gebhart/patrepeval huggingface dataset:
Production of heavy-chain class-switch variants of human monoclonal antibody by recombinant DNA technology. (1988)

We have previously established a human-mouse heterohybridoma (H6-3C4), which produced a human sperm-immobilizing antibody (mu, lambda of human type). The human rearranged immunoglobulin mu-chain and lambda-chain genes were cloned from the hybridoma H6-3C4. The cloned V region of the heavy chain (VH) gene was ligated to human immunoglobulin gamma 1-heavy chain constant region (C gamma 1) genes. This resulted in the heavy-chain class-switch from mu-chain to gamma 1-chain of H6-3C4 antibody. The class-switched heavy-chain gene as well as the cloned lambda-chain gene were introduced into mouse myeloma cell line X63Ag8.653 by protoplast fusion and electroporation. The stable transformants produced the human IgG monoclonal antibody, which fully retained specificity to human sperm cells and sperm-immobilizing activity.
Opportunities and Challenges in the Development of Experimental Drug Combinations for Cancer (2011)

It is becoming increasingly evident that cancers are dependent on a number of altered molecular pathways and can develop diverse mechanisms of resistance to therapy with single agents. Therefore, combination regimens may provide the best hope for effective therapies with durable effects. Despite preclinical data to support this notion, there are many challenges to the development of targeted combinations including scientific, economic, legal, and regulatory barriers. A discussion of these challenges and identification of models and best practices are presented with intent of aiding the research community in addressing real and perceived barriers to the development of combination therapies for cancer.
Posttranslational Formation of Formylglycine in Prokaryotic Sulfatases by Modification of Either Cysteine or Serine (1998)

Eukaryotic sulfatases carry an alpha-formylglycine residue that is essential for activity and is located within the catalytic site. This formylglycine is generated by posttranslational modification of a conserved cysteine residue. The arylsulfatase gene of Pseudomonas aeruginosa also encodes a cysteine at the critical position. This protein could be expressed in active form in a sulfatase-deficient strain of P. aeruginosa, thereby restoring growth on aromatic sulfates as sole sulfur source, and in Escherichia coli. Analysis of the mature protein expressed in E. coli revealed the presence of formylglycine at the expected position, showing that the cysteine is also converted to formylglycine in a prokaryotic sulfatase. Substituting the relevant cysteine by a serine codon in the P. aeruginosa gene led to expression of inactive sulfatase protein, lacking the formylglycine. The machinery catalyzing the modification of the Pseudomonas sulfatase in E. coli therefore resembles the eukaryotic machinery, accepting cysteine but not serine as a modification substrate. By contrast, in the arylsulfatase of Klebsiella pneumoniae a formylglycine is found generated by modification of a serine residue. The expression of both the Klebsiella and the Pseudomonas sulfatases as active enzymes in E. coli suggests that two modification systems are present, or that a common modification system is modulated by a cofactor.
Intracellular cysteine and glutathione delivery systems. (1986)

Glutathione functions in catalysis, metabolism, transport, and reductive processes and in protection of cells by destruction of free radicals, reactive oxygen intermediates, and other toxic compounds of endogenous and exogenous origin. It also functions as a storage and transport form of cysteine. Depletion of glutathione (effectively accomplished by inhibition of its synthesis) increases sensitivity to radiation and to certain toxic compounds and is of value in combination with radiation therapy or chemotherapy in situations in which cell selectivity can be achieved. Increased cellular levels of glutathione protect cells against radiation and certain toxic compounds. Glutathione levels can be increased by administration of cysteine or of glutathione, but these approaches are not entirely satisfactory. Cellular glutathione levels can be increased by supplying substrate for gamma-glutamylcysteine synthetase or for glutathione synthetase. L-2-Oxothiazolidine-4-carboxylate is well transported into many cells and is converted by 5-oxoprolinase to cysteine, a substrate of gamma-glutamylcysteine synthetase. gamma-Glutamylcysteine and related compounds are effectively transported, especially into renal cells, thus providing substrate for glutathione synthetase; higher than normal levels of glutathione can be achieved because this enzyme is not significantly inhibited by glutathione, whereas gamma-glutamylcysteine synthetase is feedback-inhibited. Derivatives of glutathione that are effectively transported into cells (glutathione itself is not) offer another means of increasing glutathione levels. The monoethyl ester of glutathione (in which the glycine carboxyl group is esterified) is well transported in vivo into liver and kidney and into cultured fibroblasts and lymphoid cells. Glutathione levels much higher than usual can be obtained by this procedure, which protects lymphoid cells against the lethal effects of irradiation and mice against acetaminophen, and which therefore may be a relatively safe way to increase cellular resistance to radiation and certain toxic compounds.
Oxide-confinement vertical-cavity surface-emittinglasers grown on GaAs(311)A substrates with dynamically stable polarisation (1998)

An experimental investigation of dynamic lasing characteristics in oxide-confinement InGaAs/GaAs vertical-cavity surface-emitting lasers (VCSELs) grown on GaAs(311)A substrates is presented. A stable single polarisation mode was exhibited along the [2̄33] crystallographic direction under continuous wave (CW) operation and under high-speed direct modulation with a data rate of 1 Gbit/s.
Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice. (1991)

A general strategy for selecting insertion mutations in mice has been devised. Constructs lacking a promoter and including a beta-galactosidase gene, or a reporter gene encoding a protein with both beta-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. Such insertion events create a mutation in the tagged gene and allow its expression to be followed by beta-galactosidase activity. Introduction of promoter trap constructs into embryonic stem (ES) cells by electroporation or retroviral infection has led to the derivation of transgenic lines that show a variety of beta-galactosidase expression patterns. Intercrossing of heterozygotes from 24 strains that express beta-galactosidase identified 9 strains in which homozygosity leads to an embryonic lethality. Because no overt phenotype was detected in the remaining strains, these results suggest that a substantial proportion of mammalian genes identified by this approach are not essential for development.
Hyperproduction of Tryptophan by Corynebacterium glutamicum with the Modified Pentose Phosphate Pathway (1999)

A classically derived tryptophan-producing Corynebacterium glutamicum strain was recently significantly improved both by plasmid-mediated amplification of the genes for the rate-limiting enzymes in the terminal pathways and by construction of a plasmid stabilization system so that it produced more tryptophan. This engineered strain, KY9218 carrying pKW9901, produced 50 g of tryptophan per liter from sucrose after 80 h in fed-batch cultivation without antibiotic pressure. Analysis of carbon balances showed that at the late stage of the fermentation, tryptophan yield decreased with a concomitant increase in CO2 yield, suggesting a transition in the distribution of carbon flow from aromatic biosynthesis toward the tricarboxylic acid cycle via glycolysis. To circumvent this transition by increasing the supply of erythrose 4-phosphate, a direct precursor of aromatic biosynthesis, the transketolase gene of C. glutamicum was coamplified in the engineered strain by using low- and high-copy-number plasmids which were compatible with the resident plasmid pKW9901. The presence of the gene in low copy numbers contributed to improvement of tryptophan yield, especially at the late stage, and led to accumulation of more tryptophan (57 g/liter) than did its absence, while high-copy-number amplification of the gene resulted in a tryptophan production level even lower than that resulting from the absence of the gene due to reduced growth and sugar consumption. In order to assemble all the cloned genes onto a low-copy-number plasmid, the high-copy-number origin of pKW9901 was replaced with the low-copy-number one, generating low-copy-number plasmid pSW9911, and the transketolase gene was inserted to yield pIK9960. The pSW9911-carrying producer showed almost the same fermentation profiles as the pKW9901 carrier in fed-batch cultivation without antibiotic pressure. Under the same culture conditions, however, the pIK9960 carrier achieved a final tryptophan titer of 58 g/liter, which represented a 15% enhancement over the titers achieved by the pKW9901 and pSW9911 carriers.
Novel Prodrugs of Alkylating Agents Derived from 2-Fluoro- and 3-Fluorobenzoic Acids for Antibody-Directed Enzyme Prodrug Therapy (1994)

The synthesis of six novel fluorinated potential prodrugs for antibody-directed enzyme prodrug therapy is described. The [2- and 3-fluoro-4-[bis(2-chloroethyl)amino]benzoyl]-L-glutamic acid (9 and 21), their bis(mesyloxy)ethyl derivatives (7 and 19), and their chloroethyl (mesyloxy)-ethyl derivatives (8 and 20) are bifunctional alkylating agents in which the activating effect of the ionized carboxyl function is masked through an amide bond to the glutamic acid residue. These compounds were designed to be activated to their corresponding benzoic acid alkylating agents at a tumor site by prior administration of a monoclonal antibody conjugated to the bacterial enzyme carboxypeptidase G2 (CPG2). The synthesis of the analogous novel parent drugs 2- and 3-fluoro-4-[bis(2-chloroethyl)amino]benzoic acid (12 and 24), their bis(mesyloxy)ethyl derivatives (10 and 22), and their chloroethyl (mesyloxy)ethyl derivatives (11 and 23) is also described. The viability of a colorectal cell line was monitored with the six potential prodrugs in the presence of CPG2 and with the parent drugs alone. Compounds 19-21 demonstrated substantial prodrug activity, with activation by CPG2 leading to cytotoxicities comparable to those of 22-24, respectively. The Km and kcat values for 7-9 and 19-21 were determined for CPG2. All potential prodrugs except 7 proved to be excellent substrates. A comparison of the relative chemical reactivity of the compounds as determined by their half-life measurements showed that the 2-fluoro substituent deactivated while the 3-fluoro substituent activated the alkylating moieties.
Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer (2016)

Eight differentially methylated CpGs that distinguish patients with metastatic-lethal from nonrecurrent tumors were validated. These novel epigenetic biomarkers warrant further investigation as they may improve prognostic classification of patients with clinically localized prostate cancer and provide new insights on tumor aggressiveness. Clin Cancer Res; 23(1); 311-9. ©2016 AACR.
Cytotoxic T lymphocytes with a grafted recognition specificity for ERBB2-expressing tumor cells. (1994)

Experimental approaches which exploit the targeted cytolytic activity of lymphocytes are being developed for cancer therapy. We generated cytotoxic T lymphocytes (CTLs) with specificity for ERBB2 receptor-expressing tumor cells. A binding function was conferred directly on the zeta chain of the T-cell receptor (TCR) complex to circumvent major histocompatibility complex-restricted antigen recognition through the alpha and beta chains of the TCR. A chimeric gene was constructed which encoded a single-chain Fv antibody (scFv, consisting of the joined heavy- and light-chain variable domains of a monoclonal antibody against the extracellular domain of the ERBB2 receptor), a hinge region as a spacer, and the zeta chain of the TCR. This gene was introduced into CTLs by retroviral gene transfer. The signaling potential of the scFv/hinge/zeta receptors was demonstrated by secretion of interferon gamma upon coincubation with ERBB2-expressing cells. Target cells expressing the ERBB2 gene were lysed in vitro with high specificity by the scFv/hinge/zeta-expressing T cells. The growth of ERBB2-transformed cells in athymic nude mice was retarded by adoptively transferred scFv/hinge/zeta-expressing CTLs. Transduced CTLs labeled with a fluorescent dye were specifically detected in tumor sections. Our results suggest that tumor cell lysis by CTLs grafted in vitro with a major histocompatibility complex-independent recognition could become a gene-therapy approach to cancer treatment.
[Contribution of flow cytometry in virology]. (1993)

The development of commercial multichannel air-cooled laser flow cytometers which allow measurement of one or more characteristic parameters of particles or cells has been furthered due to advances in probes and fluorochromes. FITC-conjugated antibodies specific for selected cell surface molecules or for viral antigen expression in infected cells, fluorescein diacetate for labeling cells as a parameter of viability and propidium iodide as a DNA stain are generally used. Flow cytometric assays have been developed in virology to study the interactions of viruses with the immune system (Hantan Virus), to evaluate the diagnosis of secondary immunodeficiency syndromes (HIV), to analyze the protein and DNA content of virally infected cells during the cell cycle (SV40), to detect immediate early, early or late antigens in HCMV-infected cells, to assess the HCMV persistence in mononuclear cells, for use as a model for studying virus attachment to cellular receptors (EBV-echovirus), to screen and evaluate antiviral agents (Influenza C, HCMV, HSV, HIV) and to quantify antigens or antibodies simultaneously against various viruses (HCMV and HSV) or against different antigenic glycoproteins (HIV). This technology has thus become an important tool for the clinical virology and microbial serology laboratories.
Immunolocalization of Cellular Fibronectins in the Normal Liver, Cirrhosis, and Hepatocellular Carcinoma (1995)

Cellular (c) fibronectins (Fn) differ biochemically, immunologically, and functionally from plasma fibronectins (pFn). Most existing data on Fn distribution in the normal and diseased liver require revision because those studies were based on reagents that did not distinguish pFn from cFn and predated the development of specific cFn monoclonal antibodies (Mabs). We immunostained cryosections of normal adult livers (n = 5), cirrhotic livers (n = 20), and livers with hepatocellular carcinoma (HCC) (n = 10) by the avidin-biotin-complex method with specific Mabs to the extradomains A and B (EDA, EDB) and oncofetal (Onc) isoforms of cFn. Selected samples were stained with an antiserum to pFn; fetal livers served as controls. Normal and cirrhotic livers showed EDA-cFn staining in the portal, septal, and perisinusoidal matrix; its distribution was more restricted than that of pFn. In cirrhosis, EDA-cFn reactions were strongest at sites of piecemeal necrosis and around proliferating ductules in biliary cirrhosis. EDA-cFn reactions were consistently most intense in the matrix of HCC. Distinct from adult normal and cirrhotic livers, reactions for EDB- and Onc-cFn were noted exclusively in most cases of HCC. We conclude that the only cFn isoform indigenous to the normal adult liver matrix is EDA-cFn. Enhanced EDA-cFn in cirrhotic livers may serve as indicator of active stromal remodeling. The restriction of EDB- and Onc-cFn to a large subset of HCC and the putative role of cFn in modulating cell-matrix adhesive interactions would suggest that the emergence of these molecules may be related to the variably invasive and metastatic properties of these tumors.
Effects of estrone, estradiol, and estriol on hormone-responsive human breast cancer in long-term tissue culture. (1977)

The effects of estrone, estradiol, and estriol on MCF-7 human breast cancer are compared. In this estrogen-responsive cell line, all three estrogens are capable of inducing equivalent stimulation of amino acid and nucleoside incorporation. Estriol is capable of partially overcoming antiestrogen inhibition with Tamoxifen (lCl 46474), even when antiestrogen is present in 1000-fold excess. Antiestrogen effects are completely overcome by 100-fold less estriol. Studies of metabolism of estrogens by MCF-7 cells revealed no conversion of estriol to either estrone or estradiol. All three steroids bind to a high-affinity estrogen receptor found in these cells. The apparent dissociation constant is lower for estradiol than for estrone and estriol, but all three bind to an equal number of sites when saturating concentrations are used. Tritiated estrogens used in binding studies were shown to be radiochemically pure. We conclude that estriol can bind to estrogen receptor and stimulate human breast cancer in tissue culture. Our data do not support an antiestrogenic role for estriol in human breast cancer.
Limits for compression of quantum information carried by ensembles of mixed states (1998)

We consider the problem of compression of the quantum information carried by ensemble of mixed states. We prove that for arbitrary coding schemes the least number of quantum bits (qubits) per message needed to convey the signal states asymptotically faithfully is bounded from below by the Holevo function $S(\ensuremath{\varrho})\ensuremath{-}{\ensuremath{\sum}}_{i}{p}_{i}S({\ensuremath{\varrho}}_{i})$. We also show that a compression protocol can be composed with another one, provided that the latter offers perfect transmission. Such a compound protocol is applied to the case of binary source. It is conjectured to reach the obtained bound. Finally, we point out that in the case of mixed signal states there could be a difference between the maximal compression rates at the coding schemes that are ``blind'' to the signal and the ones that assume the knowledge about the identities of the signal states.
Functions of the extracellular matrix and matrix degrading proteases during tumor progression (1999)

Cell interactions with extracellular matrices are important to pathological changes that occur during cell transformation and tumorigenesis. Several extracellular matrix proteins including fibronectin, thrombospondin-1, laminin, SPARC, and osteopontin have been suggested to modulate tumor phenotype by affecting cell migration, survival, or angiogenesis. Likewise, proteases including the matrix metalloproteinases (MMPs) are understood to not only facilitate migration of cells by degradation of matrices, but also to affect tumor formation and growth. We have recently demonstrated an in vivo role for the RGD-containing protein, osteopontin, during tumor progression, and found evidence for distinct functions in the host versus the tumor cells. Because of the compartmentalization and temporal regulation of MMP expression, it is likely that MMPs may also function dually in host stroma and the tumor cell. In addition, an important function of proteases appears to be not only degradation, but also cleavage of matrix proteins to generate functionally distinct fragments based on receptor binding, biological activity, or regulation of growth factors.
Interaction of West Nile virus with primary murine macrophages: role of cell activation and receptors for antibody and complement (1986)

We have measured growth of West Nile virus in mouse primary peritoneal macrophages (resident, thioglycolate elicited, and Mycobacterium bovis BCG activated) and in macrophagelike (P338D1) and nonmacrophage (L929, PS clone D) cell lines infected in the absence or presence of specific antibodies (immunoglobulin G ([IgG], IgM), and complement. Monoclonal antibodies directed against Fc receptors (IgG1/2b, 2.4G2) and type 3 complement receptors (Mac-1) were used to define the role of each receptor. Virus yield depended on a balance between enhancement and neutralization and was influenced by the physiologic state of the macrophage, the receptor pathway of viral entry, the mouse strain and age of donor. BCG-activated macrophages displayed a greater ability to restrict West Nile virus than nonactivated cells only in the presence of antiviral IgM, with or without complement; the Fc receptors for various classes of IgG mediated striking enhancement. These studies identify some of the complex innate and acquired factors that determine the interaction between West Nile virus and primary macrophages in vitro.
Phosphorylation and Regulation of Akt/PKB by the Rictor-mTOR Complex (2005)

Deregulation of Akt/protein kinase B (PKB) is implicated in the pathogenesis of cancer and diabetes. Akt/PKB activation requires the phosphorylation of Thr308 in the activation loop by the phosphoinositide-dependent kinase 1 (PDK1) and Ser473 within the carboxyl-terminal hydrophobic motif by an unknown kinase. We show that in Drosophila and human cells the target of rapamycin (TOR) kinase and its associated protein rictor are necessary for Ser473 phosphorylation and that a reduction in rictor or mammalian TOR (mTOR) expression inhibited an Akt/PKB effector. The rictor-mTOR complex directly phosphorylated Akt/PKB on Ser473 in vitro and facilitated Thr308 phosphorylation by PDK1. Rictor-mTOR may serve as a drug target in tumors that have lost the expression of PTEN, a tumor suppressor that opposes Akt/PKB activation.
ChemInform Abstract: Synthesis, X‐Ray Crystal Structure, and Biological Activity of FR186054, a Novel, Potent, Orally Active Inhibitor of Acyl‐CoA:Cholesterol O‐Acyltransferase (ACAT) Bearing a Pyrazole Ring. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Laminin gene LAMB4 is somatically mutated and expressionally altered in gastric and colorectal cancers (2014)

Laminins are important in tumor invasion and metastasis as well as in maintenance of normal epithelial cell structures. However, mutation status of laminin chain-encoding genes remains unknown in cancers. Aim of this study was to explore whether laminin chain genes are mutated and expressionally altered in gastric (GC) and colorectal cancers (CRC). In a public database, we found that laminin chain genes LAMA1, LAMA3, LAMB1 and LAMB4 had mononucleotide repeats in the coding sequences that might be mutation targets in the cancers with microsatellite instability (MSI). We analyzed the genes in 88 GC and 139 CRC [high MSI (MSI-H) or stable MSI/low MSI (MSS/MSI-L)] by single strand conformation polymorphism analysis and DNA sequencing. In the present study, we found LAMB4 (11.8% of GC and 7.6% of CRC with MSI-H), LAMA3 (2.9% of GC and 2.5 of CRC with MSI-H), LAMA1 (5.9% of GC with MSI-H) and LAMB1 frameshift mutations (1.3% of CRC with MSI-H). These mutations were not found in MSS/MSI-L (0/114). We also analyzed LAMB4 expression in GC and CRC by immunohistochemistry. Loss of LAMB4 expression was identified in 17-32% of the GC and CRC. Of note, the loss expression was more common in the cancers with LAMB4 mutation or those with MSI-H. Our data show that frameshift mutations of LAMA1, LAMA3, LAMB1 and LAMB4, and loss of LAMB4 may be features of GC and CRC with MSI-H.