Role of procoagulant lipids in human prothrombin activation. 1. Prothrombin activation by factor X(a) in the absence of factor V(a) and in the absence and presence of membranes.

Activation of prothrombin by factor X(a) requires proteolysis of two bonds and is commonly assumed to occur via by two parallel, sequential pathways. Hydrolysis of Arg(322)-Ile(323) produces meizothrombin (MzII(a)) as an intermediate, while hydrolysis of Arg(273)-Thr(274) produces prethrombin 2-fragment 1.2 (Pre2-F1.2). Activation by human factor X(a) of human prothrombin was examined in the absence of factor V(a) and in the absence and presence of bovine phosphatidylserine (PS)/palmitoyloleoylphosphatidylcholine (25:75) membranes. Four sets of data were collected: fluorescence of an active site probe (DAPA) was sensitive to thrombin, MzII(a), and Pre2-F1.2; a synthetic substrate (S-2238) detected thrombin or MzII(a) active site formation; and SDS-PAGE detected both intermediates and thrombin. The fluorescence data provided an internal check on the active site and SDS-PAGE measurements. Kinetic constants for conversion of intermediates to thrombin were measured directly in the absence of membranes. Both MzII(a) and Pre2-F1.2 were consumed rapidly in the presence of membranes, so kinetic constants for these reactions had to be estimated as adjustable parameters by fitting three data sets (thrombin and MzII(a) active site formation and Pre2 appearance) simultaneously to the parallel-sequential model. In the absence of membranes, this model successfully described the data and yielded a rate constant, 44 M(-1) s(-1), for the rate of MzII(a) formation. By contrast, the parallel-sequential model could not describe prothrombin activation in the presence of optimal concentrations of PS-containing membranes without assuming that a pathway existed for converting prothrombin directly to thrombin without release from the membrane-enzyme complex. The data suggest that PS membranes (1) regulate factor X(a), (2) alter the substrate specificity of factor X(a) to favor the meizothrombin intermediate, and (3) "channel" intermediate (MzII(a) or Pre2-F1.2) back to the active site of factor X(a) for rapid conversion to thrombin.     

Structural dynamics of the cell wall precursor lipid II in the presence and absence of the lantibiotic nisin

Representing a physiological “Achilles' heel”, the cell wall precursor lipid II (L_II) is a prime target for various classes of antibiotics. Over the years L_II-binding agents have been recognized as promising candidates and templates in the search for new antibacterial compounds to complement or replace existing drugs. To elucidate the molecular structural basis underlying L_II functional mechanism and to better understand if and how lantibiotic binding alters the molecular behavior of L_II, we performed molecular dynamics (MD) simulations of phospholipid membrane-embedded L_II in the absence and presence of the L_II-binding lantibiotic nisin. In a series of 2 × 4 independent, unbiased 100 ns MD simulations we sampled the conformational dynamics of nine L_II as well as nine L_II–nisin complexes embedded in an aqueous 150 mM NaCl/POPC phospholipid membrane environment. We found that nisin binding to L_II induces a reduction of L_II mobility and flexibility, an outward shift of the L_II pentapeptide, an inward movement of the L_II disaccharide section, and an overall deeper insertion of the L_II tail group into the membrane. The latter effect might indicate an initial step in adopting a stabilizing, scaffold-like structure in the process of nisin-induced membrane leakage. At the same time nisin conformation and L_II interaction remain similar to the 1WCO L_II–nisin NMR solution structure.     

Formation of meizothrombin as intermediate in factor Xa-catalyzed prothrombin activation

The conversion of prothrombin into thrombin by Factor Xa requires the cleavage of two peptide bonds in prothrombin. Dependent on the order of cleavage, prethrombin 2 or meizothrombin occurs as intermediate. Since prethrombin 2 has as yet been the only observed intermediate, prothrombin activation is generally considered to proceed via prethrombin 2. In this paper we present new methods that allow differentiation between meizothrombin and thrombin formed during the initial phase of prothrombin activation. These methods, which make use of the different reactivities of meizothrombin and thrombin toward fibrinogen and antithrombin III plus heparin, enabled us to show the generation of considerable amounts of meizothrombin during Factor Xa-catalyzed prothrombin activation. Both meizothrombin and thrombin incorporated the active site-directed fluorescent chloromethyl ketone 5-dimethylaminonaphthalene-1-sulfonyl-Glu-Gly-Arg-CH2Cl. Gel electrophoretic analysis of chloromethyl ketone-treated aliquots of prothrombin activation mixtures confirmed meizothrombin formation. These observations demonstrate that prothrombin may also be converted into thrombin via meizothrombin.     

Structural analysis of fibrinogen synthesized by cultured chicken hepatocytes in the presence or absence of dexamethasone

Hepatocyte monolayers, derived from chick embryos and cultured in chemically defined medium without hormones, synthesize and secrete fibrinogen that resembles chicken plasma fibrinogen immunochemically and structurally. Addition of a synthetic glucocorticoid, dexamethasone, to the cultured cells resulted in an appreciable and relatively selective increase in fibrinogen synthesis. Autoradiography of fibrinogen that had been metabolically labelled with [35S]methionine and then subjected to SDS-polyacrylamide gel electrophoresis, unreduced or under disulfide-reducing conditions, revealed that only dimeric forms of fibrinogen, containing undegraded A alpha, B beta, and gamma chains, were secreted under stimulated and unstimulated culture conditions.     

The prothrombinase-catalyzed activation of prothrombin proceeds through the intermediate meizothrombin in an ordered, sequential reaction

The activation of bovine prothrombin by prothrombinase (Factor Xa, Factor Va, synthetic phospholipid vesicles, and calcium ion) was studied in the presence of the fluorescent, reversible thrombin inhibitor dansylarginine-N-(3-ethyl-1,5-pentanediyl) amide (DAPA). Recordings of fluorescence intensity during prothrombin activation exhibited maxima that decreased to stable limiting values. These data suggested the transient appearance of the meizothrombin-DAPA complex, which exhibits fluorescence with 1.5-fold greater intensity than the thrombin-DAPA complex. At substrate concentrations well below Km, progress curves could be fitted by equations describing an ordered, sequential conversion of prothrombin to thrombin through the intermediate meizothrombin via two pseudo-first order steps. The pseudo-first order rate constants for both steps varied linearly with enzyme concentration, indicating that both steps are catalyzed by prothrombinase. The progress of the reaction was also monitored by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and densitometry analyses of aliquots removed at intervals spanning the reaction. These analyses confirmed both the existence of meizothrombin and its time course as predicted from the equations used to analyze fluorescence intensity profiles. Meizothrombin levels peaked at about 0.3 mol/mol initial prothrombin under the conditions typically studied. In addition, prethrombin 2, which is the intermediate expected from cleavages occurring in the order opposite that required to form meizothrombin, was not observed under any of the conditions examined. These data indicate that prothrombin activation catalyzed by the fully assembled prothrombinase complex proceeds via an ordered, sequential reaction with meizothrombin as the sole intermediate.     

The formation of vacuole membranes in the presence and absence of cell nucleus in amoebae

The formation of new vacuoles around injected algae was studied in amoebae at intervals after enucleation. Algae initially lay free for 3 h within the amoeba cytoplasm, after which they gradually became individually enclosed within single-vacuole membranes. During the initial stage of vacuole formation (4–24 h), discontinuous pieces of non-trilaminar membrane-like structures appeared around the algae, which were not associated with any preexisting membranes. Over 85 and 50% of injected algae became enclosed in vacuoles in amoebae that had been without nuclei between 0–16 and 18–36 h, respectively. Thus, it appeared that vacuole-forming activity was not under the immediate control of cell nuclei. This mode of vacuole formation suggested that the initial vacuole membranes might arise de novo.     

Sex differences in brain developing in the presence or absence of gonads

Brain sexual differentiation results from the interaction of genetic and hormonal influences. This study used a unique agonadal mouse model to determine relative contributions of genetic and gonadal hormone influences in the differentiation of selected brain regions. SF-1 knockout (SF-1 KO) mice are born without gonads and adrenal glands and are not exposed to endogenous sex steroids during fetal/neonatal development. Consequently, male and female SF-1 KO mice are born with female external genitalia and if left on their own, die shortly after birth due to adrenal insufficiency. In this study, SF-1 KO mice were rescued by neonatal adrenal transplantation to examine their brain morphology in adult life. To determine potential brain loci that might mediate functional sex differences, we examined the area and distribution of immunoreactive calbindin and neuronal nitric oxide synthase in the preoptic area (POA) and ventromedial nucleus of the hypothalamus, two areas previously reported to be sexually dimorphic in the mammalian brain. A sex difference in the positioning of cells containing immunoreactive calbindin in a group within the POA was clearly gonad dependent based on the elimination of the sex difference in SF-1 KO mice. Several other differences in the area of ventromedial hypothalamus and in POA were maintained in male and female SF-1 KO mice, suggesting gonad-independent genetic influences on sexually dimorphic brain development.     

Habitat factors and the presence or absence of otters Lutra lutra in Denmark

The purpose of the present study was to examine the relative influence of different habitat factors on ottersLutra lutra (Linnaeus, 1758) and to develop a predictive model to better understand the distribution of the otter in Denmark. During the National Otter Survey in 1991 data were collected on 19 variables which reflected aspects of habitat structure, composition, organic pollution and human disturbance. Multiple logistic regression analysis was used to estimate probabilities of the presence of otters as a function of one or more explanatory variables. Six variables (county, pH, water depth, presence of trees, bottom substrate and Saprobien-Index) were identified. In Denmark, otter habitat typically consists of water courses with depths > 1 m over a varied bottom, with pH > 7.0, Saprobien-Index on II–III to III (indicating slight organic pollution) with no trees on the banks. Some of these variables reflect highly productive waters. The use of the otter as an indicator of good water quality and/or aquatic habitat should be used with care.     

Centrin: its secondary structure in the presence and absence of cations

Centrin is a low molecular mass (20 kDa) protein that belongs to the EF-hand superfamily of calcium-binding proteins. Local and overall changes were investigated for interactions between cations and Chlamydomonas centrin using Fourier transform infrared (FT-IR) and circular dichroic (CD) spectroscopies. FT-IR spectral features studied included the amide I' band and the side-chain absorbances for aspartate residues located almost exclusively at the calcium-binding sites in the spectral region of 1700-1500 cm(-1). The amide I' band is exquisitely sensitive to changes in protein secondary structure and is observed to shift from 1626.5 to 1642.7 cm(-1) in the presence and absence of calcium. These spectral bands are complex and were further studied using two-dimensional Fourier transform infrared (2D-FT-IR) correlation along with curve-fitting routines. Using these methods the secondary structure contributions were determined for holocentrin and apocentrin. The alpha-helical content in centrin was determined to be 60%-53% in the presence and absence of cations, respectively. Furthermore, the beta-strand content was determined to be 12%-36%, while the random coil component remained almost constant at 7%-13.5% in the presence and absence of cations, respectively. Changes in the side-chain band are mostly due to the monodentate coordination of aspartate to the cation. A shift of approximately 4 cm(-1) (for the COO- antisymmetric stretch in Asp) from 1565 to 1569 cm(-1) is observed for apocentrin and holocentrin, respectively. Thermal dependence revealed reversible conformational transition temperatures for apocentrin at 37 degrees C and holocentrin at 45 degrees C, suggesting greater stability for holocentrin.     

Measuring agreement between two judges on the presence or absence of a trait.

At least a dozen indexes have been proposed for measuring agreement between two judges on a categorical scale. Using the binary (positive-negative) case as a model, this paper presents and critically evaluates some of these proposed measures. The importance of correcting for chance-expected agreement is emphasized, and identities with intraclass correlation coefficients are pointed out.     

Characteristics of interhemispheric relationships in the absence or presence of a skill

A comparative analysis of the time and amplitude characteristics of the negative N200 and positive P300 components of visual evoked potentials recorded at symmetric points of the frontal, parietal, temporal, and occipital areas of the right and left hemispheres of the cerebral cortex has been performed in subjects with or without the skill of operating a computer. Subjects inexperienced in an operator’s work exhibited an interhemispheric difference in the time and amplitude characteristics of the studied components. In subjects that had the skill of operating a computer, the interhemispheric difference was little, which suggests that the cortex plays only a small role in the cerebral control of this activity.     

EPR investigation of clomipramine interaction with phosphatidylcholine membranes in presence and absence of cholesterol

The effects of tricylic antidepressant clomipramine (CLO) on the membrane properties of saturated dimyristoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine as well as on unsaturated egg yolk phosphatidylcholine liposomes were investigated by the electron paramagnetic resonance spin-labeling technique, in combination with the simulation of the spectra, taking into account that the membrane is heterogeneous and composed of the regions with different fluidity characteristics. Different spin labels, monitoring membrane properties in the upper and inner parts of the membrane, were used. In general, two spectral components, having different motional characteristics, were detected in all liposomes investigated. In liposomes with saturated chains, CLO decreased the phase-transition temperature, disordered the membrane, and increased polarity in the upper part of the membrane. However, less impact was observed in liposomes with unsaturated chains. In dipalmitoyl phosphatidylcholine liposomes, it also induced molecular rearrangements near the pretransition temperature. The presence of 30 mol% cholesterol increased the fluidizing effect of CLO and modified the lateral diffusion of nitroxide in the inner part of the membrane. A unique anomalous increase in diffusion of nitroxide, dependent on CLO concentration, was detected in the temperature region where the phosphatidylcholine membrane without cholesterol experiences the phase transitions. Since the changes in the central part of the membrane were even more pronounced than in the upper part of the membrane, it could be concluded that CLO incorporates into the membrane with its hydrophobic ring parallel to the phospholipid chains.     

Censored linear regression in the presence or absence of auxiliary survival information

There has been a rising interest in better exploiting auxiliary summary information from large databases in the analysis of smaller-scale studies that collect more comprehensive patient-level information. The purpose of this paper is twofold: first, we propose a novel approach to synthesize information from both the aggregate summary statistics and the individual-level data in censored linear regression. We show that the auxiliary information amounts to a system of nonsmooth estimating equations and thus can be combined with the conventional weighted log-rank estimating equations by using the generalized method of moments (GMM) approach. The proposed methodology can be further extended to account for the potential inconsistency in information from different sources. Second, in the absence of auxiliary information, we propose to improve estimation efficiency by combining the overidentified weighted log-rank estimating equations with different weight functions via the GMM framework. To deal with the nonsmooth GMM-type objective functions, we develop an asymptotics-guided algorithm for parameter and variance estimation. We establish the asymptotic normality of the proposed GMM-type estimators. Simulation studies show that the proposed estimators can yield substantial efficiency gain over the conventional weighted log-rank estimators. The proposed methods are applied to a pancreatic cancer study for illustration.     

Formation of meizothrombin as intermediate in factor Xa-catalyzed prothrombin activation on endothelial cells. The influence of thrombin on the reaction mechanism

Incubation of prothrombin on cultured human umbilical vein endothelial cells with factor Xa and calcium ions induced the activation of prothrombin. The mechanism of prothrombin activation was analyzed on sodium dodecyl sulfate gels using immuno- and amido-blotting techniques. It was demonstrated that meizothrombin was formed as an intermediate in prothrombin activation on the endothelial cell surface. In addition, considerable amounts of meizothrombin des-fragment-1 accumulated during prothrombin activation and were not further converted to thrombin. Although preincubation of the endothelial cells with thrombin did not influence the formation of meizothrombin, addition of hirudin to the prothrombin activation mixture inhibited the formation of meizothrombin and meizothrombin des-fragment-1 almost completely. This indicated that the activity of endogenously formed thrombin influenced the formation of meizothrombin via a feedback mechanism. The increased formation of meizothrombin and accumulation of meizothrombin des-fragment-1 in a latter phase of prothrombin activation points to a regulatory mechanism in hemostasis which subdues the formation of the procoagulant alpha-thrombin.     

Activation of the chick oviduct progesterone receptor by heparin in the presence or absence of hormone.

Activation (transformation) of the chick oviduct progesterone receptor was found to be induced at 0 degrees C by heparin free in solution as well as by chromatography on a column of heparin linked to acrylamide/agarose. The transformed molecule displayed properties of the activated form of [3H]progesterone-receptor complex obtained by heat treatment or by high ionic strength: smaller size (s20,w = 3.9 S, Stokes radius = 5.2 nm), lower rate of dissociation (t 1/2 approx. 50 h at 0 degrees C compared with approx. 20 h for the 'native' form) and increased binding to phosphocellulose. In all cases, molybdate was an effective inhibitor of transformation and stabilized a large 'native' form (s20,w = 7.9 S, Stokes radius = 7.6 nm). Transformation by neither KCl nor heparin depended on the presence of ligand bound to the receptor, and the properties of the receptor molecule produced by treatment of ligand-free receptor with high ionic strength or with heparin were identical with those of the activated progesterone-receptor complex, demonstrating that receptor activation can be obtained experimentally in the absence of hormone. Our data are compatible with a model in which activation implies separation of the 4 S units, which compose the approx. 8 S 'native' form.     

Double base lesions in DNA X-irradiated in the presence or absence of oxygen

Previously, double lesions in which two adjacent bases are modified were identified in DNA oligomers exposed in solution to ionizing radiation. However, the formation of such lesions in polymer DNA had not been demonstrated. Using reference oligomer containing a specific double lesion and employing liquid chromatography-mass spectrometry (LC-MS), it was possible to show directly that double lesions are formed in irradiated calf thymus DNA. The double lesion in which a pyrimidine base is degraded to a formamido remnant and an adjacent guanine base is oxidized to 8-oxoguanine was detected in DNA X-irradiated in oxygenated aqueous solution. The double lesion in which the methyl carbon atom of a thymine base is covalently linked to carbon at the 8-position of an adjacent guanine base was detected in DNA irradiated in a deoxygenated environment.     

Glycolate biosynthesis by Scenedesmus and Chlorella in the presence or absence of NaHCO3

Summary Both Scenedesmus and Chlorella excreted comparable quantities of glycolate. Glycolate formation was dependent upon light and oxygen, but occured in the absence of added CO₂ or NaHCO₃ for net photosynthesis. In an environment of 3000 ft. c. light and an atmosphere of oxygen, about 35 g glycolate were excreted per hour per milliliter 1% (v/v) algae without NaHCO₃ or CO₂. Upon addition of NaHCO₃ the rate increased to about 55 g. Glycolate formation in the light in the absence of CO₂ may result from photometabolism of algal polysaccharides.Glycolate excretion by Scenedesmus occurred at all pH values between 6.5 and 9.5 and was not related to utilization of bicarbonate. Scenedesmus obliquus excreted glycolate when existing in plates of four or eight cells, but not when present as small individual cells.At pH 9 ¹⁴C fixation by Scenedesmus was faster than fixation by Chlorella. There was no significant difference in products of ¹⁴C fixation formed by Scenedesmus at pH values between 6.5 and 9.5.For unknown reasons -hydroxy-2-pyridinemethanesulfonate stimulated CO₂ fixation by Scenedesmus by at least 100%. This sulfonate had no effect on glycolate excretion nor upon the distribution of ¹⁴C among the products of ¹⁴CO₂ fixation by Scenedesmus.Supported in part by NSF Grant GB-4154 and published with the approval of the Director of the Michigan Agricultural Experiment Station as journal article No. 3946. The research was initiated during the period when N. E. Tolbert was supported in part by a National Institutes of Health Senior Fellowship at the Biochemisches Institut, Universität, Freiburg/Br., Germany.