Thermal transitions of myosin and its helical fragments. II. Solvent-induced variations in conformational stability.

The melting behavior of myosin and myosin rod has been studied over the pH range 5.4-7.0, in 0.5 M KCl. Both proteins exhibit almost identical T-m values, which increase from about 37 to 43 degrees as the pH is elevated through the range of study, T-m follows a sigmoidal dependence upon pH, and the inflection point occurs near pH 6.5. The influence of salt concentration on T-m was studied, by the variation of KCl from 0.15 to 2.92 M. With an increasing KCl concentration, both proteins exhibit similar, sigmoidal declines in T-m from about 44 to 34 degrees. Under all conditions of pH and ionic strength studied, melting is accompanied by an absorption of H+ by the protein. The concentration of the protein, the age of the preparation, and the presence of divalent metal ions fail to exert a significant effect on the T-m values obtained by our methods. The effects of salt concentration and pH on the thermal stability of myosin and myosin rod are discussed in terms of the location of the melting process within the myosin molecule. Myosin is shown to possess several of the requisite features for energy transduction via a proton-coupling mechanism. These features provide a framework for investigating some aspects of the molecular basis of muscle contraction within the context of the sliding filament model.     

Finding local genome rearrangements

Background

The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions.

Results

We establish a link between the minimum number of unlikely rearrangements required by a scenario and the problem of finding a maximum edge-disjoint cycle packing on a certain transformed version of the adjacency graph. This link leads to a 3/2-approximation as well as an exact integer linear programming formulation for our problem, which we prove to be NP-complete. We also present experimental results on fruit flies, showing that Hi-C data is informative when used as a criterion for rearrangements.

Conclusions

A new variant of the weighted DCJ distance problem is addressed that ignores scenario length in its objective function. A solution to this problem provides a lower bound on the number of unlikely moves necessary when transforming one gene order into another. This lower bound aids in the study of rearrangement scenarios with respect to chromatin structure, and could eventually be used in the design of a fixed parameter algorithm with a more general objective function.

     

Altered ion transporter expression in bronchial epithelium in mountaineers with high-altitude pulmonary edema.

Hypoxia inhibits activity and expression of transport proteins of cultured lung alveolar epithelial cells. Here we tested whether hypoxia at high altitude affected the expression of ion transport proteins in tissues obtained from controls and mountaineers with high-altitude pulmonary edema (HAPE) at the Capanna Margherita (4,559 m). Expression was determined by RT-PCR and Western blots from brush biopsies of bronchial epithelium and from leukocytes obtained before and during the stay at high altitude. At low altitude, amounts of mRNAs were not different between control and HAPE-susceptible subjects. At high altitude, the amount of mRNA of Na-K-ATPase, CFTR, and beta-actin of brush biopsies did not change in controls but decreased significantly (-60%) in HAPE-susceptible subjects. There was no change in Na channel mRNAs at high altitude in controls and HAPE. No statistically significant correlation was found between the expression of Na transporters and PO2 and O2 saturation. In leukocytes, 28S-rRNA and Na-K-ATPase decreased at altitude in control and HAPE-susceptible subjects, but no significant change in Na-K-ATPase protein was found. Hypoxia-inducible factor-1alpha mRNA and GAPDH mRNA tended to increase in leukocytes obtained from HAPE-susceptible subjects at high altitude but did not change in controls. These results show that hypoxia induces differences in mRNA expression of ion transport-related proteins between HAPE-susceptible and control subjects but that these changes may not necessarily predict differences in protein concentration or activity. It is therefore unclear whether these differences are related to the pathophysiology of HAPE.     

Death Through Respiratory Failure of a Fraction of Ultraviolet-Irradiated Escherichia coli B/r Cells

Escherichia coli B/r cells grown on a glycerol-containing medium and ultraviolet (UV)-irradiated to about 0.5% survival respire for about 1 hr and then cease for several hours. The cells that have completed repair and recovery processes begin to divide about 120 min after UV treatment, but this division is completely inhibited in liquid medium by caffeine, which delays repair of the irradiated deoxyribonucleic acid (DNA). When 5-fluorouracil (FU) is used to maintain respiration, the number of cells which form colonies when plated increases about 60-fold within 1 hr after irradiation. At least part of this increase does not involve repair while the cells are in the liquid medium because when caffeine is present there is still a 20-fold increase in colony formation. We conclude that many irradiated cells, although capable of carrying out complete and accurate repair of their DNA, die of respiratory failure; only when continuance of respiration is favored by FU treatment is their colony-forming potential realized. After an early increase, the number of cells able to form colonies in medium that contains FU remains constant while the completion of repair and recovery occurs. After these processes are completed, the number of cells able to form colonies increases slowly, except in the presence of caffeine, presumably because the late increase requires that repair steps take place while the cells are in liquid medium prior to cell division.     

The Epstein-Barr Virus Protein BRLF1 Activates S Phase Entry through E2F1 Induction

The Epstein-Barr Virus (EBV) immediate-early protein BRLF1 is one of two transactivators which mediate the switch from latent to lytic replication in EBV-infected cells. DNA viruses often modulate the function of critical cell cycle proteins to maximize the efficiency of virus replication. Here we have examined the effect of BRLF1 on cell cycle progression. A replication-deficient adenovirus expressing BRLF1 (AdBRLF1) was used to infect normal human fibroblasts and various epithelial cell lines. BRLF1 expression induced S phase entry in contact-inhibited fibroblasts and in the human osteosarcoma cell line U-2 OS. AdBRLF1 infection produced a dramatic increase in the level of E2F1 but not E2F4. In contrast, the levels of Rb, p107, and p130 were decreased in AdBRLF1-infected cells. Electrophoretic mobility shift assays confirmed an increased level of free E2F1 in the AdBRLF1-infected human fibroblasts. Consistent with the previously described effect of E2F1, AdBRLF1-infected fibroblasts had increased levels of p53 and p21 and died by apoptosis. BRLF1-induced activation of E2F1 may be required for efficient EBV lytic replication, since at least one critical viral replication gene (the viral DNA polymerase) is activated by E2F (C. Liu, N. D. Sista, and J. S. Pagano, J. Virol. 70:2545-2555, 1996).     

Phylogenetic alpha and beta diversity in tropical tree assemblages along regional-scale environmental gradients in northwest South America

Aims Environmental gradients are drivers of species diversity; however, we know relatively little about the evolutionary processes underlying these relationships. A potentially powerful approach to studying diversity gradients is to quantify the phylogenetic structure within and between assemblages arrayed along broad spatial and environmental gradients. Here, we evaluate the phylogenetic structure of plant assemblages along an environmental gradient with the expectation that the habitat specialization of entire lineages is an important evolutionary pattern influencing the structure of tree communities along environmental gradients.Methods We evaluated the effect of several environmental variables on the phylogenetic structure of plant assemblages in 145 plots distributed in northwestern South America that cover a broad environmental gradient. The phylogenetic alpha diversity was quantified for each plot and the phylogenetic beta diversity between each pair of plots was also quantified. Both the alpha and beta diversity measures were then related to spatial and environmental gradients in the study system.Important findings We found that gradients in temperature and potential evapotranspiration have a strong relationship with the phylogenetic alpha diversity in our study system, with phylogenetic overdispersion in low temperatures and phylogenetic clustering at higher temperatures. Further, the phylogenetic beta diversity between two plots increases with an increasing difference in temperature, whereas annual precipitation was not a significant predictor of community phylogenetic turnover. We also found that the phylogenetic structure of the plots in our study system was related to the degree of seasonal flooding and seasonality in precipitation. In particular, more stressful environments such as dry forests and flooded forests showed phylogenetic clustering. Finally, in contrast with previous studies, we find that phylogenetic beta diversity was not strongly related to the spatial distance separating two forest plots, which may be the result of the importance of the three independent mountain ranges in our study system, which generate a high degree of environmental variation over very short distances. In conclusion, we found that environmental gradients are important drivers of both phylogenetic alpha and phylogenetic beta diversities in these forests over spatial distance.     

Mechanistic basis for differential inhibition of the F1Fo‐ATPase by aurovertin

The mitochondrial F₁F_o‐ATPase performs the terminal step of oxidative phosphorylation. Small molecules that modulate this enzyme have been invaluable in helping decipher F₁F_o‐ATPase structure, function, and mechanism. Aurovertin is an antibiotic that binds to the β subunits in the F₁ domain and inhibits F₁F_o‐ATPase‐catalyzed ATP synthesis in preference to ATP hydrolysis. Despite extensive study and the existence of crystallographic data, the molecular basis of the differential inhibition and kinetic mechanism of inhibition of ATP synthesis by aurovertin has not been resolved. To address these questions, we conducted a series of experiments in both bovine heart mitochondria and E. coli membrane F₁F_o‐ATPase. Aurovertin is a mixed, noncompetitive inhibitor of both ATP hydrolysis and synthesis with lower K_i values for synthesis. At low substrate concentrations, inhibition is cooperative suggesting a stoichiometry of two aurovertin per F₁F_o‐ATPase. Furthermore, aurovertin does not completely inhibit the ATP hydrolytic activity at saturating concentrations. Single‐molecule experiments provide evidence that the residual rate of ATP hydrolysis seen in the presence of saturating concentrations of aurovertin results from a decrease in the binding change mechanism by hindering catalytic site interactions. The results from these studies should further the understanding of how the F₁F_o‐ATPase catalyzes ATP synthesis and hydrolysis. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 830–840, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Reactions of nitrite with hemoglobin measured by membrane inlet mass spectrometry

Membrane inlet mass spectrometry was used to observe nitric oxide in the well-studied reaction of nitrite with hemoglobin. The membrane inlet was submerged in the reaction solutions and measured NO in solution via its flux across a semipermeable membrane leading to the mass spectrometer detecting the mass-to-charge ratio m/z 30. This method measures NO directly in solution and is an alternate approach compared with methods that purge solutions to measure NO. Addition to deoxy-Hb(Fe(II)) (near 38 microM heme concentration) of nitrite in a range of 80 microM to 16 mM showed no accumulation of either NO or N(2)O(3) on a physiologically relevant time scale with a sensitivity near 1 nM. The addition of nitrite to oxy-Hb(Fe(II)) and met-Hb(Fe(III)) did not accumulate free NO to appreciable extents. These observations show that for several minutes after mixing nitrite with hemoglogin, free NO does not accumulate to levels exceeding the equilibrium level of NO. The presence of cyanide ions did not alter the appearance of the data; however, the presence of 2 mM mercuric ions at the beginning of the experiment with deoxy-Hb(Fe(II)) shortened the initial phase of NO accumulation and increased the maximal level of free, unbound NO by about twofold. These experiments appear consistent with no role of met-Hb(Fe(III)) in the generation of NO and an increase in nitrite reductase activity caused by the presumed binding of mercuric to cysteine residues. These results raise questions about the ability of reduction of nitrite mediated by deoxy-Hb(Fe(II)) to play a role in vasodilation.