PLD activation in Chinese hamster ovary (CHO) cells transfected with PGF2α receptor cDNA

Pertussis toxin-insensitive GTP-binding protein was observed to be involved in prostaglandin F2α(PGF2α)-induced phosphoinositide metabolism in Chinese hamster ovary (CHO) cells transfected with PGF2α receptor cDNA (CHO-PGF2α·R cells) (Ito, S. et al. Biochem. Biophys. Res. Commun. 200: 756, 1994). In the present study, we investigated PGF2α-induced PLD activation in CHO-PGF2α·R cells. PLD activation was examined by measuring the production of [³H]phosphatidylbutanol ([³H]PBut), a specific product of the PLD-catalyzed transphosphatidylation reaction. PGF2α-induced [³H]PBut formation was concentration-dependent with the maximal level obtained at 1 μM PGF2α. The maximal [³H]PBut formation was observed at 2 min after addition of PGF2α. Depletion of extracellular Ca²⁺ with EGTA suppressed PGF2α-induced PLD activation by 50%. PKC inhibitors Ro31–8425 and calphostin C inhibited PGF2α-induced [³H]PBut formation by 50%. PTK inhibitors genistein and herbimycin A failed to inhibit PGF2α-induced PLD activation. A combination of maximal effective concentrations of PGF2α (1 μM) and PMA (100 nM) enhanced PLD activation in an additive manner. Pretreatment of the cells with PMA for 2 h down-regulated PKCα and decreased PGF2α-induced PLD activation. These results suggest that PLD activation by PGF2α is mediated by both PKC-dependent and -independent pathways and that PKCα is involved in the former pathway.     

How reliable are our vegetation analyses?

Abstract. Two sets of 40 relevés, made independently by two observers on the same 5m x 5m sample plots, were compared to estimate the sampling error and to assess the effect of this sampling error on (1) estimates of species richness and diversity (2) results of multivariate analyses, and (3) estimation of species turnover in repeated sampling. The relevés were made according to the standard Braun-Blanquet method. The sampling error was estimated for (1) recording of species in sample plots and (2) visual estimation of the degree of cover (or of the general population size). Despite the fact that the sample plots were searched thoroughly for 30 - 40 min, the number of overlooked species was high with a discrepancy of 13% between corresponding relevés. Regarding multivariate analysis, the error caused by missing species was at least as important as the error in visual estimation of species cover. The estimates of degree of cover using the Braun-Blanquet scale are sufficiently reliable for use in multivariate analysis when they are subjected to ordinal transformation. When average cover values are used, the patterns detected are based solely on dominants. Species richness and species diversity could be reliably estimated from the relevés, but the estimates of equitability are very unreliable. The classical relevé method remains one of the most efficient survey methods for recognition of vegetation types on the macro-community and landscape scales.     

How reliable are experimental protein-protein interaction data?

Data of protein-protein interactions provide valuable insight into the molecular networks underlying a living cell. However, their accuracy is often questioned, calling for a rigorous assessment of their reliability. The computation offered here provides an intelligible mean to assess directly the rate of true positives in a data set of experimentally determined interacting protein pairs. We show that the reliability of high-throughput yeast two-hybrid assays is about 50%, and that the size of the yeast interactome is estimated to be 10,000-16,600 interactions.     

Engineering Chinese hamster ovary (CHO) cells to achieve an inverse growth – associated production of a foreign protein, β-galactosidase

Protein synthesis in mammalian cells can be observed in two strikingly different patterns: 1) production of monoclonal antibodies in hybridoma cultures is typically inverse growth associated and 2) production of most therapeutic glycoproteins in recombinant mammalian cell cultures is found to be growth associated. Production of monoclonal antibodies has been easily maximized by culturing hybridoma cells at very low growth rates in high cell density fed- batch or perfusion bioreactors. Applying the same bioreactor techniques to recombinant mammalian cell cultures results in drastically reduced production rates due to their growth associated production kinetics. Optimization of such growth associated production requires high cell growth conditions, such as in repeated batch cultures or chemostat cultures with attendant excess biomass synthesis. Our recent research has demonstrated that this growth associated production in recombinant Chinese hamster ovary (CHO) cells is related to the S (DNA synthesis)-phase specific production due to the SV40 early promoter commonly used for driving the foreign gene expression. Using the stably transfected CHO cell lines synthesizing an intracellular reporter protein under the control of SV40 early promoter, we have recently demonstrated in batch and continuous cultures that the product synthesis is growth associated. We have now replaced this S-phase specific promoter in new expression vectors with the adenovirus major late promoter which was found to be active primarily in the G1-phase and is expected to yield the desirable inverse growth associated production behavior. Our results in repeated batch cultures show that the protein synthesis kinetics in this resulting CHO cell line is indeed inverse growth associated. Results from continuous and high cell density perfusion culture experiments also indicate a strong inverse growth associated protein synthesis. The bioreactor optimization with this desirable inverse growth associated production behavior would be much simpler than bioreactor operation for cells with growth associated production. This revised version was published online in August 2006 with corrections to the Cover Date.     

How robust are neural network models of stimulus generalization?

Artificial feed-forward neural networks are commonly used as a tool for modelling stimulus selection and animal signalling. A key finding of stimulus selection research has been generalization: if a given behaviour has been established to one stimulus, perceptually similar novel stimuli are likely to induce a similar response. Stimulus generalization, in feed-forward neural networks, automatically arises as a property of the network. This network property raises understandable concern regarding the sensitivity of the network to variation in its internal parameter values used in relation to its structure and to its training process. Researchers must have confidence that the predictions of their model follow from the underlying biology that they deliberately incorporated in the model, and not from often arbitrary choices about model implementation. We study how network training and parameter perturbations influence the qualitative and quantitative behaviour of a simple but general network. Specifically, for models of stimulus control we study the effect that parameter variation has on the shape of the generalization curves produced by the network. We show that certain network and training conditions produce undesirable artifacts that need to be avoided (or at least understood) when modelling stimulus selection.     

How reliable are molecular dynamics simulations of membrane active antimicrobial peptides?

Membrane-active antimicrobial peptides (AMPs) are challenging to study experimentally, but relatively easy to investigate using molecular dynamics (MD) computer simulations. For this reason, a large number of MD studies of AMPs have been reported over recent years. Yet relatively little effort has focused on the validity of such simulations. Are these results reliable, and do they agree with what is known experimentally? And how much meaningful information can be obtained? To answer these questions, we demonstrate here some of the requirements and limitations of running MD simulations for several common AMPs: PGLa, melittin, maculatin and BP100. The two most important findings are: (a) simulation results depend strongly on force field parameters, making experimental verification of the simulations obligatory, and (b) slow orientational and conformational fluctuations mean that much longer sampling timescales (multi-μs) are needed if quantitative agreement between simulation averages and experimental data is to be achieved. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.     

Platelet derived growth factor recruits lactosylceramide to induce cell proliferation in UDP Gal:GlcCer: β1 → 4Galactosyltransferase (GalT-V) mutant Chinese hamster ovary cells

Recent molecular cloning studies have suggested the presence of at least two β4Gal transferase genes (β4GalT-V and β4GalT-VI) that may encode lactosylceramide synthase but whether they are functional in vivo and whether they mediate growth factor induced phenotypic change such as cell proliferation is not known. Our previous studies lead to the suggestion that various risk factors in atherosclerosis such as oxidized LDL, shear stress, nicotine, tumor necrosis factor-α converge upon LacCer synthase to induce critical phenotypic changes such as cell proliferation and cell adhesion [1]. However, whether platelet-derived growth factor also recruits LacCer synthase in mediating cell proliferation is not known. Here we have employed a Chinese hamster ovary mutant cell line Pro⁻5Lec20 to determine whether this enzyme physiologically functions to mediate cell proliferation. We show that PDGF stimulates the activity of UDP galactose:glucosylceramide, β1,4galactosyltransferase. The activity of LacCer synthase increased about 2.5 fold within 2.5–5 min of incubation with PDGF in both wild type and Pro⁻5Lec20 cells. Concomitantly, there was an increase in the generation of superoxide radicals, p⁴⁴MAPK phosphorylation and cell proliferation in CHO cells. D-phenyl-2-decanoylamino-3-morpholino-1-propanol (D-PDMP), a potent inhibitor of GlcCer synthase/LacCer synthase impaired PDGF mediated induction of LacCer synthase activity, superoxide generation, p⁴⁴ MAPK activation and cell proliferation in Pro⁻5Lec20 cells. PDGF-induced superoxide generation was also mitigated by the use of diphenylene iodonium; an inhibitor of NADPH oxidase activity that is required for superoxide generation. This inhibition was bypassed by the addition of lactosylceramide. Thus, β4GalT-V gene produces a bona fide LacCer synthase that can function in vivo to generate LacCer. Moreover, this enzyme alone can mediate PDGF induced activation of a signal transduction cascade involving superoxide generation, p⁴⁴MAPK activation, phosphorylation of Akt and cell proliferation.     

How good are comparative models in the understanding of protein dynamics?

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.     

Protection of Chinese hamster ovary cells from heat killing by treatment with cycloheximide or puromycin: involvement of HSPs?

Cycloheximide (CHM) or puromycin (PUR) added for 2 h before heating at 43 degrees C followed by either PUR or CHM during heat greatly protected cells from heat killing. This protection increased with inhibition of protein synthesis. Since treatment with a drug both before and during heating was required for heat protection, and since one drug could be exchanged for the other after the 2-h pretreatment without affecting the heat protection, a common mode of action involving inhibition of protein synthesis is suggested for the two drugs. Drug treatment reduced the synthesis of heat-shock proteins (HSPs) as studied by one-dimensional gel electrophoresis by 80-98% relative to 37 degrees C untreated controls. Synthesis of large molecules (greater than 30 kDa) was preferentially inhibited by PUR but not by CHM. Also for CHM, but not for PUR treatment, a 42 kDa band appeared along with a great reduction in the 43 kDa actin band during CHM treatment at both 37 and 43 degrees C. Furthermore, during CHM or PUR treatment, incorporation of [35S]methionine into HSP families 70, 87, or 110 was not increased relative to incorporation into total protein. However, synthesis of the 70 kDa HSP family was selectively suppressed when cells were incubated at 37 degrees C after CHM treatment, but when cells were incubated at 37 degrees C after treatment at 43 degrees C with CHM, synthesis of the 70 kDa HSP family resumed. When cells were labeled for 3 days, there was no preferential accumulation or turnover of HSP families during heating with or without CHM. Therefore, heat protection caused by treatment with CHM or PUR apparently involves a common mode of action not associated with changes in either total levels or synthesis of HSP families during drug treatment before and during heating. The significance of the changes observed in the synthesis of the HSP 70 family after heat is unknown. As thermotolerance developed during 5 h at 42 degrees C without drugs, synthesis of HSP families 70, 87, and 110, as studied with one-dimensional gels, increased 1.4-fold relative to synthesis of total protein, but compared to HSP families in cells labeled for 5 h at 37 degrees C incorporation was reduced by 40%. The increase of unique HSPs, if studied with two-dimensional gels, would probably be much greater.(ABSTRACT TRUNCATED AT 400 WORDS)     

How reliable are harvesting data for analyses of spatio‐temporal population dynamics?

Harvest data are commonly used as proxy for count data, especially in studies of long‐term temporal and spatial patterns of population fluctuations. However, usually the concurrence of the conclusions based on different types of data is impossible to verify due to the lack of count data. Here, we use annual (1964–2004) harvest and population census data for capercaillie, black grouse and hazel grouse from 14 game management districts covering Finland, and demonstrate some mismatch in the information that these data sets provide. Overall, linear regressions of annual harvest against population count give a reasonable fit, but the slopes are less than 1 in every species. Harvest bags have been proportionally larger in north and eastern Finland than in southwestern Finland, with marked species‐specific differences. Considering population variation, the CV% in the census data (30–50%) is consistently smaller than it is in the harvest data (60–70%). Most importantly, conclusions on the spatio‐temporal patterns of the population dynamics are different if based on harvest rather than count data. In capercaillie, synchrony decreases faster with distance according to the harvest data, while in black grouse and hazel grouse the census data show the steeper decline. In addition, the autocorrelation coefficients in the census time series are higher in capercaillie and black grouse than in harvest data, but in hazel grouse the opposite is true. Finally, the parameter estimates for a second order autoregressive model using different data sets differ, and these differences are species‐specific. Despite the fact that annual harvest is a positive and linear function of annual grouse population density, the pattern of population dynamics derived from the bag data is different from that shown by the census data. This result urges caution in using wildlife bag data as reliable indices of population dynamics. deceased August 2008.     

How are the cellular functions of myosin VI regulated within the cell?

This review, dedicated to the memory of Professor Setsuro Ebashi, focuses on our current work investigating the cellular functions and regulation of the unique unconventional motor, myosin VI. This myosin, unlike all the other myosins so far studied, moves towards the minus end of actin filaments and has been implicated in a wide range of cellular processes such as endocytosis, exocytosis, cell migration, cell division and cytokinesis. Myosin VI’s involvement in these cellular pathways is mediated by its interaction with specific adaptor proteins and is regulated by multiple regulatory signals and modifications such as calcium ions, PtdIns(4,5)P₂ (PIP₂) and phosphorylation. Understanding the functions of myosin VI within the cell and how it is regulated is now of utmost importance given the recent observations that it is associated with a number of human disorders such as deafness and cancers.     

Competition patterns among phytoplankton functional groups: How useful are the complex mathematical models?

Simple models have significant contribution to the development of ecological theory. However, these minimalistic modeling approaches usually focus on a small subset of the causes of a phenomenon and neglect important aspects of system dynamics. In this study, we use a complex aquatic biogeochemical model to examine competition patterns and structural shifts in the phytoplankton community under nutrient enrichment conditions. Our model simulates multiple elemental cycles (org. C, N, P, Si, O), multiple functional phytoplankton (diatoms, green algae and cyanobacteria) and zooplankton (copepods and cladocerans) groups. It also takes into account recent advances in stoichiometric nutrient recycling theory, and the zooplankton grazing term is reformulated to include algal food quality effects on zooplankton assimilation efficiency. The model provided a realistic platform to examine the functional properties (e.g., kinetics, growth strategies, intracellular storage capacity) and the abiotic conditions (temperature, nutrient loading) under which the different phytoplankton groups can dominate or can be competitively excluded in oligo, meso and eutrophic environments. Based on the results of our analysis, the intergroup variability in the minimum cell quota and maximum transport rate at the cell surface for phosphorus along with the group-specific metabolic losses can shape the structure of plankton communities. We also use classification tree analysis to elucidate aspects (e.g., relative differences in the functional group properties, critical values of the abiotic conditions, levels of the other plankton community residents) of the complex interplay among physical, chemical and biological factors that drive epilimnetic plankton dynamics. Finally, our study highlights the importance of improving the mathematical representation of phytoplankton adaptive strategies for resources procurement (e.g., regulation of transport kinetics, effects of transport kinetics on the kinetics of assimilation, relationship between assimilation and growth) to effectively link variability at the organismal level with ecosystem-scale patterns.     

How genetically variable are Neottia ovata (Orchidaceae) populations in northeast Poland?

Using 32 allozyme loci, we examined the genetic diversity of ten populations of Neottia ovata differing in size and located in different regions of northeast Poland. Within‐population genetic variation was low (P_pl = 9.4–31.2%, A = 1.09–1.34 and H_E = 0.044–0.128) relative to taxa with similar life histories. In the majority of N. ovata populations (excluding those in Biebrza), we noted high genotypic diversity (0.49?1.00) and high proportions of unique genotypes (86–100%). Neottia ovata shows a strong pattern of genetic differentiation among populations in northeast Poland, reflected in the high overall F_ST value (0.409). There was a weak, but significant, relationship between genetic and geographical distance (r = 0.09, P < 0.05). We discuss the breeding system, small population sizes and population subdivision as the most important factors affecting the genetic diversity of this species. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 40–49