Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Quantitative Modeling of GRK-Mediated β2AR Regulation

We developed a unified model of the GRK-mediated β2 adrenergic receptor (β2AR) regulation that simultaneously accounts for six different biochemical measurements of the system obtained over a wide range of agonist concentrations. Using a single deterministic model we accounted for (1) GRK phosphorylation in response to various full and partial agonists; (2) dephosphorylation of the GRK site on the β2AR; (3) β2AR internalization; (4) recycling of the β2AR post isoproterenol treatment; (5) β2AR desensitization; and (6) β2AR resensitization. Simulations of our model show that plasma membrane dephosphorylation and recycling of the phosphorylated receptor are necessary to adequately account for the measured dephosphorylation kinetics. We further used the model to predict the consequences of (1) modifying rates such as GRK phosphorylation of the receptor, arrestin binding and dissociation from the receptor, and receptor dephosphorylation that should reflect effects of knockdowns and overexpressions of these components; and (2) varying concentration and frequency of agonist stimulation “seen” by the β2AR to better mimic hormonal, neurophysiological and pharmacological stimulations of the β2AR. Exploring the consequences of rapid pulsatile agonist stimulation, we found that although resensitization was rapid, the β2AR system retained the memory of the previous stimuli and desensitized faster and much more strongly in response to subsequent stimuli. The latent memory that we predict is due to slower membrane dephosphorylation, which allows for progressive accumulation of phosphorylated receptor on the surface. This primes the receptor for faster arrestin binding on subsequent agonist activation leading to a greater extent of desensitization. In summary, the model is unique in accounting for the behavior of the β2AR system across multiple types of biochemical measurements using a single set of experimentally constrained parameters. It also provides insight into how the signaling machinery can retain memory of prior stimulation long after near complete resensitization has been achieved.     

Enzymatic System of Metabolism and Detoxication of Xenobiotics as a Basis of Metabolic Portraiting during Prognostication of Risk of Pathological Processes

We studied intraspecific features of the main enzymes of metabolism and detoxication of xenobiotics on mice (eight inbred lines) and rats (five lines) for estimation of possible variants of complete or incomplete metabolic equality. Significant genetically determined intraspecific differences for activities of the enzymes of metabolism and detoxication of xenobiotics were described. Generalized criteria for comparison of the metabolic status were proposed on the basis of activities of the main enzymes: cytochrome P-450 (hydroxylation and epoxidation), epoxyhydrolase, glutathione-S-transferase, UDP-glucuronosyl transferase, and sulfotransferase. The proposed criteria for estimation of the metabolic parameters of an individual can serve as a basis of metabolic portraiting.     

Novel inhibition of proteoglycan synthesis and exocytosis by diethylcarbamazine in the Swarm rat chondrocyte

Pretreatment of cultured chondrosarcoma chondrocytes at 37 degrees C for 15 min with 15 mM diethylcarbamazine (DEC) followed by a 60-min pulse with [35S] sulfate in the presence of DEC resulted in an approximate 40% inhibition of synthesis and a 75% inhibition of secretion of 35S-proteoglycan. The inhibition was dose-related and was not due to a decrease in protein synthesis. Chondrocytes exposed for 75 min to 15 mM DEC, washed, incubated for 17 h in DEC-free medium, and then pulsed with [35S]sulfate showed no inhibition in the rate of synthesis of proteoglycan or in the per cent of radiolabeled proteoglycans exocytosed into the culture medium, indicating full reversibility of the inhibitory effect. When chondrocytes were incubated for 75 min with both 1 mM beta-D-xyloside and 15 mM DEC, secretion of beta-D-xyloside-bound 35S-glycosaminoglycan was inhibited by more than 70% despite an approximate 3-fold increase in intracellular 35S-macromolecules, as compared to cells exposed to beta-D-xyloside alone. Upon removal of DEC, the block in the secretion of beta-D-xyloside-bound 35S-glycosaminoglycans was reversed, although there was a 15-30-min lag in the initiation of exocytosis. Light and electron microscopic examination of chondrocytes after 75 min of incubation with 15 mM DEC revealed large vacuoles, a distended Golgi apparatus, and a distended endoplasmic reticulum which contained electron dense material. Upon removal of DEC, the vacuoles disappeared and distended organelles returned to their normal appearance between 15 and 30 min, coincident with the start of exocytosis of 35S-proteoglycan and beta-D-xyloside-bound 35S-glycosaminoglycan. These biochemical and morphological studies indicate that DEC treatment of chondrosarcoma chondrocytes alters the transport of molecules from the endoplasmic reticulum to the Golgi and the transport of molecules from the Golgi to the cell surface.     

Effect of tranquilizers on the total acetylcholine content and acetylcholinesterase activity in the brain tissue of Arvicanthis niloticus

The effect of reserpine and meprobamate on the total acetylcholine content and acetylcholinesterase activity in the brain tissue of the kusu rat, Arvicanthis niloticus, was studied. The total acetylcholine content and acetylcholinesterase activity were determined 1 hr after i.p. injection of different doses of reserpine (0.25, 0.5 and 1 mg/ml/100 g body wt) and meprobamate (6.25, 12.5 and 25 mg/ml/100 g body wt). The effect of different time intervals (1, 10, 30 min, 1, 2.5, 5, 8, 12, 24 and 48 hr) on the total acetylcholine content and acetylcholinesterase activity was investigated after i.p. injection of 0.5 mg of reserpine and 12.5 mg of meprobamate/ml/100 g body wt. Both reserpine and meprobamate caused an increase in the total ACh content in the brain tissue of Arvicanthis niloticus which was suggested to be due to a decrease in the release of ACh, since both reserpine and meprobamate inhibited AChE activity after some tested periods. The effect of meprobamate was observed to be stronger than that of reserpine.     

Antibodies to the hepatitis A virus in the healthy population of Moscow

Serum specimens collected from 1002 persons in Moscow were tested for the presence of antibodies to hepatitis A virus (anti-HAV antibodies) by solid-phase enzyme immunoassay. The prevalence of these antibodies increased progressively with age from 10% in children aged 5-9 years to over 90% in the age groups of 40-49 years and over, the 50% immunity level being established at the age of 18 years. 79% of infants under 1 year were found to be immune, which was obviously due to the placental transfer of antibodies from mother to child. In a considerable part of seropositive persons over 30 years high or medium antibody titers were detected. These age groups showed a stable proportion of the low, medium and high level of anti-HAV antibodies. The prevalence of such antibodies was not related to sex. The presence of an ample amount of anti-HAV antibodies was determined in all of 18 tested lots of commercial serum immunoglobulin obtained from 3 different manufacturers.     

Vegetative fallows and potential value of the neem tree (Azadirachta indica) in the tropics

Research into the systems of agriculture based on vegetative fallows should begin from enquiries into the shrubs and trees most efficient in restoring soil productivity and providing firewood, timber, fodder and other products essential to meeting basic needs at the rural household and community level. Local processing of such products can give rise to the establishment of thriving village industries and thus generate employment and additional income. Neem tree,Azadirachta indica, of the semiarid regions is one outstanding example of a species which is not only an efficient soil ameliorant but can also provide a series of products highly competitive in price and quality with petroleum-based synthetics. Enough scientific evidence has been gathered from several hundred references on the subject to warrant the launching of a well coordinated multidisciplinary research and development programme leading to agricultural, industrial and commercial exploitation of this tree. Proposals for the implementation of several projects within the programme are briefly outlined in this paper.     

A chronobiological study of delta-amino levulinic acid urinary excretion

Determination of urinary delta-amino levulinic acid (ALA) is now systematically used in occupational health to detect an excessive exposure to lead in professionally exposed workers. However, to determine whether circadian changes of the urinary excretion of ALA alter the significance of the test, we quantified the ALA levels in the urine of 19 healthy young adults. Urine samples were taken every 3 hr between 0700 and 2300 hr and ALA levels were determined by a spectrocolorimetric method. The data indicated that the 24-hr mean ALA level was: 1.81 mg/g creatinine. The peak values (2.24 +/- 0.24) were obtained between 1400 and 1700 hr whereas the lowest ALA levels were found between 2200 and 0300 hr. Cosinor analysis revealed a significant circadian rhythm while no significant difference could be found according to sex. Possible explanations of our findings are discussed.