Knotting dynamics during DNA replication

The topology of plasmid DNA changes continuously as replication progresses. But the dynamics of the process remains to be fully understood. Knotted bubbles form when topo IV knots the daughter duplexes behind the fork in response to their degree of intertwining. Here, we show that knotted bubbles can form during unimpaired DNA replication, but they become more evident in partially replicated intermediates containing a stalled fork. To learn more about the dynamics of knot formation as replication advances, we used two-dimensional agarose gel electrophoresis to identify knotted bubbles in partially replicated molecules in which the replication fork stalled at different stages of the process. The number and complexity of knotted bubbles rose as a function of bubble size, suggesting that knotting is affected by both precatenane density and bubble size.     

Strand opening by the UvrA(2)B complex allows dynamic recognition of DNA damage.

Repair proteins alter the local DNA structure during nucleotide excision repair (NER). However, the precise role of DNA melting remains unknown. A series of DNA substrates containing a unique site-specific BPDE-guanine adduct in a region of non-complementary bases were examined for incision by the Escherichia coli UvrBC endonuclease in the presence or absence of UvrA. UvrBC formed a pre-incision intermediate with a DNA substrate containing a 6-base bubble structure with 2 unpaired bases 5' and 3 unpaired bases 3' to the adduct. Formation of this bubble served as a dynamic recognition step in damage processing. UvrB or UvrBC may form one of three stable repair intermediates with DNA substrates, depending upon the state of the DNA surrounding the modified base. The dual incisions were strongly determined by the distance between the adduct and the double-stranded-single-stranded DNA junction of the bubble, and required homologous double-stranded DNA at both incision sites. Remarkably, in the absence of UvrA, UvrBC nuclease can make both 3' and 5' incisions on substrates with bubbles of 3-6 nucleotides, and an uncoupled 5' incision on bubbles of >/=>/=10 nucleotides. These data support the hypothesis that the E.coli and human NER systems recognize and process DNA damage in a highly conserved manner.     

The structure-specific nicking of small heteroduplexes by the RAG complex: implications for lymphoid chromosomal translocations

During V(D)J recombination, the RAG complex binds at recombination signal sequences and creates double-strand breaks. In addition to this sequence-specific recognition of the RSS, the RAG complex has been shown to be a structure-specific nuclease, cleaving 3' overhangs and 3' flaps, and, more recently, 10 nucleotides (nt) bubble (heteroduplex) structures. Here, we assess the smallest size heteroduplex that core and full-length RAGs can cleave. We also test whether bubbles adjacent to a partial RSS are nicked any differently or any more efficiently than bubbles that are surrounded by random sequence. These points are important in considering what types and what size of non-B DNA structure that the RAG complex can nick, and this helps assess the role of the RAG complex in mediating lymphoid chromosomal translocations. We find that the smallest bubble nicked by the RAG complex is 3nt, and proximity to a partial or full RSS sequence does not affect the nicking by RAGs. RAG nicking efficiency increases with the size of the heteroduplex and is only about two-fold less efficient than an RSS when the bubble is 6nt. We consider these findings in the context of RAG nicking at non-B DNA structures in lymphoid chromosomal translocations.     

Bubble splitting in bifurcating tubes: a model study of cardiovascular gas emboli transport.

The transport of long gas bubbles, suspended in liquid, through symmetric bifurcations, is investigated experimentally and theoretically as a model of cardiovascular gas bubble transport in air embolism and gas embolotherapy. The relevant dimensionless parameters in the models match the corresponding values for arteries and arterioles. The effects of roll angle (the angle the plane of the bifurcation makes with the horizontal), capillary number (a dimensionless indicator of flow), and bubble volume (or length) on the splitting of bubbles as they pass through the bifurcation are examined. Splitting is observed to be more homogenous at higher capillary numbers and lower roll angles. It is shown that, at nonzero roll angles, there is a critical value of the capillary number below which the bubbles do not split and are transported entirely into the upper branch. The value of the critical capillary number increases with roll angle and parent tube diameter. A unique bubble motion is observed at the critical capillary number and for slightly slower flows: the bubble begins to split, the meniscus in the lower branch then moves backward, and finally the entire bubble enters the upper branch. These findings suggest that, in large vessels, emboli tend to be transported upward unless flow is unusually strong but that a more homogeneous distribution of emboli occurs in smaller vessels. This corresponds to previous observations that air emboli tend to lodge in the upper regions of the lungs and suggests that relatively uniform infarction of tumors by gas embolotherapy may be possible.     

Analysis of human flap endonuclease 1 mutants reveals a mechanism to prevent triplet repeat expansion

Flap endonuclease 1 (FEN1), involved in the joining of Okazaki fragments, has been proposed to restrain DNA repeat sequence expansion, a process associated with aging and disease. Here we analyze properties of human FEN1 having mutations at two conserved glycines (G66S and G242D) causing defects in nuclease activity. Introduction of these mutants into yeast led to sequence expansions. Reconstituting triplet repeat expansion in vitro, we previously found that DNA ligase I promotes expansion, but FEN1 prevents the ligation that forms expanded products. Here we show that among the intermediates that could generate sequence expansion, a bubble is necessary for ligation to produce the expansion product. Severe exonuclease defects in the mutant FEN1 suggested that the inability to degrade bubbles exonucleolytically leads to expansion. However, even wild type FEN1 exonuclease cannot compete with DNA ligase I to degrade a bubble structure before it can be ligated. Instead, we propose that FEN1 suppresses sequence expansion by degrading flaps that equilibrate with bubbles, thereby reducing bubble concentration. In this way FEN1 employs endonuclease rather than exonuclease to prevent expansions. A model is presented describing the roles of DNA structure, DNA ligase I, and FEN1 in sequence expansion.     

Bubble stimulation efficiency of dinoflagellate bioluminescence

Dinoflagellate bioluminescence , a common source of bioluminescence in coastal waters , is stimulated by flow agitation . Although bubbles are anecdotally known to be stimulatory , the process has never been experimentally investigated . This study quantified the flash response of the bioluminescent dinoflagellate Lingulodinium polyedrum to stimulation by bubbles rising through still seawater . Cells were stimulated by isolated bubbles of 0 . 3–3 mm radii rising at their terminal velocity , and also by bubble clouds containing bubbles of 0 . 06–10 mm radii for different air flow rates . Stimulation efficiency , the proportion of cells producing a flash within the volume of water swept out by a rising bubble , decreased with decreasing bubble radius for radii less than approximately 1 mm . Bubbles smaller than a critical radius in the range 0 . 275–0 . 325 mm did not stimulate a flash response . The fraction of cells stimulated by bubble clouds was proportional to the volume of air in the bubble cloud , with lower stimulation levels observed for clouds with smaller bubbles . An empirical model for bubble cloud stimulation based on the isolated bubble observations successfully reproduced the observed stimulation by bubble clouds for low air flow rates . High air flow rates stimulated more light emission than expected , presumably because of additional fluid shear stress associated with collective buoyancy effects generated by the high air fraction bubble cloud . These results are relevant to bioluminescence stimulation by bubbles in two‐phase flows , such as in ship wakes , breaking waves , and sparged bioreactors . Copyright © 2015 John Wiley & Sons, Ltd.     

Interactions between animal cells and gas bubbles: The influence of serum and pluronic F68 on the physical properties of the bubble surface

We describe a method by which the degree of bubble saturation can be determined by measuring the velocity of single bubbles at different heights from the bubble source in pure water containing increasing concentrations of surfactants. The highest rising velocities were measured in pure water. Addition of surfactants caused a concentration-dependent and height-dependent decrease in bubble velocity; thus, bubbles are covered with surfactants as they rise, and the distance traveled until saturation is reached decreases with increased concentration of surfactant. Pluronic F68 is a potent effector of bubble saturation, 500 times more active than serum. At Pluronic F68 concentrations of 0.1% (w/v), bubbles are saturated essentially at their source. The effect of bubble saturation on the interactions between animal cells and gas bubbles was investigated by using light microscopy and a micromanipulator. In the absence of surfactants, bubbles had a killing effect on cells; hybridoma cells and Chinese hamster ovary (CHO) cells were ruptured when coming into contact with a bubble. Bubbles only partially covered by surfactants adsorbed the cells. The adsorbed cells were not damaged and they also could survive subsequent detachment. Saturated bubbles, on the other hand, did not show any interactions with cells. It is concluded that the protective effect of serum and Pluronic F68 in sparged cultivation systems is based on covering the medium-bubble interface with surfaceactive components and that cell death occurs either after contact of cells with an uncovered bubble or by adsorption of cells through partially saturated bubbles and subsequent transport of cells into the foam region. (c) 1994 John Wiley & Sons, Inc.     

Cell death from bursting bubbles: Role of cell attachment to rising bubbles in sparged reactors

Bursting bubbles are thought to be the dominant cause of cell death in sparged animal or insect cell cultures. Cells that die during the bubble burst can come from three sources: cells suspended near the bubble; cells trapped in the bubble lamella; and cells that attached to the rising bubble. This article examines cell attachment to rising bubbles using a model in which cell attachment depends on cell radius, bubble radius, and cell–bubble attachment time. For bubble columns over 1 m in height and without protective additives, the model predicts significant attachment for 0.5‐ to 3‐mm radius bubbles, but no significant attachment in the presence of protective additives. For bubble columns over 10 cm in height, and without protective additives, the model predicts significant attachment for 50‐ to 100‐μm radius bubbles, but not all protective additives prevent attachment for these bubbles. The model is consistent with three sets of published data and with our experimental results. Using hybridoma cells, serum‐free medium with antifoam, and 1.60 ± 0.05 mm (standard error) radius bubbles, we measured death rates consistent with cell attachment to rising bubbles, as predicted by the model. With 1.40 ± 0.05 mm (SE) radius bubbles and either 0.1% w/v Pluronic‐F68 or 0.1% w/v methylcellulose added to the medium, we measured death rates consistent with no significant cell attachment to rising bubbles, as predicted by the model. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 62: 468–478, 1999.     

Differential reaction kinetics, cleavage complex formation, and nonamer binding domain dependence dictate the structure-specific and sequence-specific nuclease activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the "nonamer binding region," which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease.     

Damage mechanisms of suspended animal cells in agitated bioreactors with and without bubble entrainment

We show that when freely suspended hybridoma cells are cultured in an agitated bioreactor, two fluid-mechanical mechanisms can cause cell damage and growth retardation. The first is present only when there is a gas phase, and is associated with vortex formation accompanied by bubble entrainment and breakup. In the absence of a vortex and bubble entrainment, cells can be damaged only at very high agitation rates, above approximately 700 rpm, by stresses in the bulk turbulent liquid. Cell damage then correlates with Kolmogorov eddy sizes similar to or smaller than the cell size. In the absence of a vortex, the entrainment and motion of very fine bubbles cause no growth retardation even at agitation rates as high as 600 rpm.     

Analysis of freeze-thaw embolism in conifers. The interaction between cavitation pressure and tracheid size

Ice formation in the xylem sap produces air bubbles that under negative xylem pressures may expand and cause embolism in the xylem conduits. We used the centrifuge method to evaluate the relationship between freeze-thaw embolism and conduit diameter across a range of xylem pressures (Px) in the conifers Pinus contorta and Juniperus scopulorum. Vulnerability curves showing loss of conductivity (embolism) with Px down to -8 MPa were generated with versus without superimposing a freeze-thaw treatment. In both species, the freeze-thaw plus water-stress treatment caused more embolism than water stress alone. We estimated the critical conduit diameter (Df) above which a tracheid will embolize due to freezing and thawing and found that it decreased from 35 microm at a Px of -0.5 MPa to 6 microm at -8 MPa. Further analysis showed that the proportionality between diameter of the air bubble nucleating the cavitation and the diameter of the conduit (kL) declined with increasingly negative Px. This suggests that the bubbles causing cavitation are smaller in proportion to tracheid diameter in narrow tracheids than in wider ones. A possible reason for this is that the rate of dissolving increases with bubble pressure, which is inversely proportional to bubble diameter (La Place's law). Hence, smaller bubbles shrink faster than bigger ones. Last, we used the empirical relationship between Px and Df to model the freeze-thaw response in conifer species.     

Phenomena at the advancing ice-liquid interface: solutes, particles and biological cells

Ice formation in aqueous solutions and suspensions involves a number of significant changes and processes in the residual liquid. The resulting effects were described concerning the redistribution of dissolved salts, the behaviour of gaseous solutes and bubble formation, the rejection and entrapment of second-phase particles. This set of conditions is also experienced by biological cells subjected to freezing. The influences of ice formation in that respect and their relevance for cryopreservation were considered as well. A model of transient heat conduction and solute diffusion with a planar ice front, propagating through a system of finite length was found to be in good agreement with measured salt concentration profiles. The spacing of the subsequently developing columnar solidification pattern was of the same order of magnitude as the pertubation wavelengths predicted from the stability criterion. Non-planar solidification of binary salt solutions was described by a pure heat transfer model under the assumption of local thermodynamic equilibrium. The rejection of gaseous solutes and the resulting gas concentration profile ahead of a planar ice front has been estimated by means of a test bubble method, yielding a distribution coefficient of 0.05 for oxygen. The nucleation of gas bubbles has been observed to occur at slightly less than 20-fold supersaturation. The subsequent radial growth of the bubbles obeys a square-root time dependence as expected from a diffusion controlled model until the still expanding bubbles become engulfed by the advancing ice-liquid interface. The maximum bubble radii decrease for increasing ice front velocities. The transition between repulsion and entrapment of spherical latex particles by an advancing planar ice-front has been characterized by a critical value of the velocity of the solidification interface. The critical velocity is inversely proportional to the particle radius as suggested by models assuming an undisturbed ice front. The increase of the critical velocity for increasing thermal gradients shows good agreement with a theoretically predicted square-root type of dependence. Critical velocities have also been measured for yeast and red blood cells. The effect of freezing on biological cells has been analyzed for human lymphocytes and erythrocytes. The reduction of cell volume observed during non-planar freezing agrees reasonably well with shrinkage curves calculated from a water transport model. The probability of intracellular ice formation has been characterized by threshold cooling rates above which the amount of water remaining within the cell is sufficient for crystallization.(ABSTRACT TRUNCATED AT 400 WORDS)     

Mathematical model of gas bubble evolution in a straight tube.

Deep sea divers suffer from decompression sickness (DCS) when their rate of ascent to the surface is too rapid. When the ambient pressure drops, inert gas bubbles may form in blood vessels and tissues. The evolution of a gas bubble in a rigid tube filled with slowly moving fluid, intended to simulate a bubble in a blood vessel, is studied by solving a coupled system of fluid-flow and gas transport equations. The governing equations for the fluid motion are solved using two techniques: an analytical method appropriate for small nondeformable spherical bubbles, and the boundary element method for deformable bubbles of arbitrary size, given an applied steady flow rate. A steady convection-diffusion equation is then solved numerically to determine the concentration of gas. The bubble volume, or equivalently the gas mass inside the bubble for a constant bubble pressure, is adjusted over time according to the mass flux at the bubble surface. Using a quasi-steady approximation, the evolution of a gas bubble in a tube is obtained. Results show that convection increases the gas pressure gradient at the bubble surface, hence increasing the rate of bubble evolution. Comparing with the result for a single gas bubble in an infinite tissue, the rate of evolution in a tube is approximately twice as fast. Surface tension is also shown to have a significant effect. These findings may have important implications for our understanding of the mechanisms of inert gas bubbles in the circulation underlying decompression sickness.     

Rates of Shrinkage and Growth of Air Bubbles Entrained in Wheat Flour Dough

The rates of shrinkage at constant temperature, and growth under a temperature rise below 100°C, of bubbles entrained in wheat flour dough were analyzed and compared with those of a bubble in water. The rate of shrinkage of bubbles in flour dough was controlled by the diffusion of dissolved air from the surface of bubbles to the bulk of flour dough. The apparent diffusion coefficient of the dissolved air in wheat flour dough with the water fraction of 0.49 calculated from the shrinkage of bubbles, was (3.2 ± 1.5) × 10^1?1 m²/sec (19°C), and (6.4 ± 2.0) × 10^?11 m²/sec (42°C). However, the growth behavior of bubbles in flour dough under a temperature rise was very different from that predicted from the diffusion theory. The critical radius of bubbles to grow was larger than that estimated from the diffusion theory. The mechanism of growth of bubbles in wheat flour dough, which was different from that of a bubble in water, is a subject that needs to be clarified.     

Exploiting radiation damage to map proteins in nucleoprotein complexes: The internal structure of bacteriophage T7

In the final stage of radiation damage in cryo-electron microscopy of proteins, bubbles of hydrogen gas are generated. Proteins embedded in DNA bubble sooner than free-standing proteins and DNA does not bubble under the same conditions. These properties make it possible to distinguish protein from DNA. Here we explored the scope of this technique (“bubblegram imaging”) by applying it to bacteriophage T7, viewed as a partially defined model system. T7 has a thin-walled icosahedral capsid, 60 nm in diameter, with a barrel-shaped protein core under one of its twelve vertices (the portal vertex). The core is densely wrapped with DNA but details of their interaction and how their injection into a host bacterium is coordinated are lacking. With short (10 s) intervals between exposures of 17 electrons/Ų each, bubbling starts in the third exposure, with 1–4 bubbles nucleating in the core: in subsequent exposures, these bubbles grow and merge. A 3D reconstruction from fifth-exposure images depicts a bipartite cylindrical gas cloud in the core. In its portal-proximal half, the axial region is gaseous whereas in the portal-distal half, it is occupied by a 3 nm-wide dense rod. We propose that they respectively represent core protein and an end of the packaged genome, poised for injection into a host cell. Single bubbles at other sites may represent residual scaffolding protein. Thus, bubbling depends on dose rate, protein amount, and tightness of the DNA seal.     

Physical modeling of animal cell damage by hydrodynamic forces in suspension cultures

Physical damage of animal cells in suspension culture, due to stirring and sparging, is coupled with complex metabolic responses. Nylon microcapsules, therefore, were used as a physical model to study the mechanisms of damage in a stirred bioreactor and in a bubble column. Microcapsule breaskage folowed first-order kinetices in all experiments Entrainment of bubbles into the liquid phase in the stirred bioreactor gave more microcapsule breakage. In the bubble column, the bubble bursting zone at gas-liquid interface was primarilu responsible for microcapsule breakage. The forces on the microcapsules were equivalent to an external pressure of approximately 4 x 10(4) N . m(-2), based on the critical microcapsule diameter for survival of 190 mum. A stable foam layer, however, was found to be effective in protecting microcapsules from damage. The microcapsule transport to the gas-liquid interface and entrainment into the foam phase was consistent with flotation by air bubbles. This result implies that additives and operation of bioreactors should be selected to minimize flotation of cells. (c) 1992 John Wiley & Sons, Inc.