Evidence that both kinetic and thermodynamic factors govern DNA toroid dimensions: effects of magnesium(II) on DNA condensation by hexammine cobalt(III)

Millimolar concentrations of divalent cations are shown to affect the size of toroids formed when DNA is condensed by multivalent cations. The origins of this effect were explored by varying the order in which MgCl(2) was added to a series of DNA condensation reactions with hexammine cobalt chloride. The interplay between Mg(II), temperature, and absolute cation concentration on DNA condensation was also investigated. These studies reveal that DNA condensation is extremely sensitive to whether Mg(II) is associated with DNA prior to condensation or Mg(II) is added concurrently with hexammine cobalt(III) at the time of condensation. It was also found that, in the presence of Mg(II), temperature and dilution can have opposite effects on the degree of DNA condensation. A systematic comparison of DNA condensates observed in this study clearly illustrates that, under our low-salt conditions, toroid size is determined by the kinetics of toroid nucleation and growth. However, when Mg(II) is present during condensation, toroid size can also be limited by a thermodynamic parameter (e.g., undercharging). The path dependence of DNA condensation presented here illustrates that regardless of which particular factors limit toroid growth, toroids formed under the various conditions of this study are largely nonequilibrium structures.     

Plastid degeneration induced by vanadium

In the cells of primary cortex in the roots of horse bean and of root cap of maize, vanadium induced striking changes in the shape of plastids,i.e. the origin of amoeboid, ribbonlike plastids and plastid protrusions.     

Measurement of pulmonary blood flow by fractal analysis of flow heterogeneity in isolated canine lungs

Barman, Scott A., Laryssa L. McCloud, John D. Catravas, andIna C. Ehrhart. Measurement of pulmonary blood flow by fractalanalysis of flow heterogeneity in isolated canine lungs. J. Appl. Physiol. 81(5):2039-2045, 1996.Regional heterogeneity of lung blood flow can bemeasured by analyzing the relative dispersion (RD) of mass(weight)-flow data. Numerous studies have shown that pulmonary bloodflow is fractal in nature, a phenomenon that can be characterized bythe fractal dimension and the RD for the smallest realizable volumeelement (piece size). Although information exists for theapplicability of fractal analysis to pulmonary blood flow in wholeanimal models, little is known in isolated organs. Therefore, thepresent study was done to determine the effect of blood flow rate onthe distribution of pulmonary blood flow in the isolated blood-perfusedcanine lung lobe by using fractal analysis. Four different radiolabeledmicrospheres (¹⁴¹Ce,⁹⁵Nb,⁸⁵Sr, and⁵¹Cr), each 15 µm in diameter,were injected into the pulmonary lobar artery of isolated canine lunglobes (n = 5) perfused at fourdifferent flow rates ( flow1 = 0.42 ± 0.02 l/min;flow2 = 1.12 ± 0.07 l/min;flow 3 = 2.25 ± 0.17 l/min; flow 4 = 2.59 ± 0.17 l/min), and the pulmonary blood flow distribution was measured. Theresults of the present study indicate that under isogravimetric bloodflow conditions, all regions of horizontally perfused isolated lunglobes received blood flow that was preferentially distributed to themost distal caudal regions of the lobe. Regional pulmonary blood flowin the isolated perfused canine lobe was heterogeneous and fractal innature, as measured by the RD. As flow rates increased, fractal dimension values (averaging 1.22 ± 0.08) remained constant, whereas RD decreased, reflecting more homogeneous blood flowdistribution. At any given blood flow rate, high-flow areas of the lobereceived a proportionally larger amount of regional flow, suggestingthat the degree of pulmonary vascular recruitment may also be spatially related.

     

Double-stranded DNA organization in bacteriophage heads: an alternative toroid-based model.

Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent will all available data. Recently we proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here we propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.     

The energetics and evolution of oxidoreductases in deep time

The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation–reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox ( https://protein-redox-potential.web.app ), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation–reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.     

Chemical analysis of stalk components of Dictyostelium discoideum

Structural components of the stalks of mature fruiting bodies of Dictyostelium discoideum have been isolated and characterized after solubilizing non-structural components with urea and sodium dodecyl sulfate. The urea/sodium dodecyl sulfate-insoluble stalks are composed of about 52% cellulose, 15% proteins and 3% of a non-cellulosic heteropolymer in a covalently bound matrix. Non-covalently bound fatty acid containing material was also found. The composition and structural interrelationships of these components are essentially identical to that of the urea/sodium dodecyl sulfate-insoluble surface sheath which is produced earlier in development before culmination. These results suggest that the same components are involved in making structural elements which differ substantially in their functional role in the developmental sequence as well as in their spatial and temporal localization and morphological appearance.