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PubMed2004

A proposed mechanism for the reductive ring opening of the cyclodiphosphate MEcPP, a crucial transformation in the new DXP/MEP pathway to isoprenoids based on modeling studies and feeding experiments.

Experimental and theoretical investigations concerning the second-to-last step of the DXP/MEP pathway in isoprenoid biosynthesis in plants are reported. The proposed intrinsic or late intermediates 4-oxo-DMAPP (12) and 4-hydroxy-DMAPP (11) were synthesized in deuterium- or tritium-labeled form according to new protocols especially adapted to work without protection of the diphosphate moiety. When the labeled compounds MEcPP (7), 11, and 12 were applied to chromoplast cultures, aldehyde 12 was not incorporated. This finding is in agreement with a mechanistic and structural model of the responsible enzyme family: a three-dimensional model of the fragment L271-A375 of the enzyme GcpE of Streptomyces coelicolor including NADPH, the Fe(4)S(4) cluster, and MEcPP (7) as ligand has been developed based on homology modeling techniques. The model has been accepted by the Protein Data Bank (entry code 1OX2). Supported by this model, semiempirical PM3 calculations were performed to analyze the likely catalysis mechanism of the reductive ring opening of MEcPP (7), hydroxyl abstraction, and formation of HMBPP (8). The mechanism is characterized by a proton transfer (presumably from a conserved arginine 286) to the substrate, accompanied by a ring opening without high energy barriers, followed by the transfer of two electrons delivered from the Fe(4)S(4) cluster, and finally proton transfer from a carboxylic acid side chain to the hydroxyl group to be removed from the ligand as water. The proposed mechanism is in agreement with all known experimental findings and the arrangement of the ligand within the enzyme. Thus, a very likely mechanism for the second to last step of the DXP/MEP pathway in isoprenoid biosynthesis in plants is presented. A principally similar mechanism is also expected for the reductive dehydroxylation of HMBPP (8) to IPP (9) and DMAPP (10) in the last step.

Catalysis↗

PubMedDate not supplied

Development of a new model to investigate the fetal nociceptive pathways.

OBJECTIVE: The aim of the study was to develop an experimental model to investigate the fetal nociceptive pathways and fetal analgesia. METHODS: We tested the electromyographic (EMG) response from the biceps femoris to electrical stimulation of the sural nerve in chronically-prepared fetal lambs with and without sufentanil. RESULTS: An EMG response could be recorded 140 ms after the electrical stimulation above a threshold of current's intensity. The response presents the characteristics of a nociceptive flexion reflex. The reflex magnitude increased with the stimulus intensity. Sufentanil decreased the response. Bradycardia was noted 10 s after the stimulation and was not observed after sufentanilinfusion. Catecholamine concentrations were not altered by the stimulation. CONCLUSION: Our study shows that a nociceptive flexion reflex can be recorded in the ovine fetus. We suggest that this reflex can be used as a new tool to study the ontogenesis of the nociceptive pathways and the effects of analgesic drugs during fetal life.

Analgesia↗

PubMed1993

Magnocellular pathway for rotation invariant Neocognitron.

In the mammalian visual system, magnocellular pathway and parvocellular pathway cooperatively process visual information in parallel. The magnocellular pathway is more global and less particular about the details while the parvocellular pathway recognizes objects based on the local features. In many aspects, Neocognitron may be regarded as the artificial analogue of the parvocellular pathway. It is interesting then to model the magnocellular pathway. In order to achieve "rotation invariance" for Neocognitron, we propose a neural network model after the magnocellular pathway and expand its roles to include surmising the orientation of the input pattern prior to recognition. With the incorporation of the magnocellular pathway, a basic shift in the original paradigm has taken place. A pattern is now said to be recognized when and only when one of the winners of the magnocellular pathway is validified by the parvocellular pathway. We have implemented the magnocellular pathway coupled with Neocognitron parallel on transputers; our simulation programme is now able to recognize numerals in arbitrary orientation.

Algorithms↗

PubMed2002

Noninvasive imaging of spontaneous retinoblastoma pathway-dependent tumors in mice.

Identification of the critical pathways involved in tumorigenesis should ultimately lead to the design of better anticancer agents that target specific components of the disrupted pathways. Murine models of spontaneous cancer in which tumor formation is dependent on defined genetic alterations provide a powerful test system for evaluating the therapeutic efficacy of pathway-specific antineoplastics. We have generated a conditional mouse model for retinoblastoma-dependent sporadic cancer that permits noninvasive monitoring of pituitary tumor development in live animals via in vivo bioluminescence imaging of luciferase expression. We show that the high sensitivity of bioluminescence imaging can be used for noninvasive detection of luciferase expression in pituitary glands from tumor-free animals and for in vivo quantitation of tumor burden over a large dynamic range. This mouse model permits longitudinal monitoring of tumor onset, progression, and response to therapy and may be used effectively for testing cancer prevention and treatment strategies based on therapeutics that specifically target the retinoblastoma pathway.

Animals↗

PubMed1999

IgG and complement-mediated tissue damage in the absence of C2: evidence of a functionally active C2-bypass pathway in a guinea pig model.

In vitro complement-mediated lysis of heavily sensitized sheep erythrocytes by C4-deficient (C4D) guinea pig and C2-deficient (C2D) human sera was demonstrated some years ago. It was postulated that these "complement-bypass" pathways resulted from activation of C1 and components of the alternative pathway. We used normal, C2D, and C4D guinea pigs in a Forssman shock model to test the in vivo relevance of the C2- and C4-bypass pathways of complement activation. High concentrations of both anti-Forssman Ab and C2D or C4D guinea pig serum induced efficient lysis of sheep erythrocytes in vitro. The most efficient lysis was observed when IgG Ab and C2D guinea pig serum were used. Blocking either the classical pathway (treatments with EGTA-Mg2+ or soluble recombinant complement receptor type 1 (sCR1)) or the alternative pathway (treatment with heating at 50 degrees C, sCR1, or soluble recombinant CR1 lacking the first of the four long homologous repeat sequences (sCR1[desLHR-A])) inhibited lysis; both pathways were required for lysis of sheep erythrocytes by C2D and C4D guinea pig sera. i.v. injection of anti-Forssman Ab in normal guinea pigs resulted in rapid death from pulmonary shock, whereas C4D guinea pigs had no adverse effect. Surprisingly, C2D guinea pigs either died in a delayed fashion or had a sublethal reaction. sCR1 treatment prevented Forssman shock in both normal and C2D guinea pigs, whereas sCR1[desLHR-A] prevented Forssman shock only in C2D animals. Our results suggest that the C2-bypass pathway occurs in vivo to produce tissue damage. Activation of complement in the absence of C2 appears to be far more efficient than in the absence of C4.

Anaphylaxis↗

PubMed2000

GSH extrusion and and the mitochondrial pathway of apoptotic signalling.

New evidence suggests that physiological and damaging agents activate two different pathways of apoptotic signalling, which are mediated by protein-protein interactions and mitochondrial alterations respectively. The two pathways converge at the activation of caspase 3, the key effector of the execution phase of apoptosis, thus giving similar final results. The knowledge that different biochemical routes exist allows us to re-evaluate previous apparently contradictory results concerning the events occurring during apoptosis, and their respective roles. In particular, this applies to the role of oxidative stress and redox imbalance in the signal transduction events of apoptosis. It now appears that oxidative alterations are absent, or at least unnecessary, for the development of the physiological pathway. Instead, clear indications are emerging showing that redox imbalance is required for the damage-induced mitochondrial pathway. This is suggested by the finding that the depletion of glutathione, a common event in damage-induced apoptosis, is necessary and sufficient to induce cytochrome c release, the key event of this pathway. A model is proposed with GSH efflux as the backbone of the damage-induced apoptotic pathway.

Animals↗

PubMed2005

Causal models of attention-deficit/hyperactivity disorder: from common simple deficits to multiple developmental pathways.

Until recently, causal models of attention-deficit/hyperactivity disorder (ADHD) have tended to focus on the role of common, simple, core deficits. One such model highlights the role of executive dysfunction due to deficient inhibitory control resulting from disturbances in the frontodorsal striatal circuit and associated mesocortical dopaminergic branches. An alternative model presents ADHD as resulting from impaired signaling of delayed rewards arising from disturbances in motivational processes, involving frontoventral striatal reward circuits and mesolimbic branches terminating in the ventral striatum, particularly the nucleus accumbens. In the present article, these models are elaborated in two ways. First, they are each placed within their developmental context by consideration of the role of person x environment correlation and interaction and individual adaptation to developmental constraint. Second, their relationship to one another is reviewed in the light of recent data suggesting that delay aversion and executive functions might each make distinctive contributions to the development of the disorder. This provides an impetus for theoretical models built around the idea of multiple neurodevelopmental pathways. The possibility of neuropathologic heterogeneity in ADHD is likely to have important implications for the clinical management of the condition, potentially impacting on both diagnostic strategies and treatment options.

Animals↗

PubMed2005

How growth affects the fate of cellular metabolites.

Cellular metabolites frequently have more than a single function in the cell. For example they may be sources of energy as well as building blocks for several macromolecules. The relative cellular needs for these different functions depend on environmental and intracellular factors. The intermediary products of phosphorylation of pyruvate by mitochondria, for example, are used for growth, while the released ATP is used for both growth and maintenance. Since maintenance has priority over growth, and maintenance is proportional to a cell's mass, a cell's need for ATP vs. building blocks depends on the growth rate, and hence on substrate availability. We show how the concept of Synthesising Units (SUs) in linear and cyclic pathways takes care of the correct variation of the ATP/building block ratio in the context of the Dynamic Energy Budget (DEB) theory. This can only be achieved by an interaction between subsequent SUs in transferring metabolites. Apart from this interaction we also needed an essential feature of the performance of the pathway in the DEB context: the relative amount of enzymes varies with the growth rate in a special way. We solved an important consistency problem between the DEB model at the whole-cell level and a model for pathway dynamics. We observe that alternative whole-cell models, such as the Marr-Pirt model, that keep the relative amount of enzymes constant, and hence independent of the growth rate, will have problems in explaining how pathways can meet cells' growth-dependent needs for building blocks vs. ATP.

Adenosine Triphosphate↗

PubMed1984

Regulation of human B-cell activation, proliferation, and differentiation by soluble factors.

This review describes a series of studies performed in our laboratory which have focused on the activation and subsequent proliferation and differentiation of human B lymphocytes. Utilizing polyclonal signals which activate B cells by interacting with their surface membrane Ig, we have examined the events in the transition of a resting B lymphocyte to an Ig-secreting cell. A major theme in these studies is the role of soluble factors in B cell proliferation and B cell differentiation. Specific B cell growth and differentiation factors are described. Data on their sources, biochemical characterization, and methods of assay are included. Additionally, the potential role of interleukin 2 in human B cell function is discussed. The recognition that B cells exist in a variety of activation states and that transition between different states is dependent upon different signals was the impetus for a series of studies which more precisely delineated these states and the signals involved. These findings and the observations from other investigators led to a proposed model of the sequential steps in a factor-dependent B cell differentiation pathway. This model is discussed and related to the mechanisms of T cell activation and growth. Finally, the effects of two pharmacologic agents, glucocorticoids and cyclosporin A, on human B cell function are described and discussed in the context of this model.

Antigens, Differentiation, B-Lymphocyte↗

PubMed1997

Contrast gain control and fine spatial discriminations.

The effect of contrast gain control mechanisms on discrimination between highly similar simple and complex stimuli is examined, with a focus on how discrimination accuracy changes as a function of the contrast of stimulus components. Two models of contrast gain control are evaluated. In both, the response of each pathway is attenuated by a factor determined by the total activity in a large pool of pathways. One model bases attenuation on the sum of linear filter responses within this pool; the other, based on Heeger's contrast energy-driven model [J. Neurophysiol. 70, 1985 (1993)], uses squared filter response. Predictions generated from the models are compared with data from experiments reported here and from the literature. Predictions are made for simple grafting stimuli of different sizes and for stimuli to which a second grafting component is added either as a second cue or as a mask. With one exception, predictions of the models agree closely with each other and with the data. The exception is a masking study that differentiates the models and supports the filter-driven model over the energy-driven model.

Contrast Sensitivity↗

PubMed2000

The Saccharomyces cerevisiae RAD6 group is composed of an error-prone and two error-free postreplication repair pathways.

The RAD6 postreplication repair and mutagenesis pathway is the only major radiation repair pathway yet to be extensively characterized. It has been previously speculated that the RAD6 pathway consists of two parallel subpathways, one error free and another error prone (mutagenic). Here we show that the RAD6 group genes can be exclusively divided into three rather than two independent subpathways represented by the RAD5, POL30, and REV3 genes; the REV3 pathway is largely mutagenic, whereas the RAD5 and the POL30 pathways are deemed error free. Mutants carrying characteristic mutations in each of the three subpathways are phenotypically indistinguishable from a single mutant such as rad18, which is defective in the entire RAD6 postreplication repair/tolerance pathway. Furthermore, the rad18 mutation is epistatic to all single or combined mutations in any of the above three subpathways. Our data also suggest that MMS2 and UBC13 play a key role in coordinating the response of the error-free subpathways; Mms2 and Ubc13 form a complex required for a novel polyubiquitin chain assembly, which probably serves as a signal transducer to promote both RAD5 and POL30 error-free postreplication repair pathways. The model established by this study will facilitate further research into the molecular mechanisms of postreplication repair and translesion DNA synthesis. In view of the high degree of sequence conservation of the RAD6 pathway genes among all eukaryotes, the model presented in this study may also apply to mammalian cells and predicts links to human diseases.

Adenosine Triphosphatases↗

PubMed1997

A blinded trial of local recombinant tissue factor pathway inhibitor versus either local or systemic heparin in a vein bypass model.

PURPOSE: Tissue factor pathway inhibitor (TFPI), an endogenous protease, is a potent inhibitor of the extrinsic pathway of coagulation. To determine whether TFPI could be used as an alternative to systemic heparin and dextran in vein bypass grafting procedures, we compared the efficacy of these agents in a blinded trial using a pig model of lower extremity vein bypass grafting. METHODS: Yorkshire pigs (60 to 75 kg) were divided into four groups of five each: systemic heparin (5 ml 10(3) U heparin, 50 ml intravenous dextran, and 10 U heparin/ml flush), local heparin (5 ml saline solution, 50 ml intravenous dextran, and 10 U heparin/ml flush), recombinant TFPI (rTFPI) (5 ml saline solution, 50 ml intravenous saline, and rTFPI 90 micrograms/ml flush), and control (5 ml and 50 ml intravenous saline and intravenous phosphate-buffered saline solution flush). The pigs were anesthetized and the lesser saphenous vein was harvested and reversed to construct a bypass from the common femoral artery to the saphenous artery at the hock. Each pig received two intravenous infusions before cross-clamping, and the artery and vein were flushed locally according to the protocol for each treatment group. Coagulation parameters were drawn 30 minutes after cross-clamping. The surgical team was blinded as to the pigs' treatment group throughout the protocol. RESULTS: The time from initial infusion until bypass completion averaged 80 minutes. Conduit patency rates at 7 days were as follows: four of five in the rTFPI group, three of five in the systemic heparin group, one of five in the local heparin group, and zero of five in the control group. The activated partial thromboplastin time was elevated (50.1 +/- 13.8 seconds) with systemic heparin but not in the other groups. CONCLUSIONS: Local administration of TFPI prevents thrombosis as effectively as systemic heparin and dextran and is superior to local heparin flush plus dextran (p = 0.02). Thus local TFPI offers an excellent alternative to systemic heparin plus dextran and avoids the risks of systemic anticoagulation.

Animals↗

PubMed2002

Modelling the effect of incorporated halogenated pyrimidine on radiation-induced DNA strand breaks.

PURPOSE: To estimate the enhancement of DNA strand breaks induced by low linear energy transfer (LET) radiation in the presence of halogenated pyrimidines and to examine complexity and clustering properties of damage that could provide a correlation between DNA damage and lethality. MATERIALS AND METHODS: Monte Carlo track structure methods were used to model and estimate the induction of strand breakage by X-ray photons with and without the incorporated Br/I deoxyuridine in cell-mimetic conditions. The increase of DNA strand break induction was modelled by taking into account the direct energy deposition and the reactions of radicals. The yield and spectrum of strand breaks were calculated at various degrees of Br/IdU incorporation. The excess strand breaks due to Br/IdU incorporation was assumed to be induced by highly reactive uracilyl radicals. Four mechanisms were considered for the production of uracilyl radicals classified into three groups, by hydrated electrons, by direct energy deposition, and by both hydrated electrons and direct energy depositions. In total, nine different models were considered to test the excess strand breaks by incorporated Br/IdU assuming different pathways. RESULTS: Model calculations show the following: the yield of strand breaks is enhanced by both the e(aq)(-) reaction and the direct energy deposition on base moiety; there is a significant contribution to the enhancement of yield of strand breaks due to energy transfer about four bases along the DNA to Br/IdU and DNA strand break complexity increases with degree of Br/IdU incorporation. Enhancement ratios of 1.8 and 2.5 for 40% Br/IdU substitution were obtained for single- and double-strand breaks, respectively. CONCLUSIONS: The increase in the yield of strand breaks due to Br/IdU incorporation could be explained by the mechanism of uracilyl radical production by e(aq)(-) and direct energy deposition. The importance of energy transfer along the DNA is demonstrated. It is shown that the incorporation of Br/IdU causes a spectral shift towards a greater complexity of clustered DNA damage.

Base Sequence↗

PubMed2005

A mathematical model for regulating monomer composition of the microbially synthesized polyhydroxyalkanoate copolymers.

A mathematical model is proposed for predicting the copolymer composition of the microbially synthesized polyhydroxyalkanoate (PHA) copolymers. Based on the biochemical reactions involved in the precursor formation and polymerization pathways, the model correlates the copolymer composition with the cultivation conditions, the enzyme levels and selectivity, and the metabolic pathways. It suggests the following points: (1) in the case of a sole carbon source, the copolymer composition depends mainly on the topology of the metabolic pathways and the selectivity of both the enzymes involved in the precursor formation and the polymerization route; (2) the copolymer composition can be varied in a wide range via alteration of the flux ratio of different types of monomers channeled from two or more independent and simultaneous pathways; (3) the enzymes which should be over-expressed or inhibited to obtain the desired copolymer composition can be predicted. For example, inhibition of the beta-oxidation pathway will increase the content of the monomer units with longer chain length. To test the model, various experiments were envisaged by varying cultivation time, concentration and chain length of the sole carbon source, and molar ratio of the cosubstrates. The predictions from the model agree well with the experimental results. Therefore, the proposed model will be useful in predicting the PHA copolymer composition under different biochemical reaction conditions. In other words, it can provide a guide for the synthesis of desired PHA copolymers.

Computer Simulation↗

PubMed1999

FGF-2/fibroblast growth factor receptor/heparin-like glycosaminoglycan interactions: a compensation model for FGF-2 signaling.

Heparin-like glycosaminoglycans (HLGAGs) play a central role in the biological activity and signaling behavior of basic fibroblast growth factor (FGF-2). Recent studies, however, indicate that FGF-2 may be able to signal in the absence of HLGAG, raising the question of the nature of the role of HLGAG in FGF-2 signaling. In this study, we present a conceptual framework for FGF-2 signaling and derive a simple model from it that describes signaling via both HLGAG-independent and HLGAG-dependent pathways. The model is validated with F32 cell proliferation data using wild-type FGF-2, heparin binding mutants (K26A, K119A/R120A, K125A), and receptor binding mutants (Y103A, Y111A/W114A). In addition, this model can predict the cellular response of FGF-2 and its mutants as a function of FGF-2 and HLGAG concentration based on experimentally determined thermodynamic parameters. We show that FGF-2-mediated cellular response is a function of both FGF-2 and HLGAG concentrations and that a reduction of one of the components can be compensated for by an increase in the other to achieve the same measure of cellular response. Analysis of the mutant FGF-2 molecules show that reduction in heparin binding interactions and primary receptor site binding interactions can also be compensated for in the same manner. These results suggest a molecular mechanism that could be used by cells in physiological systems to modulate the FGF-2-mediated cellular response by controlling HLGAG expression.

Binding Sites↗

PubMed1995

Collapse and repair of replication forks in Escherichia coli.

Single-strand interruptions in a template DNA are likely to cause collapse of replication forks. We propose a model for the repair of collapsed replication forks in Escherichia coli by the RecBCD recombinational pathway. The model gives reasons for the preferential orientation of Chi sites in the E. coli chromosome and accounts for the hyper-rec phenotype of the strains with increased numbers of single-strand interruptions in their DNA. On the basis of the model we offer schemes for various repeat-mediated recombinational events and discuss a mechanism for quasi-conservative DNA replication explaining the recombinational repair-associated mutagenesis.

Chromosomes, Bacterial↗

PubMed2006

Thematic review series: patient-oriented research. Design and analysis of lipoprotein tracer kinetics studies in humans.

Lipoprotein tracer kinetics studies have for many years provided new and important knowledge of the metabolism of lipoproteins. Our understanding of kinetics defects in lipoprotein metabolism has resulted from the use of tracer kinetics studies and mathematical modeling. This review discusses all aspects of the performance of kinetics studies, including the development of hypotheses, experimental design, statistical considerations, tracer administration and sampling schedule, and the development of compartmental models for the interpretation of tracer data. In addition to providing insight into new metabolic pathways, such models provide quantitative information on the effect of interventions on lipoprotein metabolism. Compartment models are useful tools to describe experimental data but can also be used to aid in experimental design and hypothesis generation. The SAAM II program provides an easy-to-use interface with which to develop and test compartmental models against experimental models. The development of a model requires that certain checks be performed to ensure that the model describes the experimental data and that the model parameters can be estimated with precision. In addition to methodologic aspects, several compartment models of apoprotein and lipid metabolism are reviewed.

Computer Simulation↗

PubMed2004

Mathematical model of NF-kappaB regulatory module.

The two-feedback-loop regulatory module of nuclear factor kappaB (NF-kappaB) signaling pathway is modeled by means of ordinary differential equations. The constructed model involves two-compartment kinetics of the activators IkappaB (IKK) and NF-kappaB, the inhibitors A20 and IkappaBalpha, and their complexes. In resting cells, the unphosphorylated IkappaBalpha binds to NF-kappaB and sequesters it in an inactive form in the cytoplasm. In response to extracellular signals such as tumor necrosis factor or interleukin-1, IKK is transformed from its neutral form (IKKn) into its active form (IKKa), a form capable of phosphorylating IkappaBalpha, leading to IkappaBalpha degradation. Degradation of IkappaBalpha releases the main activator NF-kappaB, which then enters the nucleus and triggers transcription of the inhibitors and numerous other genes. The newly synthesized IkappaBalpha leads NF-kappaB out of the nucleus and sequesters it in the cytoplasm, while A20 inhibits IKK converting IKKa into the inactive form (IKKi), a form different from IKKn, no longer capable of phosphorylating IkappaBalpha. After parameter fitting, the proposed model is able to properly reproduce time behavior of all variables for which the data are available: NF-kappaB, cytoplasmic IkappaBalpha, A20 and IkappaBalpha mRNA transcripts, IKK and IKK catalytic activity in both wild-type and A20-deficient cells. The model allows detailed analysis of kinetics of the involved proteins and their complexes and gives the predictions of the possible responses of whole kinetics to the change in the level of a given activator or inhibitor.

Animals↗