The time course of repair of ultraviolet-induced DNA damage; implications for the structural organisation of repair

Alternative molecular mechanisms can be envisaged for the cellular repair of UV-damaged DNA. In the "random collision" model, DNA damage distributed throughout the genome is recognised and repaired by a process of random collision between DNA damage and repair enzymes. The other model assumes a "processive" mechanism, whereby DNA is scanned for damage by a repair complex moving steadily along its length. These two models give different predictions concerning the time course of repair. Random collision should result in a declining rate of repair with time as the concentration of lesions in the DNA falls; but the processive model predicts a constant rate of repair until scanning is complete. We have examined the time course of DNA repair in human fibroblasts given low (generally sublethal) doses of UV light. Using 3 distinct assays, we find no sign of a constant repair rate after 4 J/m2 or less, even when the first few hours after irradiation are examined. Thus DNA repair is likely to depend on random collision. The implications of this finding for the structural organisation of repair are discussed.     

Transverse and longitudinal permittivities of a gaseous plasma with an electron collision frequency proportional to the electron velocity

The transverse and longitudinal plasma permittivities, ?^tr and ? ^l , are analyzed for the case where the electron collision frequency in the Bhatnagar-Gross-Krook collision integral is proportional to the absolute value of the electron velocity. It is found that, in both the low-and high-frequency limits, the expressions for ?^tr and ? ^l derived for the case of a variable electron collision frequency coincide with the classical formulas obtained under the assumption of a constant collision frequency, whereas for frequencies close to the electron collision frequency, these expressions differ significantly from the classical ones.     

Liquid chromatography-mass spectrometry/mass spectrometry method development for drug metabolism studies: Examining lipid matrix ionization effects in plasma

Glycerophosphocholines (GPCho's) are known to cause liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) matrix ionization effects during the analysis of biological samples (i.e. blood, plasma). We have developed a convenient new method, which we refer to as "in-source multiple reaction monitoring" (IS-MRM), for detecting GPCho's during LC-MS/MS method development. The approach uses high energy in-source collisionally induced dissociation (CID) to yield trimethylammonium-ethyl phosphate ions (m/z 184), which are formed from mono- and disubstituted GPCho's. The resulting ion is selected by the first quadrupole (Q1), passed through the collision cell (Q2) in the presence of collision gas at low energy to minimize fragmentation, and m/z 184 selected by the third quadrupole. This approach can be combined with standard multiple reaction monitoring (MRM) transitions with little compromise in sensitivity during method development and sample analysis. Hence, this approach was used to probe ionization matrix effects in plasma samples. The resulting information was employed to develop LC-MS/MS analyses for drugs and their metabolites with cycle times less than 5 min.     

Ab initio molecular dynamics simulation on the formation process of He@C60 synthesized by explosion

The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C₆₀ at fairly high yield, but the mechanism of He inserting into C₆₀ cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C₆₀ molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C₆₀, and the self-healing capability of the defects was also observed.

Activity in the myelin fibers of the cat cutaneous nerve in response to heating]

The collision method combined with some techniques improving the signal-to-noise ratio showed that the activation in the nerve fiber group A gamma 1, A delta, A delta 2 and in "mixed" fibers group was changed by hairy skin heating. A relatively great number of nerve fibers of these groups were activated and only an insignificant part of them inhibited their activity in response to the cutaneous receptor heating. A spontaneous activity increase and skin relaxation under heating. were shown.     

Helical nature of sperm swimming affects the fit of fertilization-kinetics models to empirical data

Models of fertilization kinetics rely upon estimates of the swimming velocity of sperm to predict collision rates between egg and sperm. Most investigators measure sperm swimming velocity without accounting for the helical motion of sperm, thereby obtaining an inflated estimate of the velocity with which sperm approach eggs. In turn, models of fertilization predict inflated rates of sperm/egg collision. I observed sea urchin sperm colliding with eggs, quantified the rate of sperm/egg collision, and measured sperm velocity as a component of the helix through which they swim. I also adjusted the "target size" of eggs to reflect the diameter of the helix. My estimate of sperm swimming velocity is an order of magnitude lower than other estimates for the same species. By using helical parameters in fertilization kinetics models and accounting for dead sperm in laboratory trials, I was able to accurately predict lower rates of sperm/egg collision. Moreover, making these adjustments in the model increased the estimated proportion of sperm that initiate fertilization by 6- to 7-fold, suggesting that a better understanding of sperm swimming might lead to a more complete understanding of fertilization biology and natural selection on gamete traits.     

THE PHAGOCYTOSIS OF SOLID PARTICLES : I. QUARTZ.

1. A new quantitative method of measuring phagocytosis of solid particles is described. 2. A method of calculating the chances of collision between leucocytes and quartz particles of different sizes is developed. 3. The speed with which three suspensions of different sized quartz particles should be ingested by leucocytes is predicted from the calculated chances of collision, and the prediction is verified experimentally. 4. The formula for the chances of collision is also verified by varying the speed of rotation of the tubes in which the phagocytic mixtures are incubated.     

ATPase mechanism of Eg5 in the absence of microtubules: insight into microtubule activation and allosteric inhibition by monastrol

The ATPase mechanism of kinesin superfamily members in the absence of microtubules remains largely uncharacterized. We have adopted a strategy to purify monomeric human Eg5 (HsKSP/Kinesin-5) in the nucleotide-free state (apoEg5) in order to perform a detailed transient state kinetic analysis. We have used steady-state and presteady-state kinetics to define the minimal ATPase mechanism for apoEg5 in the absence and presence of the Eg5-specific inhibitor, monastrol. ATP and ADP binding both occur via a two-step process with the isomerization of the collision complex limiting each forward reaction. ATP hydrolysis and phosphate product release are rapid steps in the mechanism, and the observed rate of these steps is limited by the relatively slow isomerization of the Eg5-ATP collision complex. A conformational change coupled to ADP release is the rate-limiting step in the pathway. We propose that the microtubule amplifies and accelerates the structural transitions needed to form the ATP hydrolysis competent state and for rapid ADP release, thus stimulating ATP turnover and increasing enzymatic efficiency. Monastrol appears to bind weakly to the Eg5-ATP collision complex, but after tight ATP binding, the affinity for monastrol increases, thus inhibiting the conformational change required for ADP product release. Taken together, we hypothesize that loop L5 of Eg5 undergoes an "open" to "closed" structural transition that correlates with the rearrangements of the switch-1 and switch-2 regions at the active site during the ATPase cycle.     

The effect of divalent metals and laminar shear on the formation of large freshwater aggregates

Aquatic sediment from Hamilton Harbor were suspended under controlled Couette shear to measure the changes in particle size distribution when the bulk concentration of divalent cations Cd²⁺, Cu²⁺, Ni²⁺ and Zn²⁺ was increased 500 ppb above ambient values. The size distribution of particles followed a bimodal distribution, at diameters of 20 and 200 m, and was modeled with a curvilinear collision model, using a logarithmic size scale to compensate for the decreasing density of larger aggregates. Although collision frequencies decreased with particle size, there was a limit (160 m) above which shear no longer affected collision. Addition of divalent metals caused formation of non-porous large aggregates greater than 300 m, at shears lower than 3 dynes cm^–2. The sharp increase in aggregate volume that resulted from metal addition indicated that a partitioning threshold exists in the harbor, coinciding with an imaginary line along the shore, where wind driven agitation causes a bottom shear of 3 dynes cm^–2. This threshold can be visualized as the area near shore where bottom sediments consist of sands with nominal size greater than 250 m. Calculations, using Stoke's settling, predict settling of large aggregates near thermocline depth, coincident with the appearance of fine clays on the sediment surface.     

Theory of harmonic generation in a plasma produced by the photoionization of gas atoms with electrons in the <Emphasis Type="Italic">np</Emphasis> states

For a plasma produced by the photoionization of hydrogen-like atoms with electrons in the np states, a theory is developed that describes the nonlinear plasma polarizability due to electron-ion collisions, which governs the bremsstrahlung-induced coherent harmonic generation. The effective partial collision frequencies are obtained as functions of the pump field intensity for the first four p states of hydrogen-like atoms and for the third, fifth, seventh, ninth, and eleventh harmonics. These analytic results make it possible to establish the scalings of the collision frequencies with pump field intensity, the principal quantum number, and the number of the generated harmonic. In the case of pump fields of comparatively low intensities, some qualitative differences are revealed between these scalings and the corresponding scalings obtained for the Bethe regime of suppression of the photoionization barrier in a gas of hydrogen-like atoms with electrons in the ns states.     

Determination of electrostatic potentials at biological interfaces using electron-electron double resonance.

A new general method for the determination of electrostatic potentials at biological surfaces is presented. The approach is based on measurement of the collision frequency of a charged nitroxide in solution with a nitroxide fixed to the surface at the point of interest. The collision frequency is determined with 14N:15N double label electron-electron double resonance (ELDOR). As a test, the method is shown to give values for phospholipid bilayer surface potentials consistent with the Gouy-Chapman theory, a simple model shown by many independent tests to accurately describe charged, planar surfaces. In addition, the method is applied to determine the electrostatic potential near the surface of DNA. The results indicate that the potential is significantly smaller than that predicted from Poisson-Boltzmann analysis, but is in qualitative agreement with that predicted by Manning's theory of counter ion condensation. The method is readily extended to measurement of surface potentials of proteins.     

A theory of Brownian coagulation in a bounded planar region

A method for calculating time-dependent probabilities and rates of coagulation is given for particles on a bounded two-dimensional region. Equations are derived and solved for the random variations of displacements between two particles which undergo independent Brownian motion and bind irreversibly upon collision. The solution is used to calculate expected times required for collisions of particles. Comparison with earlier models shows that revised boundary values and initial conditions predictably lengthen required collision times by about a factor of four. Applicatons of the methodology are discussed.     

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.

The rate constant for the transition between the equatorial and axial conformations of N-acetylalanyl-N'-methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency gamma = 2 ps-1, shows diffusive character for gamma greater than or equal to 10 ps-1, but does not approach zero even at gamma = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., gamma approximately 2 ps-1). This method is expected to be more efficient than either molecular dynamics in vacuo (which corresponds to LD with gamma = 0) or molecular dynamics in solvent (where dynamics is largely diffusive).     

Reaction of c-Type Cytochromes with the Iron Hexacyanides: Mechanistic Implications

The reaction of c-cytochromes with iron hexacyanides is similar in mechanism to the interaction of cytochromes with their physiological oxidants and reductants in that the formation of complexes precedes electron transfer. Analysis of the kinetics of oxidation and reduction of a number of c-cytochromes by solving the simultaneous differential equations defining the mechanism is possible, and allows assignment of all six rate constants describing a minimum three-step mechanism [cyto(Fe(+3)) + Fe(+2) right harpoon over left harpoon cyto (Fe(+3)) - Fe(+2) right harpoon over left harpoon cyto(Fe(+2)) - Fe(+3) right harpoon over left harpoon cyto(Fe(+2)) + Fe(+3)]. We find that the usual steady-state approximations are not valid. Furthermore, the ratio of first-order rate constants for electron transfer was approximately 1.0, and no correlation was found between any of the six rate constants and the differences in oxidation-reduction potential of the iron-hexacyanides and different cytochromes c. However, it was found that the ratio of the rate constants for complex formation between ferricytochrome c and potassium ferrocyanide and ferrocytochrome c and potassium ferricyanide was proportional to the difference in oxidation-reduction potentials. Thus the minimum three-step mechanism given above accurately describes the observed kinetic data. However, this mechanism leads to a number of conceptual difficulties. Specifically, the mechanism requires that the collision complexes formed [cyto(Fe(+3)) - Fe(CN)(6) (-4) and cyto(Fe(+2)) - Fe(CN)(6) (-3)] have very different equilibrium constants, and further requires that formation of the collision complexes be accompanied by "chemistry" to make the intermediates isoenergetic. A more complex five-step mechanism which requires that the reactants [Fe(CN)(6) (-4) and ferricytochrome c or Fe(CN)(6) (-3) and ferrocytochrome c] form a collision complex followed by a first-order process before electron transfer, was found to yield results similar to those of the three-step mechanism. However, describing the formation of the collision complex in terms of a rapid equilibrium circumvents conceptual difficulties and leads to a physically reasonable mechanism. In this mechanism the reactants are in rapid equilibrium with the collision complexes and the rate constants for complex formation are controlled by diffusion and accessibility. The collision complexes then rearrange, possibly through conformational changes and/or solvent reorganization, to yield isoenergetic intermediates that can undergo rapid reversible electron transfer. The five-step mechanism can be described by the same rate constants obtained from the three-step mechanism with the appropriate adjustments to account for rapid equilibrium. This more complex analysis associates the oxidation-reduction potential of a particular cytochrome with the relative magnitude of the first-order conversion of the oxidant and reductant collision complexes to their respective intermediates. Thus the cytochromes c control their oxidation-reduction potential by chemical and/or structural alterations. This mechanism appears to be general in that it is consistent with the observed kinetics of 11 different cytochromes c from a wide variety of sources with a range of oxidation-reduction potentials.     

Collision mortality has no discernible effect on population trends of North American birds

Avian biodiversity is threatened by numerous anthropogenic factors and migratory species are especially at risk. Migrating birds frequently collide with manmade structures and such losses are believed to represent the majority of anthropogenic mortality for North American birds. However, estimates of total collision mortality range across several orders of magnitude and effects on population dynamics remain unknown. Herein, we develop a novel method to assess relative vulnerability to anthropogenic threats, which we demonstrate using 243,103 collision records from 188 species of eastern North American landbirds. After correcting mortality estimates for variation attributable to population size and geographic overlap with potential collision structures, we found that per capita vulnerability to collision with buildings and towers varied over more than four orders of magnitude among species. Species that migrate long distances or at night were much more likely to be killed by collisions than year-round residents or diurnal migrants. However, there was no correlation between relative collision mortality and long-term population trends for these same species. Thus, although millions of North American birds are killed annually by collisions with manmade structures, this source of mortality has no discernible effect on populations.     

Identification of protein side chains near the membrane-aqueous interface: a site-directed spin labeling study of KcsA.

This study presents an approach to identifying surface residues on membrane proteins that are exposed toward the membrane-aqueous interface. The method employs a lipid Ni(II) chelate that localizes the metal ion to a region near the membrane-aqueous interface. Lateral diffusion of the lipid chelate results in Heisenberg exchange (HE) with nitroxide side chains in the protein only if direct contact occurs between the paramagnetic species during a collision. Thus, HE serves as a signature for residues facing the bilayer in the neighborhood of the membrane-aqueous interface. To evaluate the method, 13 surface residues on the extracellular half of KcsA, a prokaryotic potassium channel of known structure, were examined for HE with the Ni(II) chelate. The HE rate between the two species is found to depend strongly on the vertical position of the nitroxide with respect to the membrane-aqueous interface. Nitroxides introduced near the interface experience relatively high HE rates, whereas nitroxides that are immersed in the bilayer interior or sterically sheltered from collision experience low or undetectable rates. The results indicate that residues near the interface can be identified on the basis of their high rates of collision with the headgroup region of the bilayer.     

Ungulate: vehicle collision rates are associated with the phase of the moon

The phase of the moon can affect activity patterns of nocturnal animals, and may also affect visibility for motorists. However, surprisingly little is known about whether the risk of a wildlife-vehicle collision (WVC) is associated with lunar phase. We investigated the relationship between frequency of WVC at night and lunar phase for four large ungulate species that account for a high proportion of serious WVC along roads in agricultural and forested landscapes of two continents: wild boar Sus scrofa, roe deer Capreolus capreolus, and red deer Cervus elaphus in Castile and Leon, Spain, and white-tailed deer Odocoileus virginianus in New York State, USA. Three of the four species most frequently collided with vehicles at night during the full moon phase of the lunar cycle; this pattern was evident throughout the year but was stronger during some months. For roe deer, the species for which WVC was most closely associated with the lunar cycle, the frequency of WVC was 71.3% greater during the full than new moon period. Our results indicate that rates of ungulate WVC at night cycle on a period of a lunar month, which has implications for traffic safety planning and for motor vehicle collision emergency response preparation.     

A biomechanical evaluation of whiplash using a multi-body dynamic model

This paper presents a biomechanical evaluation of whiplash injury potential during the initial extension motion of the head in a rear-end collision. A four-segment dynamic model is developed in the sagittal plane for the analysis. The model response is validated using the existing experimental data and is shown to simulate the "S-shape" kinematics of the cervical spine and the resulting dynamics observed in human and cadaver experiments. The model is then used to evaluate the effects of parameters such as collision severity, head/headrest separation, and the initial head orientation in the sagittal plane on the "S-shape" kinematics of the cervical spine and the resulting neck loads. It is shown, for example, that the cervical spine forms an "S-shape" for a range of change in speeds and that at lower and higher speeds changes the spine does not form the "S-shape." Furthermore, it is shown that the "S-shape" formation also depends on the head to headrest separation distance.     

Impacts of onshore wind energy production on birds and bats: recommendations for future life cycle impact assessment developments

Purpose

Models for quantifying impacts on biodiversity from renewable energy technologies are lacking within life cycle impact assessment (LCIA). We aim to provide an overview of the effects of wind energy on birds and bats, with a focus on quantitative methods. Furthermore, we investigate and provide the necessary background for how these can be integrated into new developments of LCIA models in future.

Methods

We reviewed available literature summarizing the effects of wind energy developments on birds and bats. We provide an overview of available quantitative assessment methods that have been employed outside of the LCIA framework to model the different impacts of wind energy developments on wildlife. Combining the acquired knowledge on impact pathways and associated quantitative methods, we propose possibilities for future approaches for a wind energy impact assessment methodology for LCIA.

Results and discussion

Wind energy production has impacts on terrestrial biodiversity through three main pathways: collision, disturbance, and habitat alterations. Birds and bats are consistently considered the most affected taxonomic groups, with different responses to the before-mentioned impact pathways. Outside of the LCIA framework, current quantitative impact assessment prediction models include collision risk models, species distribution models, individual-based models, and population modeling approaches. Developed indices allow scaling of species-specific vulnerability to mortality, disturbance, and/or habitat alterations.

Conclusions

Although insight into the causes behind collision risk, disturbance, and habitat alterations for bats and birds is still limited, the current knowledge base enables the development of a robust assessment tool. Modeling the impacts of habitat alterations, disturbance, and collisions within an LCIA framework is most appropriate using species distribution models as those enable the estimation of species’ occurrences across a region. Although local-scale developments may be more readily feasible, further up-scaling to global coverage is recommended to allow comparison across regions and technologies, and to assess cumulative impacts.