Dynamics of electron transfer from high-potential cytochrome <Emphasis Type="Italic">c</Emphasis> to bacteriochlorophyll dimer in photosynthetic reaction centers as probed using laser-induced temperature jump

Laser-induced temperature jump experiments were used for testing the rates of thermoinduced conformational transitions of reaction center (RC) complexes in chromatophores of Chromatium minutissimum. The thermoinduced transition of the macromolecular RC complex to a state providing effective electron transport from the multiheme cytochrome c to the photoactive bacteriochlorophyll dimer within the temperature range 220–280 K accounts for tens of seconds with activation energy 0.166 eV/molecule. The rate of the thermoinduced transition in the cytochrome–RC complex was found to be three orders of magnitude slower than the rate of similar thermoinduced transition of the electron transfer reaction from the primary to secondary quinone acceptors studied in the preceding work (Chamorovsky et al. in Eur Biophys J 32:537–543, 2003). Parameters of thermoinduced activation of the electron transfer from the multiheme cytochrome c to the photoactive bacteriochlorophyll dimer are discussed in terms of cytochrome c docking onto the RC.     

Sequence stratigraphy of Eocene incised valley clastics and associated sediments,Island of Rab,northern Adriatic Sea,Croatia

Clastic sediments of Middle–Late Eocene age were studied on the Island of Rab (northern Adriatic Sea, Croatia) in order to reconstruct their depositional history, depositional environments, and geometry of sandstone bodies. Detailed outcrop logging and mapping revealed the response of depositional systems to frequent relative sea-level changes, which initiated significant basinward and landward shifts of facies, respectively. Tidal sandstones are commonly underlain by shoreface sandstones, and overlain by offshore sandy marls, whereas the latter are again overlain by shoreface sandstones. Major relative sea-level falls initiated basinward shift of depositional systems and the incision of incised valleys or estuaries, and consequently truncated the underlying shelf sediments. In some cases, the accelerated sea-level fall caused rapid shoreface progradation which is interpreted as a forced regression. Relative sea-level rise caused flooding of the incised relief, and deposition of tidal sandstone bodies which overlie type-I sequence boundaries. The coarse lag sediment of these sequence boundaries locally disappears laterally, and the boundary is granulometrically less prominent. All of the major bounding surfaces have been recognized in the sections studied, although the maximum flooding surface is recognized as a thin “zone” instead of a single surface. Altogether, 28 complete sequences, and 15 parasequences are recognized in the informal unit of the Lopar sandstones, documenting the depositional response to high-frequency relative sea-level oscillations. They have so far not been recognized in the Eocene of the eastern Adriatic region.     

Evolution of Hyperactive,Repetitive Antifreeze Proteins in Beetles

Some organisms that experience subzero temperatures, such as insects, fish, bacteria, and plants, synthesize antifreeze proteins (AFPs) that adsorb to surfaces of nascent ice crystals and inhibit their growth. Although some AFPs are globular and nonrepetitive, the majority are repetitive in both sequence and structure. In addition, they are frequently encoded by tandemly arrayed, multigene families. AFP isoforms from the mealworm beetle, Tenebrio molitor, are extremely potent and inhibit ice growth at temperatures below −5°C. They contain a 12-amino acid repeat with the sequence TCTxSxxCxxAx, each of which makes up one coil of the β-helix structure. TxT motifs are arrayed to form the ice-binding surface in all three known insect AFPs: the homologous AFPs from the two beetles, T. molitor and Dendroides canadensis, and the nonhomologous AFP from the spruce budworm, Choristoneura fumiferana. In this study, we have obtained the cDNA and genomic sequences of additional T. molitor isoforms. They show variation in the number of repeats (from 6 to 10) which can largely be explained by recombination at various TCT motifs. In addition, phylogenetic comparison of the AFPs from the two beetles suggests that gene loss and amplification may have occurred after the divergence of these species. In contrast to a previous study suggesting that T. molitor genes have undergone positive Darwinian selection (selection for heterogeneity), we propose that the higher than expected ratio of nonsynonymous-to-synonymous substitutions might result from selection for higher AT content in the third codon position. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. [Reviewing Editor: Dr. John Oakeshott]     

Mechanokinetic model of cell membrane: theoretical analysis of plasmalemma homeostasis, growth and division

A theoretical model dealing with endocytosis, exocytosis and caveolae invagination, describing plasmalemma homeostasis during cell growth and division, is proposed. It considers transmembrane pressure, membrane tension and mechanosensitivity of membrane processes. Membrane hydraulic conductivity and the flux of transmembrane nonvesicular transport are taken into account. The developed mathematical analysis operates with a formulated set of constitutive equations describing the mechanical state and kinetics of changes in an open dynamic membrane system. The standard version of a model with adjusted parameters was implemented, and predictions including a discussion on the effect of possible parameter modifications were presented. Computer simulations indicate big changes in the magnitude of membrane tension and elasticity, and in the number of membrane buddings in young cells and during mitosis. They also show the extent of cell growth inhibition resulting from a decrease in transmembrane transport or an increase in the exerted difference in osmotic pressure. Moreover, the simulations reveal that exocytosis regulated during mitosis may not be as important for cell growth, as sometimes presumed. Finally, practical application and possible extension of the model are discussed.     

Numerical and Demographic Responses of Pumas to Changes in Prey Abundance: Testing Current Predictions

ABSTRACT Information on factors affecting population size of pumas (Puma concolor) can be important because their principal prey over most of the western United States are valued big game species (e.g., mule deer [Odocoileus hemionus], elk [Cervus elaphus], and bighorn sheep [Ovis canadensis]). Based on the hypothesis that puma numbers are limited by their food supply, puma populations should track changes in prey abundance by growing exponentially with increases in prey and by declining with a lag response when prey decreases. Additional predictions proposed by researchers are that body mass of pumas, female productivity, kitten survival, and adult survival should decrease after a prey decline. We used a 15-year database from a hunted population of pumas in southern Idaho and northwestern Utah to test these predictions. During the 15-year time span of the database, a major decline in mule deer abundance occurred. Estimates of puma numbers and demographic characteristics came from intensive capture and radiocollaring efforts. We calculated kitten and adult survival with MICROMORT software. We found that adult puma numbers increased exponentially at r = 0.07 during a period of increasing mule deer numbers. Four years after the mule deer abundance declined, puma numbers decreased at a rate of r = −0.06. Body mass of female pumas was lower after the decline in puma numbers (42.6 ± SE = 1.2 kg, n = 40 vs. 40.1 ± 0.64 kg, n = 34, t = 5.06, P = 0.045). Kitten survival was less after the decline in deer abundance (0.573 ± 0.016, n = 30 vs. 0.856 ± 0.015, n = 25, Z = 2.40, P < 0.01). Survival of resident females was significantly less after the decline in puma numbers (0.783 ± 0.03 vs. 0.929 ± 0.019, U = 55.0, P = 0.009). Female productivity did not differ before or after the decline in deer abundance. Our results supported the majority of the predictions concerning the impact of changing deer abundance, which supported the hypothesis that the abundance of mule deer limited our population of pumas.     

Prehistoric Pile Dwellers within an Emergent Ecosystem: An Archaeological Case of Hunters and Gatherers at the Mouth of the Savannah River during the Mid-Holocene

Evidence of a pile-dwelling community and seral environmental conditions during the late Mid-Holocene (ca 4,000–3,000 years b.p.) is explored through archaeological data and paleoecological information from the Bilbo Site at the mouth of the Savannah River along the Georgia coast, U.S.A. It is argued that pile dwellings were a central feature of the cultural adaptive system, allowing settlements to be located in wetlands that provided optimal access to the evolving food resources of multiple, dynamic environments. It also is suggested that the adaptive strategy included residential stability and a more complex organizational structure than that exhibited by modern hunter-gatherers living in marginal environments. An erratum to this article can be found at     

Unfolding energetics and conformational stability of DLC8 monomer

To understand the rules governing the protein folding process it is essential to study the stability and unfolding of small monomeric proteins. Here, I present the pH dependent thermal unfolding energetics and conformational stability analysis of monomeric Dynein light chain protein (DLC8) in the pH range 3.5-2.0. DLC8 is the smallest and the most conserved light chain among the light chains of the dynein motor assembly. Thermal unfolding of DLC8 monomer is much complex with the presence of transient intermediates, which is in contrast to the notion that small proteins unfold via simple two-state process. The unfolding seems to be more cooperative at lower pH and the temperature of highest conformational stability (T(s)) is found to be maximum (295.7 K) at pH 2.76. Stability curves have been simulated to understand the thermodynamic parameters that govern the shapes of the experimentally obtained curves. Further, an effort has been made to correlate the observed differences in the denaturation energetics with the protein sequence in order to throw light on the structure-folding paradigm of the DLC8 monomer.     

Electron and nuclear dynamics in many-electron atoms, molecules and chlorophyll-protein complexes: A review

It has been shown [V.A. Shuvalov, Quantum dynamics of electrons in many-electron atoms of biologically important compounds, Biochemistry (Mosc.) 68 (2003) 1333-1354; V.A. Shuvalov, Quantum dynamics of electrons in atoms of biologically important molecules, Uspekhi biologicheskoi khimii, (Pushchino) 44 (2004) 79-108] that the orbit angular momentum L of each electron in many-electron atoms is L = mVr = n? and similar to L for one-electron atom suggested by N. Bohr. It has been found that for an atom with N electrons the total electron energy equation E = −(Z^eff)²e⁴m/(2n²?²N) is more appropriate for energy calculation than standard quantum mechanical expressions. It means that the value of L of each electron is independent of the presence of other electrons in an atom and correlates well to the properties of virtual photons emitted by the nucleus and creating a trap for electrons. The energies for elements of the 1st up to the 5th rows and their ions (total amount 240) of Mendeleev' Periodical table were calculated consistent with the experimental data (deviations in average were 5 × 10^− 3). The obtained equations can be used for electron dynamics calculations in molecules. For H₂ and H₂⁺ the interference of electron-photon orbits between the atoms determines the distances between the nuclei which are in agreement with the experimental values. The formation of resonance electron-photon orbit in molecules with the conjugated bonds, including chlorophyll-like molecules, appears to form a resonance trap for an electron with E values close to experimental data. Two mechanisms were suggested for non-barrier primary charge separation in reaction centers (RCs) of photosynthetic bacteria and green plants by using the idea of electron-photon orbit interference between the two molecules. Both mechanisms are connected to formation of the exciplexes of chlorophyll-like molecules. The first one includes some nuclear motion before exciplex formation, the second one is related to the optical transition to a charge transfer state.     

Long-term changes in a benthic assemblage associated with artificial reefs

The aim of the study was to evaluate the long-term development of a hard bottom benthic assemblage over a period of 20 years in an area off the mouth of a large river. The artificial reef of Fregene was selected because benthic assemblage data were available for the period 1981–1992. This artificial reef is located in the mid Tyrrhenian Sea, 5 nautical miles north of the two mouths of the Tevere River (Latium, Italy) and 1.5 nautical miles offshore from Fregene (Rome, Italy). The artificial reef was deployed in March 1981 for fisheries enhancement in 10–14 m of water on a sandy-silty seabed. The Tevere River carries suspended materials and a heavy load of organics since it transports Rome’s effluent, resulting in the eutrophic state of area waters. Benthic sampling was conducted in 2001 by SCUBA diving; two standard surfaces of 400 cm² were scraped from the vertical walls of the same uppermost block in four different periods. All organisms were identified and counted. The methodology used is the same as that adopted in the previous periods, so that the 2001 data could be compared with past collected data. The benthic assemblage was analysed by cluster analysis using the Bray-Curtis index and clustered using the group average clustering algorithm. The SIMPER procedure was used to identify those taxa that characterize each station group identified by cluster analysis. Changes in benthic assemblages and hydrological trends of the Tevere River were investigated using the cumulative sum series method. The 20-year development of the benthic community, starting from the new substratum, is composed of different phases characterised by different benthic assemblages. In particular five different phases were distinguished: 1. Pioneer species recruitment (May 1981–June 1981); 2. Mytilus galloprovincialis (mussel) dominance (August 1981–November 1983); 3. M. galloprovincialis regression (July 1984–October 1985); 4. M. galloprovincialis absence (91–92); 5. Bryozoans bioconstruction dominance (2001). The dynamic succession of the observed benthic assemblages exhibited a good relation with the Tevere River flow. The Tevere River flow, and the subsequent sedimentation process, seems to have strongly influenced the benthic assemblage succession of the Fregene artificial reef. Guest editors: G. Relini & J. Ryland Biodiversity in Enclosed Seas and Artificial Marine Habitats     

Allelopathic effects of the submerged macrophyte <Emphasis Type="Italic">Potamogeton malaianus</Emphasis> on <Emphasis Type="Italic">Scenedesmus obliquus</Emphasis>

Allelopathic effects of the submerged macrophyte Potamogeton malaianus on Scenedesmus obliquus were assessed using a two-phase approach under controlled laboratory conditions. In the co-culture experiment (phase І), the growth of S. obliquus at two different initial cell densities was significantly inhibited by P. malaianus. Moreover, the growth inhibition was dependent on the biomass density of P. malaianus. Antioxidant enzymes (SOD, CAT and POD), MDA, APA, total soluble protein, protein electrophoretic pattern and morphology of S. obliquus were determined after the co-culture experiment was terminated. The activities of SOD, CAT, POD and APA at the low initial cell density were stimulated, the contents of MDA and total soluble protein were increased, and some special protein bands disappeared in P. malaianus treatments. The macrophyte had no effect on the activities of SOD and APA at the high initial cell density, but significantly influenced other physiological parameters of S. obliquus with the increase of biomass density. The morphology of S. obliquus showed no difference in the macrophyte treatments and the controls, and the cultures were dominated by 4-celled coenobia. The results indicated P. malaianus had significant allelopathic effects on the growth and physiological processes of S. obliquus. Moreover, the allelopathic effects depended on initial algal cell density, biomass density of the macrophyte, and their interaction. In the experiment of P. malaianus culture filtrates (phase II), filtrates from combined culture of plant and S. obliquus at the low initial cell density exhibited no apparent growth inhibitory effect on S. obliquus. The result showed that initial addition of growth-inhibiting plant filtrates had no allelopathic effect on S. obliquus. We concluded that the allelopathic effects on S. obliquus were found in the presence of P. malaianus, but not in P. malaianus filtrates. However, the absence of allelopathic effect on S. obliquus might be due to the very low concentrations of allelochemicals in the filtrates. Handling editor: S. M. Thomas