-2 administration. Correlations were not significant between LAK precursor frequency during IL-2 therapy and the total number of circulating lymphocytes, the percentage of CD56+ lymphocytes, IL-2 proliferative responses, or LAK activity of peripheral blood lymphocytes, indicating that the precursor frequency identification based on functional testing of individual cells is not accurately reflected by these analyses of heterogeneous bulk populations. Selective cell depletion analyses revealed that the majority of LAK precursors after in vivo IL-2 therapy were cells with the natural killer phenotype. Analysis of LAK precursors may help define the in vivo IL-2 administration, alone or in combination with other hematopoietic or immunodifferentiative cytokines, necessary to further augment in vivo effector cell numbers and activity for patients with cancer.
Effective Stabilization and Delivery of siRNA: Reversible siRNA−Phospholipid Conjugate in Nanosized Mixed Polymeric Micelles (2010)

siRNA is a powerful tool to control cellular processes at the post-transcriptional level. However, its therapeutic potential is limited because of low stability in biological fluids and the lack of simple and efficient delivery systems. Chemical modification of siRNA could be used to increase its intracellular delivery, but may affect its specific activity. To overcome these obstacles, we suggest a simple and effective system capable of stabilization, delivery, and subsequent release of free active siRNA within cells. With this in mind, we reversibly modified the double-stranded GFP-siRNA with a phosphothioethanol (PE) portion via the reducible disulfide bond and incorporated the resulting siRNA-S-S-PE conjugate in nanosized PEG-PE micelles. In the mixed siRNA-S-S-PE/PEG-PE micelles obtained, siRNA was well-protected against degradation by nucleases for at least 24 h, and was released easily from these nanoparticles in free form in the presence of glutathione (GSH) at a concentration mimicking the intracellular levels. In GFP-C166 endothelial cells, mixed GFP-siRNA-S-S-PE/PEG-PE micelles down-regulate the GFP production 50-fold more effectively than free siRNA. In addition, siRNA-containing micelles showed none of the cytotoxic side effects typical for siRNA delivery systems that are based on electrostatic association of siRNA with cationic carriers. Thus, a reversible siRNA-phospholipid conjugate formulated into mixed micelles with PEG-PE can be an effective, nontoxic system for stabilization and delivery of siRNA.
Selective Histone Deacetylase 6 Inhibitors Bearing Substituted Urea Linkers Inhibit Melanoma Cell Growth (2012)

The incidence of malignant melanoma has dramatically increased in recent years thus requiring the need for improved therapeutic strategies. In our efforts to design selective histone deactylase inhibitors (HDACI), we discovered that the aryl urea 1 is a modestly potent yet nonselective inhibitor. Structure-activity relationship studies revealed that adding substituents to the nitrogen atom of the urea so as to generate compounds bearing a branched linker group results in increased potency and selectivity for HDAC6. Compound 5 g shows low nanomolar inhibitory potency against HDAC6 and a selectivity of ∼600-fold relative to the inhibition of HDAC1. These HDACIs were evaluated for their ability to inhibit the growth of B16 melanoma cells with the most potent and selective HDAC6I being found to decrease tumor cell growth. To the best of our knowledge, this work constitutes the first report of HDAC6-selective inhibitors that possess antiproliferative effects against melanoma cells.
Adenovirus-mediated p16/CDKN2 gene transfer induces growth arrest and modifies the transformed phenotype of glioma cells. (1996)

The p16 (MTS1/CDKN2) gene localized at the 9p21 chromosomal region encodes for a cell cycle inhibitor protein and is altered in many human cancers. The frequency of p16 alterations in gliomas exceeds 50%. To restore the missing wild-type p16 gene efficiently in glioma cells an adenovirus vector carrying the full length coding sequence of the wild-type p16 cDNA, Ad5RSV-p16, was constructed. Three human glioma cell lines, U251 MG, U-87 MG and D54 MG, that did not express endogenous p16/CDKN2 gene and were easily infected with adenovirus vectors were selected for these experiments. Introduction of the Ad5RSV-p16 in these malignant glioma cell lines directed the biosynthesis of functional p16 protein in the majority of the exposed cells, significantly inhibited cell growth, influenced cell morphology and modified the transformed phenotype of cells including the ability to form colonies in soft agar. Flow cytometric studies revealed that the majority of the Ad5RSV-p16 infected glioma cells were arrested in the G0-G1 phases of the cell cycle. These results suggest that p16/CDKN2 inactivation is a significant factor in the genesis and progression of gliomas and that the restoration of the wild-type p16 protein could have clinical and therapeutic utility.