Automatic pathway building in biological association networks

Background  

Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved by automatic fact extraction using various text-mining algorithms. Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined.     

Functional photoacoustic microscopy for high-resolution and noninvasive in vivo imaging

Although optical absorption is strongly associated with the physiological status of biological tissue, existing high-resolution optical imaging modalities, including confocal microscopy, two-photon microscopy and optical coherence tomography, do not sense optical absorption directly. Furthermore, optical scattering prevents these methods from imaging deeper than approximately 1 mm below the tissue surface. Here we report functional photoacoustic microscopy (fPAM), which provides multiwavelength imaging of optical absorption and permits high spatial resolution beyond this depth limit with a ratio of maximum imaging depth to depth resolution greater than 100. Reflection mode, rather than orthogonal or transmission mode, is adopted because it is applicable to more anatomical sites than the others. fPAM is demonstrated with in vivo imaging of angiogenesis, melanoma, hemoglobin oxygen saturation (sO2) of single vessels in animals and total hemoglobin concentration in humans.     

Influence of Dalargin, a Peripheral Opiate Receptor Agonist, on Exercise Tolerance in Patients with Coronary and Peripheral Artery Atherosclerosis

The study showed that chronic stimulation of peripheral - and -opiate receptors by a course of intravenous D-Ala²–Leu⁵-Arg⁶-enkephalin (dalargin) causes an antianginal effect in patients with ischemic heart disease (IHD) and increases tolerance to exercise in patients with atherosclerosis of coronary and peripheral arteries. Prolonged activation of peripheral - and -receptors causes a venodilator effect and decreases the tone of peripheral arteries in patients with IHD and atherosclerosis of lower extremities. After a course of dalargin, the chronotropic response to exercise strengthens in patients with IHD and the hypertensive response to threshold exercise weakens in patients with atherosclerosis of lower extremities.     

Activation of peripheral δ2 opioid receptors increases cardiac tolerance to ischemia/reperfusion injury: Involvement of protein kinase C,NO-synthase,KATP channels and the autonomic nervous system

AimsThis study aims to investigate the role of peripheral δ₂ opioid receptors in cardiac tolerance to ischemia/reperfusion injury and to examine the contribution of PKC, TK, K_ATP channels and the autonomic nervous system in δ₂ cardioprotection.Main methodsDeltorphin II and various inhibitors were administered in vivo prior to coronary artery occlusion and reperfusion in a rat model. The animals were monitored for the development of arrhythmias, infarct development and the effects of selected inhibitors.Key findingsPretreatment with peripheral and δ₂ specific opioid receptor (OR) antagonists completely abolished the cardioprotective effects of deltorphin II. In contrast, the selective δ₁ OR antagonist 7-benzylidenenaltrexone (BNTX) had no effect. The protein kinase C (PKC) inhibitor chelerythrine and the NO-synthase inhibitor L-NAME (N-nitro-l-arginine methyl ester) also reversed both deltorphin II effects. The nonselective ATP-sensitive K+ (K_ATP) channel inhibitor glibenclamide and the selective mitochondrial K_ATP channel inhibitor 5-hydroxydecanoic acid only abolished the infarct-sparing effect of deltorphin II. Inhibition of tyrosine kinase (TK) with genistein, the ganglion blocker hexamethonium and the depletion of endogenous catecholamine storage with guanethidine reversed the antiarrhythmic action of deltorphin II but did not change its infarct-sparing action.SignificanceThe cardioprotective mechanism of deltorphin II is mediated via stimulation of peripheral δ₂ opioid receptors. PKC and NOS are involved in both its infarct-sparing and antiarrhythmic effects. Infarct-sparing is dependent upon mitochondrial K_ATP channel activation while the antiarrhythmic effect is dependent upon TK activation. Endogenous catecholamine depletion reduced antiarrhythmic effects but did not alter the infarct-sparing effect of deltorphin II.     

Effect of stimulation of mu-opiate receptors on contractility of the isolated heart in normal oxygenation and during ischemia-reperfusion]

Activation of mu-opioid receptor (OR) in rats prevented development of reperfusion-induced myocardial cell damage. In contrast, direct cardiac mu-OR stimulation with the opioid receptor agonist DAMGO decreased cardiac contractility in normal oxygenation and aggravated the reperfusion-induced myocardial cell damage. The findings suggest that the cardioprotective effect of mu-OR stimulation is not mediated via cardiac mu-OR activation.     

On the possibilities of diagnosis of the state of the phytoplankton photosynthetic apparatus by the method of nonlinear laser fluorimetry

The possibilities of diagnosis of the state of the phytoplankton photosynthetic apparatus by the method of nonlinear laser fluorimetry (saturation fluorimetry), which can be realized in remote sensing mode, were investigated. A procedure for the determination of the nonsaturated fluorescence parameter phi0, which is proportional to the concentration of chlorophyll a molecules, and the parameter A, which is a product of three photophysical parameters of chlorophyll a molecule in native chloroplast, was elaborated. Laboratory experiments with the axenic culture of eurihaline Thalassiosira weissflogii showed that the parameter A depends on the state of the photosynthetic apparatus of the alga, which was varied by either DCMU treatment or exposure to actinic light.     

Description of the Photosynthetic Apparatus of <Emphasis Type="Italic">Fucus vesiculosus</Emphasis> L. in Early Embryogenesis

Dynamics of some photosynthetic parameters was studied in gametes, zygotes, and embryos of kelp Fucus vesiculosus L. The following indices were determined at different stages of seaweed early development: the contents of pigments and ribulose-1,5-bisphosphate carboxylase/oxygenase, the rates of photosynthesis and dark respiration, and the activities of photosystems I and II. The dynamics of photosynthetic activity in the zygotes and embryos of F. vesiculosus proved to reflect the main physiological processes of its early development.     

Activation of δ-opioid receptors increases resistance of isolated heart to ischemia/reperfusion: The role of cAMP and intracellular calcium

Activation of cardiac -opioid receptors (ORs) by their selective agonist DPDPE (154 nM) increased the resistance of perfused rat heart to ischemia/reperfusion injury. Decreased release of creatine phosphokinase to the perfusate and decreased incidence of arrhythmias were observed during reoxygenation. At the same time, opioidergic decrease in left ventricular developed pressure took place both during the preischemic period and after restoring the coronary circulation. All these effects could be prevented by blocking -ORs by naltrindole or inhibition of Ca²⁺-ATPase of sarcoplasmic reticulum by cyclopiazonic acid. -OR agonist DPDPE had no effect on cAMP levels in myocardial tissue during the whole experiment. The obtained data suggest that the antiarrhythmic and cytoprotective effects observed after -OR stimulation can be realized through the changes in Ca²⁺ transport at the level of the sarcoplasmic reticulumTranslated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 1, 2005, pp. 55–62.Original Russian Text Copyright © 2005 by Lishmanov, Maslov, Lasukova, Platonov, Oeltgen.