Modelling and simulation of biased agonism dynamics at a G protein-coupled receptor.

Theoretical models of G protein-coupled receptor (GPCR) concentration-response relationships often assume an agonist producing a single functional response via a single active state of the receptor. These models have largely been analysed assuming steady-state conditions. There is now much experimental evidence to suggest that many GPCRs can exist in multiple receptor conformations and elicit numerous functional responses, with ligands having the potential to activate different signalling pathways to varying extents-a concept referred to as biased agonism, functional selectivity or pluri-dimensional efficacy. Moreover, recent experimental results indicate a clear possibility for time-dependent bias, whereby an agonist's bias with respect to different pathways may vary dynamically. Efforts towards understanding the implications of temporal bias by characterising and quantifying ligand effects on multiple pathways will clearly be aided by extending current equilibrium binding and biased activation models to include G protein activation dynamics. Here, we present a new model of time-dependent biased agonism, based on ordinary differential equations for multiple cubic ternary complex activation models with G protein cycle dynamics. This model allows simulation and analysis of multi-pathway activation bias dynamics at a single receptor for the first time, at the level of active G protein (αGTP), towards the analysis of dynamic functional responses. The model is generally applicable to systems with NG G proteins and N* active receptor states. Numerical simulations for NG=N*=2 reveal new insights into the effects of system parameters (including cooperativities, and ligand and receptor concentrations) on bias dynamics, highlighting new phenomena including the dynamic inter-conversion of bias direction. Further, we fit this model to 'wet' experimental data for two competing G proteins (Gi and Gs) that become activated upon stimulation of the adenosine A1 receptor with adenosine derivative compounds. Finally, we show that our model can qualitatively describe the temporal dynamics of this competing G protein activation.

Exchange of Nitrogen through an Urban Tidal Freshwater Wetland in Philadelphia, Pennsylvania.

Tidal freshwater wetlands in urban settings can be subject to elevated N concentrations, which can promote the exchange of N between the marsh, water, and atmosphere, including denitrification. We used a multitiered approach consisting of direct measurements of N fluxes and denitrification, tidal hypsometry, and N load modeling to examine N exchanges in an urban tidal freshwater wetland of the Delaware River Estuary, Philadelphia, PA. Sediment cores and aboveground biomass were collected at 20 locations across a range of elevations and plant communities in April, July, and October 2010. Nitrate was taken up by the marsh during all seasons. In the spring, the high rate of NH production from the sediment was correlated with NO uptake, suggesting dissimilatory reduction to NH as a potentially important process. Denitrification rates were greatest in July, averaging 5.5 ± 0.6 mg N m h. Adjusted for tidal inundation using a refined digital elevation model, denitrification averaged 0.08, 0.5, and 0.2 g N m mo for April, July, and October, respectively. Less than 10% of the modeled N load was estimated to have been removed in the months measured. A combination of high N load, limited marsh area that represented ∼1% of the watershed area, and conservative extrapolation of denitrification rates contributed to the low estimate of the N load attenuated.

Cryptosporidium parvum antigens induce mouse and human dendritic cells to generate Th1-enhancing cytokines.

Cryptosporidium parvum is an opportunistic intracellular parasite that causes mild to severe diarrhoea, which can be life-threatening in an immunocompromised host. To increase our understanding of the mechanisms that play a role in host immune responses, we investigated the effects of C. parvum antigens on the phenotype of mouse and human dendritic cells (DCs). Cryptosporidium parvum antigens induced DC activation as indicated by upregulation of the maturation marker CD209, as well as by the production of the cytokines interleukin-12 p70, IL-2, IL-1beta, IL-6. In particular, significant increases in the expression of IL-12 p70 were observed from mouse DCs derived from bone marrow in response to solubilized sporozoite antigen and the recombinant cryptosporidial antigens, Cp40 and Cp23. We observed a small but significant increase in IL-18 expression following the exposure to Cp40. We found that the induction of Th1 cytokines was MyD88 dependent (MyD88 knockout mouse DCs were unresponsive). Additionally, both sporozoite preparations (solubilized and live) significantly induced IL-12 production by human monocytic dendritic cells (MoDCs). This finding indicates that solubilized as well as recombinant antigens can induce the maturation of DCs and subsequently initiate an innate immune response.

Pulmonary ventilation measured from body surface movements.

Changes in anteroposterior diameters of the rib cage and abdomen are sensed with magnetometers and summed to give outputs which are very nearly linearly related to changes in lung volume. The volume events of breathing can be measured without recourse to a mouthpiece or face mask, other than for calibration, and with minimal encumbrance to the subject.

Thermoregulation in the mouths of feeding gray whales.

Vascular structures for heat conservation in the tongue of the gray whale (Eschrichtius robustus) are reported here. Numerous individual countercurrent heat exchangers are found throughout the massive tongue. These converge at the base of the tongue to form a bilateral pair of retia. Temperature measurements from the oral cavity of a live gray whale indicate that more heat may be lost through the blubber layer over the body than through the tongue, despite the fact that the tongue is far more vascularized and has much less insulation. These heat exchangers substantially reduce heat loss when these whales feed in cold waters.

Altered DNA recognition and bending by insertions in the alpha 2 tail of the yeast a1/alpha 2 homeodomain heterodimer.

The yeast MAT alpha 2 and MATa1 homeodomain proteins bind cooperatively as a heterodimer to sites upstream of haploid-specific genes, repressing their transcription. In the crystal structure of alpha 2 and a1 bound to DNA, each homeodomain makes independent base-specific contacts with the DNA and the two proteins contact each other through an extended tail region of alpha 2 that tethers the two homeodomains to one another. Because this extended region may be flexible, the ability of the heterodimer to discriminate among DNA sites with altered spacing between alpha 2 and a1 binding sites was examined. Spacing between the half sites was critical for specific DNA binding and transcriptional repression by the complex. However, amino acid insertions in the tail region of alpha 2 suppressed the effect of altering an a1/alpha 2 site by increasing the spacing between the half sites. Insertions in the tail also decreased DNA bending by a1/alpha 2. Thus tethering the two homeodomains contributes to DNA bending by a1/alpha 2, but the precise nature of the resulting bend is not essential for repression.

Lipids of the living coelacanth, Latimeria chalumnae.

The muscle of Latimeria chalumnae contains 30 to 71 percent (dry weight) of lipid deposited extracellularly. Wax esters constituted 90 percent or more of the lipids from muscle and fat storage tissues. These esters, by gaschromatographic analysis, consisted of C(30) to C(40) homologs with one or two double bonds.

Enhanced adhesion of ZnO nanowires during in situ scanning electron microscope peeling.

The interfacial adhesion behaviour of a ZnO nanowire-Si substrate system is investigated using an in situ scanning electron microscope (SEM) mechanical peeling technique. The peel front of a nanowire advances via stick-slip events, and an equilibrium between the driving and resistant force to separation occurs immediately prior to a slip event. The interfacial adhesion energy is one order higher than that predicted theoretically by van der Waals interactions. The enhanced adhesion is primarily attributed to chemical and electrostatic interfacial interactions induced by electron irradiation. This work demonstrates that the operating environment of a nanoscale system could dramatically influence its adhesion behaviour. These findings are expected to have significant implications for interpreting the adhesion behaviour exhibited by a 1D nanostructure-substrate system when applying different testing methodologies, and for the fabrication of future NEMS devices.

Relative contributions of large and small airways to flow limitation in normal subjects before and after atropine and isoproterenol.

Bronchodilatation was produced in normal subjects by the inhalation of atropine, a parasympatholytic agent, and isoproterenol, a beta adrenergic stimulator. Density dependence of maximal expiratory flow (Vmax), expressed as a ratio of Vmax with an 80% helium-20% oxygen gas mixture to Vmax with air at isolung volumes, indicated that the predominant flow regimes across upstream airways changed differently after each agent was given separately. After atropine Vmax increased, elastic recoil pressure did not change, and density dependence decreased. Utilizing the equal pressure points analysis which defines upstream and downstream segments of the intrathoracic airways at flow limitation, these results suggest a greater relative dilatation of the larger upstream airways such that more of the driving pressure is dissipated across the smaller airways in which flow is less dependent upon gas density. After isoproterenol Vmax increased, elastic recoil pressure did not change, and density dependence increased. This suggests a preferential dilatation of the smaller and more peripheral airways with less density-dependent flow regimes such that more of the driving pressure would be dissipated in the larger airways in which flow is more dependent upon gas density. Systematic decreases after isoproterenol lead independently to the same conclusion. After both agents together, Vmax increased and density dependence and critical alveolar pressures did not change from control, suggesting a relatively uniform dilatation of all the airways comprising the upstream segment.

Frequency dependence of flow resistance in patients with obstructive lung disease.

Total respiratory, pulmonary, and chest wall flow resistances were determined by means of forced pressure and flow oscillations (3-9 cps) superimposed upon spontaneous breathing in a group of patients with varying degrees of obstructive lung disease. Increased total respiratory and pulmonary resistances were found, whereas the chest wall resistance was normal or subnormal. The total respiratory and pulmonary resistances decreased with increasing frequencies. Static compliance of the lung was measured during interrupted slow expiration, and dynamic compliance was measured during quiet and rapid spontaneous breathing. Compliance was found to be frequency-dependent. The frequency dependence of resistance and compliance are interpreted as effects of uneven distribution of the mechanical properties in the lungs. The practical application of the oscillatory technique to the measurement of flow resistance in patients with lung disease is discussed. Measurements of total respiratory resistance by the forced oscillatory technique at frequencies less than 5 cps appear to be as useful for assessing abnormalities in airway resistance as either the plethysmographic or esophageal pressure techniques.

Scanning mutagenesis of Mcm1: residues required for DNA binding, DNA bending, and transcriptional activation by a MADS-box protein.

MCM1 is an essential gene in the yeast Saccharomyces cerevisiae and is a member of the MADS-box family of transcriptional regulatory factors. To understand the nature of the protein-DNA interactions of this class of proteins, we have made a series of alanine substitutions in the DNA-binding domain of Mcm1 and examined the effects of these mutations in vivo and in vitro. Our results indicate which residues of Mcm1 are important for viability, transcriptional activation, and DNA binding and bending. Substitution of residues in Mcm1 which are highly conserved among the MADS-box proteins are lethal to the cell and abolish DNA binding in vitro. These positions have almost identical interactions with DNA in both the serum response factor-DNA and alpha2-Mcm1-DNA crystal structures, suggesting that these residues make up a conserved core of protein-DNA interactions responsible for docking MADS-box proteins to DNA. Substitution of residues which are not as well conserved among members of the MADS-box family play important roles in contributing to the specificity of DNA binding. These results suggest a general model of how MADS-box proteins recognize and bind DNA. We also provide evidence that the N-terminal extension of Mcm1 may have considerable conformational freedom, possibly to allow binding to different DNA sites. Finally, we have identified two mutants at positions which are critical for Mcm1-mediated DNA bending that have a slow-growth phenotype. This finding is consistent with our earlier results, indicating that DNA bending may have a role in Mcm1 function in the cell.

The yeast alpha2 and Mcm1 proteins interact through a region similar to a motif found in homeodomain proteins of higher eukaryotes.

Homeodomain proteins are transcriptional regulatory factors that, in general, bind DNA with relatively low sequence specificity and affinity. One mechanism homeodomain proteins use to increase their biological specificity is through interactions with other DNA-binding proteins. We have examined how the yeast (Saccharomyces cerevisiae) homeodomain protein alpha2 specifically interacts with Mcm1, a MADS box protein, to bind DNA specifically and repress transcription. A patch of predominantly hydrophobic residues within a region preceding the homeodomain of alpha2 has been identified that specifies direct interaction with Mcm1 in the absence of DNA. This hydrophobic patch is required for cooperative DNA binding with Mcm1 in vitro and for transcriptional repression in vivo. We have also found that a conserved motif, termed YPWM, frequently found in homeodomain proteins of insects and mammals, partially functions in place of the patch in alpha2 to interact with Mcm1. These findings suggest that homeodomain proteins from diverse organisms may use analogous interaction motifs to associate with other proteins to achieve high levels of DNA binding affinity and specificity.

Use of Trichomonas vaginalis clinical isolates to evaluate correlation of gene expression and metronidazole resistance.

We investigated whether variations in gene expression of enzymes associated with anaerobic resistance of laboratory-derived strains of Trichomonas vaginalis could be detected in a group of 28 clinical isolates with variations in metronidazole sensitivity. We compared isolates by real-time PCR because this method allows for highly sensitive quantification of mRNA and for evaluation of several genes simultaneously. We found that PFOR gene A mRNA levels were highly correlated with PFOR gene B levels, as well as the D subunit of malic enzyme and ferrodoxin. Ferrodoxin mRNA expression was also significantly correlated with that of malic enzyme and hydrogenase. However, when we evaluated relationships between these enzymes and resistance to metronidazole, we found no significant correlations between aerobic or anaerobic in vitro sensitivity to drug and mRNA levels of any of the enzymes tested. Similarly, using a Student's t-test, no significant differences in enzyme mRNA levels were observed between isolates separated by metronidazole resistance or susceptibility. The lack of correlation between gene expression and resistance or susceptibility could be the result of differences in expression at the protein level or because other biochemical pathways or genes are involved in the resistance observed in clinical settings.

Transforming growth factor receptors in liver regeneration following partial hepatectomy in the rat.

Transforming growth factors alpha and beta (TGF-alpha and TGF-beta) are produced in the liver and appear to play an important role in the regulation of hepatic growth. We investigated changes in receptors for these polypeptide growth factors in regenerating liver after partial hepatectomy in the rat with comparisons to livers from normal and sham-operated animals. In normal rats, binding of 125I-epidermal growth factor (EGF) to liver membranes was fully and competitively displaced by TGF-alpha, indicating that these two growth factors share similar sites on the same hepatic receptor. Scatchard analyses revealed that EGF receptors bound EGF with 4- to 8-fold higher affinity than TGF-alpha. Following partial hepatectomy or sham operation, EGF/TGF-alpha receptor number decreased by 25, 40, and 55% at 12, 24, and 72 h, respectively. In all cases. Scatchard analysis obtained with EGF yielded a linear plot indicating a single population of binding sites with a dissociation constant (Kd) of approximately 0.9 nM. Scatchard analysis of TGF-beta binding showed that liver membranes from sham-operated and normal rats express binding sites with a Kd of approximately 35 pM. In contrast, membranes obtained from 12-, 24-, and 72-h regenerating livers were altered in a manner consistent with uncovering or appearance of a higher affinity site. Affinity labeling of liver plasma membranes with 125I-TGF-beta revealed two predominant proteins with Mr 85,000 and 66,000. In unfractionated membrane preparations, two other proteins with Mr 105,000 and approximately 150,000 were seen. Following partial hepatectomy the major change in affinity-labeled proteins was a small (10-25%) but consistent decrease in the Mr 85,000 species. These results show that receptors for TGF-alpha and TGF-beta are modulated after partial hepatectomy, a further indication that these polypeptides may have an important role in liver regeneration.

Induction of replicative competence ("priming") in normal liver.

We have used a system of nutritional manipulation to investigate whether hepatocytes of the normal liver can be primed for replication in vivo. In this system, rats that are denied protein for 3 days undergo a burst of hepatic DNA synthesis and mitosis when they are refed amino acids, while normally fed or starved rats do not respond. To determine if hepatocytes of protein deprived (PD) rats have been "primed" for replication, we examined changes in protooncogene expression in livers of PD rats to see if they would mimic the pattern of gene expression that is induced early after partial hepatectomy. c-jun, c-myc, and p53 mRNAs were elevated in livers of PD rats, while c-fos and c-ras genes were not expressed. The administration of amino acids to PD rats stimulated hepatic DNA synthesis in a shorter period than is required after partial hepatectomy and induced p53 and c-ras expression. In culture, hepatocytes from PD rats had higher levels of c-myc mRNA, underwent morphological changes more rapidly, and reached maximum rates of DNA synthesis earlier than normal hepatocytes. In both normal and primed hepatocyte cultures, transforming growth factor alpha stimulated DNA synthesis more effectively than epidermal growth factor. We conclude that hepatocytes pass through a priming stage before they proliferate and that replicative competence without DNA synthesis can be induced in hepatocytes in the normal liver.

Sequential protooncogene expression during rat liver regeneration.

When growth is stimulated in the normally quiescent adult rat liver by partial hepatectomy, steady state levels of messenger RNAs (mRNAs) for c-fos, c-myc, and p53 increase sequentially during the prereplicative phase which precedes DNA synthesis. Levels of c-fos mRNA are elevated at least 4-fold within 15 min after partial hepatectomy and decrease rapidly by 2 h; c-myc mRNA reaches maximal levels (5-fold over normal) between 30 min and 2 h after the operation. A second, transient phase of expression for both c-fos and c-myc occurs around 8 h after partial hepatectomy. p53 mRNA levels increase between 8 and 12 h after the operation (5-fold over normal) and are reflected in an elevation of steady state levels of p53 protein between 12 and 15 h after partial hepatectomy. The levels of ras p21 protein increase much later at a time of active DNA replication and cell division. Actinomycin D injected at the time of partial hepatectomy blocks the increase in c-myc at 2 h but has no effect on c-fos mRNA levels. Actinomycin D injected at 6 h only partially blocks the increase in c-myc and p53 mRNA at 8 h but does not affect c-fos mRNA. Our results suggest that the transient and sequential expression of protooncogenes during the prereplicative stage of liver regeneration is likely to reflect events associated with entry and progression of hepatocytes into the cell cycle and can serve as markers for identifying specific humoral factors involved in liver regeneration.

Lipid epoxide hydrolase in rat lung preparations.

The activity of rat lung epoxide hydrolase (epoxide hydrolase, EC 3.3.2.3) was studied using two lipid epoxides which can be isolated from lung tissue. These epoxides displayed different Km,app and hydration rates. Methyl cis-9,10-epoxystearate was hydrated 20-times more rapidly than cholest-5 alpha,6 alpha-epoxy-3 beta-ol. The Km for the lung microsomal enzyme was variable and dependent on the microsome concentration in the medium. A soluble epoxide hydrolase was also detected in both lung and liver. This enzyme appears similar to the microsomal enzyme in its activity toward methyl epoxystearate. The measured activities for liver microsomal epoxide hydrolase were over 8-times those for lung microsomes; activity against cholesterol epoxide was 40-times greater for liver. In spite of the slow rates measured with cholesterol epoxide in lung preparations, this compound was an effective competitive inhibitor against methyl epoxystearate over a wide concentration range. This suggests that cholesterol epoxide readily binds to epoxide hydrolase and is an effective competitive inhibitor against a much more actively metabolized substrate, methyl epoxystearate. Such circumstances indicate that cholesterol epoxide binds with a high degree of nonproductivity to lung microsomal epoxide hydrolase. This attribute of lung epoxide hydrolase may relate to the relatively high concentrations of cholesterol epoxide found in lung tissue.

Isolation of the gene coding for elongation factor-1alpha in Cryptosporidium parvum.

A gene encoding for Cryptosporidium parvum (C. parvum) elongation factor 1alpha (EF-1alpha) was isolated and sequenced from a cDNA expression library. The recombinant protein cross-reacted with a monoclonal antibody that was raised to a sporozoite cell surface antigen. The gene encoded a 435 amino acid protein with a predicted molecular weight of 48.1 kDa. The predicted C. parvum EF-1alpha protein sequence showed extensive homology with the EF-1alpha proteins of other eukaryotic organisms and included three conserved sequence motifs implicated in GTP binding.

Fetal growth factors as determinants of intrauterine hepatic growth.

To understand mechanisms at the cellular level that may lead to the selective organomegaly seen in fetuses of diabetic mothers, we examined the role of insulin and autocrine-paracrine growth factors in the regulation of hepatic growth in the fetal rat. Analyses of fetal liver from the last one-third of gestation demonstrated the presence of specific mRNAs for the transforming growth factors (TGFs) TGF-alpha and TGF-beta. TGF-alpha, a homologue of epidermal growth factor (EGF), acts through EGF receptors. Levels of mRNA for TGF-alpha increased dramatically postnatally, whereas EGF receptor number increased just before term. In contrast, levels of mRNA for TGF-beta, an inhibitor of epithelial cell growth, were greater in fetal liver than in adult liver, as was TGF-beta-receptor binding. Other analyses demonstrated increases in tyrosine kinase activities of the insulin receptor, EGF receptor, and insulinlike growth factor I receptor as term approached. Proliferation of fetal rat hepatocytes in primary culture did not require mitogens or serum, consistent with production and activity of autocrine-paracrine growth factors. TGF-beta was a potent inhibitor of fetal hepatocyte proliferation in culture, whereas insulin potentiated fetal hepatocyte growth above "mitogen-independent" levels. The regulatory mechanisms controlling fetal hepatic growth involve a complex interaction between stimulatory and inhibitory factors. Growth factor expression, receptor expression, receptor tyrosine kinase activity, and postreceptor signal transmission represent potential loci for insulin action that might be involved in the pathogenesis of fetal macrosomia seen in diabetic pregnancies.

Growth-promoting effects of relaxin and related compositional changes in the uterus, cervix, and vagina of the rat.

Although the precise role of relaxin has yet to be elucidated, it has been implicated in the regulation of physiological and biochemical processes in the reproductive tract during pregnancy and parturition. In this study, the growth-promoting effects of relaxin and related compositional changes in the uterus, cervix, and vagina of immature ovariectomized estrogen-primed rats were examined. Relaxin increased the wet weight of the uterus, cervix, and vagina in a significant and linear manner over the log of the dose range (1-30 micrograms; 6 h). The increase in uterine weight was due to increases in both dry weight and water content at all doses. A dose of 1 microgram relaxin induced maximal increases in dry weights in the cervix and vagina over control values; higher doses increased wet weight, but these changes were due solely to increases in water content. Thirty micrograms of relaxin were found to increase total soluble protein and glycogen content of the vagina above control values after 6 h. Relaxin did not alter the total collagen levels of the uterus or cervix, and collagen concentrations were significantly reduced in these organs 6 and 24 h after treatment. Total glycosaminoglycan levels were elevated by relaxin in the uterus (6 h) and cervix (24 h). Total vaginal collagen was increased 24 h after relaxin injection, but the collagen concentration was decreased over the time interval studied, and glycosaminoglycan levels in the vagina were unaltered. In summary, relaxin stimulates growth of the uterus, cervix, and vagina by increasing water content and tissue mass. The increases in distensibility that relaxin induces in these organs appear to be related to changes in the fluid matrix and proteoglycan metabolism rather than alterations in collagen concentration, at least 6-24 h after a single injection. These results support the hypothesis that relaxin plays a significant role in the maintenance of pregnancy through its contribution to fetal accommodation and in the facilitation of parturition through expansion of the entire birth canal.