gebhart/patrepeval huggingface dataset:
Substrate specificities of recombinant murine Golgi 1,2-mannosidases IA and IB and comparison with endoplasmic reticulum and Golgi processing 1,2-mannosidases (1998)

The catalytic domains of murine Golgi alpha1,2-mannosidases IA and IB that are involved in N-glycan processing were expressed as secreted proteins in P.pastoris . Recombinant mannosidases IA and IB both required divalent cations for activity, were inhibited by deoxymannojirimycin and kifunensine, and exhibited similar catalytic constants using Manalpha1,2Manalpha-O-CH3as substrate. Mannosidase IA was purified as a 50 kDa catalytically active soluble fragment and shown to be an inverting glycosidase. Recombinant mannosidases IA and IB were used to cleave Man9GlcNAc and the isomers produced were identified by high performance liquid chromatography and proton-nuclear magnetic resonance spectroscopy. Man9GlcNAc was rapidly cleaved by both enzymes to Man6GlcNAc, followed by a much slower conversion to Man5GlcNAc. The same isomers of Man7GlcNAc and Man6GlcNAc were produced by both enzymes but different isomers of Man8GlcNAc were formed. When Man8GlcNAc (Man8B isomer) was used as substrate, rapid conversion to Man5GlcNAc was observed, and the same oligosaccharide isomer intermediates were formed by both enzymes. These results combined with proton-nuclear magnetic resonance spectroscopy data demonstrate that it is the terminal alpha1, 2-mannose residue missing in the Man8B isomer that is cleaved from Man9GlcNAc at a much slower rate. When rat liver endoplasmic reticulum membrane extracts were incubated with Man9GlcNAc2, Man8GlcNAc2was the major product and Man8B was the major isomer. In contrast, rat liver Golgi membranes rapidly cleaved Man9GlcNAc2to Man6GlcNAc2and more slowly to Man5GlcNAc2. In this case all three isomers of Man8GlcNAc2were formed as intermediates, but a distinctive isomer, Man8A, was predominant. Antiserum to recombinant mannosidase IA immunoprecipitated an enzyme from Golgi extracts with the same specificity as recombinant mannosidase IA. These immunodepleted membranes were enriched in a Man9GlcNAc2to Man8GlcNAc2-cleaving activity forming predominantly the Man8B isomer. These results suggest that mannosidases IA and IB in Golgi membranes prefer the Man8B isomer generated by a complementary mannosidase that removes a single mannose from Man9GlcNAc2.
Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes (1984)

Protein genes can be found either by searching the DNA sequence for signals such as ribosome binding sites or by looking for the effects that coding for a protein has on the coding sequence. This paper describes how these coding effects can be measured and used to detect protein coding regions.
Nonribosomal Peptide Synthetases Involved in the Production of Medically Relevant Natural Products (2008)

Natural products biosynthesized wholly or in part by nonribosomal peptide synthetases (NRPSs) are some of the most important drugs currently used clinically for the treatment of a variety of diseases. Since the initial research into NRPSs in the early 1960s, we have gained considerable insights into the mechanism by which these enzymes assemble these natural products. This review will present a brief history of how the basic mechanistic steps of NRPSs were initially deciphered and how this information has led us to understand how nature modified these systems to generate the enormous structural diversity seen in nonribosomal peptides. This review will also briefly discuss how drug development and discovery are being influenced by what we have learned from nature about nonribosomal peptide biosynthesis.
An anti-CD45RO immunotoxin kills HIV-latently infected cells from individuals on HAART with little effect on CD8 memory (2004)

CD4+ CD45RO+ T cells are the major latent viral reservoir in HIV-infected individuals and hence a major obstacle in curing the disease. An anti-CD45RO immunotoxin (IT) can decrease the number of both productively and latently infected CD4+ T cells obtained from HIV-infected individuals with detectable viremia. In this study, we determined whether this IT could also kill latently infected replication-competent CD4+ T cells obtained from infected individuals without detectable plasma viremia. Our results demonstrate that ex vivo treatment with the anti-CD45RO IT significantly reduced the frequency of these cells. In contrast, the IT had only a modest effect on the cytomegalovirus-specific memory responses of CD8+ T cells. These results suggest that purging latent cells from infected individuals on highly active antiretroviral therapy with the anti-CD45RO IT might reduce the HIV latent reservoir without seriously compromising CD8+ T cell memory responses.
SOI: materials to systems (2002)

The continuing volume growth of portable systems with their increasing demand for better performance and autonomy makes SOI a very attractive approach for large volume IC's production dedicated to low voltage, low power, high speed systems. The capability of SOI circuits to operate at 1 V or below even in the case of DRAM's has been demonstrated as the best compromise between speed and power consumption. SOI is also appropriate for the Gigabit DRAM generation and the "system on chip" approach. These market segments will be the volume drivers for SOI but they are not the only markets for which SOI will be a key technology. Radiation-hard circuits, Smart power, MEMS, Mixed signal, High temperature electronics, and integrated optics all profit from the unique SOI structure. Up to now production volume of SOI circuits has been limited by SOI material availability. A new approach called Smart Cut(R) offers an answer both for the high volume production of SOI wafers and also for quality and cost issues. This approach is based on hydrogen implantation and wafer bonding and allows cutting of thin slices of material at the atomic scale. Trends in the SOI activity from material to systems are discussed.
Direct and Indirect Mechanisms for Regulation of Fatty Acid Synthase Gene Expression by Liver X Receptors (2002)

The nuclear receptors LXRalpha and LXRbeta have been implicated in the control of lipogenesis and cholesterol homeostasis. Ligand activation of these receptors in vivo induces expression of the LXR target gene SREBP-1c and increases plasma triglyceride levels. Expression of fatty acid synthase (FAS), a central enzyme in de novo lipogenesis and an established target of the SREBP-1 pathway, is also induced by LXR ligands. The effects of LXR ligands on FAS expression have been proposed to be entirely secondary to the induction of SREBP-1c. We demonstrate here that LXRs regulate FAS expression through direct interaction with the FAS promoter as well as through activation of SREBP-1c expression. Induction of FAS expression in HepG2 cells by LXR ligands is reduced, but not abolished, under conditions where SREBP processing is suppressed. Moreover, LXR ligands induce FAS expression in CHO-7 cells without altering expression of SREBP-1. We demonstrate that in addition to tandem SREBP sites, the FAS promoter contains a high affinity binding site for the LXR/RXR heterodimer that is conserved in diverse animal species including birds, rodents, and humans. The LXR and SREBP binding sites independently confer LXR responsiveness on the FAS promoter, and maximal induction requires both transcription factors. Transient elevation of plasma triglyceride levels in mice treated with a synthetic LXR agonist correlates with transient induction of hepatic FAS expression. These results indicate that the LXR signaling pathway modulates FAS expression through distinct but complementary mechanisms and suggest that the FAS gene may be a critical target in the control of lipogenesis by LXRs.
Helicobacter pylori Infection in the Colombian Andes: A Population-based Study of Transmission Pathways (1996)

In 1992, the authors studied Helicobacter pylori infection and exposures relevant to person-to-person, waterborne, foodborne, and zoonotic transmission in a census sample of 684 2-9-year-old children in Aldana, Nariño, a rural community in the Colombian Andes. H. pylori prevalence, as determined by the 13C-urea breath test, was 69%, and prevalence increased from 53% in 2 year-olds to 87% in 9 year-olds. Beginning at 3 years of age, a higher percentage of males compared with females were infected. Odds ratios were estimated by multivariate logistic regression to control for mutual confounding by transmission-pathway proxy variables and socioeconomic indicators. Among transmission-pathway proxies, the strongest predictor of H. pylori status was the number of persons who lived in the home, with the number of children apparently being of greater importance than the number of adults. Swimming in rivers, streams, or pools increased the odds of infection, as did using streams as a drinking water source. Children who frequently consumed raw vegetables were more likely to have the infection, and children who had contact with sheep also had increased prevalence odds. Because the results did not implicate a single mode of transmission, the possibility of multiple pathways is indicated.
Tetracycline Analogs Affecting Binding to Tn10-Encoded Tet Repressor Trigger the Same Mechanism of Induction (1996)

We examined the influence of substituents in tetracycline (tc) analogs modified at positions 2 and 4-9 and anhydrotetracycline (atc) on induction of the Tn10-encoded Tet repressor (TetR) by a quantitative in vitro induction assay. The equilibrium association constants of the modified tc to TetR were independently determined to distinguish effects on binding from those on induction. We found a correlation between the binding affinity and induction of TetR for most tc analogs. While a substitution at position 5 revealed only minor effects, changes at position 6 increased binding and induction efficiencies up to 20-fold. A chlorine at position 7 or 8 enhanced binding and induction about 4- and 9-fold, respectively. Substituents at position 9 decreased binding up to 5-fold. Epimerization of the dimethylamino function at position 4 in 4-epi-tc resulted in about 300-fold-reduced binding and 80-fold-reduced induction. Substitution of this grouping by hydrogen in 4-de(dimethylamino)-tc resulted in no binding and no induction. The respective atc analog failed to induce as well, although binding was still observed. The dimethylamino function may, thus, play a role in triggering the conformational change of TetR necessary for induction. Substitution of the 2-carboxamido by a nitrilo function did not influence binding and induction efficiencies. Atc showed about 30-fold increased binding and induction, being the most effective inducer tested in this study. The equilibrium association constants of most TetR-[Mg-tc]+ and TetR-([Mg-tc]+)2 analog complexes with tet operator are decreased about 10(2)- and 10(8)-fold, respectively, as compared to those of free TetR. This suggests that these tc analogs share the same molecular mechanism of TetR induction.
Dissection of the functional domains of Escherichia coli carbamoyl phosphate synthetase by site-directed mutagenesis. (1990)

The catalytic functions of the amino-terminal and carboxyl-terminal halves of the large subunit of carbamoyl phosphate synthetase from Escherichia coli have been identified using site-directed mutagenesis. Glycine residues at positions 176, 180, and 722 within the putative mononucleotide-binding site were replaced with isoleucine residues. Each of these mutations resulted in at least a 1 order of magnitude reduction in the Vmax for carbamoyl phosphate synthesis. The mutations on the amino-terminal half, G176I and G180I, caused slight reduction in the rate of synthesis of ATP from ADP and carbamoyl phosphate (the partial ATP synthesis reaction) but the bicarbonate-dependent ATPase reaction velocity was reduced to less than 10% of the wild-type rate. The mutant G722I, which is on the carboxy-terminal half, caused the partial ATP synthesis reaction to be reduced by 1 order of magnitude but the bicarbonate-dependent ATPase reaction was reduced only slightly. All three mutations are within regions which show homology to the putative glycine-rich loops of many ATP-binding proteins. These results have been interpreted to suggest that the two homologous halves of the large subunit of carbamoyl phosphate synthetase each contain a binding site for ATP. The NH2-terminal domain contains the portion of the large subunit that is primarily involved with the phosphorylation of bicarbonate to carboxy phosphate while the COOH-terminal domain contains the region of the enzyme that catalyzes the phosphorylation of carbamate to carbamoyl phosphate.
Polyglutamation of methotrexate with common polymorphisms in reduced folate carrier, aminoimidazole carboxamide ribonucleotide transformylase, and thymidylate synthase are associated with methotrexate effects in rheumatoid arthritis (2004)

These data suggest that measuring RBC MTXPG levels and/or the common polymorphisms in the folate-purine-pyrimidine pathway may help in monitoring MTX therapy.
Molecular cloning and functional expression of human acyl-coenzyme A:cholesterol acyltransferase cDNA in mutant Chinese hamster ovary cells. (1993)

Accumulation of cholesterol esters as cytoplasmic lipid droplets within macrophages and smooth muscle cells is a characteristic feature of early lesions of atherosclerotic plaque. Intracellularly, an essential element in forming cholesterol ester from cholesterol is the enzyme acyl-coenzyme A:cholesterol acyltransferase (ACAT). ACAT is a membrane protein located in the endoplasmic reticulum. The ACAT protein has never been purified to homogeneity, and no antibodies directed against ACAT have been reported. The gene(s) encoding this enzyme had not been isolated. This laboratory had previously reported the isolation of Chinese hamster ovary cells expressing human ACAT activity. From DNAs of these cells, we have cloned a 1.2-kb exonic human genomic DNA. This led to the eventual cloning of a 4-kb cDNA clone (K1) from a human macrophage cDNA library. Transfection of K1 in ACAT-deficient mutant Chinese hamster ovary cells complemented the mutant defect and resulted in the expression of human ACAT activity. K1 contained an open reading frame of 1650 bp encoding an integral membrane protein of 550 amino acids. Protein homology analysis showed that the predicted K1 protein shared homologous peptide sequences with other enzymes involved in the catalysis of acyl adenylate formation followed by acyl thioester formation and acyl transfer. These results indicate that K1 encodes a structural gene for ACAT. The cDNA reported here should facilitate future molecular studies on ACAT.
Metabolic fate of irinotecan in humans: correlation of glucuronidation with diarrhea. (1994)

Irinotecan (7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxy-camptotheci n (CPT-11) is hydrolyzed by the enzyme carboxyl esterase to 7-ethyl-10-hydroxycamptothecin (SN-38), which further undergoes glucuronic acid conjugation to form the corresponding SN-38 glucuronide (SN-38G). SN-38 is believed to be the cause of treatment-related diarrhea, a dose-limiting toxicity of CPT-11 observed in phase I clinical trials. This study investigated the effect of glucuronidation on the concentrations of SN-38 following CPT-11 infusion in 21 patients undergoing a phase I trial. To assess the relationship between gastrointestinal toxicity and pharmacokinetics of CPT-11 and its metabolites, we defined a "biliary index" of SN-38 which was the product of the relative area ratio of SN-38 to SN-38G and the total CPT-11 area under the plasma concentration-time curve. Nine patients with grade 3-4 diarrhea had higher biliary indexes than 12 patients with grade 0-2 diarrhea (median 2228 versus 5499, P = 0.0004). The relatively higher index values, suggestive of higher biliary concentrations of SN-38, were possibly due to low glucuronidation rates. Hence, modulation of glucuronidation may be effective in increasing the therapeutic index of CPT-11.
New hybrid of PTS-CAPPR methods using GA for PAPR reduction in OFDM systems (2009)

In this paper, we propose a new PAPR reduction by using the hybrid of partial transmit sequences (PTS) and cascade adaptive peak power reduction (CAPPR) methods with coded side information (SI) technique design by genetic algorithm (GA). These methods are used in an orthogonal frequency division multiplexing (OFDM) system. The OFDM employs orthogonal sub-carriers for data modulation. These sub-carriers unexpectedly present a large peak to average power ratio (PAPR) in some cases. A proposed reduction method consists of these two methods and realizes both advantages at the same time. In order to obtain the optimum condition on PTS for PAPR reduction, a quite large calculation cost must be demanded and thus it is impossible to obtain the optimum PTS. In the proposed method, by using the pseudo-optimum condition with a coded SI technique designed by GA, the total calculation cost becomes drastically reduced. In simulation results, the proposed method shows the improvement on PAPR and also reveals the high performance on bit error rate (BER) of an OFDM system.
Association of a plasminogen activator inhibitor (PAI-1) with the growth substratum and membrane of human endothelial cells. (1987)

We have studied the distribution of the plasminogen activator inhibitor type 1 (PAI-1) in cultures of confluent human umbilical vein endothelial cells. Plasminogen activator inhibitor activity measured by the 125I-fibrin plate assay was detected in the cytosol (2.85 +/- 0.16 U), 100,000 g particulate fraction (1.26 +/- 0.30 U), and in the growth substratum (9.82 +/- 1.80 U). Characterization of the protein responsible for this activity by reverse fibrin autography, immunoprecipitation, and immunoblotting demonstrated that it had an Mr of 46,000 and was antigenically related to PAI-1. Only the active form of the inhibitor was found in all three fractions. Inhibitor in the cytosol and particulate fraction converted to the latent form during 37 degrees C incubation while the substratum inhibitor remained fully active. Extracellular PAI-1 was detected in the growth substratum before its appearance in conditioned medium and represented the major protein deposited beneath the cells. The inhibitor was only transiently localized in the substratum, disappearing within 6 h and concomitantly appearing in the culture medium. Incubation of isolated metabolically labeled substratum with tissue plasminogen activator (tPA) resulted in the appearance and release of an immunologically related inactive 44,000 Mr form as well as the tPA-PAI-1 complex (110,000 Mr). PAI-1 was also converted into its 44,000-Mr form and released by treatment of the substratum with human leukocyte elastase. The rapid deposition and predominance of PAI-1 in the underlying compartment of endothelial cells may explain how the basement membrane is protected from proteolytic degradation by plasmin-generating enzymes.
Comparative Gastric Irritation of the Fumaric Acid Esters Dimethyl Fumarate (DMF) and XP23829 in Rat and Monkey (P01.159) (2013)

OBJECTIVE: To compare the potential for oral XP23829 and DMF to cause persistent GI irritation in animals after repeated dosing.
Cell‐penetrating peptides: 20 years later, where do we stand? (2013)

Twenty years ago, the discovery of peptides able to cross cellular membranes launched a novel field in molecular delivery based on these non-invasive vectors, most commonly called cell-penetrating peptides (CPPs) or protein transduction domains (PTDs). These peptides were shown to efficiently transport various biologically active molecules inside living cells, and thus are considered promising devices for medical and biotechnological developments. Moreover, CPPs emerged as potential tools to study the prime mechanisms of cellular entry across the plasma membrane. This review is dedicated to CPP fundamentals, with an emphasis on the molecular requirements and mechanism of their entry into eukaryotic cells.
Small-signal analysis of modulation characteristics in a semiconductor laser subject to strong optical injection (1996)

Injection locking of a semiconductor laser can induce major changes in the modulation characteristics of the laser. A small-signal analysis using the lumped element model shows that both the frequency and damping of the characteristic resonances of the coupled complex field and free carriers (gain medium) are modified. The detuning between the injected field and the free-running oscillating field, the amplitude of the injection field relative to the free-running field, the linewidth enhancement factor, the cavity photon and spontaneous carrier decay rates, and the field enhancement of the decay rate are all key parameters in determining the changes to the modulation characteristics. For a broad range of parameters, there is simultaneous enhancement of the modulation bandwidth and stable, locked operation. The enhancement is a cavity phenomena and does not occur in a traveling wave amplifier. It requires that the frequency of the locking field be detuned from the injection-modified frequency of the cavity resonance. This causes a resonant enhancement of the modulation sideband associated with the preferred frequency of the optical cavity. Bandwidth enhancements beyond the free-running laser limit are possible over a range of injection levels and injection frequency detunings.
Spectrin and Ankyrin-Based Pathways: Metazoan Inventions for Integrating Cells Into Tissues (2001)

The spectrin-based membrane skeleton of the humble mammalian erythrocyte has provided biologists with a set of interacting proteins with diverse roles in organization and survival of cells in metazoan organisms. This review deals with the molecular physiology of spectrin, ankyrin, which links spectrin to the anion exchanger, and two spectrin-associated proteins that promote spectrin interactions with actin: adducin and protein 4.1. The lack of essential functions for these proteins in generic cells grown in culture and the absence of their genes in the yeast genome have, until recently, limited advances in understanding their roles outside of erythrocytes. However, completion of the genomes of simple metazoans and application of homologous recombination in mice now are providing the first glimpses of the full scope of physiological roles for spectrin, ankyrin, and their associated proteins. These functions now include targeting of ion channels and cell adhesion molecules to specialized compartments within the plasma membrane and endoplasmic reticulum of striated muscle and the nervous system, mechanical stabilization at the tissue level based on transcellular protein assemblies, participation in epithelial morphogenesis, and orientation of mitotic spindles in asymmetric cell divisions. These studies, in addition to stretching the erythrocyte paradigm beyond recognition, also are revealing novel cellular pathways essential for metazoan life. Examples are ankyrin-dependent targeting of proteins to excitable membrane domains in the plasma membrane and the Ca(2+) homeostasis compartment of the endoplasmic reticulum. Exciting questions for the future relate to the molecular basis for these pathways and their roles in a clinical context, either as the basis for disease or more positively as therapeutic targets.
Repeated Intravesical Instillations of an Adenoviral Vector in Patients With Locally Advanced Bladder Cancer: A Phase I Study of p53 Gene Therapy (2003)

Intravesical instillation of Ad5CMV-p53 is safe, feasible, and biologically active when administered in multiple doses to patients with bladder cancer. Observations from this study indicate that this treatment has an antitumor effect in superficial transitional-cell carcinoma. Improvements in the efficiency of gene transfer and the levels of gene expression are required to develop more effective gene therapy for bladder cancer.