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PubMed1996

Protein kinase C activation and phosphate uptake are altered in intact mucolipidosis type-4 skin fibroblasts.

Mucolipidosis type 4 (ML-4) is an autosomal recessive inborn error of metabolism, the pathogenesis of which is not known. We characterized protein kinase C (PKC) activation and cellular phosphate uptake in intact quiescent ML-4 skin fibroblasts and after stimulation with phorbol myristate acetate (PMA). [3H]Phorbol dibutyrate uptake was not altered in ML-4 compared to control cells. Translocation of PKC from the cytosolic to the membranous compartment upon stimulation with PMA was perturbed in ML-4 cells. Phosphate uptake was reduced in both cytosolic and membranous fractions of quiescent ML-4 cells. Stimulation with PMA did not elicit an increase in phosphate uptake in the cytosolic fraction of ML-4 cells compared with control cells, but led to comparable phosphate uptake in the membranous fraction of both cell types. The data indicate that PKC-mediated signal transduction may be perturbed in ML-4. Other kinases and phosphatases may be involved. These alterations may play an important role in the pathogenesis of this disorder.

Blotting, Western↗
PubMed2006

Phylogenetic and functional biomakers as indicators of bacterial community responses to mixed-waste contamination.

Few studies have demonstrated changes in community structure along a contaminant plume in terms of phylogenetic, functional, and geochemical changes, and such studies are essential to understand how a microbial ecosystem responds to perturbations. Clonal libraries of multiple genes (SSU rDNA, nirK, nirS, amoA, pmoA, and dsrAB) were analyzed from groundwater samples (n = 6) that varied in contaminant levels, and 107 geochemical parameters were measured. Principal components analyses (PCA) were used to compare the relationships among the sites with respect to the biomarker (n = 785 for all sequences) distributions and the geochemical variables. A major portion of the geochemical variance measured among the samples could be accounted for by tetrachloroethene, 99Tc, No3, SO4, Al, and Th. The PCA based on the distribution of unique biomarkers resulted in different groupings compared to the geochemical analysis, but when the SSU rRNA gene libraries were directly compared (deltaC(xy) values) the sites were clustered in a similar fashion compared to geochemical measures. The PCA based upon functional gene distributions each predicted different relationships among the sites, and comparisons of Euclidean distances based upon diversity indices for all functional genes (n = 432) grouped the sites by extreme or intermediate contaminant levels. The data suggested that the sites with low and high perturbations were functionally more similar than sites with intermediate conditions, and perhaps captured the overall community structure better than a single phylogenetic biomarker. Moreover, even though the background site was phylogenetically and geochemically distinct from the acidic sites, the extreme conditions of the acidic samples might be more analogous to the limiting nutrient conditions of the background site. An understanding of microbial community-level responses within an ecological framework would provide better insight for restoration strategies at contaminated field sites.

Bacteria↗
PubMed1996

Measurement of respiratory parameters by using inspired oxygen sinusoidal forcing signals.

A companion paper (C. E. W. Hahn. J. Appl. Physiol 81: 985-997, 1996) described a continuous-flow gas-exchange mathematical model, which predicted that forced inspired oxygen sinusoids could be used to measure respiratory parameters rapidly, in place of the inert gas argon. We therefore made simultaneous measurements of dead space volume (VD) and alveolar volume (VA) in an animal model, using argon and oxygen inspired gas concentration sinusoid forcing signals, and then compared the results. Our data confirmed the model prediction that the attenuations of the oxygen and argon sinusoid perturbations are identical in the alveolar gas space, even though there is a net uptake of oxygen by the body. Our results show that the calculated values of VD and VA, obtained by using inspired oxygen forcing signals, were independent of both the mean fractional inspired oxygen concentration (FIO2; range 0.18-0.80% vol/vol) and the oxygen forcing signal amplitude (range +/- 2-6% vol/vol). In these studies, oxygen forcing signals, with forcing periods between 1 and 2 min, were able to measure controlled changes in instrument dead space to within 16 ml and also measure positive end-expiratory pressure-induced changes in VA. Under hyperoxic conditions, intravascular oxygen sensors confirmed that the sinusoidal PO2 signal passed into the arterial blood but not into the mixed-venous blood. However, the sinusoid perturbation PO2 signal did pass into the mixed-venous blood when the mean FIO2 was mildly hypoxic (FIO2 = 0.18% vol/vol). These data show that oxygen can be used instead of argon to measure airways dead space and VA.

Animals↗
PubMed2004

Reduced growth hormone secretion prolongs puberty but does not delay the developmental increase in luteinizing hormone in the absence of gonadal negative feedback.

Previous studies have shown that the growth hormone (GH) axis is important for timing the later stages of puberty in female monkeys. However, it is not clear whether these growth-related signals are important for the initiation of puberty and early pubertal events. The present study, using female rhesus monkeys, used two approaches to answer this question. Experiment 1 tested the hypothesis that reduced GH secretion would blunt the rise in nocturnal LH secretion in young (17 mo; n = 7) but not older adolescent ovariectomized females (29 mo; n = 6). Reduced GH secretion was induced by treating females with the sustained release somatostatin analogue formulation, Sandostatin LAR (625 microg/kg). Morning (0900-0930 h) and evening (2200-2230 h) concentrations of bioactive LH were higher in older adolescent compared to young adolescent females. However, diurnal concentrations were not affected by the inhibition of GH secretion in either age group when compared to the placebo-treated, control condition. Experiment 2 tested the hypothesis that reduced GH secretion induced in young juvenile females would delay the initial increase in nocturnal LH secretion and subsequent early signs of puberty. In order to examine this hypothesis, puberty in control females (n = 7) was compared to those in which puberty had been experimentally arrested until a late adolescent age (29 mo) by the use of a depot GnRH analogue, Lupron (750 microg kg(-1) mo(-1); n = 7). Once the analogue treatment was discontinued, the progression of puberty was compared to a group treated in a similar fashion but made GH deficient by continuous treatment with Sandostatin LAR (n = 6). Puberty occurred as expected in control females with the initial rise in evening LH at 21 mo, menarche at 22 mo, and first ovulation at 30 mo. As expected, Lupron arrested reproductive maturation, but elevations in morning and evening LH and menarche occurred within 2 mo of the cessation of Lupron in both Lupron and Lupron-GH-suppressed females. In contrast, first ovulation was delayed significantly in the Lupron-GH-suppressed females (41 mo) compared to the Lupron-only females (36 mo). These data indicate that within this experimental model, reduced GH secretion does not perturb the early stages of puberty but supports previous observations that the GH axis is important for timing the later stages of puberty and attainment of fertility. Taken together, the data indicate that factors that reduce GH secretion may have a deleterious effect on the completion of puberty.

Animals↗
PubMed1999

Heterotropic effectors exert more significant strain on monoligated than on unligated hemoglobin.

The effect of allosteric effectors, such as inositol hexakisphosphate and/or bezafibrate, has been investigated on the unliganded human adult hemoglobin both spectroscopically (employing electronic absorption, circular dichroism, resonance Raman, and x-ray absorption near-edge spectroscopies) and functionally (following the kinetics of the first CO binding step up to a final 4% ligand saturation degree). All data indicate that the unliganded T-state is not perturbed by the interaction with either one or both effectors, suggesting that their functional influence is only exerted when a ligand molecule is bound to the heme. This is confirmed by the observation that CO dissociation from partially liganded hemoglobin ( </= 0.04) is strongly altered by the presence of either effector, and the effect is enhanced whenever the two effectors are simultaneously present. Altogether, these data are a direct demonstration of the occurrence of a strain induced by the presence of a ligand molecule bound to the heme, and for the first time there is a clear indication that the expression of the functional heterotropic effect by these non-heme ligands requires this strain, which is not present in the unliganded molecule.

Adult↗
PubMed2000

Perturbation of EGF-activated MEK1 and PKB signal pathways by TGF-beta1 correlates with perturbation of EGF-induced cyclin D1 and DNA synthesis by TGF-beta1 in C3H 10T1/2 cells.

In mouse C3H 10T1/2 cells, we previously reported that TGF-beta1 first delays and later potentiates EGF-induced DNA synthesis corresponding to an inhibition of EGF-induced cyclin D1 expression at t = 13 h. We report here that in accord with DNA synthesis kinetics, TGF-beta1 initially suppresses EGF-induced cyclin D1 expression then later releases the inhibition. Furthermore, TGF-beta1 also first decreases and later potentiates the levels of EGF-activated MEK1/MAPK and PKB, indicating the existence of cross talk between TGF-beta 1- and EGF-activated signal transduction pathways. PD98059, the specific inhibitor of MEK1, significantly blocks EGF-induced DNA synthesis, whereas wortmannin, the PI3K inhibitor, exerts a modest inhibitory effect, which suggests that the activation of MEK1-MAPK pathway plays a major role in EGF-induced DNA synthesis and the activation of PI3K-PKB pathway plays a minor role. Upon examination of mechanisms underlying the cross talk, it was discovered that application of TGF-beta1 triggers a rapid association between Raf-1 and catalytic subunits of PKA, which are reported to be able to inactivate Raf-1 upon activation. Therefore, TGF-beta1 may activate PKA to inhibit the EGF-activated MEK1-MAPK pathway. The wortmannin-sensitive phosphorylation at the thr(389) site is necessary for activation of p70s6K, an important kinase involved in mitogen-stimulated protein synthesis. Although we found that EGF-stimulated p70s6K phosphorylates through a MAPK-dependent and a MAPK-independent (wortmannin-sensitive) pathway, TGF-beta1 failed to block EGF-triggered phosphorylation of p70s6K at thr(389) and thr(421)/ser(424) sites, implying that PKB inhibition by TGF-beta1 may result from inhibition of PDK1 activity instead of inhibition of PI3K activity. These data also suggest that TGF-beta1 may selectively perturb certain EGF-activated MAPK pools.

Animals↗
PubMed2002

Modulation of voltage sensitivity by N-terminal cytoplasmic residues in human Kv1.2 channels.

Potassium channels are now among the best understood membrane proteins and most salient functions have been mapped onto distinct portions of the protein. The detailed mechanism by which movement of the voltage sensor is transduced into channel opening is yet to be understood. We have constructed chimaeras from our collection of human voltage-gated potassium channels and expressed them in Xenopus oocytes. Here we report on a chimaeric construct, 1N/2, generated by swapping the N-terminal cytoplasmic residues of hKv1.1 onto the transmembrane body of hKv1.2. This chimaera functions as a classic outward rectifier but with a 25 mV hyperpolarizing shift in the mid-point of channel activation. The conductance of oocytes expressing this construct decreases significantly on depolarizing beyond +5 mV, unlike full-length hKv1.2. Other parameters such as ionic selectivity and charybdotoxin blockage are unaffected in making the chimaera. These observations suggest that the introduction of the "foreign" chain from hKv1.1 does not cause a large-scale perturbation of channel structure. Loss of the N-terminus from hKv1.2 is not responsible for the shift in voltage dependence, as a truncation construct, delta75N2, starting at the splice junction, has the same voltage-dependence as full-length hKv1.2. Both constructs show a maximum in their conductance-voltage curves. This decline in conductance on extensive depolarization may arise due to perturbations to the machinery that locks channels into their open state on depolarization. Taken together with our observations on other N-terminal swapped chimaeras, our data imply that N-terminal residues can interact with transmembrane regions and perturb the machinery mediating voltage-dependent channel gating.

Animals↗
PubMed2004

Bifurcation and stability analysis in musculoskeletal systems: a study in human stance.

Reflexes are important in the control of such daily activities as standing and walking. The goal of this study is to establish how reflexive feedback of muscle length, velocity, and force can lead to stable equilibria (i.e., posture) and limit cycles (e.g., ankle clonus and gait). The influence of stretch reflexes on the behavior and stability of musculoskeletal systems was examined using a model of human stance. We computed branches of fold and Hopf bifurcations by numerical bifurcation analysis of the model. These fold and Hopf branches divide the parameter space, constructed by the reflexive feedback gains, into regions of different behavior: unstable posture, stable posture, and stable limit cycles. These limit cycles correspond to a neural deficiency, termed ankle clonus. We also linked bifurcation analysis to known biomechanical concepts by linearizing the model: the fold branch corresponds to zero ankle stiffness and defines the minimal muscle length feedback necessary for stable posture; the Hopf branch is related to unstable reflex loops. Crossing the Hopf branch can lead to the above-mentioned stable limit cycles. The Hopf branch reduces with increasing time delays, making the subject's posture more susceptible to unstable reflex loops. This might be one of the reasons why elderly people, or those with injuries to the central nervous system, often have trouble with standing and other posture tasks. The influence of cocontraction and force feedback on the behavior of the posture model was also investigated. An increase in cocontraction leads to an increase in ankle stiffness (i.e., intrinsic muscle stiffness) and a decrease in the effective reflex loop gain. On the one hand, positive force feedback increases the ankle stiffness (i.e., intrinsic and reflexive muscle stiffness); on the other hand it makes the posture more susceptible to unstable reflex loops. For negative force feedback, the opposite is true. Finally, we calculated areas of reflex gains for perturbed stance and quiet stance in healthy subjects by fitting the model to data from the literature. The overlap of these areas of reflex gains could indicate that stretch reflexes are the major control mechanisms in both quiet and perturbed stance. In conclusion, this study has successfully combined bifurcation analysis with the more common biomechanical concepts and tools to determine the influence of reflexes on the stability and quality of stance. In the future, we will develop this line of research to look at rhythmic tasks, such as walking.

Ankle↗
PubMed1994

Hydration and partial compressibility of biological compounds.

We review the results of compressibility studies on proteins, nucleic acids, and systematically altered low molecular weight compounds that model the constituents of these biopolymers. The model compound data allow one to define the compressibility properties of water surrounding charged, polar, and nonpolar groups. These results, in conjunction with compressibility data on proteins and nucleic acids, were used to define the properties of water that is perturbed by the presence of these biopolymers in aqueous solutions. Throughout this review, we emphasize the importance of compressibility data for characterizing the hydration properties of solutes (particularly, proteins, nucleic acids, and their constituents), while describing how such data can be interpreted to gain insight into role that hydration can play in modulating the stability of and recognition between biologically important compounds.

Animals↗
PubMed1984

Teflon injection in 16 patients with paralytic dysphonia: perceptual and acoustic evaluations.

Sixteen patients with paralytic dysphonia were treated with Teflon injection in the paralyzed vocal fold. Trained voice pathologists rated the pre- and postinjection voices on a 5-point scale for each 11 voice characteristics. Among these, aphonia, breathiness, and hypofunction diminished significantly after injection. The perceptual evaluation was correlated with acoustic data from long-time-average spectrum analysis, fundamental frequency distribution analysis, and waveform perturbation analysis. In this acoustic assessment, systematic changes were found in the long-time-average spectra, which agreed well with the perceptual data. In 12 of 16 patients the voice was both perceptually and acoustically improved after Teflon injection.

Adult↗
PubMed1996

Interaction of oxytocin with Ca2+: II. Proton magnetic resonance and molecular modeling studies of conformations of the hormone and its Ca2+ complex.

Drastic changes in the CD and fluorescence spectra of oxytocin [cyclo(Cys1-Tyr2-Ile3-Gln4-Asn5-Cys6)-Pro7-Leu8-Gly 9-NH2] occur on binding Ca2+ in trifluoroethanol (Ananthanarayanan and Brimble, preceding paper). To further characterize the conformation of the Ca(2+)-bound hormone, we carried out 1H-nmr measurements in deuterated trifluorethanol of oxytocin and its 1:1 Ca2+ complex. The one-dimensional nmr data identified residues involved in Ca2+ binding and the extent of their perturbation on Ca2+ addition. The 3JNH-CH coupling constants and two-dimensional nuclear Overhauser effect (NOE) spectral cross peaks confirmed the helical nature of the Ca2+ complex deduced from CD data. Interproton distances in the free hormone and its Ca2+ complex were estimated from the respective NOE data. Apparent global minimum-energy conformations of free and Ca2+ bound oxytocin were computed using the Monte Carlo with energy minimization protocol, with and without incorporating the NOE-derived distance constraints. Taken together, our results show Ca2+ binding to oxytocin to be a two-step process. The binding of the first Ca2+ brings the otherwise extended tail segment of oxytocin closer to the ring moiety so that it wraps around the cation. This causes the maximal extent of change in all the spectral parameters. The subsequent formation of the 2:1 Ca-oxytocin complex results in the tail detaching itself away from the ring so as to bind the second Ca2+ ion. This leads to further spectral changes in the hormone molecule. The tail segment plays a major role in both steps. These observations may be useful in understanding the structural basis of oxytocin action.

Calcium↗
PubMed2005

A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

Computational Biology↗
PubMed2026

MAdLandExpression: integrating sexual reproduction into the Physcomitrium patens expression atlas.

Physcomitrium patens is a bryophyte model system particularly valuable for evolutionary developmental and comparative genomics studies. Sexual reproduction in bryophytes offers unique insights into the evolution of land plant reproduction. Unlike seed plants, bryophytes have a dominant gametophyte phase and provide significant advantages for studying sexual reproduction, such as the possibility to maintain embryo-lethal mutants through vegetative propagation or the presence of motile male gametes. More than 25&#x2009;years after the first publications of transcriptomic data for P. patens, expression data of most developmental stages of P. patens as well as its responses to various biotic and abiotic perturbations have been represented by microarrays or RNA-seq datasets. To facilitate the use of such data, we introduce the MAdLandExpression atlas as a successor of PEATmoss (Physcomitrium Expression Atlas Tool), integrating its 109 P. patens expression experiments and expanding it with 20 recently published RNA-seq samples of sexual reproduction stages, thus completing the coverage of the P. patens life cycle. The MAdLandExpression atlas also introduces new features for data visualization and analysis, such as the comparison of samples from multiple datasets and gene set normalization. Using this tool, the sexual reproduction dataset was analyzed, identifying genes potentially important for egg and sperm cell development, and confirming the behavior of known key genes in sexual development observed in previous studies.

Bryopsida↗
PubMed2000

A model of HIV-1 pathogenesis that includes an intracellular delay.

Mathematical modeling combined with experimental measurements have yielded important insights into HIV-1 pathogenesis. For example, data from experiments in which HIV-infected patients are given potent antiretroviral drugs that perturb the infection process have been used to estimate kinetic parameters underlying HIV infection. Many of the models used to analyze data have assumed drug treatments to be completely efficacious and that upon infection a cell instantly begins producing virus. We consider a model that allows for less then perfect drug effects and which includes a delay in the initiation of virus production. We present detailed analysis of this delay differential equation model and compare the results to a model without delay. Our analysis shows that when drug efficacy is less than 100%, as may be the case in vivo, the predicted rate of decline in plasma virus concentration depends on three factors: the death rate of virus producing cells, the efficacy of therapy, and the length of the delay. Thus, previous estimates of infected cell loss rates can be improved upon by considering more realistic models of viral infection.

Anti-HIV Agents↗
PubMed1993

Schistosoma mansoni: membranes from adult worms reversibly perturb shape, volume, and membrane organization of intact human red blood cells.

Adult forms of Schistosoma mansoni ingest host (human) red blood cells (RBCs). To elucidate potential mechanisms by which contact with adult parasites perturbs RBC membranes, we studied the effects of the membrane fraction of isolated schistosomes on RBC shape, volume, potassium ion content, and phospholipid and transmembrane protein lateral mobility. S. mansoni-treated RBCs exhibited rapid but spontaneously reversible shape change from discocytes to spheroechinocytes, reversible decrease in cell volume, and rapid loss of intracellular potassium ions. Treated RBCs also showed rapid but spontaneously reversible immobilization of membrane phospholipids and of band 3, the major transmembrane protein. These data suggest that components of adult S. mansoni membranes can perturb host RBC volume and membrane organization. In the absence of RBC lysis, RBC metabolic and repair mechanisms can reverse these effects.

Animals↗
PubMed1990

Inhibition of neutrophil superoxide secretion by the preservative, methylhydroxybenzoate: effects mediated by perturbation of intracellular Ca2+?

The preservative, methylhydroxybenzoate inhibited O2- secretion from human neutrophils activated by both the chemotactic peptide fMet-Leu-Phe and phorbol myristate acetate (PMA): the low level of oxidant secretion activated by the ionophore A23187 was similarly reduced in preservative-treated suspensions. Oxidant secretion was similarly reduced in fMet-Leu-Phe and A23187 treated suspensions in which intracellular Ca2+ was buffered by loading with Quin-2, indicating that methylhydroxybenzoate may exert its effects by perturbation of intracellular Ca2(+)-dependent processes. Methylhydroxybenzoate could mimic EGTA in preventing the Ca2+ dependent enhancement of trypsin activity and could also bind this cation in experiments using a Ca2+ electrode, although the preservative bound Ca2+ more slowly and had a lower affinity than EGTA. These data indicate that methylhydroxybenzoate may exert its effects on neutrophils by perturbation of Ca2(+)-dependent activation pathways and this phenomenon may also explain its other known pharmacological effects. Furthermore, these observations provide an insight into the mechanisms by which intracellular Ca2+ may regulate oxidant secretion.

Calcium↗
PubMed2005

How much NMR data is required to determine a protein-ligand complex structure?

Here we present an NMR-based approach to solving protein-ligand structures. The procedure is guided by biophysical, biochemical, or knowledge-based data. The structures are mainly derived from ligand-induced chemical-shift perturbations (CSP) induced in the resonances of the protein and ligand-detected saturated transfer difference signals between ligands and selectively labeled proteins (SOS-NMR). Accuracy, as judged by comparison with X-ray results, depends on the nature and completeness of the experimental data. An experimental protocol is proposed that starts with calculations that make use of readily available chemical-shift perturbations as experimental constraints. If necessary, more sophisticated experimental results have to be added to improve the accuracy of the protein-ligand complex structure. The criteria for evaluation and selection of meaningful complex structures are discussed. These are exemplified for three complexes, and we show that the approach bridges the gap between theoretical docking approaches and complex NMR schemes for determining protein-ligand complexes; especially for relatively weak binders that do not lead to intermolecular NOEs.

Cyclic AMP-Dependent Protein Kinases↗
PubMed2003

Atomic refinement with correlated solid-state NMR restraints.

The orientation data provided by solid-state NMR can provide a great deal of structural information about membrane proteins. The quality of the information provided is, however, somewhat degraded by sign degeneracies in measurements of the dipolar coupling tensor. This is reflected in the dipolar coupling penalty function used in atomic refinement, which is less capable of properly restraining atoms when dipolar sign degeneracies are present. In this report we generate simulated solid-state NMR data using a variety of procedures, including back-calculation from crystal structures of alpha-helical and beta-sheet membrane proteins. We demonstrate that a large fraction of the dipolar sign degeneracies are resolved if anisotropic dipolar coupling measurements are correlated with anisotropic chemical shift measurements, and that all sign degeneracies can be resolved if three data types are correlated. The advantages of correlating data are demonstrated with atomic refinement of two test membrane proteins. When refinement is performed using correlated dipolar couplings and chemical shifts, perturbed structures converge to conformations with a larger fraction of correct dipolar signs than when data are uncorrelated. In addition, the final structures are closer to the original unperturbed structures when correlated data are used in the refinement. Thus, refinement with correlated data leads to improved atomic structures. The software used to correlate dipolar coupling and chemical shift data and to set up energy functions and their derivatives for refinement, CNS-SS02, is available at our web site.

Algorithms↗