Neutral mutations and repetitive DNA

We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.     

The cell wall-plasmalemma interface in sieve tubes of barley

Both thick- and thin-walled sieve tubes in leaf-blade veins of Hordeum vulgare L. exhibit a distinct, electron-opaque inner wall layer after fixation in glutaraldehyde-osmium tetroxide and staining with uranyl acetate and lead citrate. This inner wall layer is thickest at the sieve plates and lateral sieve areas where it is permeated by a labyrinth of tubules formed by the plasmalemma. Along the lateral walls between sieve areas the inner wall layer apparently is penetrated by numerous microvilli-like evaginations of the plasmalemma, giving the cell wall-plasmalemma interface the appearance of a brush border. It is suggested that a similar brush-border-like structure may occur at the cell wall-plasmalemma interface of sieve elements in a wide variety of vascular plants.Abbreviation ER endoplasmic reticulum     

X-ray and model-building studies on the specificity of the active site of proteinase K

Proteinase K, the extracellular serine endopeptidase (E.C. 3.4.21.14) from the fungus Tritirachium album limber, is homologous to the bacterial subtilisin proteases. The binding geometry of the synthetic inhibitor carbobenzoxy-Ala-Phechloromethyl Ketone to the active site of proteinase K was the first determined from a Fourier synthesis based on synchrotron X-ray diffraction data between 1.8 Å and 5.0 Å resolution. The protein inhibitor complexes was refined by restrained least-squares minimization with the data between 10.0 and 1.8 Å. The final R factor was 19.1% and the model contained 2,018 protein atoms, 28 inhibitors atoms, 125 water molecules, and two Ca²⁺ ions. The peptides portion of the inhibitor is bound to the active center of proteinase K by means of a three-stranded antiparallel pleated sheet, with the side chain of the phenylalanine located in the P1 site. Model building studies, with lysine replacing phenylalanine in the inhibitor, explain the relatively unspecific catalytic activity of the enzyme.     

A new device for collection of interstitial water from wetland sediments

A sampler for collection of interstitial water from wetland sediments is described. It differs from other sampling devices because it does not have to be filled with solution to facilitate diffusion, it does not have to be removed from the wetland to collect samples, and it can be used to draw repeated samples over time from identical locations. The device facilitates in situ measurement of a wide range of abiotic parameters such as electrical conductivity, redox potential, and pH in wetland sediments. The device has application in ecological investigations of sediment-borne wildlife diseases, studies of benthic invertebrates, measurement of nutrient exchange, and other aspects of wetland ecology.     

Studies on graft unions

Summary The occurrence of plasmodesmata in the graft interfaces of two heteroplastic grafts (Impatiens walleriana onImpatiens olivieri andHelianthus annum onVicia faba) has been studied. For both systems two types of intercellular strand are described: 1. Continuous plasmodesmata interconnecting the cells of stock and scion and 2. half plasmodesmata traversing the wall part of one partner cell without connection to the abutting cell. Single strands or branched forms occur in both types of plasmodesma. In the case of half plasmodesmata, branchings with extended median nodules predominate. The distribution of half and continuous plasmodesmata varies with the different areas of a graft interface: in the region of bridging vascular tissues most cell connections are continuous. In areas where cortex or pith-derived callus cells and those of misaligned tissues (cortex/vascular tissue; cortex/pith; pith/vascular tissue) match, discontinuous strands predominate.Branched half plasmodesmata also occur in presumably fused walls between related callus cells; they are typical structures secondarily formed in non-division walls.The results are discussed with regard to compatibility/incompatibility phenomena in heterografts and the development and function of interspecific cell bridges.     

On the oscillatory phenomenon in an oil/water interface

A simple theoretical model is presented for simulating the self-sustained oscillations of electric potential and pH at an oil/water interface appearing in a two-phase system composed of 2-nitropropane solution containing picrate acid and an aqueous solution of cetyltrimethylammonium bromide. In the present model, a well-known condition necessary for the occurrence of self-sustained oscillations, i.e., the presence of a positive feedback process far from equilibrium, is taken into account in a set of kinetic equations to describe simplified characters of the following two processes: (i) a cooperative formation of ion pair complexes at the interface, and (ii) supply of picrate anions and cetyltrimethylammonium cations to the interface accompanied by release of ion pair complexes to the organic phase. The numerical solutions of the present equations are shown to reproduce fairly well the characteristic properties of the oscillation of electric potential and pH such as wave forms and frequencies.     

Tidal flushing of ammonium from intertidal sediments of Ria Formosa,Portugal

Ammonium concentrations were determined in near-bottom water and intertidal surface sediments collected in February and July 1993 at five stations of Ria Formosa, a shallow meso-tidal coastal lagoon in southern Portugal. At each station, samples were taken a few minutes before tidal inundation, and subsequently 2, 10, 15 and 20 minutes thereafter. Ammonium concentration in near-bottom waters increased dramatically in the first 2 minutes followed by a decrease during the 18 minutes of flooding (maximum range 10.3-2.2 M). The highest levels in the flooding water were concomitant with a decrease of extractable ammonium recorded in the upper sediment layer (2 cm). Laboratory experiments indicated that ammonium is easily extracted from the sediment solids by physical perturbation, as one would expect when tidal water flushes over the intertidal area. This perturbation results in the export of ammonium from the sediment, by pulse mechanisms of short time intervals. On a daily scale this amount is two orders of magnitude higher than transport resulting from molecular diffusion.     

A 43 kDa protein inserted at the plasma membrane-cytoskeleton interface in rumen entodiniomorphid ciliates

Summary The P-43 ofEudiplodinium and homologous proteins in three other entodiniomorphid species, free-living ciliates, flagellates, and HeLa cells, were identified at the plasma membrane-cytoskeleton interface. Proteins cross-reacting with MAb B6 were also located at the ciliary inner surface of the plasma membrane. Due to the strong adhesion of the plasma membrane to the underlying cytoskeleton, classical extraction with detergents, urea, NaOH, and PTA, failed to separate the two components completely. However, the extraction properties of P-43, associated with its membrane-cytoskeleton interactive functions, suggest that this unglycosylated protein may present some analogies with proteins of the intermediate filaments. Their ubiquity and localization suggest that P-43 and MAb B6 crossreacting proteins may not be strictly epiplasmic but could be amphitropic proteins, strongly anchored to both the plasma membrane and the underlying microfilament framework, via protein-protein binding or by direct insertion in the lipid bilayer.Abbreviations BSA bovine serum albumin - Con A concanavalin A - EDTA ethylene diamine tetraacetic acid - EM electron microscopy - IF intermediate filaments - MAb monoclonal antibody - MET 2-mercaptoethanol - MW molecular weight - PAb polyclonal antibody - PBS phosphate buffered saline - PMSF phenylmethylsulfonyl fluoride - PTA phosphotungstic acid - SDS sodiumdodecyl sulfate - TAME Na-p-tosyl-arginine methyl ester - TLCK Na-p-tosyl-lysine chloromethyl ketone     

Subunit interface mutants of rabbit muscle aldolase form active dimers.

We report the construction of subunit interface mutants of rabbit muscle aldolase A with altered quaternary structure. A mutation has been described that causes nonspherocytic hemolytic anemia and produces a thermolabile aldolase (Kishi H et al., 1987, Proc Natl Acad Sci USA 84:8623-8627). The disease arises from substitution of Gly for Asp-128, a residue at the subunit interface of human aldolase A. To elucidate the role of this residue in the highly homologous rabbit aldolase A, site-directed mutagenesis is used to replace Asp-128 with Gly, Ala, Asn, Gln, or Val. Rabbit aldolase D128G purified from Escherichia coli is found to be similar to human D128G by kinetic analysis, CD, and thermal inactivation assays. All of the mutant rabbit aldolases are similar to the wild-type rabbit enzyme in secondary structure and kinetic properties. In contrast, whereas the wild-type enzyme is a tetramer, chemical crosslinking and gel filtration indicate that a new dimeric species exists for the mutants. In sedimentation velocity experiments, the mutant enzymes as mixtures of dimer and tetramer at 4 degrees C. Sedimentation at 20 degrees C shows that the mutant enzymes are > 99.5% dimeric and, in the presence of substrate, that the dimeric species is active. Differential scanning calorimetry demonstrates that Tm values of the mutant enzymes are decreased by 12 degrees C compared to wild-type enzyme. The results indicate that Asp-128 is important for interface stability and suggest that 1 role of the quaternary structure of aldolase is to provide thermostability.