The functional relationship between the polymerization and catalytic activity of beef liver glutamate dehydrogenase. III. Analysis of Thusius' critique.

Thusius' critique (1977) of our work (Cohen et al., 1975,1976; Cohen &; Benedek, 1976), on the functional relationship between the equilibrium polymerization and catalytic activity of beef liver glutamate dehydrogenase, is refuted on a point by point basis. Thusius' critique is primarily based on data relating to the kinetics of the polymerization-depolymerization reaction. It is shown that such data are not in contradiction to our equilibrium thermodynamic analysis, for this analysis makes absolutely no predictions regarding the kinetics of the polymerization-depolymerization reaction. Moreover, the important functional relationship between the polymerization and allosteric control of beef liver glutamate dehydrogenase has, in any event, been clearly demonstrated on a purely experimental basis. Furthermore, our theoretical model is the only proposed model capable of quantitatively explaining the available data on the detailed equilibrium polymer distribution and the associated level of catalytic activity as functions of effector and enzyme concentrations.     

Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition.

An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared with available data. The method is based on entirely physical model of van der Waals interactions that reflects as illustrated in this work the distribution of electron density. Various levels of hierarchy in the protein spatial structure are discerned by analysis of the energy interaction between structural units of different scales. Thus the level of energy hierarchy plays role of sole parameter, and the method obviates the use of complicated geometrical criteria with numerous fitting parameters. The algorithm readily and accurately locates domains formed by continuous segments of the protein chain as well as those comprising non-sequential segments, sets no limit to the number of segments in a domain. We have analyzed 309 protein structures. Among 277 structures for which our results could be compared with the domain definitions made in other works, 243 showed complete or partial coincidence, and only in 34 cases the domain structures proved substantially different. The domains delineated with our approach may coincide with reference definition at different levels of the globule hierarchy. Along with defining the domain structure, our approach allows one to consider the protein spatial structure in terms of the spatial distribution of the interaction energy in order to establish the correspondence between the hierarchy of energy distribution and the hierarchy of structural elements.     

Fine-tuned distribution of feather mites (Astigmata) on the wing of birds: the case of blackcaps Sylvia atricapilla

The distribution of feather mites (Astigmata) along the wing of passerine birds could change dramatically within minutes because of the rapid movement of mites between feathers. However, no rigorous study has answered how fine-tuned is the pattern of distribution of feather mites at a given time. Here we present a multiscale study of the distribution of feather mites on the wing of non-moulting blackcaps Sylvia atricapilla in a short time period and at a single locality. We found that the number and distribution of mites differed among birds, but it was extremely similar between the wings of each bird. Moreover, mites consistently avoided the first secondary feather, despite that it is placed at the centre of the feathers most used by them. Thus, our results suggest that feather mites do precise, feather-level decisions on where to live, contradicting the current view that mites perform "mass", or "blind" movements across wing feathers. Moreover, our findings indicate that "rare" distributions are not spurious data or sampling errors, but each distribution of mites on the wing of each bird is the outcome of the particular conditions operating on each ambient-bird-feather mite system at a given time. This study indicates that we need to focus on the distribution of feather mites at the level of the individual bird and at the feather level to improve our understanding of the spatial ecology of mites on the wings of birds.     

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realization from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is, however, often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated data sets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen and the other studying host range distribution in a lineage of Salmonella enterica, and we discuss many other potential applications.     

Fine‐tuned distribution of feather mites (Astigmata) on the wing of birds: the case of blackcaps Sylvia atricapilla

The distribution of feather mites (Astigmata) along the wing of passerine birds could change dramatically within minutes because of the rapid movement of mites between feathers. However, no rigorous study has answered how fine‐tuned is the pattern of distribution of feather mites at a given time. Here we present a multiscale study of the distribution of feather mites on the wing of non‐moulting blackcaps Sylvia atricapilla in a short time period and at a single locality. We found that the number and distribution of mites differed among birds, but it was extremely similar between the wings of each bird. Moreover, mites consistently avoided the first secondary feather, despite that it is placed at the centre of the feathers most used by them. Thus, our results suggest that feather mites do precise, feather‐level decisions on where to live, contradicting the current view that mites perform “mass”, or “blind” movements across wing feathers. Moreover, our findings indicate that “rare” distributions are not spurious data or sampling errors, but each distribution of mites on the wing of each bird is the outcome of the particular conditions operating on each ambient‐bird‐feather mite system at a given time. This study indicates that we need to focus on the distribution of feather mites at the level of the individual bird and at the feather level to improve our understanding of the spatial ecology of mites on the wings of birds.     

The morphology of the cerebellum the last 25 years.

Advances in our knowledge of the subdivision and the development of the cerebellum during the last 25 years are reviewed. It is concluded that the longitudinal subdivision of the cerebellum has become firmly established in studies of the morphogenesis, the connections and the chemoarchitecture of the cerebellum. A complicated relationship exists between the transverse, lobular subdivision of the cerebellum and the distribution of different mossy fiber systems.     

Macromolecular transport in heart valves. III. Experiment and theory for the size distribution of extracellular liposomes in hyperlipidemic rabbits

The heart valve leaflets of 29-day cholesterol-fed rabbits were examined by ultrarapid freezing without conventional chemical fixation/processing, followed by rotary shadow freeze-etching. This procedure images the leaflets' subendothelial extracellular matrix in extraordinary detail, and extracellular lipid liposomes, from 23 to 220 nm in diameter, clearly appear there. These liposomes are linked to matrix filaments and appear in clusters. Their size distribution shows 60.7% with diameters 23-69 nm, 31.7% between 70 and 119 nm, 7.3% between 120 and 169 nm, and 0.3% between 170 and 220 nm (superlarge) and suggests that smaller liposomes can fuse into larger ones. We couple our model from Part II of this series (Zeng Z, Yin Y, Jan KM, Rumschitzki DS. Am J Physiol Heart Circ Physiol 292: H2671-H2686, 2007) for lipid transport into the leaflet to the nucleation-polymerization model hierarchy for liposome formation proposed originally for aortic liposomes to predict liposome formation/growth in heart valves. Simulations show that the simplest such model cannot account for the observed size distribution. However, modifying this model by including liposome fusing/merging, using parameters determined from aortic liposomes, leads to predicted size distributions in excellent agreement with our valve data. Evolutions of both the liposome size distribution and total liposome mass suggest that fusing becomes significant only after 2 wk of high lumen cholesterol. Inclusion of phagocytosis by macrophages limits the otherwise monotonically increasing total liposome mass, while keeping the excellent fit of the liposome size distribution to the data.     

Rapid significance estimation in local sequence alignment with gaps.

In order to assess the significance of sequence alignments, it is crucial to know the distribution of alignment scores of pairs of random sequences. For gapped local alignment, it is empirically known that the shape of this distribution is of the Gumbel form. However, the determination of the parameters of this distribution is a computationally very expensive task. We present a new algorithmic approach which allows estimation of the more important of the Gumbel parameters at least five times faster than the traditional methods. Actual runtimes of our algorithm between less than a second and a few minutes on a workstation bring significance estimation into the realm of interactive applications.     

Statistics of divergence times.

Given the number of nucleotide substitutions between two species (K) and the substitution rate nu, the expectation of the corresponding divergence time is usually calculated as K/(2 nu). This is strictly true only if nu is regarded as a constant because the ratio of two random variables, such as K/(2 nu), has distributional properties different from those of the distribution of K. Therefore, both the mean and any confidence interval for divergence times are unknown in this situation. We model the distribution of K and nu using the Gamma distribution and calculate the mean and 95% confidence interval for the corresponding divergence time. These calculations are compared with results obtained by bootstrapping sequence data from the model plant Arabidopsis thaliana and its relatives. We show that for nonoverlapping pairs of phylogenetic distances, our method approaches the bootstrap results very closely. In contrast, regarding the mutation rate as a constant leads to strong underestimation of the confidence interval. An implementation of our method of computing divergence times is accessible through a web interface at http://www.soft.ice.mpg.de/cite.     

Quantitative interrelationship between Gibbs-Donnan equilibrium, osmolality of body fluid compartments, and plasma water sodium concentration.

The presence of negatively charged, impermeant proteins in the plasma space alters the distribution of diffusible ions in the plasma and interstitial fluid (ISF) compartments to preserve electroneutrality. We have derived a new mathematical model to define the quantitative interrelationship between the Gibbs-Donnan equilibrium, the osmolality of body fluid compartments, and the plasma water Na+ concentration ([Na+]pw) and validated the model using empirical data from the literature. The new model can account for the alterations in all ionic concentrations (Na+ and non-Na+ ions) between the plasma and ISF due to Gibbs-Donnan equilibrium. In addition to the effect of Gibbs-Donnan equilibrium on Na+ distribution between plasma and ISF, our model predicts that the altered distribution of osmotically active non-Na+ ions will also have a modulating effect on the [Na+]pw by affecting the distribution of H2O between the plasma and ISF. The new physiological insights provided by this model can for the first time provide a basis for understanding quantitatively how changes in the plasma protein concentration modulate the [Na+]pw. Moreover, this model defines all known physiological factors that may modulate the [Na+]pw and is especially helpful in conceptually understanding the pathophysiological basis of the dysnatremias.     

Molecular and morphological evidence reveals introgression in swarms of the invasive taxa Fallopia japonica, F. sachalinensis, and F. xbohemica (Polygonaceae) in the United States

Fallopia japonica (Japanese knotweed, Polygonaceae) is a well-known East Asian perennial that is established throughout the U.S. and Europe. Another congener, F. sachalinensis, and their hybrid, F. ×bohemica, also persist on both continents. Their invasive success is primarily attributed to their ability to spread via clonal growth. However, mounting evidence suggests invasion history and dynamics differ between continents and that sexual reproduction is more common than previously assumed. We used published morphological traits designed to distinguish the three taxa to characterize their distribution in 24 New England towns. We found continuous variation of all five traits, with 84% of our 81 individuals having at least one trait outside parental limits. Hierarchical cluster analysis, along with two chloroplast and one nuclear species-specific markers, suggests the presence of intercrossing, segregating hybrids, and likely introgression between F1 hybrids and F. japonica. Our markers also show the first evidence of bidirectional hybridization between parental taxa in the U.S., emphasizing the complex structure of populations in our region. This study is a first step toward unraveling the evolutionary forces that have made these taxa such aggressive invaders in the U.S. The data may also affect management strategies originally designed for largely monomorphic, clonal populations.     

Mapping the three-dimensional locations of ribosomal RNA and proteins.

Seven regions of 16S rRNA have been located on the surface of the 30S ribosomal subunit by DNA hybridization electron microscopy in our laboratory. In addition, we have recently mapped the three-dimensional locations of an additional seven small ribosomal proteins by immunoelectron microscopy. The information from the direct mapping of the sites on rRNA has been incorporated into a model for the tertiary structure of 16S rRNA, accounting for approximately 40% of the total 16S rRNA. A novel structure, the platform ring, is proposed for a region of rRNA within the central domain. This structure rings the edges of the platform and includes regions 655-751 and 769-810. Another region, the recognition complex, consists of nucleotides 500-545, and occupies a region on the exterior surface of the subunit, near the EF-Tu binding site. In addition, 19 of the 21 small subunit ribosomal proteins have been mapped by immunoelectron microscopy in our laboratory. In order to evaluate the reliability of our model for the three-dimensional distribution of 16S rRNA, we have predicted which sites of rRNA are adjacent to ribosomal proteins and compared these predictions with r-protein protection studies of others. Good correlation between the model, the locations of rRNA sites, the locations of ribosomal proteins, and regions of rRNA protected by ribosomal proteins, provides independent support for this model.     

Sequence organization of the rat genome by electron microscopy.

The size and arrangement of repetitive and inverted repeat (foldback) sequences in rat DNA were studied by visualization of hybrid and heteroduplex structures in the electron microscope. The self-reassociation of repetitive sequence-bearing DNA strands often results in the formation of four-ended "H" structures, whose duplex regions equal the repetitive sequence length and can be measured in the electron microscope. In this way, it was determined that the average size of the class of numerous short repetitive sequences is 0.40 +/- 0.15 kbp. Heteroduplex structures were prepared between long whole DNA single strands and short repeat-sequence-bearing strands. The analysis of these structures confirms that the size of the repetitive sequences in 0.4 kbp on average. Length measurements between adjacent duplexes show that the average spacing between two interspersed repeats is at least 1.5-1.8 kbp. By examining 29.4-kbp single strands after brief renaturation, the size and distribution of foldback sequences were determined. There are 1.9 X 10(5) foldback apirs per rat genome, spaced an average of 9.7 kbp apart according to our measurement. Repetitive, inverted repeat and unique sequences are interspersed with each other in at least half the genome.     

Nonparametric simulation-based statistics for detecting linkage in general pedigrees.

We present here four nonparametric statistics for linkage analysis that test whether pairs of affected relatives share marker alleles more often than expected. These statistics are based on simulating the null distribution of a given statistic conditional on the unaffecteds' marker genotypes. Each statistic uses a different measure of marker sharing: the SimAPM statistic uses the simulation-based affected-pedigree-member measure based on identity-by-state (IBS) sharing. The SimKIN (kinship) measure is 1.0 for identity-by-descent (IBD) sharing, 0.0 for no IBD status sharing, and the kinship coefficient when the IBD status is ambiguous. The simulation-based IBD (SimIBD) statistic uses a recursive algorithm to determine the probability of two affecteds sharing a specific allele IBD. The SimISO statistic is identical to SimIBD, except that it also measures marker similarity between unaffected pairs. We evaluated our statistics on data simulated under different two-locus disease models, comparing our results to those obtained with several other nonparametric statistics. Use of IBD information produces dramatic increases in power over the SimAPM method, which uses only IBS information. The power of our best statistic in most cases meets or exceeds the power of the other nonparametric statistics. Furthermore, our statistics perform comparisons between all affected relative pairs within general pedigrees and are not restricted to sib pairs or nuclear families.     

Statistical analysis of structural and kinetic characteristics of fungal colony growth with Trichoderma viride PERS.: S.F. Gray

The mycelial colonies of Trichoderma viride were grown between two thin cellophane films for exact measurements. The results obtained testify to the fact that in a mature colony the average length of intercalary cells, the average number of intercalary cells in an internode and the average internode length are stable. At this stage of morphogenesis the mean internode length is shown to be equal to the product of the average intercalary cell length and the average number of intercalary cells in an internode. The coefficients of variation of the internode length and the number of intercalary cells in an internode are found to be equal. The length of an intercalary cell and duration of the doubling cycle of an apical cell of T. viride obey the law of Gamma distribution. According to our observations, the Gamma distribution is typical for the length and duration of the doubling cycle of any bacterial cells and cells of any multicellular organisms.     

Different distribution of daunomycin in plasma membranes from drug-sensitive and drug-resistant P388 leukemia cells.

When the anthracycline daunomycin (DNM) is incorporated into isolated plasma membranes from P388 murine leukemia cells, the drug partitions between 'deep' and 'surface' membrane domains. Such domains have been characterized on the basis of: (1) fluorescence resonance energy transfer between 1,6-diphenylhexa-1,3,5-triene or 1-[4-(trimethylamino)phenyl]-6-phenylhexa-1,3,5-triene as energy donors, which are well known in their positioning within the membrane, and daunomycin as the energy acceptor, and (2) quenching of the fluorescence of the membrane-associated drug by the water-soluble quencher iodide. The distribution of DNM between the two plasma membrane domains is different depending on the cellular phenotype. Thus, in membranes from drug-sensitive cells, DNM is preferentially confined to 'surface' domains, while in membranes from drug-resistant cells, the drug distributes more homogeneously between 'surface' and 'deep' domains. Experiments using artificial lipid vesicles suggest that differences in the relative levels of certain lipids in the plasma membranes from drug-sensitive and drug-resistant cells, namely phosphatidylserine and cholesterol, are partly responsible for the observed differences in the distribution of DNM. Since drug-membrane interactions are important in anthracycline cytotoxicity, it is possible that our observations on a different membrane distribution of daunomycin, may be related to the different sensitivity to the drug exhibited by these cells.     

Analysis of polymer molecular weight distributions in aqueous two-phase systems.

The partitioning of proteins and other biomaterials between two aqueous phases containing polyethyleneglycol and dextran is a strong function of the molecular weight of the two polymers. Although both polymers are polydispersed (especially Dx) most theoretical treatments refer only to the average molecular weight (number or mass) and assume that the molecular weight distribution of each polymer is the same in both phases. In this work the molecular weight distribution of each polymer is the same in both phases. In this work the molecular weight distributions of four stock solutions of PEG (4000, 6000, 10,000 and 20,000) and four stock solutions of Dx (10,000, 40,000, 110,000 and 500,000) were measured using High Performance Gel Chromatography. The measurements were repeated on the phases formed by the polymer solutions after they were mixed and allowed to equilibrate. The molecular weight distribution of the Dx differed in the top and bottom phase; both differed from that of the stock solution. Although we believe that the molecular weight distribution for PEG also differs in the top and bottom phases, we were unable to determine this within the resolution of our instruments.     

Compartmentation of free amino acids for protein biosynthesis. Influence of diurnal changes in hepatic amino acid concentrations of the composition of the precursor pool charging aminoacyl-transfer ribonucleic acid.

To investigate further the mechanisms by which amino acids are segregated for protein biosynthesis, the distribution of a pulse of [3H]valine was monitored in hepatic amino acid pools at seven intervals in the diurnal cycle of meal-fed rats. Although each condition was characterized by a unique balance between intracellular and extracellular valine, in every case the specific radioactivity of valyl-tRNA at steady state was higher that that of intracellular valine but below the extracellular value. Further, the specific radioactivity of the valyl-tRNA could be accurately predicted if extracellular and intracellular valine were combined in proportions specified by the transmembrane concentration gradient. These observations not only substantiate our earlier conclusions that the amino acids used for protein synthesis do not originate exclusively from either the intracellular or extracellular pools, but also strengthen our theory that the membrane transport system is the physical basis for such compartmentation. On the basis of these data we present a method for measuring the specific radioactivity of the precursor pool for protein biosynthesis in cases where the actual isolation of the aminoacyl-tRNA is not technically feasible, and also suggest a theoretical basis for interpreting the unequal distribution of both total and [3H]valine between intracellular and extracellular fluids.     

The importance of electric field distribution for effective in vivo electroporation of tissues.

Cells exposed to short and intense electric pulses become permeable to a number of various ionic molecules. This phenomenon was termed electroporation or electropermeabilization and is widely used for in vitro drug delivery into the cells and gene transfection. Tissues can also be permeabilized. These new approaches based on electroporation are used for cancer treatment, i.e., electrochemotherapy, and in vivo gene transfection. In vivo electroporation is thus gaining even wider interest. However, electrode geometry and distribution were not yet adequately addressed. Most of the electrodes used so far were determined empirically. In our study we 1) designed two electrode sets that produce notably different distribution of electric field in tumor, 2) qualitatively evaluated current density distribution for both electrode sets by means of magnetic resonance current density imaging, 3) used three-dimensional finite element model to calculate values of electric field for both electrode sets, and 4) demonstrated the difference in electrochemotherapy effectiveness in mouse tumor model between the two electrode sets. The results of our study clearly demonstrate that numerical model is reliable and can be very useful in the additional search for electrodes that would make electrochemotherapy and in vivo electroporation in general more efficient. Our study also shows that better coverage of tumors with sufficiently high electric field is necessary for improved effectiveness of electrochemotherapy.