Semiotes: a semantics for sharing.

MOTIVATION: Reliable, automated communication of biological information requires methods to declare the information's semantics. In this paper I describe an approach to semantic declaration intended to permit independent, distributed databases, algorithms, and servers to exchange and process requests for information and computations without requiring coordination or agreement among them on universe of discourse, data model, schema, or implementation. RESULTS: This approach uses Glossa, a formal language defining the semantics of biological ideas, information, and algorithms, to executably define the semantics of complex ideas and computations by constructs of semiotes, terms which axiomatically define very simple notions. A database or algorithm wishing to exchange information or computations maintains a set of mappings between its particular notions and semiotes, and a parser to translate between its indigenous ideas and implementation and the semiotes. Requests from other databases or algorithms are issued as semiotic messages, locally interpreted and processed, and the results returned as semiotes to the requesting entity. Thus, semiotes serve as a shared, abstract layer of definitions which can be computably combined by each database or algorithm according to its own needs and ideas. By combining the explicit declaration of semantics with the computation of the semantics of complex ideas, Glossa and its semiotes permit independent computational entities to lightly federate their capabilities as desired while maintaining their unique perspectives on both scientific and technical questions.

Differential effects of pinacidil and levcromakalim on the contractions elicited electrically or by noradrenaline in the portal vein of the rabbit.

The present study was undertaken to examine the antivasoconstrictor effects of pinacidil and levcromakalim, two potassium channel openers (PCOs), on the isolated rabbit portal vein and to define the role for different subtypes of pre- and/or post-synaptic K+ channels in the antivasoconstrictor action of the PCOs. The vein strips were contracted by electrical field stimulation (EFS) or by exogenous noradrenaline (NA). The results of this study showed that pinacidil produced a more potent inhibition of the neurogenic contractions (pD2 = 6.04 +/- 0.05) than of contractions induced by exogenous NA (pD2 = 4.90 +/- 0.10). Glibenclamide (1 microM), a selective blocker of adenosine triphosphate (ATP)-sensitive K+ channels (K(ATP)), did not affect the pinacidil-induced inhibition of contractions evoked by exogenous NA. In contrast, glibenclamide (0.1-10 microM) significantly antagonized the effect of pinacidil on EFS evoked contractions in a noncompetitive manner. There was no difference between the inhibitory effects of levcromakalim on neurogenic contractions (pD2 = 7.58 +/- 0.05) and contractions evoked by exogenous NA (pD2 = 7.64 +/- 0.08). Glibenclamide (1 microM) antagonized in the same manner the levcromakalim-induced inhibition of neurogenic contractions and contractions evoked by exogenous NA. Moreover, glibenclamide competitively antagonized the effect of levcromakalim on EFS induced contractions of the rabbit portal vein (pA2 = 6.40 +/- 0.10). Charybdotoxin (0.4 microM) and apamin (0.1 microM) did not influence the inhibitory effects of pinacidil and levcromakalim, both on contractions evoked by EFS and contractions evoked by exogenous NA. These results suggest that the antivasoconstrictor effect of levcromakalim might be postsynaptic and associated with opening of the smooth muscle K(ATP) channels. In contrast, it is hypothesized that the effect of pinacidil on neurogenic contractions is due to an interference with K(ATP) channels in the neuromuscular synapse. It seems that the action of pinacidil on the NA contractions is mediated by another still undefined mechanisms of pinacidil.

Elements of a more comprehensive theory of computing.

Problems implementing DNA computers stem from the physical nature of molecules and their reactions. The present theory of computation requires assumptions that, at best, are extremely crude approximations of the physical chemistry. Here, I consider the hypothesis that discarding those assumptions in favor of more physically realistic descriptions would produce a more comprehensive theory of computing, yielding both theoretical insights and help in designing better molecular computers. I describe the discordances between the theories of physical biochemistry and computation, indicate some elements of a more comprehensive theory, and discuss some of the challenges the construction of a unified theory faces.

[Potassium channels and the development of new drugs]. / Kalijumski kanali i razvoj novih lekova.

Ion channel modulation has recently become an attractive target for experimental and clinical research in a never-ending quest for drug development. Following the decades of domination of calcium channel blockers, currently the focus is on potassium channels and their modulators; this is one of the most rapidly developing fields of research. Because potassium channels have an important role in maintaining the membrane potential in all tissues and in shaping the action potential in the heart, potassium channel modulators are expected to provide better therapies primarily in cardiology (acute coronary syndromes, arrhythmias) but also in other branches of medicine.

The effects of levcromakalim and pinacidil on the human internal mammary artery.

The present study was undertaken to examine the effects of pinacidil and levcromakalim, two potassium, channel openers, on human internal mammary artery (HIMA) obtained from patients undergoing coronary artery bypass surgery, and to clarify the contribution of different K+ channel subtypes in pinacidil and levcromakalim action in this blood vessel. Pinacidil and levcromakalim induced a concentration-dependent relaxation of the precontracted arterial segments (pEC50 = 5.77 +/- 0.05 and 6.89 +/- 0.03, respectively), 4-Aminopyridine (3 mM), a non-selective blocker of K+ channels, induced significant shifts to the right of the concentration-response curves for pinacidil and levcromakalim. Tetraethylammonium (6 mM), charybdotoxin (0.4 microM) and apamin (0.1 microM), blockers of Ca(2+)-sensitive K+ channels, had no effect on the pinacidil- and levcromakalim-evoked relaxation. Glibenclamide (0.1-10 microM), a selective blocker of adenosine triphosphate (ATP)-sensitive K+ channels, competitively antagonized the response to levcromakalim (pKB = 7.92 +/- 0.07). In contrast, glibenclamide, in significantly higher concentrations (3-30 microM), non-competitively antagonized the response to pinacidil. High concentrations of pinacidil (> 10 microM) relaxed arterial rings bathed by a medium containing 100 mM K+ with maximum response 83 +/- 6%. Under the same conditions, the maximum levcromakalim-induced relaxation on HIMA was almost abolished (15 +/- 2%). It is concluded that pinacidil and levcromakalim do not relax the HIMA through the same subtype of K+ channel. ATP-sensitive K+ channels are probably involved in levcromakalim- but not in a pinacidil-induced relaxation in the HIMA. In addition, in pinacidil-induced relaxation of the HIMA, K+ channel-independent mechanisms seem to be involved.

[Pharmacotherapy of cancer pain]. / Farmakoterapija kancerskog bola.

Pain is the most frequent cause of suffering of cancer patients. Recent improvements in pharmacotherapy of cancer pain have made management successful in the majority of patients. Optimal pharmacotherapy program requires careful assessment of the origin and cause of pain. The choice of analgetics should be sequentional using WHO stepladder. Oral application by the clock in an individually titrated dosage is recommended. Morphine remains the most useful opioid. Some drugs without being classic analgetics contribute considerably to the treatment of cancer pain of specific origin. Membrane-stabilisers, antidepressants and steroids are effective in the treatment of neurogenic pain. Anxiolytics should be avoided bacause they cause sedation without improving the quality of analgesia. Finally, it is necessary to treat the side effects of analgetics.

A comparison of the relaxant effects of pinacidil in rabbit renal and mesenteric artery.

1. The relaxant effects of pinacidil were compared in isolated rabbit renal and mesenteric artery. 2. Pinacidil (10 nm-300 microM) relaxed renal and mesenteric arterial rings precontracted with phenylephrine with pD2 values of 5.11 +/- 0.03 and 6.27 +/- 0.04, respectively. 3. The inhibitory effect of pinacidil on the rabbit mesenteric artery was competitively antagonized by glibenclamide (1-10 microM). The calculated pKB value was 6.37 +/- 0.04. On the renal artery, glibenclamide (2-20 microM) did not significantly affect pinacidil-induced relaxation (P > 0.05). 4. Tetraethylammonium (TEA, 1-10 mM) competitively antagonized the pincaidil induced relaxation of the rabbit renal artery. The pKB value was 3.22 +/- 0.08. On the mesenteric artery TEA antagonized the effect of pinacidil in a noncompetitive manner. 5. The concentration-response curves for pinacidil on the rabbit renal and mesenteric artery were not affected by apamin (0.1 microM). 6. It is concluded that ATP-sensitive K+ channels (KATP) are not involved in pinacidil action on the rabbit renal artery. On the contrary, KATP are probably major sites of pinacidil action on the rabbit mesenteric artery.

Relaxation of human uterine artery in response to pinacidil: predominant role for ATP-dependent potassium channels.

The effect of pinacidil on human isolated uterine artery rings was investigated. Pinacidil (10 nM-300 microM) induced a concentration-dependent relaxation of the precontracted arterial segments (pD2: 6.26; maximal response: 98.5%). Apamin (1 microM) and tetraethylammonium (6 mM) had no effects on the pinacidil-evoked relaxation, while 4-aminopyridine (0.1-6 mM) and glibenclamide (1-10 microM) competitively antagonized the response to pinacidil. The dissociation constants for 4-aminopyridine and glibenclamide were 240 microM and 0.40 microM, respectively. It is concluded that, in human uterine arteries, pinacidil induces relaxation. On the basis of differential antagonist affinities, we suggest that pinacidil produces a relaxation of this blood vessel through activation of glibenclamide-sensitive, ATP-dependent potassium channels.

[Pharmacology of beta blockers]. / Farmakologija beta blokatora.

Beta blockers possess several pharmacologic characteristics which highly recommend them for use in the therapeutic branches of medicine: their actions are mild and develop slowly, providing thus a fine regulation of cardiovascular functions; no tolerance occurs to the pharmacodynamic actions of beta blockers, and therefore they ean be used for years without loss of activity; pharmacokinetics of beta blockers is adjusted to the current therapeutic needs by molecular manipulation and/or pharmaceutical technology, and nowadays many members of this group may be used 1-2 times daily which is optimal dosage schedule for chronic diseases. Due to the convenient pharmacologic profile, beta blockers are widely used in clinical medicine, first of all in cardiology for the treatment of hypertension, ischaemic heart disease, cardiac arrhythmias, in acute myocardial infarction and its primary and secondary prevention, and, to a lesser degree, in ophthalmology, neurology, psychiatry and other branches of medicine.

Context effects in the formation of deletions in Escherichia coli.

We have examined the frequency with which identical deletions are formed in different chromosomal contexts. A panel of six mutant bla genes containing palindrome/direct repeat structures were moved from pBR322 to three locations: at lambda att, at chromosomal lac, and at F'lac. Deletion of the palindromes and one of the direct repeats results in reversion to Ampr. The frequency of deletion for all alleles declines beyond the reduction in copy number when they are moved from the multicopy plasmid environment to a single-copy chromosome. The magnitude of the declines varies in an allele-specific and location-specific manner. Our data support the hypothesis that context can influence the frequency of mutation independent of the immediate DNA sequence.

Formation of supercoiling domains in plasmid pBR322.

Twin domains of positive and negative supercoiling are thought to form in DNA molecules whenever free rotation of a transcription complex around the DNA helix is impeded. Evidence for these domains has come from findings with Escherichia coli strains that are deficient in DNA topoisomerase I (top mutants) or that have been treated with DNA gyrase inhibitors. Plasmid pBR322 is highly supercoiled in these strains, whereas some of its deletion derivatives are not. The studies of pBR322 derivatives presented here show that high negative supercoiling in top strains requires translation as well as transcription of the first 98 codons of the tet gene and does not require the divergently transcribed amp gene. The N-terminal region of the TetA protein is thought to insert into the inner membrane. Our results favor models in which supercoiling domains are created when DNA segments are anchored to a large cellular structure via coupled transcription, translation, and membrane insertion of a nascent protein.

The effect of ergot alkaloids ergosinine, dihydroergosine and dihydroergotamine on neurotransmission and contractility of the isolated ileum of the guinea-pig.

The effects of ergosinine (ESNN), dihydroergosine (DHESN) and dihydroergotamine (DHE) on contractions of the isolated terminal and middle segments of the guinea-pig ileum were studied in-vitro. Responses to cholinergic (3 Hz) and adrenergic stimulation (30 Hz in the presence of atropine) were inhibited, albeit at high concentrations of all three alkaloids (1-30 micrograms ml-1). Cholinergic neurotransmission was surprisingly more affected than adrenergic transmission. Noradrenaline (NA) contractions, however, were inhibited at very low concentrations (1-30 ng ml-1) with the following order of potency: DHESN = DHE greater than ESNN. Prazosin was equally as potent as DHESN in inhibiting NA contractions and similarly potent in inhibiting responses to adrenergic stimulation. ESNN, DHESN and DHE when used at concentrations from 1-30 micrograms ml-1 were also found to inhibit 5-hydroxytryptamine greater than histamine greater than acetylcholine greater than KCl contractions. The results suggest that the principal pharmacological action of ESNN, DHESN and DHE on the guinea-pig isolated ileum is the antagonism to NA on the postsynaptic and extrajunctional population of alpha-adrenoceptors. The neurotransmission, adrenergic as well as cholinergic, appeared to be inhibited via a non-specific presynaptic mechanism presumably regulating the transmitter release. Anti-5-hydroxytryptamine, anti-acetylcholine and antihistamine actions were obtained at similar and relatively high concentrations, thus pointing to a non-specific depressant action upon a common mechanism regulating the contractility of the smooth muscle.(ABSTRACT TRUNCATED AT 250 WORDS)

Calcium antagonistic action of pentobarbitone on the isolated terminal ileum of the guinea-pig.

Action of pentobarbitone was studied on isolated segments of the terminal and middle ileum of the guinea-pig and compared with the effects of verapamil. Pentobarbitone (10(-4)-10(-3) M) was found to almost equally inhibit responses produced by ES at 3 Hz and ACH, and those elicited by ES at 30 Hz and NA. Increase in the extracellular calcium did not antagonize the effects of pentobarbitone on both types of ES. These results are an indication of a postsynaptic site of action. The concentration-response curves to calcium-induced contractions (3-300 microM) were displaced to the right by both drugs; however, unlike verapamil, pentobarbitone markedly reduced the maximum response to calcium. Calcium-induced contractions after reaching the plateau level were relaxed both by pentobarbitone and verapamil. Pentobarbitone lowered the resting tone even in the high-KCl depolarizing solution, while verapamil produced no change in this series of experiments. It could be concluded that pentobarbitone when used in anesthetic concentrations might affect contractility of the intestinal smooth muscle by an action located at the postsynaptic membrane or beyond it. The antagonism between pentobarbitone and calcium appeared to be noncompetitive and is presumed to be effected via an indirect action on the functioning of calcium channels.

Interaction between adenosine triphosphate and noradrenaline in the isolated vas deferens of the guinea-pig.

1 An interaction between adenosine triphosphate (ATP) and noradrenaline (NA) was investigated in the isolated vas deferens of the guinea-pig. 2 ATP (1.7 to 50 microM) enhanced contractions due to transmural electrical stimulation (ES; parameters: 30 Hz, 0.2 to 0.3 ms, 10 to 30 V; 1 s train duration). Responses to exogenous NA (12 microM) were also potentiated by ATP while contractions to acetylcholine (6 microM) were inhibited. 3 NA (1.2 microM) potentiated ATP-induced contractions and prevented the development of tachyphylaxis to ATP (510 microM). 4 Phentolamine (12.5 microM) prevented the potentiation by NA of ATP-induced contractions; these contractions were insensitive to phentolamine (up to 25 microM). 5 Removal of potassium chloride from the Tyrode solution for 10 min abolished the potentiating actions of both ATP and NA. 6 The present results suggest that the effect of ATP may be functionally closely related to that of NA at alpha-adrenoceptors in the vas deferens of the guinea-pig.

Late replication and recombination in the vegetative pool of T4.

The rates and extents of replication are the same for all members of the vegetative pool, whether already residing (progeny) or newly entered (superinfecting). Thus, no member of the pool is sequestered in a replicative complex. Amber N82 infections of nonpermissive host result in extensive breakdown of phage DNA. The extent of fragmentation observed depends on the multiplicity of infection and whether phage ligase is present. Hence, parental DNA suffers single-strand nicks which can be repaired by ligase only if recombination does not interfere. The physiological role of ligase in compensating for such nicks is reemphasized. Superinfecting genomes recombine very rapidly with progeny molecules whose combined lengths are approximately six times that of the superinfecting genomic fragment. The superinfecting phage does not replicate before recombining. Therefore, the lack of replication poses no barrier to efficient recombination.

Influence of pyridylisatogen tosylate on contractions produced by ATP and by purinergic stimulation in the terminal ileum of the guinea-pig.

2-2'Pyridylisatogen tosylate (PIT), which antagonizes the inhibitory action of ATP in the taenia caeci, did not antagonize the excitatory effects of exogenous ATP and of purinergic stimulation of the terminal guinea-pig ileum. PIT (0-5--2-5 muM) potentiated the ATP-induced contractions and also the contractions produced by potassium chloride, though the potentiation could not be related to the dose in every experiment. The responses to noradrenaline, adrenaline and histamine were slightly inhibited. PIT also potentiated the contractions produced by electrical stimulation of intramural purinergic nerves when either an alternate or uniform stimulation pattern was used. The present results in which the preparation is contracted by ATP are opposite to those obtained with PIT on the taenia caeci, which is relaxed by ATP. This raises a question of duality or plurality of receptors for ATP.

Action of methylxanthines and imidazole on the contractility of the terminal ileum of the guinea pig.

Methylxanthines (aminophylline and caffeine) and imidazole, substances with an opposite action on phosphodiesterase (PDE), were found to contract the terminal ileum and to potentiate nerve-mediated responses--contractions elicited by electrical stimulation (ES) at 3 Hz and 30 Hz. Imidazole-induced contractions which were partly reduced by atropine, potentiated both responses to ES to about the same extent, and enhanced contractility of the preparation to histamine and potassium. The action of imidazole on the terminal ileum could be related to its influence on PDE in the smooth muscle. The effects of aminophylline and caffeine were found to be more complex, possibly involving some mechanisms other than inhibition of PDE. They produced atropine-sensitive contractions of the terminal ileum, which were potentiated by physostigmine and strongly depressed by hemicholinium. In the presence of atropine, they potentiated ES-induced contractions, particularly those elicited by ES at 30 Hz, which are thought to be of adrenergic origin. Both actions appeared to be due to presynaptic effects -- activation of cholinergic and adrenergic neurons in the intestinal wall, possibly by enhanced influx of calcium, and facilitated release of acetylcholine and noradrenaline. Aminophylline, in concentrations which potentiated nerve-mediated contractions elicited by ES, did not affect direct smooth muscle-contracting action of drugs. Higher concentrations of aminophylline, above 0.1 mM, were found to inhibit histamine- and noradrenaline-induced contractions presumably due to inhibition of PDE in the smooth muscle and subsequent elevation of cAMP levels.

Reduction in brain tyrosine hydroxylase activity following acetylcholinesterase blockade in rats.

Activation of cholinergic neurons in the brain is produced by administration of the acetylcholinesterase inhibitors physostigmine and diisopropylfluorophosphate (DFP). This activation has a biphasic effect on tyrosine hydroxylase (EC 4.14.3-) activity. The acute effect of DFP, 1 mg/kg, intraperitoneally, or physostigmine, 0.2 mg/kg, intravenously, or 10 mug, intraventricularly, was a rapid reduction in tyrosine hydroxylase activity in the hypothalamus. The activities of DOPA decarboxylase (EC 4.1.1.28) and dopamine-beta-hydroxylase (EC 1.14.17.1) were not changed. In contrast to the acute effect, chronic administration of physostigmine, 0.2 mg/kg, intravenously, twice daily for 7 days produced an increase in tyrosine hydroxylase activity in the hypothalamus. The rapid acute effects may be due to an allosteric inactivation of tyrosine hydroxylase, while the chronic effects may reflect enzyme induction.

Influence of adenosine, cAMP and db-cAMP on responses of the isolated terminal guinea-pig ileum to electrical stimulation.

Adenosine, cAMP and db-cAMP were found to inhibit nerve-mediated contractions of the terminal ileum elicited by electrical stimulation (ES). Responses to ES at 30 Hz, which are believed to be of adrenergic origin, were considerably more affected than the responses to ES at 3 Hz, which may be of purinergic orign. The following order of relative inhibitory potencies was established: adenosine greater than cAMP greater than db-cAMP. Adenosine, cAMP and db-cAMP did not affect the contractile responses of the preparation to histamine, potassium and noradrenaline. Therefore, the observed inhibition of nerve-mediated contractions was thought to be due to an action on presynaptic sites, i.e. on the neural network within the intestine. This action was antagonized by an increase in external calcium and by aminophylline, which is known to increase intracellular calcium. The present experiments suggests that the inhibitory action of adenosine, cAMP and db-cAMP results from a reduction of calcium fluxes across the neural membrane and to a subsequent reduction in the release of neurotransmitter(s). The inhibitory effect of cAMP appeared to be nonspecific and was presumably related to adenosine in its molecule.