Self-organization of the vascular system in plant leaves: inter-dependent dynamics of auxin flux and carrier proteins

The vegetative hormone Auxin is involved in vascular tissues formation throughout the plant. Trans-membrane carrier proteins transporting auxin from cell to cell and distributed asymmetrically around each cell give to auxin a polarized movement in tissues, creating streams of auxin that presume future vascular bundles. According to the canalization hypothesis, auxin transport ability of cells is thought to increase with auxin flux, resulting in the self-enhancement of this flux along auxin paths. In this study we evaluate a series of models based on canalization hypothesis using carrier proteins, under different assumptions concerning auxin flux formation and carrier protein dynamics. Simulations are run on a hexagonal lattice with uniform auxin production. A single cell located in the margin of the lattice indicates the petiole, and acts as an auxin sink. The main results are: (1) We obtain branching auxin distribution patterns. (2) The type of self-enhancement described by the functional form of the carrier proteins regulation responding to the auxin flux intensity in different parts of a cell, has a strong effect on the possibility of generating the branching patterns. For response functions with acceleration in the increase of carrier protein numbers compared to the auxin flux, branching patterns are likely to be generated. For linear or decelerating response functions, no branching patterns are formed. (3) When branching patterns are formed, auxin distribution greatly differs between the case in which the number of carrier proteins in different parts of a cell are regulated independently, and the case in which different parts of a cell compete for a limited number of carrier proteins. In the former case, the auxin level is lower in veins than in the surrounding tissue, while in the latter, the auxin is present in greater abundance in veins. These results suggest that canalization is a good candidate for describing plant vein pattern formation.     

Profiling cytogenetic diversity with entropy-based karyotypic analysis

Regardless the high degree of variation observed in solid tumor karyotypes, the use of diversity as a measurable phenomenon remains unexplored. Here we present a systematic cytogenetic analysis using Shannon's entropy as a measure for karyotypic diversity. Karyotypes from 14 epithelial tumor types (n = 1232) have the aneuploidy status scored, resulting in highly asymmetrical sample distribution, for which we determine the index of diversity (Shannon H') of structural and numerical chromosomal aberrations. Since karyotypic diversity is tissue-specific, this approach may give rise to new insights into the processes that may account for aneuploidy progression and solid tumor outcomes.     

Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference

RNA-mediated interference (RNAi) has emerged recently as one of the most powerful functional genomics tools. RNAi has been particularly effective in the nematode worm C. elegans where RNAi has been used to analyse the loss-of-function phenotypes of almost all predicted genes. In this review, we illustrate how RNAi has been used to analyse gene function in C. elegans as well as pointing to some future directions for using RNAi to examine genetic interactions in a systematic manner.     

Rapid screening procedures for identification of succinic acid producers

Succinic acid, an intermediate of tricarboxylic acid cycle, is produced and accumulated by anaerobic microorganisms. The long-standing interest in the production of this organic acid is because it is a key compound in producing more than 30 commercially important products. The detection of succinic acid is generally carried out by gas chromatography (GC), enzymatic assays, ion-exclusion chromatography (IEC) or by high performance liquid chromatography (HPLC). However, these methods are time consuming, require sophisticated instrumentation and are expensive. In the present investigation we are reporting two rapid, cost effective screening methods for the detection of this important organic acid. These methods can be utilized to screen a large number of microbes producing succinic acid in a very short span of time.     

Fourier shell correlation threshold criteria

The resolution value claimed for an electron microscopical three-dimensional reconstruction indicates the overall quality of the experiment. The Fourier shell correlation (FSC) criterion has now become the standard quality measure. However, what has continued to be controversial is the issue of the FSC threshold level at which one defines the reproducible resolution. Here, we discuss the theoretical behaviour of the FSC in conjunction with the various factors which influence it: the number of "voxels" in a given Fourier shell, the symmetry of the structure, and the size of the structure within the reconstruction volume. Both the theoretical considerations and our model experiments show that fixed-valued FSC threshold (like "0.5") may never be used in a reproducible criterion. Fixed threshold values are-as we show here-simply the result of incorrect assumptions in the basic statistics. Two families of FSC threshold curves are discussed: the sigma-factor curves and the new family of bit-based information threshold curves. Whereas sigma-factor curves indicate the resolution level at which one has collected information significantly above the noise level, the information curves indicate the resolution level at which enough information has been collected for interpretation.     

An assessment of dead space in pulmonary ventilation of the toad Bufo schneideri

The respiratory cycles of Rana and Bufo has been disputed in relation to flow patterns and to the respiratory dead-space of the buccal volume. A small tidal volume combined with a much larger buccal space motivated the "jet steam" model that predicts a coherent expired flow within the dorsal part of the buccal space. Some other studies indicate an extensive mixing of lung gas within the buccal volume. In Bufo schneideri, we measured arterial, end-tidal and intrapulmonary PCO(2) to evaluate dead-space by the Bohr equation. Dead-space was also estimated as: V(D)=(total ventilation-effective ventilation)/f(R), where total ventilation and f(R) were measured by pneumotachography, while effective ventilation was derived from the alveolar ventilation equation. These approaches were consistent with a dead space of 30-40% of tidal volume, which indicates a specific pathway for the expired lung gas.     

Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?

Although most genetic estimates of contemporary effective population size (Ne) are based on models that assume Ne is constant, in real populations Ne changes (often dramatically) over time, and estimates (Ne) will be influenced by Ne in specific generations. In such cases, it is important to properly match Ne to the appropriate time periods (for example, in computing Ne/N ratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity--the 'salmon' model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following. Discrete generations: (i) Temporal samples from generations 0 and t estimate the harmonic mean Ne in generations 0 through t - 1 but do not provide information about Ne in generation t; (ii) Single samples provide an estimate of Ne in the parental generation, not the generation sampled; (iii) single-sample and temporal estimates never provide information about Ne in exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations. Salmon model: (i) A pair of single-cohort (typically juvenile) samples from years 0 and t provide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (N b(0) and N b(t)), but adult samples are more difficult to interpret because they are influenced by Nb in a number of previous years; (ii) For single-cohort samples, both one-sample and temporal methods provide estimates of Nb in the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single-sample estimates of Nb as much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates of Ne in iteroparous species with overlapping generations and identify areas in need of further research.     

Heterokaryon formation and parasexual recombination between vegetatively incompatible lineages in a population of the chestnut blight fungus, Cryphonectria parasitica

Heterokaryosis was recently reported in the chestnut blight fungus, Cryphonectria parasitica, in which individuals contain nuclei that are isogenic except at the mating-type locus (MAT). MAT heterokaryons were found in several natural populations, including a putatively clonal population in West Salem, Wisconsin, providing an opportunity to address the question of how heterokaryons arise. We represented relationships among RFLP fingerprint haplotypes as networks in which loop formation is considered evidence of recombination. From 1990 to 1995, this population was clonal, as indicated by a simple haplotype network without loops, and the correlation of vegetative compatibility (vc) types and mating types with haplotype lineages. By 1999, we observed loops in the haplotype network involving isolates of two vc types (WS-2 and WS-3). Isolates with haplotypes in the loops were either MAT heterokaryons, carried the opposite mating type from other isolates of the same vc type, and/or had two alleles at two or more codominant SCAR (sequence-characterized amplified region) loci. Segregation of markers and recombination were evident among single-spore isolates from one heterokaryon; these single-spore isolates had novel fingerprint haplotypes, also within the loops. In contrast, vc type WS-1, which comprises 85% of the population, was represented by a simple network with no loops, indicating a clonal lineage varying only by mutation. Almost all isolates of WS-1 had the same mating type; the exceptions were five isolates that were MAT heterokaryons. These results are consistent with the hypothesis that heterokaryons formed between vegetatively incompatible individuals, and recombination occurred by a parasexual process.     

Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data

The number of structures of protein-protein complexes deposited to the Protein Data Bank is growing rapidly. These structures embed important information for predicting structures of new protein complexes. This motivated us to develop the PPISP method for predicting interface residues in protein-protein complexes. In PPISP, sequence profiles and solvent accessibility of spatially neighboring surface residues were used as input to a neural network. The network was trained on native interface residues collected from the Protein Data Bank. The prediction accuracy at the time was 70% with 47% coverage of native interface residues. Now we have extensively improved PPISP. The training set now consisted of 1156 nonhomologous protein chains. Test on a set of 100 nonhomologous protein chains showed that the prediction accuracy is now increased to 80% with 51% coverage. To solve the problem of over-prediction and under-prediction associated with individual neural network models, we developed a consensus method that combines predictions from multiple models with different levels of accuracy and coverage. Applied on a benchmark set of 68 proteins for protein-protein docking, the consensus approach outperformed the best individual models by 3-8 percentage points in accuracy. To demonstrate the predictive power of cons-PPISP, eight complex-forming proteins with interfaces characterized by NMR were tested. These proteins are nonhomologous to the training set and have a total of 144 interface residues identified by chemical shift perturbation. cons-PPISP predicted 174 interface residues with 69% accuracy and 47% coverage and promises to complement experimental techniques in characterizing protein-protein interfaces. .