Steady-State Analysis and Scheduling of Cyclic Job Shops with Overtaking

A cyclic shop is a production system that repeatedly produces identical sets of parts of multiple types, called minimal part sets (MPSs), in the same loading and processing sequence. A different part type may have a different machine visit sequence. We consider a version of cyclic job shop where some operations of an MPS instance are processed prior to some operations of the previous MPS instances. We call such a shop an overtaking cyclic job shop (OCJS). The overtaking degree can be specified by how many MPS instances the operations of an MPS instance can overtake. More overtaking results in more work-in-progress, but reduces the cycle time, in general. We prove that for a given processing sequence of the operations at each machine, under some conditions, an OCJS has a stable earliest starting schedule such that each operation starts as soon as its preceding operations are completed, the schedule repeats an identical timing pattern for each MPS instance, and the cycle time is kept to be minimal. To do these, we propose a specialized approach to analyzing steady states for an event graph model of an OCJS that has a cyclic structure, which can keep the MPS-based scheduling concept. Based on the steady-state results, we develop a mixed integer programming model for finding a processing sequence of the operations at each machine and the overtaking degrees, if necessary, that minimize the cycle time.     

Rationally designed neuropeptide antagonists: A novel approach for generation of environmentally friendly insecticides

We report our approach for the generation of a novel type of putative insecticides based on backbone cyclic peptidomimetic antagonists of insect neuropeptides using pheromone biosynthesis activating neuropeptide (PBAN) as a model. This approach, called the backbone cyclic neuropeptide based antagonist (BBC-NBA), includes the following steps: (i) elucidation of the active sequence of the chosen insect neuropeptide; (ii) disclosure of a lead antagonist based on the sequence found in step (i); (iii) design and synthesis of backbone cyclic peptide libraries (cycloscan) based on the sequence of the lead antagonist; and (iv) design and synthesis of a peptidomimetic prototype insecticide. The BBC-NBA approach was applied to PBAN and led to the discovery of a potent linear lead antagonist and a potent backbone cyclic antagonist devoid of agnoistic activity which inhibited sex pheromone biosynthesis inHeliothis peltigera female moths.     

Structure and Energetics of Allosteric Regulation of HCN2 Ion Channels by Cyclic Nucleotides

Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels play an important role in regulating electrical activity in the heart and brain. They are gated by the binding of cyclic nucleotides to a conserved, intracellular cyclic nucleotide-binding domain (CNBD), which is connected to the channel pore by a C-linker region. Binding of cyclic nucleotides increases the rate and extent of channel activation and shifts it to less hyperpolarized voltages. We probed the allosteric mechanism of different cyclic nucleotides on the CNBD and on channel gating. Electrophysiology experiments showed that cAMP, cGMP, and cCMP were effective agonists of the channel and produced similar increases in the extent of channel activation. In contrast, electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) on the isolated CNBD indicated that the induced conformational changes and the degrees of stabilization of the active conformation differed for the three cyclic nucleotides. We explain these results with a model where different allosteric mechanisms in the CNBD all converge to have the same effect on the C-linker and render all three cyclic nucleotides similarly potent activators of the channel.     

Modelling Dictyostelium discoideum morphogenesis: the culmination

The culmination of the morphogenesis of the cellular slime mould Dictyostelium discoideum involves complex cell movements which transform a mound of cells into a globule of spores on a slender stalk. We show that cyclic AMP signalling and differential adhesion, combined with cell differentiation and slime production, are sufficient to produce the morphogenetic cell movements which lead to culmination. We have simulated the process of culmination using a hybrid cellular automata/partial differential equation model. With our model we have been able to reproduce the main features that occur during culmination, namely the straight downward elongation of the stalk, its anchoring to the substratum and the formation of the long thin stalk topped by the spore head. We conclude that the cyclic AMP signalling system is responsible for the elongation and anchoring of the stalk, but in a roundabout way: pressure waves that are induced by the chemotaxis towards cyclic AMP squeeze the stalk through the cell mass. This mechanism forces the stalk to elongate precisely in the direction opposite to that of the chemotactically moving cells. The process turns out to be ‘guided’ by inactive ‘pathfinder’ cells, which form the tip of the stalk. We show that the entire development is enacted by means of the aforementioned building blocks. This means that no global gradients or different modes of chemotaxis are needed to complete the culmination. MPEG movies of the simulations are available on-line: http://www-binf.bio. uu.nl/stan/bmb.     

Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194

We report the molecular basis for the differences in activity of cyclic and linear antimicrobial peptides. We iteratively performed atomistic molecular dynamics simulations and biophysical measurements to probe the interaction of a cyclic antimicrobial peptide and its inactive linear analogue with model membranes. We establish that, relative to the linear peptide, the cyclic one binds stronger to negatively charged membranes. We show that only the cyclic peptide folds at the membrane interface and adopts a β-sheet structure characterised by two turns. Subsequently, the cyclic peptide penetrates deeper into the bilayer while the linear peptide remains essentially at the surface. Finally, based on our comparative study, we propose a model characterising the mode of action of cyclic antimicrobial peptides. The results provide a chemical rationale for enhanced activity in certain cyclic antimicrobial peptides and can be used as a guideline for design of novel antimicrobial peptides.     

Cyclic stretch enhances reorientation and differentiation of 3-D culture model of human airway smooth muscle

Activation of airway smooth muscle (ASM) cells plays a central role in the pathophysiology of asthma. Because ASM is an important therapeutic target in asthma, it is beneficial to develop bioengineered ASM models available for assessing physiological and biophysical properties of ASM cells. In the physiological condition in vivo, ASM cells are surrounded by extracellular matrix (ECM) and exposed to mechanical stresses such as cyclic stretch. We utilized a 3-D culture model of human ASM cells embedded in type-I collagen gel. We further examined the effects of cyclic mechanical stretch, which mimics tidal breathing, on cell orientation and expression of contractile proteins of ASM cells within the 3-D gel. ASM cells in type-I collagen exhibited a tissue-like structure with actin stress fiber formation and intracellular Ca²⁺ mobilization in response to methacholine. Uniaxial cyclic stretching enhanced alignment of nuclei and actin stress fibers of ASM cells. Moreover, expression of mRNAs for contractile proteins such as α-smooth muscle actin, calponin, myosin heavy chain 11, and transgelin of stretched ASM cells was significantly higher than that under the static condition. Our findings suggest that mechanical force and interaction with ECM affects development of the ASM tissue-like construct and differentiation to the contractile phenotype in a 3-D culture model.     

Morituri te salutant? Olfactory signal transduction and the role of phosphoinositides

During the past 150 years, researchers have investigated the cellular, physiological, and molecular mechanisms underlying the sense of smell. Based on these efforts, a conclusive model of olfactory signal transduction in the vertebrate's nose is now available, spanning from G-protein-mediated odorant receptors to ion channels, which are linked by a cyclic adenosine 3',5'-monophosphate-mediated signal transduction cascade. Here we review some historical milestones in the chronology of olfactory research, particularly emphasising the role of cyclic nucleotides and inositol trisphosphate as alternative second messengers in olfactory cells. We will describe the functional anatomy of the nose, outline the cellular composition of the olfactory epithelium, and describe the discovery of the molecular backbone of the olfactory signal transduction cascade. We then summarize our current model, in which cyclic adenosine monophosphate is the sole excitatory second messenger in olfactory sensory neurons. Finally, a possible significance of microvillous olfactory epithelial cells and inositol trisphosphate in olfaction will be discussed.     

Pacemakers in aggregation fields of Dictyostelium discoideum: does a single cell suffice?

In this paper we address the following question: can a single cell of the cellular slime mold Dictyostelium discoideum serve as a pacemaker for the aggregation phase? Whether or not this is possible is determined by the relative importance of cyclic AMP production due to self-stimulation as compared to diffusion of cyclic AMP away from the cell and extracellular degradation. We determine the conditions under which a single cell on an infinite place can emit periodic signals of cyclic AMP using a model developed previously for signal relay and adaptation in Dictyostelium. Elsewhere it has been shown that this model provides an accurate representation of the stimulus-response behavior of Dictyostelium for a variety of experimental conditions.     

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

We use flow cytometry to characterize equilibrium binding of a fluorophore-labeled trivalent model antigen to bivalent IgE-FcεRI complexes on RBL cells. We find that flow cytometric measurements are consistent with an equilibrium model for ligand-receptor binding in which binding sites are assumed to be equivalent and ligand-induced receptor aggregates are assumed to be acyclic. However, this model predicts extensive receptor aggregation at antigen concentrations that yield strong cellular secretory responses, which is inconsistent with the expectation that large receptor aggregates should inhibit such responses. To investigate possible explanations for this discrepancy, we evaluate four rule-based models for interaction of a trivalent ligand with a bivalent cell-surface receptor that relax simplifying assumptions of the equilibrium model. These models are simulated using a rule-based kinetic Monte Carlo approach to investigate the kinetics of ligand-induced receptor aggregation and to study how the kinetics and equilibria of ligand-receptor interaction are affected by steric constraints on receptor aggregate configurations and by the formation of cyclic receptor aggregates. The results suggest that formation of linear chains of cyclic receptor dimers may be important for generating secretory signals. Steric effects that limit receptor aggregation and transient formation of small receptor aggregates may also be important.     

Cyclic AMP and the control of aggregative phase gene expression in Dictyostelium discoideum.

The induction of aggregative phase functions and the acceleration of the onset of aggregation competence by nanomolar pulses of cyclic AMP can be mimicked by exposing developing cells to a high extracellular concentration of either cyclic AMP or cyclic GMP (5 × 10^?4M) during the first 1–2 hr of development. Pulses of cyclic AMP have previously been shown to result in oscillations of intracellular cyclic AMP concentration; we show that high extracellular concentrations of cyclic AMP and cyclic GMP cause intracellular cyclic AMP levels to increase. We describe a mutant, HM11, which has elevated levels of intracellular cyclic AMP from the beginning of development and which begins to accumulate cell-associated phosphodiesterase, an aggregative phase enzyme, within an hour of starvation. Our data suggest that the expression of aggregative phase functions is controlled by an elevation of intracellular cyclic AMP which may be either continuous or periodic.     

A thermodynamically motivated model for stress-fiber reorganization

We present a model for stress-fiber reorganization and the associated contractility that includes both the kinetics of stress-fiber formation and dissociation as well as the kinetics of stress-fiber remodeling. These kinetics are motivated by considering the enthalpies of the actin/myosin functional units that constitute the stress fibers. The stress, strain and strain rate dependence of the stress-fiber dynamics are natural outcomes of the approach. The model is presented in a general 3D framework and includes the transport of the unbound stress-fiber proteins. Predictions of the model for a range of cyclic loadings are illustrated to rationalize hitherto apparently contrasting observations. These observations include: (1) For strain amplitudes around 10 % and cyclic frequencies of about 1 Hz, stress fibers align perpendicular to the straining direction in cells subjected to cyclic straining on a 2D substrate while the stress fibers align parallel with the straining direction in cells constrained in a 3D tissue. (2) At lower applied cyclic frequencies, stress fibers in cells on 2D substrates display no sensitivity to symmetric applied strain versus time waveforms but realign in response to applied loadings with a fast lengthening rate and slow shortening. (3) At very low applied cyclic frequencies (on the order of mHz) with symmetric strain versus time waveforms, cells on 2D substrates orient perpendicular to the direction of cyclic straining above a critical strain amplitude.     

Photooxidase system of Rhodospirillum rubrum. I. Photooxidations catalyzed by chromatophores isolated from a mutant deficient in photooxidase activity

The aerobic photooxidations of reduced 2,6-dichlorophenolindophenol and of reaction-center bacteriochlorophyll (P-870) have been investigated in membrane vesicles (chromatophores) isolated from a non-phototrophic Rhodospirillum rubrum strain. In aerobic suspensions of wild-type chromatophores, continuous light elicits an increase of the levels of 2,6-dichlorophenolindophenol and of oxidized P-870, which reach steady-state values shortly after the onset of illumination. In contrast, light induces in mutant suspensions a transient increase of the levels of 2,6-dichlorophenolindophenol and of oxidized P-870, which fall to low steady-state values within a few seconds. These observations suggest that the mutation has altered a redox constituent located on the low-potential side of the photochemical reaction center, between a pool of acceptors and oxygen.Since endogenous cyclic photophosphorylation is catalyzed by mutant chromatophores at normal rates, it appears that the constituent altered by the mutation does not belong to the cyclic electron-transfer chain responsible for photophosphorylation. However, the system which mediates the aerobic photooxidations and the cyclic system are not completely independent: endogenous photophosphorylation is inhibited by oxygen in wild-type chromatophores but not in mutant chromatophores; in addition, the inhibitor of cyclic electron flow, 2-heptyl-4-hydroxyquinoline-N-oxide, enhances the aerobic photooxidation of reduced 2,6-dichlorophenolindophenol by chromatophores from both strains.These results support a tentative branched model for light-driven electron transfer. In that model, the constituent altered in the mutant strain is located in a side electron-transfer chain which connects the cyclic acceptors to oxygen.     

Expression and subcellular localization of CDK2 and cdc2 kinases and their common partner cyclin A in thyroid epithelial cells: Comparison of cyclic AMP-dependent and -independent cell cycles

Dog thyroid epithelial cells in primary culture constitute a model of positive control of DNA synthesis initiation and GO-S prereplicative phase progression by cyclic AMP as a second messenger for TSH. In its early steps, this mitogenic control is quite distinct from cyclic AMP-independent mitogenic cascades elicited by growth factors. We demonstrate here that TSH (cyclic AMP) and EGF + serum (cyclic AMP-independent) stimulations cooperate and finally converge on proteins that control the cell cycle machinery. This convergence included a common induction of the expression of cyclin A and p34^cdc2, and to a lesser extent of p33/38^cdk2, which was already expressed in quiescent thyroid cells, and common changes of cdc2 and CDK2 phosphorylations as evidenced by electrophoretic mobility shifts. Kinetic differences in these processes after stimulation by TSH or EGF + serum or by these factors in combination correlated with differences in cell cycle kinetics. Moreover, an immunofluorescence analysis of these proteins using the double labeling of PCNA as a marker of each cell cycle phase shows: (1) a previously undescribed nuclear translocation of CDK2 before S phase initiation; (2) a sudden increase of cdc2 nuclear immunoreactivity at G2/mitosis transition. These data support the roles of CDK2 and cdc2 at G1/S and G2/mitosis transitions, respectively. (3) We were unable to demonstrate in individual cells a strict association between the nuclear appearance of cyclin A and G1/S transition, and an association of cyclin A and CDK2 with PCNA-stained DNA replication sites. On the other hand, the lengthening of G2 phase in the TSH/cyclic AMP-dependent thyroid cell cycle was associated with a stabilization of Tyr15 inhibitory phosphorylation of cdc2 and an especially high nuclear concentration of cyclin A and CDK2. We hypothesize that high nuclear accumulation of cyclin A and CDK2 during G2 phase could be causative in the cyclic AMP-dependent delay of mitosis onset. © 1996 Wiley-Liss, Inc.     

Evolutionary branching of dispersal strategies in structured metapopulations

 Dispersal polymorphism and evolutionary branching of dispersal strategies has been found in several metapopulation models. The mechanism behind those findings has been temporal variation caused by cyclic or chaotic local dynamics, or temporally and spatially varying carrying capacities. We present a new mechanism: spatial heterogeneity in the sense of different patch types with sufficient proportions, and temporal variation caused by catastrophes. The model where this occurs is a generalization of the model by Gyllenberg and Metz (2001). Their model is a size-structured metapopulation model with infinitely many identical patches. We present a generalized version of their metapopulation model allowing for different types of patches. In structured population models, defining and computing fitness in polymorphic situations is, in general, difficult. We present an efficient method, which can be applied also to other structured population or metapopulation models. Received: 6 March 2001 / Revised version: 12 February 2002 / Published online: 17 July 2002     

Time-resolved phosphorescence of tyrosine,tyrosine analogs,and tyrosyl residues in oxytocin and small peptides

We present the time-resolved phosphorescence of oxytocin, two oxytocin derivatives, vasopressin and a series of compounds that serve as models for free tyrosine. One of the oxytocin derivatives, desaminodicarbaoxytocin, has the disulfide bridge replaced by an ethylene bridge, and lacks the N-terminus. Similar to the reported fluorescence decays of tyrosine in these peptides, the phosphorescence decays generally are not single exponentials, but can be fit as biexponentials. The decay times for the oxytocin peptides are shorter than for desaminodicarbaoxytocin or the model compounds, and this we attribute to enhanced spin-orbit coupling due to the presence of sulfur. We measured the phosphorescence decay of the model cyclic pentapeptide that contains tyrosine and compared it to that observed for the same cyclic pentapeptide in which tyrosine is replaced by tryptophan. We also report the phosphorescence of 2-tryptophan-oxytocin, and deamino-2-tryptophan-oxytocin in which biexponential phosphorescence decay is also observed.     

Topical application of integrin antagonists inhibits proliferative retinopathy.

The expression of alphav-integrins is highly selective for angiogenic endothelial cells; ligation inhibition by cyclic RGD peptides prevents pathological neovascularization in tumor or retinopathy models to a large extent. We have previously demonstrated that proliferative retinopathy in a mouse model of retinopathy of prematurity (ROP model) can be reduced by more than 70%. To minimize systemic side effects and unwanted interference with responsive angiogenesis, we investigated topical application of cyclic RGD-peptides. In preliminary experiments, we could exclude any inhibiting effects of the carrier solution containing EDTA, Na2S, mannitol, hydroxyethyl starch, and benzalconium chloride on the inhibitory effect of cyclic RGD peptides. Retinal presence of small molecular-mass integrin antagonists after topical application was confirmed using fluorescein-labeled cyclic RGD peptide. Topical application of the peptide to the eye inhibited proliferative retinopathy in a dose-dependent fashion with a maximum of almost 50%. These results suggest that small molecular-mass peptide antagonists of alphav-type integrins are efficient in inhibiting proliferative retinopathy by topical application.     

The positive control of cell proliferation by the interplay of calcium ions and cyclic nucleotides. A review

Conclusion Calcium, cyclic AMP, and cyclic GMP do not seem to be involved in proliferative activation of postmitotic differentiated cells. Instead, they are intracycle regulators, and we propose the following working model of their control of the initiation of DNA synthesis. While a role for cyclic GMP cannot yet be defined, a brief postmitotic burst of its synthesis might serve to prevent certain activated cells (e.g. 3T3 mouse cells) from being diverted into a nonproliferating (but still activated) G₀ state (Figs. 1 and 17). In a latter part of the G₁ phase, something happens to stimulate briefly the synthesis of cyclic AMP which, in turn, drives calcium ions from the mitochondria into the cytosol to activate newly synthesized thymidylate synthetase (or other primed enzymic assemblies) (Fig. 1). Having “turned on” their target enzymes, the accumulated cyclic AMP is destroyed and the excess calcium ions are reaccumulated by the mitochondria to avoid interfering with succeeding reactions. This model predicts that persistent changes in cyclic AMP metabolism and the respiration-linked, calcium-accumulating (ion-buffering) activity of mitochondria may be responsible for the sustained growth of tumors. Issued as NRCC No. 14974.     

Effects of cyclic irrigation on water and nitrogen mass balances in a paddy field

Cyclic irrigation is considered an effective water management practice for reducing pollutant loads from a paddy-field district. The objective of this study was to clarify the effects of cyclic irrigation on mass balance in paddy plots. At the study site, cyclic irrigation with a high cyclic irrigation ratio (% reused water in irrigation water) was conducted from late April to late June. We found a complementary relationship between the volume of irrigation water and rainfall, which together totaled about 1400-1600 mm during the irrigation period each year. We concluded that a cyclic irrigation system that enables the paddy-field district to use a high cyclic irrigation ratio may lead to more efficient use of rainfall for crop irrigation. Nitrogen concentrations in both irrigation water and ponded water tended to be higher during the cyclic irrigation period than during the lake water irrigation period. Nitrogen input from irrigated water accounted for about 8-16% of the total input of nitrogen. It is suggested that fertilizer application of nitrogen can be reduced by its return through cyclic irrigation.     

Development of a Transgenic Plasmodium berghei Line (Pbpfpkg) Expressing the P. falciparum cGMP-Dependent Protein Kinase,a Novel Antimalarial Drug Target

With the inevitable selection of resistance to antimalarial drugs in treated populations, there is a need for new medicines to enter the clinic and new targets to progress through the drug discovery pipeline. In this study we set out to develop a transgenic rodent model for testing inhibitors of the Plasmodium falciparum cyclic GMP-dependent kinase in vivo. A model was needed that would allow us to investigate whether differences in amino acid sequence of this enzyme between species influences in vivo efficacy. Here we report the successful development of a transgenic P. berghei line in which the cyclic GMP-dependent protein kinase (PKG) was replaced by the P. falciparum orthologue. We demonstrate that the P. falciparum orthologue was able to functionally complement the endogenous P. berghei pkg gene throughout blood stage development and early sexual development. However, subsequent development in the mosquito was severely compromised. We show that this is due to a defect in the female lineage of the transgenic by using genetic crosses with both male and female deficient P. berghei lines. This defect could be due to expression of a female-specific target in the mosquito stages of P. berghei that cannot be phosphorylated by the P. falciparum kinase. Using a previously reported anti-coccidial inhibitor of the cyclic GMP-dependent protein kinase, we show no difference in in vivo efficacy between the transgenic and control P. berghei lines. This in vivo model will be useful for screening future generations of cyclic GMP-dependent protein kinase inhibitors and allowing us to overcome any species-specific differences in the enzyme primary sequence that would influence in vivo efficacy in the rodent model. The approach will also be applicable to in vivo testing of other antimalarial compounds where the target is known.     

Intracellular and Extracellular Cyclic Nucleotides in Wild-Type and White Collar Mutant Strains of Neurospora crassa: Temperature Dependent Efflux of Cyclic AMP from Mycelia

Cyclic AMP and cyclic GMP were released into the growth medium of mycelia of Neurospora crassa wild-type strains St.L.74A and Em5297a and by white collar-1 and white collar-2 mutant strains. After growth for 6 days at 18°C, there were 2.19 (St.L.74A), 5.83 (Em5297a), 1.38 (white collar-1), and 1.10 (white collar-2) nanomoles of cyclic AMP per gram dry weight of mycelia in the growth medium. These values corresponded to concentrations of cyclic AMP of between approximately 10 and 50 nanomolar. The corresponding values for extracellular cyclic GMP were typically less than 6% of the values for cyclic AMP. Following transfer to fresh medium, cyclic AMP efflux was demonstrated for each of the strains, and the amount of cyclic AMP exported into the fresh medium was greater at 25°C than 6°C. Intracellular cyclic AMP and cyclic GMP were also measured in each of the strains. The values for cyclic AMP were in the same range as those in the literature (approximately 0.5 to 1.5 nanomoles per gram dry weight of mycelia). However, the corresponding intracellular cyclic GMP values were less than 1% of the cyclic AMP values, i.e. more than 50 times lower than the value previously reported for the St.L.74A wild-type. Transfer of mycelia after 6 days at 18°C to fresh media and incubation for 2 hours at 25°C or 6°C did not consistently affect the intracellular level of cyclic AMP or cyclic GMP in the strains examined. We could detect no change in intracellular cyclic AMP when mycelia of the St.L.74A wild-type strain were irradiated with blue light for periods of up to 3.0 hours at 18°C, or in cyclic AMP and cyclic GMP for irradiation times of up to 1 minute at 6°C. We propose that the plasma membrane of Neurospora crassa is permeable to cyclic nucleotides, and the export of cyclic nucleotides into the growth medium may be a means of regulating intracellular levels. We conclude that three factors that affect carotenogenesis in Neurospora crassa (blue light, temperature, and the white collar mutations) have no appreciable effect on the total measurable intracellular cyclic nucleotides in this organism. There was no extracellular or intracellular cyclic AMP or cyclic GMP in the crisp-1 mutant strain, which suggested either that adenylate cyclase (which is absent in crisp-1) catalyzes the synthesis of both cyclic AMP and cyclic GMP or that the crisp-1 mutation somehow results in a deficiency of two enzymes (adenylate and guanylate cyclase).