gebhart/patrepeval huggingface dataset:
Analysis, Characterization, and Loci of the tuf Genes in Lactobacillus and Bifidobacterium Species and Their Direct Application for Species Identification (2003)

We analyzed the tuf gene, encoding elongation factor Tu, from 33 strains representing 17 Lactobacillus species and 8 Bifidobacterium species. The tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. We demonstrated that the synonymous substitution affecting this gene renders elongation factor Tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. In fact, the phylogeny generated by these tuf sequences is consistent with that derived from 16S rRNA analysis. The investigation of a multiple alignment of tuf sequences revealed regions conserved among strains belonging to the same species but distinct from those of other species. PCR primers complementary to these regions allowed species-specific identification of closely related species, such as Lactobacillus casei group members. These tuf gene-based assays developed in this study provide an alternative to present methods for the identification for lactic acid bacterial species. Since a variable number of tuf genes have been described for bacteria, the presence of multiple genes was examined. Southern analysis revealed one tuf gene in the genomes of lactobacilli and bifidobacteria, but the tuf gene was arranged differently in the genomes of these two taxa. Our results revealed that the tuf gene in bifidobacteria is flanked by the same gene constellation as the str operon, as originally reported for Escherichia coli. In contrast, bioinformatic and transcriptional analyses of the DNA region flanking the tuf gene in four Lactobacillus species indicated the same four-gene unit and suggested a novel tuf operon specific for the genus Lactobacillus.
Preparation of epitaxial AlN films by electron cyclotron resonance plasma-assisted chemical vapor deposition on Ir- and Pt-coated sapphire substrates (1994)

AlN epitaxial films have been fabricated on Ir- and Pt-coated α-Al2O3 substrates via electron cyclotron resonance plasma-assisted chemical vapor deposition (ECRPACVD) using an AlBr3-N2-H2-Ar gas system at substrate temperatures ranging from 500 to 700 °C. The epitaxial relationships between AlN films and substrates were determined by x-ray diffraction, x-ray pole figure, and reflection high-energy electron diffraction. The results are useful in practical applications, such as AlN/metal/α-Al2O3 structure in surface acoustic wave (SAW) devices.
Granulocyte-macrophage colony stimulating factor gene expression and function during tumor promotion (1994)

Although recent evidense suggests that granulocyte-macrophage colony stimulating factor (GM-CSF) plays a role in cutaneous inflammation induced by topical exposure of phorbol ester tumor promoters to murine epidermis, there is little information available on the temporal sequence of gene expression of this cytokine over the time course of tumor promotion or about its function in this process. The goal of the present studies was to examine the potential role of GM-CSF in tumor promotion in SENCAR mice. Competitive reverse transcriptase polymerase chain reaction (RT-PCR) studies demonstrated that a single topical application of 12-O-tetradecanoylphorbol-13-acetate (TPA; 2 μg, 10 tg) to the dorsal epidermis of SENCAR mouse skin stimulated a dose and time dependent GM-CSF gene expression that was upregulated at 1 h after TPA exposure, peaked at 3 h and declined at 12 h. Although treatment with 7',12'-dbnethyl- benz[a] anthracene (DMBA) did not stimulate GM-CSF gene expression, GM-CSF gene expression was elevated in epidermal tissue isolated from SENCAR mice treated with a single application of 10 nmol DMBA followed by multiple applications of 2 μg TPA over a 1–22 week time course. Immunochemical and autoradiographic studies demonstrated that GM-CSF protein was produced by suprabasal keratino cytes, interfolilcular cells, nonproliferating papilloma cells and leukocytes within the dermis. Intraperitoneal injection of recombinant (r) GM-CSF into SENCAR mice at 2 h prior to topical application of 10 μg TPA induced a significant increase in epidermal keratinocyte proliferation, leukocyte infiltration into the dermis, hydroperoxide production by circulating neutrophils and chemotactic activity present within the plasma at 24 h compared to treatment with only 10 μg TPA. Intravenous injection of anti-GM-CSF antibodies significantly inhibited both local and systemic inflammatory events induced by topical application of TPA. The present studies suggest that GM-CSF has a broad spectrom of activity with at least two target cell populations, epidermal keratino cytes within the proliferative compartment and leukocytes.
Changes in the metabolic clearance of vasopressin and in plasma vasopressinase throughout human pregnancy. (1989)

Metabolic clearance rates (MCR) of arginine vasopressin (AVP) were measured serially in five women starting before conception, during gestational weeks 7-8 (early), 22-24 (middle), and 36-38 (late pregnancy), and again 10-12 wk postpartum. Hormonal disposal rates were determined after water loading to suppress endogenous AVP release using a constant infusion method designed to achieve three different steady-state concentrations of plasma AVP (PAVP) on each test occasion. Dose schedules were altered in mid- and late pregnancy to obtain comparable AVP levels at each stage of the protocol. Prehydration decreased plasma osmolality sufficiently to suppress AVP release, as circulating AVP-neurophysin measured serially in three of the women was undetectable. The MCR of AVP was similar before conception (0.75 +/- 0.31, 0.79 +/- 0.34, and 0.76 +/- 0.28 liters/min at PAVP of 2.6 +/- 1.9, 4.7 +/- 2.4, and 8.3 +/- 3.9 pg/ml), in early pregnancy (0.89 +/- 0.34, 0.97 +/- 0.04, and 0.95 +/- 0.40 liters/min at PAVP of 2.2 +/- 2.1, 3.9 +/- 3.2, and 7.9 +/- 3.4 pg/ml), and postpartum (0.70 +/- 0.21, 0.69 +/- 0.24, and 0.75 +/- 0.20 liters/min at PAVP 3.5 +/- 1.8, 5.1 +/- 3.7, and 9.1 +/- 4.2 pg/ml). Values at mid-pregnancy (2.8 +/- 1.3, 3.0 +/- 1.2, and 2.7 +/- 1.2 liters/min at PAVP 2.3 +/- 2.2, 4.0 +/- 3.6, and 7.7 +/- 3.9 pg/ml) and late pregnancy (3.2 +/- 1.4, 3.3 +/- 1.4, and 2.9 +/- 1.2 liters/min at PAVP 1.9 +/- 2.0, 3.8 +/- 2.6, and 7.4 +/- 4.1 pg/ml) increased 3-4-fold (all P less than 0.01). Plasma vasopressinase, undetectable at 7-8 gestational wk, increased markedly by mid- and slightly more by late gestation. Finally, relationships between PAVP and urine osmolality were similar before, during, and after pregnancy. We conclude that marked increments in the MCR of AVP occur between gestational weeks 7 and 8 and mid-pregnancy, which parallel the period of greatest rise in both trophoblastic mass and plasma vasopressinase. There was no evidence of a renal resistance to AVP during gestation.
Episomal vectors for gene expression in mammalian cells (2000)

An important reason for preferring mammalian cells for heterologous gene expression is their ability to make authentic proteins containing post-translational modifications similar to those of the native protein. The development of expression systems for mammalian cells has been ongoing for several years, resulting in a wide variety of effective expression vectors. The aim of this review is to highlight episomal expression vectors. Such episomal plasmids are usually based on sequences from DNA viruses, such as BK virus, bovine papilloma virus 1 and Epstein-Barr virus. In this review we will mainly focus on the improvements made towards the usefulness of these systems for gene expression studies and gene therapy.
Genetic, physiological and biochemical characterization of multiple methanol methyltransferase isozymes in Methanosarcina acetivorans C2A (2005)

Biochemical evidence suggests that methanol catabolism in Methanosarcina species requires the concerted effort of methanol:5-hydroxybenzimidazolylcobamide methyltransferase (MtaB), a corrinoid-containing methyl-accepting protein (MtaC) and Co-methyl-5-hydroxybenzimidazolylcobamide:2-mercapto-ethanesulphonic acid methyltransferase (MtaA). Here we show that Methanosarcina acetivorans possesses three operons encoding putative methanol-specific MtaB and corrinoid proteins: mtaCB1, mtaCB2 and mtaCB3. Deletion mutants lacking the three operons, in all possible combinations, were constructed and characterized. Strains deleted for any two of the operons grew on methanol, whereas strains lacking all three did not. Therefore, each operon encodes a bona fide methanol-utilizing MtaB/corrinoid protein pair. Most of the mutants were similar to the wild-type strain, with the exception of the DeltamtaCB1 DeltamtaCB2 double mutant, which grew more slowly and had reduced cell yields on methanol medium. However, all mutants displayed significantly longer lag times when switching from growth on trimethylamine to growth on methanol. This indicates that all three operons are required for wild-type growth on methanol and suggests that each operon has a distinct role in the metabolism of this substrate. The combined methanol:CoM methyltransferase activity of strains carrying only mtaCB1 was twofold higher than strains carrying only mtaCB2 and fourfold higher than strains carrying only mtaCB3. Interestingly, the presence of the mtaCB2 and mtaCB3 operons, in addition to the mtaCB1 operon, did not increase the overall methyltransferase activity, suggesting that these strains may be limited by MtaA availability. All deletion mutants were unaffected with respect to growth on trimethylamine and acetate corroborating biochemical evidence indicating that each methanogenic substrate has specific methyltransfer enzymes.
The purification and properties of human T cell growth factor. (1982)

Human T cell growth factor (TCGF) has been purified more than 800-fold from serum-free lymphocyte conditioned media by utilizing ion exchange chromatography with DEAE-Sepharose, gel filtration with Ultrogel AcA54, and preparative SDS-polyacrylamide gel electrophoresis. This mitogenic protein, which is released by T cells into the incubating media after exposure to a lectin (PHA), has a m.w. of 13,000 as determined by SDS-PAGE and 20,000 to 25,000 on gel filtration and has an isoelectric point of 6.8. The material extracted from acrylamide gels is a single band (or two nearly superimposed bands) when rerun on analytical SDS gels. Partially purified material is unstable even at -70 degrees C and requires the addition of bovine serum albumin or polyethylene glycol to maintain biologic activity. It is sensitive to proteolytic digestion but resistant to nucleases and thiol-reducing agents such as dithiothreitol. Human TCGF can be reversibly denatured with urea or SDS. Material extracted from acrylamide gels has been shown to sustain T lymphoblasts in tissue culture. In contrast to lectins, certain antigens, and crude lymphocyte conditioned media, purified TCGF does not initiate lymphocyte blastogenesis but is a highly selective mitogen for T cells previously activated by exposure to lectins or antigens.
Alkylation reactions of ethyl malonate, ethyl acetoacetate, and acetylacetone by gas–liquid phase-transfer catalysis (G.L.–P.T.C.) (1987)

Malonyl, acetoacetyl, and acetylacetonyl alkylation reactions have been carried out in the gaseous state under gas–liquid phase-transfer catalysis (g.l.–p.t.c.) conditions using potassium carbonate or sodium hydrogen carbonate as the base. No alkali metal was used to generate the reactive anion. No solvents are used in the process, and the reaction mixture requires no stirring. The phase-transfer catalysts which promote the reaction: phosphonium salts, crown ethers, and poly(ethylene glycol) are also the medium in which the reaction occurs; they direct C- or O-alkylation, as a function of the methylene compound and the alkylating agent used. The malonic ester alkylation using poly(ethylene glycol) gives rise to improved selectivity for C-monoalkylation compared with the other catalysts.
Activation of metalloproteinases-2 and -9 by interleukin-1alpha in S100A4-positive liposarcoma cell line: correlation with cell invasiveness. (2004)

These data show that S100A4-positive SW872 respond to interleukins by influencing the behavior of factors involved in extracellular matrix degradation and emphasize the predominant role of MMP activity status on the positive regulation of cell migration mechanisms.
The carboxyl-terminal region of human interferon γ is important for biological activity: mutagenic and NMR analysis (1991)

Deletion of nine amino acids from the carboxyl terminus of human IFN gamma (residues 138--146; LFRGRRASQ) resulted in a 7-fold increase in specific antiviral activity. Similar increases in receptor binding affinity were seen. Deletion of residues 136 and 137 (QM) had little additional effect, but removal of Ser135 resulted in a sharp drop in antiviral activity. Further removal of residues 133 and 134 (KR) lowered antiviral activity to 1% of the peak value. Comparison of the proton NMR spectra of selected deletions down to residue 132 showed that there was no significant change in the core protein structure. Deletions down to residue 125 had the same antiviral activity as those to 132, but changes could now be seen in the aromatic proton NMR spectrum of this shorter derivative. Substitution of the homologous murine sequence between residues 124 and 130 (human SPAAKTG; murine LPESSLR) resulted in only a small decrease in antiviral activity, further suggesting that the precise sequence in this region was not critical for activity. Ser135 was substituted with a number of other amino acids with little or no change in activity. The importance of the residues between 131 and 134 for biological activity was corroborated by mutagenesis, although some substitutions in this region were tolerated.
Probing of DNA-Binding Sites of Escherichia coli RecA Protein Utilizing 1-Anilinonaphthalene-8-sulfonic Acid (1998)

RecA protein of Escherichia coli plays an essential role in homologous recombination of DNA strands. To analyze the interaction of RecA with single-stranded DNA (ssDNA), we performed a fluorescence competition assay employing 1-anilinonaphthalene-8-sulfonic acid (ANS) as an extrinsic fluorescent probe. ANS bound to RecA at three sites, leading to enhancement of ANS fluorescence. Addition of synthetic polynucleotides to the RecA-ANS complex in the absence of a nucleotide quenched the ANS fluorescence, indicating displacement of ANS molecules by ssDNA. Less effective quenching by poly(dA) suggests that the nucleoprotein filament on poly(dA) may differ from those on poly(dT) and poly(dC). A titration experiment with poly(dT) and poly(dA) showed clear stoichiometric binding of 3.5 nucleotides per protein. The site size for poly(dC) was 7.0, which could be explained by the formation of a double helix of poly(dC). ATP and other nucleotides also displaced the ANS. To identify ANS-binding sites, ANS was incorporated into RecA by UV irradiation, and fluorescent peptides were isolated from the proteolytic digest. Sequence analysis suggested that ANS binds to or near the ATP-binding region. These results suggest that the fluorescence quenching and photoincorporation assay using ANS may be useful for the analysis of the interaction of a protein and its ligand.
Identification of genes related to invasion and metastasis in pancreatic cancer by cDNA representational difference analysis. (2003)

The difference in gene expression between the highly invasive and metastatic cell line PC-1.0 and the weakly invasive and metastatic cell line PC-1 both derived from a pancreatic ductal carcinoma induced by N-nitrosobis (2-oxopropyl) amine (BOP) in Syrian golden hamster was examined using the Representational Difference Analysis (RDA) method. Within 8 clones (cDNA fragments) successfully isolated after subtraction hybridization of PC-1 cDNA from PC-1.0, 5 clones were shown to be specific or highly expressed in PC-1.0 as confirmed by RT-PCR. Among these 5 clones, two known genes, MAP kinase kinase 2 (MKK2) and phosphatidylinositol 4-kinase (PI4K230) were detected by gene sequencing. The specific expressions of MKK2 and PI4K230 in the highly invasive and metastatic cell line PC-1.0 were confirmed by RT-PCR and Northern blotting. By adding the CM of PC1.0 which included the cancer cell dissociation factor (DF), PC-1 cells began to dissociate and migrate from the colonies, and in addition the expression of MKK2 was found to be induced. On the other hand, the expression of PI4K230 was not induced in PC-1 cells by adding the CM of PC-1.0. Interestingly, in PC-1.0 the expression of PI4K230 was completely abolished and apoptosis induced by the PI3K inhibitor wortmannin. These results suggest that both MKK2 and PI4K230 are factors of a signal transduction pathway that might play an important role related to invasion and metastasis through the induction of cell motility and/or the inhibition of apoptosis.
Dynamic Changes in Regulatory T Cells Are Linked to Levels of Diet-Induced Hypercholesterolemia (2011)

Prolonged hypercholesterolemia impairs Treg but not effector T cell accumulation in lesions, but reversal of hypercholesterolemia can prevent loss of lesional Treg. Therefore, cholesterol-lowering therapies may induce dynamic and beneficial changes in Treg:effector T cell ratios in atherosclerotic lesions.
Flow cytometry detection of caspase 3 activation in preapoptotic leukemic cells (2000)

These results demonstrate that anti-active caspase 3 labeling can be an alternative to fluorogenic substrates to efficiently detect early apoptosis by FCM in heterogeneous samples. They also confirm that anthracyclines induce blast cell apoptosis by a caspase 3-dependent pathway.
Induced pluripotent stem cells: advances to applications (2009)

Induced pluripotent stem cell (iPS) technology has enriched the armamentarium of regenerative medicine by introducing autologous pluripotent progenitor pools bioengineered from ordinary somatic tissue. Through nuclear reprogramming, patient-specific iPS cells have been derived and validated. Optimizing iPS-based methodology will ensure robust applications across discovery science, offering opportunities for the development of personalized diagnostics and targeted therapeutics. Here, we highlight the process of nuclear reprogramming of somatic tissues that, when forced to ectopically express stemness factors, are converted into bona fide pluripotent stem cells. Bioengineered stem cells acquire the genuine ability to generate replacement tissues for a wide-spectrum of diseased conditions, and have so far demonstrated therapeutic benefit upon transplantation in model systems of sickle cell anemia, Parkinson's disease, hemophilia A, and ischemic heart disease. The field of regenerative medicine is therefore primed to adopt and incorporate iPS cell-based advancements as a next generation stem cell platforms.
Tumor-Associated Hyaluronan Limits Efficacy of Monoclonal Antibody Therapy (2014)

Despite tremendous progress in cancer immunotherapy for solid tumors, clinical success of monoclonal antibody (mAb) therapy is often limited by poorly understood mechanisms associated with the tumor microenvironment (TME). Accumulation of hyaluronan (HA), a major component of the TME, occurs in many solid tumor types, and is associated with poor prognosis and treatment resistance in multiple malignancies. In this study, we describe that a physical barrier associated with high levels of HA (HA(high)) in the TME restricts antibody and immune cell access to tumors, suggesting a novel mechanism of in vivo resistance to mAb therapy. We determined that approximately 60% of HER2(3+) primary breast tumors and approximately 40% of EGFR(+) head and neck squamous cell carcinomas are HA(high), and hypothesized that HA(high) tumors may be refractory to mAb therapy. We found that the pericellular matrix produced by HA(high) tumor cells inhibited both natural killer (NK) immune cell access to tumor cells and antibody-dependent cell-mediated cytotoxicity (ADCC) in vitro. Depletion of HA by PEGPH20, a pegylated recombinant human PH20 hyaluronidase, resulted in increased NK cell access to HA(high) tumor cells, and greatly enhanced trastuzumab- or cetuximab-dependent ADCC in vitro. Furthermore, PEGPH20 treatment enhanced trastuzumab and NK cell access to HA(high) tumors, resulting in enhanced trastuzumab- and NK cell-mediated tumor growth inhibition in vivo. These results suggest that HA(high) matrix in vivo may form a barrier inhibiting access of both mAb and NK cells, and that PEGPH20 treatment in combination with anticancer mAbs may be an effective adjunctive therapy for HA(high) tumors.
Administration of a human monoclonal antibody (TUVIRUMAB) to chronic hepatitis B patients pre‐treated with lamivudine: monitoring of serum TUVIRUMAB in immune complexes (2001)

A human monoclonal anti-hepatitis B antibody preparation (TUVIRUMAB) was administered 6 times over a 2-week period in a dose-escalating scheme to chronic hepatitis B patients pre-treated with lamivudine. The capacity of the TUVIRUMAB antibody to "neutralize" hepatitis B surface antigen in the circulation was investigated by means of experimental enzyme-immunoassays. Monoclonal antibody conjugates enabled the detection of HBsAg, TUVIRUMAB, and HBsAg/TUVIRUMAB complexes. The results showed that (1) TUVIRUMAB was able partially to "neutralize" in vitro and in vivo, (2) HBsAg/TUVIRUMAB complexes can be traced by assays that capture the complex at either its HBsAg or its TUVIRUMAB component, (3) the final concentration of TUVIRUMAB at the end of therapy varied greatly but seemed to be related to HBsAg production at the start of therapy, (4) for at least 14 days after discontinuation of therapy, a minimal HBsAg level could be maintained in the presence of a declining TUVIRUMAB titer in patients with less than 3 microg/ml HBsAg before the start of therapy, (5) three months after therapy, all HBsAg levels had returned to pre-treatment levels and TUVIRUMAB had disappeared.
Method for determination of neutral atomic oxygen flux (1990)

A method for determining the flux of atomic oxygen atoms to a probe surface has been developed. Two probes are used. One is a glass probe enclosing a small, ceramic resistor heater and a thermocouple for determining the ambient local temperature. Another probe has a silver tip and inside it is only a thermocouple. In an atomic oxygen environment, such as a laboratory oxygen plasma, the silver probe will quickly develop a silver oxide coating which provides for atomic oxygen recombination. The temperature increase of the silver probe caused by energy release in the recombination reaction is matched by the glass probe using the resistive heater. The energy input to the glass probe allows determination of the atomic oxygen flux to the silver oxide probe. This is similar to other approaches using such probes except that by matching the temperature with a resistive heater in the glass probe, whose surface does not allow for recombination of atomic oxygen, a direct measure of the energy deposited on the silver probe may be obtained.