gebhart/patrepeval huggingface dataset:
Solid-Phase Minisequencing as a Tool to Detect DNA Polymorphism (2003)

Single-base substitutions, which give rise to biallelic sequence polymorphism, have been estimated to occur on the average at one out of a thousand nucleotides in the human genome (1). Analysis of this allelic variation can be utilized in population genetic studies, in genetic-linkage analysis, for the discrimination between individuals and for tissue typing. Genotyping by analyzing single-nucleotide polymorphisms provides some clear advantages compared to genotyping by analyzing multiallelic microsatellite markers. The mutation rate of single nucleotides is lower, single-base substitutions can be detected by technically simple, automatable methods, and the computational interpretation of the results is simpler.
Characterization of a type II collagen gene (COL2A1) mutation identified in cultured chondrocytes from human hypochondrogenesis. (1992)

A subtle mutation in the type II collagen gene COL2A1 was detected in a case of human hypochondrogenesis by using a chondrocyte culture system and PCR-cDNA scanning analysis. Chondrocytes obtained from cartilage biopsies were dedifferentiated and expanded in monolayer culture and then redifferentiated by culture over agarose. Single-strand conformation polymorphism and direct sequencing analysis identified a G----A transition, resulting in a glycine substitution at amino acid 574 of the pro alpha 1(II) collagen triple-helical domain. Morphologic assessment of cartilage-like structures produced in culture and electrophoretic analysis of collagens synthesized by the cultured chondrocytes suggested that the glycine substitution interferes with conversion of type II procollagen to collagen, impairs intracellular transport and secretion of the molecule, and disrupts collagen fibril assembly. This experimental approach has broad implications for the investigation of human chondrodysplasias as well as human chondrocyte biology.
The Arabidopsis eer1 Mutant Has Enhanced Ethylene Responses in the Hypocotyl and Stem (2001)

By screening for enhanced ethylene-response (eer) mutants in Arabidopsis, we isolated a novel recessive mutant, eer1, which displays increased ethylene sensitivity in the hypocotyl and stem. Dark-grown eer1 seedlings have short and thick hypocotyls even in the absence of added ethylene. This phenotype is suppressed, however, by the ethylene biosynthesis inhibitor 1-aminoethoxyvinyl-glycine. Following ethylene treatment, the dark-grown eer1 hypocotyl response is greatly exaggerated in comparison with the wild type, indicating that the eer1 phenotype is not simply due to ethylene overproduction. eer1 seedlings have significantly elevated levels of basic-chitinase expression, suggesting that eer1 may be highly sensitive to low levels of endogenous ethylene. Adult eer1 plants display exaggerated ethylene-dependent stem thickening, which is an ethylene response previously unreported in Arabidopsis. eer1 also has enhanced responsiveness to the ethylene agonists propylene and 2,5-norbornadiene. The eer1 phenotype is completely suppressed by the ethylene-insensitive mutation etr1-1, and is additive with the constitutive ethylene-response mutation ctr1-3. Our findings suggest that the wild-type EER1 product acts to oppose ethylene responses in the hypocotyl and stem.
RNA polymerase I catalysed transcription of insert viral cDNA (1993)

RNA polymerase I has been used for transcription of influenza hemagglutinin (HA) cDNA precisely linked in the anti-sense configuration to both mouse rDNA promoter and terminator segments. In transcription reactions based on Ehrlich ascites cell nuclear extracts, specific uniform RNA products are synthesized in high rates that are comparable to original rDNA template transcriptions. Primer extension reactions show the 5' ends of these RNA transcripts to be located exactly at position +1, corresponding to the 5' end of negative strand HA viral RNA. RNA 3' ends in a first series of constructs were found extended beyond the accepted location of pre-rRNA 3' ends, in using both hybrid cDNA and original rDNA templates. But upon deletion of six basepairs from the rDNA termination region RNA polymerase I transcription has been adapted to yield correctly terminated influenza viral RNA in vitro. This result has been confirmed in an in vivo experiment via synthesis of an anti-sense viral RNA molecule containing the chloramphenicol acetyltransferase (CAT) gene, which in turn is recognized at its terminal sequence by viral RNA dependent RNA polymerase for plus strand mRNA synthesis and expression of CAT activity.
Influence of IL-6 on MDR and MRP-mediated multidrug resistance in human hepatoma cells (2001)

The objective of this study was to examine effects of interleukin-6 (IL-6) on the expression and activity of the drug resistance transporters (MDR1 and MRP) in human hepatoma cell lines. Expression and activity of MDR1 and MRP transporters were examined in IL-6-treated and control HuH 7 and HepG2 cells using semi-quantitative RT-PCR analysis and by rhodamine 123 and 5-carboxyfluorescin efflux assays. Results from RT-PCR demonstrated expression of MRP3, MRP6, and MDR1 in HuH 7 cells and expression of MRP1, MRP2, MRP3, MRP6, and MDR1 in HepG2 cells. Compared with controls, treatment of HuH 7 cells with IL-6 (10 ng/mL, 24 h) resulted in a 1.8-fold increase in MRP-mediated efflux of 5-CF with a corresponding 1.5-fold induction of MRP3 mRNA levels (p < 0.05). Similarly, in HepG2 cells, a 2-fold increase in MRP functional activity and a 1.8-fold induction of MRP1 mRNA levels were seen in the IL-6 treated cells (p < 0.05). Treatment of cells with IL-6 was also found to cause significant reductions in the expression and activity of MDR1 in HuH 7 cells, but not in HepG2 cells. Our data suggest that IL-6 induces MRP expression and activity in human hepatoma cell lines. Suppressive effects of IL-6 on MDR1 expression and activity were also observed in HuH 7 cells. This underscores the importance of examining the regulation of multiple drug resistance proteins as these proteins may have opposing regulatory mechanisms in malignant cells.
Kinetic isotope effects and ‘metabolic switching’ in cytochrome P450‐catalyzed reactions (1987)

Abstract The mechanistic significance of a kinetic isotope effect on a cytochrome P‐450catalyzed reaction depends, fundamentally, on the nature of the interaction of the substrate with the active site of the enzyme as well as on the nature of the chemistry of the reaction catalyzed. Consequently, kinetic isotope effects can be used to extract information on the topology of the enzyme and the mechanism of substrate oxidation. Kinetic isotope effect studies are sometimes accompanied by ‘metabolic switching’ or a change in metabolic pathway, catalyzed either by the same enzyme or by a different enzyme. For the specific case where ‘metabolic switching’ gives rise to a change in regional specificity for the cytochrome P‐450 catalyzed metabolism of a compound, this change can be explained in terms of the topological constraints on substrate binding imposed by the active site of the enzyme.
Dynamics of Periodic Pulse Collisions in a Strongly Dissipative-Dispersive System (2005)

We report on the dynamics of the periodic collision process occurring between different pulse bound states in a stretched-pulse erbium-doped fiber laser. The acquisition of a large number of second-order correlation traces allows us to reconstruct the dynamics of a single collision event. The measurements clearly demonstrate that, unlike true solitons in the case of integrable systems, the pulses do not fully overlap in the course of a collision. Instead, the collision proceeds through the exchange of bonds between the individual pulses constituting the bound states.
Structure‐Function Studies of the Plant Cyclotides: The Role of a Circular Protein Backbone (2003)

The traditional idea of proteins as linear chains of amino acids is being challenged with the discovery of miniproteins that contain a circular backbone. The cyclotide family is the largest group of circular proteins and is characterized by an amide‐circularized protein backbone and six conserved cysteine residues. These conserved cysteines are paired to form a knotted network of disulfide bonds. The combination of the circular backbone and a cystine knot, known as the cyclic cystine knot (CCK) motif, confers exceptional stability upon the cyclotides. This review discusses the role of the circular backbone based on studies of both the oxidative folding of kalata B1, the prototypical cyclotide, and a comparison of the structure and activity of kalata B1 and its acyclic permutants.
Molecular cloning and expression of alternatively spliced PITSLRE protein kinase isoforms. (1994)

Minimal ectopic expression of the p58GTA protein kinase results in a provocative phenotype involving cell cycle delay, mitotic catastrophe, and decreased cell viability. In addition, this kinase is well conserved evolutionarily, ubiquitously expressed, and its genes map to a position on human chromosome 1 frequently deleted in the late stages of tumorigenesis. Here we report that the p58GTA protein kinase is a member of a larger subfamily of proteins. The mRNAs encoding these proteins are generated by alternative splicing from multiple duplicated genes. These isoforms range in size from 50 to 110 kDa. Divergence between the alternatively spliced isoforms is localized to the amino-terminal region of the molecule. The entire p58GTA open reading frame is conserved in most of these p58GTA isoforms. The predicted sequences of the larger isoforms encode bipartite nuclear localization signal sequences and extensive polyglutamic acid domains. Antibodies to the p58GTA isoform were used to confirm the presence of the alternatively spliced isoforms in different cell types as well as identify two additional isoforms that appear to arise from a separate gene(s). Cellular fractionation studies indicate that one of the isoforms is found only in the nucleus, and the remainder are found in both the cytoplasm and the nucleus. Expression and localization of some p58GTA isoforms suggest that they may have specialized cellular functions. Because of the large number of isoforms generated from multiple genes we propose naming these kinases PITSLRE alpha 1, alpha 2-1, alpha 2-2, alpha 2-3 alpha 2-4, beta 1, beta 2-1, and beta 2-2 based on the conserved sequence of the PSTAIRE box unique to p34cdc2 kinases and the gene from which they are transcribed.
Interleukin 2 Regulates Expression of Its Receptor and Synthesis of Gamma Interferon by Human T Lymphocytes (1984)

Interleukin 2 (IL-2) has an important role in the regulation of the expression of IL-2 receptors and the synthesis of gamma interferon (IFN-gamma) by T lymphocytes. IL-2 is required for the optimum expression of IL-2 receptors on activated T lymphocytes and for maximum synthesis of IFN-gamma in vitro. Dexamethasone, an immunosuppressant drug that inhibits IL-2 synthesis, diminished the expression of IL-2 receptors and the synthesis of IFN-gamma. Anti-Tac, a monoclonal antibody known to prevent the binding of IL-2 to its receptor without inhibiting IL-2 synthesis, down-regulated the expression of the receptor and partially inhibited synthesis of IFN-gamma. In a population of T lymphocytes prevented from synthesizing IL-2 by dexamethasone and incapable of using IL-2 as a result of blockage of IL-2 receptors by anti-Tac, the number of receptor-bearing cells and receptor density were diminished. Anti-Tac in combination with dexamethasone also exerted a synergistic effect on IFN-gamma synthesis, inhibiting it almost completely. The inhibitory effect of dexamethasone IFN-gamma synthesis may be of clinical importance, since IFN-gamma activates macrophages and thereby triggers one of the defense mechanisms against bacterial infections.
The antigen-binding capacity of the peptide chains of horse antibodies (1966)

The antigen-binding capacity of the peptide chains of horse anti-(diphtheria toxin) has been studied by using (125)I-labelled toxoid and electrophoresis of antibody-antigen mixtures on cellulose acetate. The heavy chains retained about 20% of the activity of the whole antibody and the light chains less than 5%. Recombination of specific heavy and light chains gave about 60% recovery of activity and recombination of specific heavy chains and non-specific light chains about 40% recovery. It is suggested that these results favour the heavy chain as the major site of the antigen-binding activity.
Adeno-Associated Virus Types 5 and 6 Use Distinct Receptors for Cell Entry (2006)

The transduction efficiency of adeno-associated virus (AAV) vectors in various somatic tissues is determined primarily by the viral capsid proteins. In contrast to vectors made with AAV type 2 capsids, those having type 5 or 6 capsids show high transduction rates in airway epithelial cells, in a range that should be sufficient for treating lung disease. Here we have compared the properties of vectors made with AAV5 or AAV6 capsid proteins to determine whether their receptor usage is similar, and found several differences between the viruses. First, an AAV6 vector did not hemagglutinate red blood cells, whereas an AAV5 vector did, and this property was sialic acid dependent. Second, AAV5 vector transduction required sialic acid in all cells tested, whereas AAV6 vector transduction was sialic acid dependent or independent, depending on the target cells tested. Third, levels of an AAV6 vector that interfered with entry of another AAV6 vector only poorly inhibited AAV5 vector transduction and vice versa. These results indicate that AAV5 and AAV6 vectors use distinct cellular receptors for cell entry. Although both AAV5 and AAV6 vectors exhibited high transduction rates in well-differentiated human airway epithelial cultures, they exhibited distinct cell-type transduction profiles in mouse lung that may reflect differences in receptor usage.
Multichannel bidirectional transmission using a WDM MUX/DMUX pair and unidirectional in-line amplifiers (1997)

We propose a repeated bidirectional WDM transmission system using cascaded WDM MUX/DMUX pairs as narrow-bandpass filters and reflection attenuators. Fiber span is increased by inserting unidirectional EDFAs between WDM MUX/DMUX pair as in-line amplifiers. A three-channel hybrid system with one 10-Gb/s and two 2.5-Gb/s channels is also demonstrated In the 1550-nm region for transmission over 150 km of dispersion-shifted fiber. Negligible power penalty due to back reflection was observed.
Oxidative Stress-Related Biomarkers in Essential Hypertension and Ischemia-Reperfusion Myocardial Damage (2013)

Cardiovascular diseases are a leading cause of mortality and morbidity worldwide, with hypertension being a major risk factor. Numerous studies support the contribution of reactive oxygen and nitrogen species in the pathogenesis of hypertension, as well as other pathologies associated with ischemia/reperfusion. However, the validation of oxidative stress-related biomarkers in these settings is still lacking and novel association of these biomarkers and other biomarkers such as endothelial progenitor cells, endothelial microparticles, and ischemia modified albumin, is just emerging. Oxidative stress has been suggested as a pathogenic factor and therapeutic target in early stages of essential hypertension. Systolic and diastolic blood pressure correlated positively with plasma F2-isoprostane levels and negatively with total antioxidant capacity of plasma in hypertensive and normotensive patients. Cardiac surgery with extracorporeal circulation causes an ischemia/reperfusion event associated with increased lipid peroxidation and protein carbonylation, two biomarkers associated with oxidative damage of cardiac tissue. An enhancement of the antioxidant defense system should contribute to ameliorating functional and structural abnormalities derived from this metabolic impairment. However, data have to be validated with the analysis of the appropriate oxidative stress and/or nitrosative stress biomarkers.
Cloning and Expression of a Novel MAPKK-like Protein Kinase, Lymphokine-activated Killer T-cell-originated Protein Kinase, Specifically Expressed in the Testis and Activated Lymphoid Cells (2000)

A novel protein kinase, TOPK (T-LAK cell-originated protein kinase), was isolated from a lymphokine-activated killer T (T-LAK) cell subtraction cDNA fragment library. The open reading frame of the TOPK gene encodes a protein of 322 amino acids, possessing a protein kinase domain profile. The cap site analysis of the 5'-end of TOPK mRNA revealed two forms, a major full-length form and a minor spliced form at the 5'-site, both encoding the same protein. A BLAST homology search and phylogenetic analysis indicated that TOPK is related to dual specific mitogen-activated protein kinase kinase (MAPKK). The transfection of the TOPK gene to COS-7 cells up-regulated a phosphorylation of p38 MAPK but not ERK1/2 or SAPK/JNK. Gel precipitation study indicated that TOPK protein can be associated with p38 in vitro. Tissue distribution of TOPK mRNA expression was specific for the testis, T-LAK cells, activated lymphoid cells, and lymphoid tumors. On the other hand, deactivated T-LAK cells did not show TOPK mRNA expression. These data suggest that TOPK is a newly identified member of a novel MEK3/6-related MAPKK that may be enrolled in the activation of lymphoid cells and support testicular functions.
Differential effects of nitrogen mustardin vivoon the cancer and host cells in MCa‐11 tumours (1995)

We analysed the effects of nitrogen mustard (HN2) on the growth, cell cycle distributions, and ratios of tumour cells to host cells for MCa-11 tumours grown in vivo. Treatment of tumour-bearing BALB/c mice with 3 mg/kg of HN2 produced a significant slowing of MCa-11 tumour growth. Seventy-two hours after treatment in vivo with either 3 or 4 mg/kg of HN2, the host cells in the treated tumours showed a significantly decreased G0/G1 peak and an increased G2/M peak (P < 0.01), whereas the cancer cells in the treated tumours showed significant increases in the G0/G1 peak coupled with relatively decreased proportions of S and G2/M tumour cells (P < 0.001). The ratio of the total number of cancer cells to the total number of host cells in the tumours was significantly increased 72 h after HN2 administration (P < 0.01). Thirty-two days after treatment with HN2, the cell cycle distributions of the host and tumour cells in the treatment and control tumours had returned to being identical, but the ratio of the total number of cancer cells to the total number of host cells remained increased in the treated tumours (P < 0.01). These results show that the administration in vivo of HN2 can lead to entirely different cell cycle effects for the host and cancer cells in the same tumour, and that the partial growth arrest of MCa-11 tumours from HN2 treatment may be due in part to the preferential destruction of host cells rather than solely to a direct cytotoxic effect on the cancer cells.
Erythropoietin Administration Increases Production and Reactivity of Platelets in Dogs (1997)

Administration of erythropoietin (EPO) to adult dogs resulted in a dramatic increase in the number of thiazole orange-positive (TO+) platelets, also referred to as reticulated platelets. Pre-treatment level of TO+ platelets was 6.2 +/- 0.5% (mean +/- 1 SE: n = 5); following day 5 of treatment with 500 U EPO/kg/day, the percentage of TO+ platelets peaked at 16.8 +/- 2.3% (n = 5; p <0.02). After cessation of the hormone, the number of TO+ platelets fell rapidly to below starting levels. Unexpectedly, there was a significant decline in total platelet count during EPO administration despite an increased level of TO+ platelets. To assess platelet reactivity, total platelets and TO+ platelets from EPO-treated dogs were analyzed for thrombin-responsiveness as quantitated by P-selectin expression on the cell surface; reactivity was expressed as a thrombin EC50, the thrombin concentration required to activate 50% of platelets. Both total and TO+ platelets were hyperreactive during EPO treatment when compared either to pre-treatment values or to control animals. Thrombin EC50 values for total and TO+ platelets on day 5 fell to 66.5 +/- 5.4% (mean +/- 1 SE; n = 5; p <0.02) and 62.2 +/- 8.7% (n = 5; p <0.025), respectively, of pre-treatment levels. These data indicate that EPO not only promotes the synthesis of increased numbers of TO+ platelets in the dog but that these newly produced platelets are hyperreactive when compared to TO+ platelets from control animals.
Bone turnover markers and bone density across the menopausal transition. (1996)

We measured lunbar spine and femoral neck bone mineral density (BMD); urine markers of bone resorption; serum markers of bone formation; and serum gonadotrophin, estradiol and inhibin concentrations in a population-based cohort of 281 women aged 45-57 yr. Women were classified into pre-, peri-, and postmenopausal groups, depending on menstrual bleeding patterns. Compared with premenopausal women, BMD was lower only in postmenopausal women but not in women currently using hormone replacement therapy (HRT). BMD decreased with age in the perimenopausal group. Compared with premenopausal women, perimenopausal women had 20% greater urine N-telopeptide excretion (P < 0.05) and a doubling of gonadotrophin levels (P < 0.01), whereas serum estradiol and bone formation marker concentrations were no different. Postmenopausal Women had greater levels of bone turnover markers (P < 0.0001), except free deoxypyridinoline and type I procollagen propeptide. Among postmenopausal women, bone resorption markers were lower in those using HRT. Levels of nearly all bone turnover markers were positively related to serum FSH concentrations (P < 0.0001). Overall, the major independent predictors of BMD were age, urine N-telopeptide, serum bone alkaline phosphatase, and serum, FSH, whereas urine free deoxypyridinoline was positively related to BMD in pre- and perimenopausal women. In conclusion, the perimenopause is associated with elevated bone resorption rates and declining BMD, and factors in addition to estrogen deficiency may also contribute to the pathogenesis of postmenopausal osteoporosis.
Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction (1989)

Calculations of the free energy profile for the first two (rate-limiting) steps of the staphylococcal nuclease catalyzed reaction are reported. The calculations are based on the empirical valence bond method in combination with free energy perturbation molecular dynamics simulations. The calculated activation free energy is in good agreement with experimental kinetic data, and the catalytic effect of the enzyme is reproduced without any arbitrary adjustment of parameters. The enormous reduction of the activation barrier (relative to the reference reaction in water) appears to be largely associated with the strong electrostatic effect of the Ca2+ ion and the two arginine residues in the active site. This favorable electrostatic environment reduces the cost of the general-base catalysis step by almost 15 kcal/mol (by stabilizing the OH- nucleophile) and then stabilizes the developing negative charge on the 5'-phosphate group in the second step of the reaction by about 19 kcal/mol. The basic features of the originally postulated enzyme mechanism (Cotton et al., 1979) are found to be compatible with the observed activation free energy. However, the proposed modification of the mechanism (Sepersu et al., 1987), in which Arg 87 interacts only with the pentacoordinated transition state, is supported by the simulations. Further calculations on the D21E mutant also give results in good agreement with kinetic data.