Demiarcs,creaons and genons

Useful insights into the representation of natural systems can be gained by decomposing directed graphs (digraphs) into elementary components. Arcs of digraphs can be split into male demiarcs (outarcs) which leave vertices and female demiarcs (inarcs) which enter demiarcs. Likewise, a vertex can be split into an input perceiving side called the creaon and an output generating side called the genon. Digraphs can be regarded as being hierarchically organized because each vertex in a level-1 digraph can be expanded into a level-2 digraph. In general, each vertex of a level-i digraph can be expanded into a level-(i+1) digraph. Arcs of a level-i digraph can be regarded as bundles of level-(i + 1) arcs which are split at the vertex boundary. These elementary graphical components are shown to be useful for depicting input-output systems such as organisms, ecosystems and societies.     

POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS

Abstract Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having "missing values" for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2 ^p − 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.     

CyDAS: a cytogenetic data analysis system

For statistical analyses in cancer cytogenetics, the genomic changes encoded by the karyotype must be translated into numerical codes. We developed a program, which extracts chromosomal gains and losses as well as breakpoints from the karyotype. The changes are compiled in tables according to the chromosome bands involved and/or depicted in projection to the respective chromosome ideogram. The data are ready to be integrated into further statistical analyses. The program may be run as desktop or Internet application.     

Parallel microchannel-based measurements of individual erythrocyte areas and volumes

We describe a microchannel device which utilizes a novel approach to obtain area and volume measurements on many individual red blood cells. Red cells are aspirated into the microchannels much as a single red blood cell is aspirated into a micropipette. Inasmuch as there are thousands of identical microchannels with defined geometry, data for many individual red cells can be rapidly acquired, and the fundamental heterogeneity of cell membrane biophysics can be analyzed. Fluorescent labels can be used to quantify red cell surface and cytosolic features of interest simultaneously with the measurement of area and volume for a given cell. Experiments that demonstrate and evaluate the microchannel measuring capabilities are presented and potential improvements and extensions are discussed.     

Prospects for utilising plant-adaptive mechanisms to improve wheat and other crops in drought- and salinity-prone environments

Breeding for adaptation to abiotic stress is extremely challenging due to the complexity of the target environments as well as that of the stress‐adaptive mechanisms adopted by plants. While many traits have been reported in the literature, these must be considered with respect to the type of environment for which a cultivar is targeted. In theory, stress‐adaptive traits can be divided into groups whose genes and/or physiological effects are likely to be relatively independent such that when parents with contrasting traits are crossed, adaptive genes will be pyramided. Currently the following groups of candidate traits are being considered for drought adaptation in wheat: traits relating to: (i) pre‐anthesis growth, (ii) water extraction, (iii) water use efficiency, (iv) photo‐protection. A number of mechanisms relating to root function have potential to ameliorate drought stress. Hydraulic redistribution (HR) of water by roots of dryland shrubs enables even relatively small amounts of rainwater to be moved down into the soil profile actively by the root system before it evaporates from the soil surface. Another example is the symbiotic relationship of plants with mycorrhizal fungi that produce a glycoprotein that has a positive effect on soil structure and moisture characteristics. From an agronomic point of view, crop water use efficiency can be increased by exploiting the stress‐adaptive mechanism whereby leaves reduce transpiration rate in response to a chemical root signal in response to drying soil. While there is limited genetic diversity for adaptation to salinity in wheat, tolerance has been found in the ancestral genomes of polyploid wheat and their relatives associated with sodium exclusion into the xylem. Wide crossing techniques such as production of synthetic hexaploids are being exploited to tap into this source of genetic diversity. Looking further into the future, progress is being made into understanding the regulatory mechanisms that are expressed under abiotic stress to maintain cellular homeostasis, as well as in the ability to genetically transform crop plants with genes from alien species.     

Pair formation

A multitype pair formation model for a one-sex population, without separation, with given type distribution of singles, produces a distribution of pairs with the given type distribution as a marginal distribution. The pair distribution can be seen as a nonnegative symmetric matrix. For this matrix representation formulas have been given years ago and have been widely used. The goal of the paper is to understand these formulas in probabilistic terms and give a meaning to their coefficients. Our approach connects the formulas to the problem of completing a substochastic matrix to a stochastic matrix. In this way the coefficients in the representation formula can be interpreted as preferences and insight can be gained into the set of distributions respecting given preferences. In order to put these questions into a wider perspective, the classical two-sex pair formation models are reviewed and embedded into the class of one-sex models, and dynamic models are designed that yield pair distributions as limit elements.     

Development states associated with the floral transition.

Floral initiation can be analyzed from a developmental perspective by focusing upon how developmental fates are imprinted, remembered, and expressed. This is not an altogether new perspective, since people studying flowering have been concerned for a long time with the commitment of meristems to form flowers and the morphological, cellular, and molecular changes associated with this commitment. What is novel is the emphasis on developmental states as opposed to physiological processes. This developmental focus indicates that there appear to be at least three major developmental states that are acquired and expressed in the process of a meristem initiating floral morphogenesis. The meristem cells must first become competent to respond to a developmental signal that evokes them into a florally determined state. The leaves are the usual source of this signal and a specific leaf may or may not have the capacity to be inductively active. When a leaf does develop the capacity for inductive activity, this capacity is usually correlated with the ontogeny of the leaf. Inductive activity, however, may be continually expressed as in some day-neutral plants or may be latent as in plants where the photoperiod is the external cue for activity. Competent shoot apical meristems respond to inductive leaf signal by being evoked into a florally determined state. Under permissive conditions this florally determined state is expressed as the initiation of floral morphogenesis. Many mechanisms have evolved to regulate entry into and expression of these developmental states. As we learn more about the developmental states associated with flowering and how they are acquired and expressed, we will understand better how the various patterns of flowering are related to one another as well as which developmental processes are common to all angiosperms.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

An ecological study of three freshwater ponds of hyderabad-India IV. the phytoplankton (diatoms,euglenineae and myxophyceae)

Data on the ecology of Diatoms, Euglenineae and Myxophyceae in three freshwater ponds, differing in chemical composition and algal flora, situated in the vicinity of Hyderabad-India are presented. An attempt has been made to isolate various genera into groups, as their multiplication depended on particular ranges of a single chemical factor or set of factors. Several species could be separated into seasonal forms as they occur in particular periods of the year. Others could be grouped under indifferent forms as these are neither influenced by fluctuations in chemical factors nor by seasonal changes.     

Transport of microinjected alcohol oxidase from Pichia pastoris into vesicles in mammalian cells: involvement of the peroxisomal targeting signal

This report describes the microinjection of a purified peroxisomal protein, alcohol oxidase, from Pichia pastoris into mammalian tissue culture cells and the subsequent transport of this protein into vesicular structures. Transport was into membrane-enclosed vesicles as judged by digitonin-permeabilization experiments. The transport was time and temperature dependent. Vesicles containing alcohol oxidase could be detected as long as 6 d after injection. Coinjection of synthetic peptides containing a consensus carboxyterminal tripeptide peroxisomal targeting signal resulted in abolition of alcohol oxidase transport into vesicles in all cell lines examined. Double-label experiments indicated that, although some of the alcohol oxidase was transported into vesicles that contained other peroxisomal proteins, the bulk of the alcohol oxidase did not appear to be transported to preexisting peroxisomes. While the inhibition of transport of alcohol oxidase by peptides containing the peroxisomal targeting signal suggests a competition for some limiting component of the machinery involved in the sorting of proteins into peroxisomes, the organelles into which the majority of the protein is targeted appear to be unusual and distinct from endogenous peroxisomes by several criteria. Microinjected alcohol oxidase was transported into vesicles in normal fibroblasts and also in cell lines derived from patients with Zellweger syndrome, which are unable to transport proteins containing the ser-lys-leu-COOH peroxisomal targeting signal into peroxisomes (Walton et al., 1992). The implications of this result for the mechanism of peroxisomal protein transport are discussed.     

Class IIa bacteriocins: biosynthesis, structure and activity

In the last decade, a variety of ribosomally synthesized antimicrobial peptides or bacteriocins produced by lactic acid bacteria have been identified and characterized. As a result of these studies, insight has been gained into fundamental aspects of biology and biochemistry such as producer self protection, membrane-protein interactions, and protein modification and secretion. Moreover, it has become evident that these peptides may be developed into useful antimicrobial additives. Class IIa bacteriocins can be considered as the major subgroup of bacteriocins from lactic acid bacteria, not only because of their large number, but also because of their activities and potential applications. They have first attracted particular attention as listericidal compounds and are now believed to be the next in line if more bacteriocins are to be approved in the future. The present review attempts to provide an insight into general knowledge available for class IIa bacteriocins and discusses common features and recent findings concerning these substances.     

Tumorigenicity Assays,Including Use of the Jackknife

The complexities of long-term tumorigenicity assays are discussed and statistical approaches suggested. Account must be taken of how tumors are discovered, and a reasonable distinction might be made between self-evidencing tumors (palpable tumors and rapidly lethal tumors) and those identified only on necropsy. Tumor autolysis can pose difficulties. The nature of the experimental design must be taken into account-the study can be completely randomized, or may involve litter-matching, or circumstances may require that all members of a litter be treated alike. The use of a logrank procedure or a closely equivalent Mantel-Haenszel procedure can provide a unifying approach, but modification needs to be made so as to take into account-data on non-self-evidencing tumors. Censoring plays a role, whether because of eventual study termination or because losses to competing risks are treated as censored observations. Where there are several non-zero dosage levels, the analysis can be modified according to the dosage metric used. Multiplicity of statistical tests can arise whether because a number of questions are asked or because a multiplicity of tumor sites have to be considered. Some of the kinds of questions raised have been addressed in earlier papers by various of the present authors, to which the reader is referred. Specifically new material is given on use of the jackknife so as to take into account that the unit of observation is the litter or even the group of litters caged together. Various problems were found to attend the application of the jackknife in such situations.     

Protozoa as Hosts for Endosymbioses and the Conversion of Symbionts into Organelles1,2

ABSTRACT. Protozoa may be thought of as preadapted to serve as hosts for cellular endosymbionts by virtue of their widespread ability to take up particles by endocytosis. The absence of the cell wall so characteristic of plants and fungi and the commonly large size of most protozoa are additional factors favoring protozoan cells for endosymbioses. The conversion of symbiont into a cellular organelle (e.g. a mitochondrion or chloroplast) is more complicated, especially since the latter do not code for all of their own proteins. Thus, such conversions are held to be rare. Among protozoa, numerous foraminifera appear to have characteristics making them very favorable as hosts for certain algae. Such adaptations, both physiological and morphological in nature, are discussed. Also discussed in this paper are the ways by which (present-day) chloroplasts and mitochondria may have been derived from early endosymbionts: a single ancestral cyanobacterium, in the first case, and a single ancestral purple-nonsulfur bacterium, in the second. Mechanisms for insertion of proteins into and across the organellar membranes had to be evolved for all genes transferred from the symbionts into the host nucleus.     

Brugia malayi: arachidonic acid uptake into lipid bodies of adult parasites

Lipid bodies are non-membrane bound intracellular organelles, which have been recognized morphologically in a diversity of mammalian and nonmammalian cells, but are of uncertain function. In mammalian cells, in addition to serving as a storage site of cholesterol and triglyceride, lipid bodies can be a repository of esterified arachidonic acid. Adult worms of the human filarial parasite Brugia malayi have been found to esterify exogenous [3H]arachidonic acid into parasite phospholipids and neutral lipids. Electron microscopic autoradiography demonstrated that [3H]arachidonate was preferentially incorporated into filarial lipid bodies. The dominant incorporation of arachidonate into lipid bodies of a nematode establishes that lipid bodies are a site of arachidonic acid accumulation in nonmammalian, as well as mammalian, cells.     

Caveolae: Formation,dynamics, and function

Caveolae are abundant surface pits formed by the assembly of cytoplasmic proteins on a platform generated by caveolin integral membrane proteins and membrane lipids. This membranous assembly can bud off into the cell or can be disassembled releasing the cavin proteins into the cytosol. Disassembly can be triggered by increased membrane tension, or by stress stimuli, such as UV. Here, we discuss recent mechanistic studies showing how caveolae are formed and how their unique properties allow them to function as multifunctional protective and signaling structures.     

Euclidean nature of phylogenetic distance matrices

Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical constraint and aim at partitioning trait values into a phylogenetic component (phylogenetic inertia) and one or multiple specific components related to adaptive evolution. The way phylogenetic information is incorporated into the PCMs depends on the method used. For the first group of methods, phylogenies are converted into variance-covariance matrices of traits following a given model of evolution such as Brownian motion (BM). For the second group of methods, phylogenies are converted into distance matrices that are subsequently transformed into Euclidean distances to perform principal coordinate analyses. Here, we show that simply taking the elementwise square root of a distance matrix extracted from a phylogenetic tree ensures having a Euclidean distance matrix. This is true for any type of distances between species (patristic or nodal) and also for trees harboring multifurcating nodes. Moreover, we illustrate that this simple transformation using the square root imposes less geometric distortion than more complex transformations classically used in the literature such as the Cailliez method. Given the Euclidean nature of the elementwise square root of phylogenetic distance matrices, the positive semidefinitiveness of the phylogenetic variance-covariance matrix of a trait following a BM model, or related models of trait evolution, can be established. In that way, we build a bridge between the two groups of statistical methods widely used in comparative analysis. These results should be of great interest for ecologists and evolutionary biologists performing statistical analyses incorporating phylogenies.     

Mathematical modelling of angiogenesis using continuous cell-based models

In this work, we develop a mathematical formalism based on a 3D in vitro model that is used to simulate the early stages of angiogenesis. The model treats cells as individual entities that are migrating as a result of chemotaxis and durotaxis. The phenotypes used here are endothelial cells that can be distinguished into stalk and tip (leading) cells. The model takes into account the dynamic interaction and interchange between both phenotypes. Next to the cells, the model takes into account several proteins such as vascular endothelial growth factor, delta-like ligand 4, urokinase plasminogen activator and matrix metalloproteinase, which are computed through the solution of a system of reaction–diffusion equations. The method used in the present study is classified into the hybrid approaches. The present study, implemented in three spatial dimensions, demonstrates the feasibility of the approach that is qualitatively confirmed by experimental results.     

Population and genetic structure of a male-dispersing strepsirrhine,Galago moholi (Primates,Galagidae), from northern South Africa,inferred from mitochondrial DNA

Primates - The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into...