gebhart/patrepeval huggingface dataset:
Adaptation to supraphysiologic levels of insulin gene expression in transgenic mice: evidence for the importance of posttranscriptional regulation. (1993)

Insulin production was studied in transgenic mice expressing the human insulin gene under the control of its own promoter. Glucose homeostasis during a 48-h fast was similar in control and transgenic mice, with comparable levels of serum immunoreactive insulin. Northern blot and primer extension analyses indicated that more than twice as much insulin mRNA is present in pancreata from transgenic mice. Primer extension analysis using oligonucleotides specific for mouse insulins I and II or for human insulin, showed that the excess insulin mRNA was due solely to expression of the foreign, human insulin gene. The ratio of mRNA for mouse insulin I and II was unaffected by coexpression of human insulin. There were coordinate changes in the levels of all three mRNA during the 48-h fast, or after a 24-h fast followed by 24-h refeed. Despite the supraphysiologic levels of insulin mRNA in the transgenic mice, their pancreatic content of immunoreactive insulin was not significantly different from controls. The comparison of the relative levels of human and mouse insulin mRNAs with their peptide counterparts (separated by HPLC) indicates that the efficiency of insulin production from mouse insulin mRNA is greater than that from human, stressing the importance of posttranscriptional regulatory events in the overall maintenance of pancreatic insulin content.
Targeted delivery to PEPT1-overexpressing cells: Acidic, basic, and secondary floxuridine amino acid ester prodrugs (2005)

Floxuridine is a clinically proven anticancer agent in the treatment of metastatic colon carcinomas and hepatic metastases. However, prodrug strategies may be necessary to improve its physiochemical properties and selectivity and to reduce undesirable toxicity effects. Previous studies with amino acid ester prodrugs of nucleoside drugs targeted to the PEPT1 transporter coupled with recent findings of the functional expression of the PEPT1 oligopeptide transporter in pancreatic adenocarcinoma cell lines suggest the potential of PEPT1 as therapeutic targets for cancer treatment. In this report, we show the feasibility of achieving enhanced transport and selective antiproliferative action of amino acid ester prodrugs of floxuridine in cell systems overexpressing PEPT1. All prodrugs exhibited affinity for PEPT1 (IC50, 1.1-2.3 mmol/L). However, only the prolyl and lysyl prodrugs exhibited enhanced uptake (2- to 8-fold) with HeLa/PEPT1 cells compared with HeLa cells, suggesting that the aspartyl prodrugs are PEPT1 inhibitors. The selective growth inhibition of Madine-Darby canine kidney (MDCK)/PEPT1 cells over MDCK cells by the prodrugs was consistent with the extent of their PEPT1-mediated transport. All ester prodrugs hydrolyzed to floxuridine fastest in Caco-2 cell and MDCK homogenates and slower in human plasma and were most chemically stable in pH 6.0 buffer. Prolyl and lysyl prodrugs were relatively less stable compared with aspartyl prodrugs in buffers and in cell homogenates. The results suggest that optimal design for targeted delivery would be possible by combining both stability and transport characteristics afforded by the promoiety.
Protection of Power Systems with Distributed Generation: State of the Art (2005)

The integration of distributed sources into existing networks brings up sev-eral technical, economical and regulatory questions. In terms of physical integration, protection is one of the major issues. Therefore new protec-tion schemes for both distributed generators (DG) and utility distribution networks have been developed in the recent years, but there are still open questions. This document is the result of a literature study and intends to give an overview of issues and current state concerning protection of DG. The ¯rst part gives a basic introduction to distributed generation and power system protection. In section 2 protection issues concerning DG are outlined, then the current practice is described in section 3. In section 4 some new approaches in this ¯eld are reported and ¯nally section 5 concludes with an
Accelerated Color Change of Gold Nanoparticles Assembled by DNAzymes for Simple and Fast Colorimetric Pb2+ Detection (2004)

The combination of high metal selectivity of DNAzymes with the strong distance-dependent optical properties of metallic nanoparticles has presented considerable opportunities for designing colorimetric sensors for metal ions. We previously communicated a design for a colorimetric lead sensor based on the assembly of gold nanoparticles by a Pb(2+)-dependent DNAzyme. However, heating to 50 degrees C followed by a cooling process of approximately 2 h was required to observe the color change. Herein we report a new improved design that allows fast (<10 min) detection of Pb(2+) at ambient temperature. This improvement of sensor performance is a result of detailed studies of the DNAzyme and nanoparticles, which identified "tail-to-tail" nanoparticle alignment, and large (42 nm diameter) nanoparticle size as the major determining factors in allowing fast color changes. The optimal conditions for other factors such as temperature (35 degrees C) and concentrations of the DNAzyme (2 microM), its substrate (3 nM), and NaCl (300 mM) have also been determined. These results demonstrate that fundamental understanding of the DNAzyme biochemistry and nanoparticle science can lead to dramatically improved colorimetric sensors.
Controlling gene expression in plants using synthetic zinc finger transcription factors (2002)

Synthetic zinc finger proteins can be fused to transcriptional regulatory domains to create artificial transcription factors that modulate the expression of a specific target gene. Recent studies have demonstrated that synthetic zinc finger domains can be constructed to bind DNA sequences with a high degree of specificity. To devise a general strategy for controlling plant gene expression with artificial transcription factors, a rapid transient assay was developed to test the regulatory activity of synthetic zinc finger transcription factors (effectors) on target plasmids (reporters) in plant cells. Effective activation was demonstrated with zinc finger proteins fused to a derivative of the VP16 activation domain. The mSin3 interaction domain (SID) of the human MAD1 protein provided moderate repression of target reporters. Unlike many naturally occurring transcription factors, these synthetic effectors exhibit a strong dependence on binding site position. Reporter genes that are stably integrated into plant cells responded similarly to transiently transfected reporter plasmids, verifying that this assay accurately reflects the behavior of these transcription factors on an endogenous target within the context of chromosomal DNA. These results provide evidence that synthetic zinc finger proteins can be used to manipulate the expression of endogenous genes in plants.
Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi’s sarcoma‐associated herpesvirus (2009)

The Kaposi's sarcoma-associated herpesvirus protein SOX (shut off and exonuclease) and its Epstein-Barr virus homolog, BGLF5, are active during the early lytic phase and belong to the alkaline nuclease family. Both proteins have been shown to be bifunctional, being responsible for DNA maturation as well as host shutoff at the mRNA level. We present the crystal structure of SOX determined at 1.85 A resolution. By modeling DNA binding, we have identified catalytic residues that explain the preferred 5'-exonuclease activity of the alkaline nucleases. The presence of a crevice suitable for binding duplex DNA supports a role for herpes alkaline nucleases in recombination events preceding packaging of viral DNA. Direct interaction with dsDNA is supported by oligonucleotide binding data. Mutations specifically affecting host shutoff map to a surface region of the N-terminal domain, implying an essential role in protein-protein interactions, and link the RNase activity of the enzyme to mRNA degradation pathways.
Conduction- and valence-band offsets at the hydrogenated amorphous silicon-carbon/crystalline silicon interface via capacitance techniques (1996)

Using a combination of junction capacitance techniques, we measure both the a-${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{C}}_{\mathit{x}}$:H/c-Si conduction- and valence-band offsets in a Schottky diode heterostructure sample composed of a sub-\ensuremath{\mu}m-thick layer of intrinsic hydrogenated amorphous silicon-carbon (a-${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{C}}_{\mathit{x}}$:H) deposited on an n-type crystalline silicon (c-Si) substrate. A series of these heterostructure samples with amorphous optical gaps ranging from 1.75 to 2.1 eV were fabricated using plasma-enhanced chemical-vapor deposition. First, a thermally activated capacitance step due to the response of defects at the amorphous/crystalline interface is evident in capacitance vs temperature (C-T) scans taken on all these samples. The bias dependence of this step's activation energy provides a direct measure of the a-${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{C}}_{\mathit{x}}$:H/c-Si interface potential as a function of the c-Si depletion width in each heterostructure. By application of Poisson's equation, we find that the a-${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{C}}_{\mathit{x}}$:H/c-Si conduction-band offset \ensuremath{\Delta}${\mathit{E}}_{\mathit{C}}$ increases as the optical gap widens and varies in the range of 0.00--0.20 for the samples investigated. Second, while under reverse bias at low temperature, we optically pulsed each sample with c-Si band-gap light to create trapped holes at the a-${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{C}}_{\mathit{x}}$:H/c-Si valence-band offset \ensuremath{\Delta}${\mathit{E}}_{\mathit{V}}$. By noting the threshold for the subsequent optical release of these trapped holes by subband-gap light, we found that \ensuremath{\Delta}${\mathit{E}}_{\mathit{V}}$ increases from 0.65 to 0.83 eV in the alloy range investigated. Finally, using the known crystalline silicon band gap, we directly determine the mobility gap for each of the amorphous samples. \textcopyright{} 1996 The American Physical Society.
Co‐inoculation of tumorigenic rat prostate mesenchymal cells with non‐tumorigenic epithelial cells results in the development of carcinosarcoma in syngeneic and athymic animals (1989)

Co-inoculation of NbF-I and NbE-I s.c. into either adult male syngeneic rats or athymic nude mice induced the development of tumors that resembled carcinosarcoma on histopathologic evaluation. These tumors were composed of a mixture of adenocarcinoma and fibrosarcoma and were induced by the mixtures of NbF-I and NbE-I cells at a ratio ranging from 0.001 to 3.2; inoculation of NbF-I alone resulted in the development of fibrosarcoma. Flow-cytometric analysis showed that the epithelial cells subcloned from the carcinosarcoma had a DNA profile like that of their parental cell line and remained non-tumorigenic. When co-inoculated with the tumorigenic fibroblasts in syngeneic hosts, however, the subcloned epithelial cells again formed carcinosarcomas. Our results indicate that cell fusion between epithelial cells and fibroblasts is an unlikely explanation for tumorigenicity. We propose that prostatic fibroblasts exert a directive influence on their adjacent epithelial cells through a paracrine mechanism that determines epithelial growth and tumorigenicity in vivo.
Protection of mice against tumor growth by immunization with an oncogene-encoded growth factor. (1990)

The K-fgf/hst oncogene encodes a growth factor of the fibroblast growth factor (FGF) family that is secreted and transforms cells through a mechanism of autocrine cell proliferation. K-fgf-transformed cells are highly tumorigenic in immunocompetent allogeneic and syngeneic animals. BALB/c mice were immunized with a bacterial fusion protein consisting of a portion of the MS2 polymerase and of the human K-FGF precursor lacking only the first 4 amino acids or with a recombinant protein corresponding to the mature, secreted form of K-FGF (176 amino acids). They were then challenged with syngeneic K-fgf- or H-ras-transformed cells. Vaccinated animals exhibited a significant degree of protection against tumor induction, which was specific for K-fgf-transformed cells and correlated with the ability of the immunized mice to produce high titers of anti-K-FGF antibodies. Thus immunization with a single oncogene product can protect animals against tumor cells expressing this oncogene.
The oligonucleotide probe database (1996)

Free access1 October 1996 Share on The oligonucleotide probe databaseAuthors: E W Alm, D B Oerther, N Larsen, D A Stahl, L RaskinAuthors Info & AffiliationsDOI: https://doi.org/10.1128/aem.62.10.3557-3559.1996 PDF/EPUB
TSG101 interaction with HRS mediates endosomal trafficking and receptor down-regulation (2003)

Down-regulation of mitogenic signaling in mammalian cells relies in part on endosomal trafficking of activated receptors into lysosomes, where the receptors are degraded. These events are mediated by ubiquitination of the endosomal cargo and its consequent sorting into multivesicular bodies that form at the surfaces of late endosomes. Tumor susceptibility gene 101 (tsg101) recently was found to be centrally involved in this process. Here we report that TSG101 interacts with hepatocyte growth factor-regulated tyrosine kinase substrate (HRS), an early endosomal protein, and that disruption of this interaction impedes endosomal trafficking and endocytosis-mediated degradation of mitogenic receptors. TSG101/HRS interaction occurs between a ubiquitin-binding domain of TSG101 and two distinct proline-rich regions of HRS, and is modulated by a C-terminal TSG101 sequence that resembles a motif targeted in HRS. Mutational perturbation of TSG101/HRS interaction prevented delivery of epidermal growth factor receptor (EGFR) to late endosomes, resulted in the cellular accumulation of ubiquitinated EGFR in early endosomes, and inhibited ligand-induced down-regulation of EGFR. Our results reveal the TSG101 interaction with HRS as a crucial step in endocytic down-regulation of mitogenic signaling and suggest a role for this interaction in linking the functions of early and late endosomes.
Profluorescent protease substrates: intramolecular dimers described by the exciton model. (1996)

Xanthene dyes are known to form dimers with spectral characteristics that have been interpreted in terms of exciton theory. A unique aspect of H-type dimers is the fluorescence quenching that accompanies their formation. Using the principles of exciton theory as a guide, a series of protease substrates was synthesized with a xanthene dye on each side of the cleavage site. To bring the attached dyes into spatial proximity to form a dimer, the molecular design included structure determinant regions in the amino acid sequence. In addition, chromophores were chosen such that changes in absorption spectra indicative of exciton splitting were anticipated. Cleavage of the peptides by a protease resulted in disruption of the dimers and indeed significant absorption spectral changes were observed. Furthermore, substrate cleavage was accompanied by at least an order of magnitude increase in fluorescence intensity. This has allowed determination of intracellular elastase activity using a fluorescence microscope equipped with standard optics.
Calcium/calmodulin-dependent kinase II plays an important role in prostate cancer cell survival (2007)

It has recently been shown that the androgen receptor (AR) is the main factor that required for prostate cancer cells survival. We show that knocking down AR expression by siRNA induces PI3K-independent activation of Akt, which was mediated by calcium/calmodulin-dependent kinase II (CaMKII). We further show, for the first time, that prostate cancer cells express beta,gamma and delta CaMKII genes, and the expression of these genes is under the control of AR activity: active AR in the presence of androgens inhibits CaMKII gene expression whereas inhibition of AR activity results in elevated level of kinase activity and in enhanced expression of CaMKII-beta and -gamma genes. Overexpression of CaMKII genes results in resistance to apoptosis induced by KN-93, a CaMKII inhibitor, or wortmanninn, a PI3K/Akt inhibitor, in combination with doxorubicin, thapsigargin and TRAIL. Moreover, overexpression of CaMKII increases secretion of prostate specific antigen and promotes cell growth of LNCaP in steroid-free condition. Our data show that there is cross-talk between AR- and CaMKII-mediated pathways. The results of this study suggest that CaMKII is an important player in prostate cancer cells ability to escape apoptosis under androgen ablation and facilitate the progression of prostate cancer cells to an androgen independent state.
Film dosimetry of megavoltage photon beams: A practical method of isodensity‐to‐isodose curve conversion (1981)

The central problems of photon beam film dosimetry are the dependence of film response upon photon energy, processing conditions, and film plane orientation. We have overcome these problems by accurately fitting the depth-dependent sensitometric curve of Kodak XV-2 film (exposed parallel to beam axis) to the equation OD(D,d) = ODs(1 - exp [- alpha 0[1 + beta(d-dm)]D]) where OD(D,d) is the optical density for dose D at depth d. ODs, alpha 0, and beta are constants characteristic of the film and beam energy but are independent of field size. Only central axis depth dose data for a single field are required to determine their values. A computer program based upon this equation has been written which successfully generates single field isodose curves from film data for a variety of field sizes (including wedged fields) with an accuracy of +/- 3%. Data are presented for 60Co, and 4 and 10 MV x rays.
Neuron Adhesion on a Silicon Chip Probed by an Array of Field-Effect Transistors (1996)

The interaction of an individual nerve cell with a surface of oxidized silicon is studied. ac voltages from 0.1 to 5000 Hz are applied to the neuron. The resulting voltage profiles in the cleft between cell membrane and surface are recorded by an array of sixteen field-effect transistors with open metal-free gate oxide. Using methods of the cable theory to describe the contact area (diameter around 35 \ensuremath{\mu}m), we evaluate the width of the cleft (around 20 nm) and the conductance of the membrane, which is enhanced by an order of magnitude.
Combining the Best in Triplex Recognition:  Synthesis and Nucleic Acid Binding of a BQQ−Neomycin Conjugate (2003)

Synthesis of a BQQ-neomycin conjugate is reported. The conjugate combines two ligands, one known to intercalate triplexes (BQQ) and another known to bind in the triplex groove (neomycin). The conjugate stabilizes T.A.T, as well as mixed base DNA triplex, better than neomycin, BQQ, or a combination of both. The conjugate selectively stabilizes the triplex (in the presence of physiological salt concentrations), with as little as 4 muM of the ligand leading to a DeltaTm of >60 degrees C. Competition dialysis studies show a clear preference for the drug binding to triplex DNA/RNA over the duplex/single strand structures. Modeling studies suggest a structure of neomycin bound to the larger W-H (Watson-Hoogsteen) groove with BQQ intercalated between the triplex bases.
Electricity Generation by Rhodopseudomonas palustris DX-1 (2008)

Bacteria able to generate electricity in microbial fuel cells (MFCs) are of great interest, but there are few strains capable of high power production in these systems. Here we report that the phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris DX-1, isolated from an MFC, produced electricity at higher power densities (2720 +/- 60 mW/m2) than mixed cultures in the same device. While Rhodopseudomonas species are known for their ability to generate hydrogen, they have not previously been shown to generate power in an MFC, and current was generated without the need for light or hydrogen production. Strain DX-1 utilizes a wide variety of substrates (volatile acids, yeast extract, and thiosulfate) for power production in different metabolic modes, making it highly useful for studying power generation in MFCs and generating power from a range of simple and complex sources of organic matter. These results demonstrate that a phototrophic purple nonsulfur bacterium can efficiently generate electricity by direct electron transfer in MFCs, providing another model microorganism for MFC investigations.
Phage-display library selection of high-affinity human single-chain antibodies to tumor-associated carbohydrate antigens sialyl Lewisxand Lewisx (1999)

mAbs against tumor-associated carbohydrate antigens have the potential to play a prominent role in cancer immunotherapy. However, it has not been possible to fully exploit the clinical utility of such antibodies primarily, because those of adequate affinity could be derived only from murine sources. To address this problem, we prepared a single-chain Fv (scFv) antibody library from the peripheral blood lymphocytes of 20 patients with various cancer diseases. Completely human high-affinity scFv antibodies were then selected by using synthetic sialyl Lewisx and Lewisx BSA conjugates. These human scFv antibodies were specific for sialyl Lewisx and Lewisx, as demonstrated by ELISA, BIAcore, and flow cytometry binding to the cell surface of pancreatic adenocarcinoma cells. Nucleotide sequencing revealed that at least four unique scFv genes were obtained. The Kd values ranged from 1.1 to 6.2 x 10(-7) M that were comparable to the affinities of mAbs derived from the secondary immune response. These antibodies could be valuable reagents for probing the structure and function of carbohydrate antigens and in the treatment of human tumor diseases.
HOXB4 enforces equivalent fates of ES-cell-derived and adult hematopoietic cells (2005)

Genetic manipulation of hematopoietic stem and progenitor cells is an important tool for experimental and clinical applied hematology. However, techniques that allow for gene targeting, subsequent in vitro selection, and expansion of genetically defined clones are available only for ES cells. Such molecularly defined and, hence, "safe" clones would be highly desirable for somatic gene therapy. Here, we demonstrate that in vitro differentiated ES cells completely recapitulate the growth and differentiation properties of adult bone marrow cells, in vitro and in vivo, when ectopically expressing HOXB4. Myeloid development was enforced and (T) lymphoid development suppressed over a wide range of expression levels, whereas only high expression levels of the transcription factor were detrimental for erythroid development. This indicates a close association between the amounts of ectopic HOXB4 present within a progenitor cell and and the decision to self renew or differentiate. Because HOXB4 mediates similar fates of ES-derived and bone marrow hematopoietic stem cells, the primitive embryonic cells can be considered a promising alternative for investigating hematopoietic reconstitution, in vivo, based on well defined clones. Provided that HOXB4 levels are kept within a certain therapeutic window, ES cells also carry the potential of efficient and safe somatic gene therapy.