Neutral Models with Generalised Speciation

Hubbell’s neutral theory claims that ecological patterns such as species abundance distributions can be explained by a stochastic model based on simple assumptions. One of these assumptions, the point mutation assumption, states that every individual has the same probability to speciate. Etienne et al. have argued that other assumptions on the speciation process could be more realistic, for example, that every species has the same probability to speciate (Etienne, et al. in Oikos 116:241–258, 2007). They introduced a number of neutral community models with a different speciation process, and conjectured formulas for their stationary species abundance distribution. Here we study a generalised neutral community model, encompassing these modified models, and derive its stationary distribution, thus proving the conjectured formulas.     

Numerical simulations of stochastic circulatory models

Properties of two of the stochastic circulatory models theoretically introduced by Smith et al., 1997, Bull. Math. Biol. 59, 1–22 were investigated. The models assumed the gamma distribution of the cycle time under either the geometric or Poisson elimination scheme. The reason for selecting these models was the fact that the probability density functions of the residence time of these models are formally similar to those of the Bateman and gamma-like function models, i.e., the two common deterministic models. Using published data, the analytical forms of the probability density functions of the residence time and the distributions of the simulated values of the residence time were determined on the basis of the deterministic models and the stochastic circulatory models, respectively. The Kolmogorov-Smirnov test revealed that even for 1000 xenobiotic particles, i.e., a relatively small number if the particles imply drug molecules, the probability density functions of the residence time based on the deterministic models closely matched the distributions of the simulated values of the residence time obtained on the basis of the stochastic circulatory models, provided that parameters of the latter models fulfilled selected conditions.     

The time sequence of the relation between mean crowding and mean density with some population processes

Summary The theories of the stochastic processes are applied to construct mathematical models for describing the processes of population change as an ever changing the distribution of individuals in a space. These models consist of two mathematical expressions which are named the spatial distribution probability function (Q _n (t)) and the transition probability function (P _i,n (t)), respectively. The former gives the spatial distribution at any future time. Given an actual spatial distribution at any time, the latter function converts it to the spatial distribution at any future time. According to these models, we discussed the time sequence of the mean crowding-mean density relation (Iwao andKuno, 1971) in some population processes such as mortality, birth, immigration, growth, and their combined processes.     

Cytochemical localization and function of the 3-linked glucan callose in the developing cotton fibre cell wall

Summary Several recent biochemical studies concerning the hemicellulosic content of the developing cotton fibre wall have pointed to an important increase of 1,3-linked glucans at the onset of the secondary wall formation and their slow decrease until the end of fibre development (Meinert andDelmer 1977,Huwyler et al. 1978, 1979,Maltby et al. 1979). These almost insoluble glucans are extra-cellular and possibly associated with the S₁ or winding layer, but no other data on their exact localization were given.By means of a specific fluorescence method, using a 0.05% decolourized aniline blue solution, we show that one of these 3-linked glucans,callose, is always localized, independently of the fibre age, in the innermost wall layer bordering the cell lumen, from the onset of the secondary thickening up to the end of fibre development. Some possible roles assumed by these callose deposits are suggested and discussed. They may be involved in the normal mechanism of cellulose biosynthesis, as being effectively consumed by turnover or, more probably, as forming a permanently restored interface or matrix where cellulose microfibrils undergo a sort of maturation and are oriented before their definitive incorporation in the organized cell wall. They are not to be confused with the wound callose deposits which characterize damaged or immature fibres.     

A new genus of theActinoplanaceae: Dactylosporangium,gen. nov.

Summary Two aerobic mesophilic species of a new genus belonging to the familyActinoplanaceae are described under the nameDactylosporangium (D. aurantiacum strainD/748 type species andD. thailandensis strainD/449). The new genus is characterized by the production of finger shaped sporangia emerging directly from the vegetative mycelium.The motile sporangiospores, three to four in number are arranged in a single straight row inside the sporangium.The genusActinoplanes of the familyActinoplanaceae was described in 1950 byCouch and is characterized by the bacteria-like, flagellated spores formed in sporangia. Other members of the familyActinoplanaceae have been studied byKarling (1954),Rothwell (1957) andCross et al. (1963) in the United States, byGaertner (1955) in Germany, byVan Brummelen andWent (1957) in Holland, byNonomura andOhara (1960) in Japan, byTaig et al. (1962),Tsyganov et al. (1963), andKoniev et al. (1965) in Russia. Except for the organisms studied byKarling and byRothwell, which undoubtedly belonged to theActinoplanes but were not studied in pure culture, the organisms studied by most of the other authors belonged to the genusStreptosporangium.Three new genera having motile spores were described more recently:Ampullariella andSpirillospora described byCouch (1963, 1964), andPlanomonospora byThiemann et al. (1967b).     

On the infiltration of Golgi bodies from the follicular epithelium to the egg

Summary 1. In a well advanced oocyte of the tortoise the egg membranes besides the theca and the single-layered epithelium consist of a zona pellucida often differentiated into zona striata and a homogeneous layer; underlying these two layers is a layer of cortical fibrillae or fibrillar layer, Next to this layer, is the limiting membrane of the egg which is not present in all stages and generally disappears in a well developed oocyte. In certain animals either the homogeneous layer or fibrillar layer is absent. 2. In certain animals,Golgi bodies seem to be extruded into the follicle cells from the theca cells. 3. At a particular stage of development the follicle cells become very active and produce a large number of smallGolgi bodies. TheseGolgi granules filter through canalicular passages of the zona radiata into either the homogeneous layer and from thence into the fibrillar layer or where a homogeneous layer is not present directly to the fibrillar layer. Where a fibrillar layer is not present they are transferred directly to the limiting membrane and from thence to the egg. 4. In certain cases e. g. in Fowl, Calotes and Uromastix, fairly large lumps ofGolgi bodies are extruded from the follicle cells through the zona pellucida into the egg. Here the fine canilicular passages do not seem to form a vehicle for the passage of these comparatively larger bodies. 5. The fine canalicular passages in the zona radiata ofTestudo graeca andKachuga smithii and the fibrillar prolongation of the cytoplasm which we have called the fibrillar layer are marked features of the egg membranes at certain stages of development of the egg. During the period when infiltration ofGolgi bodies through these passages takes place slides prepared by silver nitrate and osmic methods show black beaded chains ofGolgi granules in various stages of descent. 6. It is claimed that the extrusion and infiltration ofGolgi bodies from the follicular epithelium to the egg are established phenomena at least in the Vertebrates.     

Reconstruction of the flagellar apparatus and microtubular cytoskeleton inPyramimonas gelidicola (Prasinophyceae,Chlorophyta)

Summary The absolute configuration of the flagellar apparatus inPyramimonas gelidicola McFadden et al. has been determined and shows identity withP. obovata, indicating that they are closely related. Comparison with the flagellar apparatus of quadriflagellate zoospores from the more advancedChlorophyceae suggest thatPyramimonas may be a primitive ancestral form. The microtubular cytoskeleton has been examined in detail and is shown to be unusual in that it does not attach to the flagellar apparatus. Cytoskeletal microtubules are nucleated individually, and this is interpreted as an adaptation to the methods of mitosis and scale deployment. In view of the primitive nature of these processes, it is proposed that this type of cytoskeletal organization may represent a less advanced condition than that of the flagellar root MTOCs (microtubule organizing centers) observed in theChlorophyceae.     

Morphology and distribution of Müller cells in the retina of the toad Bufo marinus

We have previously shown that an antibody against neuron-specific enolase (NSE) selectively labels Müller cells (MCs) in the anuran retina (Wilhelm et al. 1992). In the present study the light- and electron-microscopic morphology of MCs and their distribution were described in the retina of the toad, Bufo marinus, using the above antibody. The somata of MCs were located in the proximal part of the inner nuclear layer and were interconnected with each other by their processes. The MCs were uniformly distributed across the retina with an average density of 1500 cells/mm². Processes of MCs encircled the somata of photoreceptor cells isolating them from each other by glial sheath, except for those of the double cones. Some of the photoreceptor pedicles remained free of glial sheath. Electron-microscopic observations confirmed that MC processes provide an extensive scaffolding across the neural retina. At the outer border of the ganglion cell layer these processes formed a non-continuous sheath. The MC processes traversed through the ganglion cell layer and spread beneath it between the neuronal somata and the underlying optic axons. These processes formed a continuous inner limiting membrane separating the optic fibre layer from the vitreous tissue. Neither astrocytic nor oligodendrocytic elements were found in the optic fibre layer. The significance of the uniform MC distribution and the functional implications of the observed pattern of MC scaffolding are discussed.     

Amino acid sequence and physico-chemical behavior of coat proteins of wild strain tobacco mosaic virus. II. Aggregation behavior and electric charge distribution in comparison to the strains vulgare and dahlemense

Summary The primary structures of the coat proteins of three strains of TMV were established (Anderer et al., 1965; Wittmann-Liebold u. Wittmann, 1963; Wittmann 1965; Rentschler part I of this paper). They differ from one another in 29, 35 and 40 positions. Since the primary structure of a protein determines its secondary and tertiary structure, the geometry of the subunits and the cause of aggregation were investigated to see how they were influenced by the primary structures.The aggregation of the native proteins as a function of pH and ionic strength was investigated by determining sedimentation coefficients. All three proteins showed a similar cause of aggregation.The geometry of the subunits was compared in experiments with mixed aggregates (Sarkar, 1960). The result was that the subunits of U2 were able to form mixed aggregates with dahlemense and vulgare subunits. From this one can conclude that the geometrical properties of the three subunits are very similar.The A-Protein, the larger aggregates, and protein denatured in 8 M urea differed in their charge distributions. The differences seem to be located in regions of the polypeptide chain where they cause no disturbances and where they do not affect the aggregation properties.How to visualize the striking similarity of aggregation behaviour in spite of the great differences in primary structures is discussed on the basis of the conception of Tanford (1962) and Epstein (1964).

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2. Teil einer Dissertation der Mathematisch-naturwissenschaftlichen Fakultät der Universität Tübingen.     

Effects of stochastic channel gating and distribution on the cardiac action potential

Ion channels exhibit stochastic conformational changes determining their gating behavior. In addition, the process of protein turnover leads to a natural variability of the number of membrane and gap junctional channels. Nevertheless, in computational models, these two aspects are scarcely considered and their impacts are largely unknown. We investigated the effects of stochastic current fluctuations and channel distributions on action potential duration (APD), intercellular conduction delays (ICDs) and conduction blocks using a modified ventricular cell model (Rudy et al.) with Markovian formulations of the principal ion currents (to simulate their stochastic open-close gating behavior) and with channel counts drawn from Poisson distributions (to simulate their natural variability). In single cells, APD variability (coefficient of variation: 1.6% at BCL=1000 ms) was essentially caused by stochastic channel gating of I_Ks, persistent I_Na and I_Ca,L. In cell strands, ICD variability induced by stochastic channel gating and Poissonian channel distributions was low under normal conditions. Nonetheless, at low intercellular coupling levels, Poissonian gap junctional channel distribution resulted in a large ICD variability (coefficient of variation >20%), highly heterogeneous conduction patterns and conduction blocks. Therefore, the stochastic behavior of current fluctuations and channel distributions can contribute to the heterogeneity of conduction patterns and to conduction block, as observed previously in experiments in cardiac tissue with altered intercellular coupling.     

Light,fluorescence and electron microscopic studies on “neurosecretion” in tritonia diomedia bergh (Mollusca,Nudibranchia)

Summary Membrane-limited electron-dense inclusions designated as elementary neurosecretory granules have a characteristic distribution in cerebropleural ganglia of the nudibranch snail Tritonia diomedia. They occur in the neuropile and also in individual nerve fibres, connectives and commissures. These granules have been found neither in perikarya of nerve cells nor in proximal segments of their processes.Specific fluorescence obtained in Tritonia preparations with Sterba's pseudoisocyanin method for neurosecretory products has the same pattern of location.The distribution of stainable material in preparations prepared with ordinary neurosecretory procedures (chrome haematoxylin-phloxin after Gomori-Bargmann and paraldehydefuchsin after Gomori-Gabe) is similar to that described by different authors in other gastropods, but strongly differs from the locationof elementary neurosecretory granules and of pseudoisocyanin-positive material. The adequacy of different histological methods for studying neurosecretion in gastropods is discussed.     

A Review and Comparison of Methods for Recreating Individual Patient Data from Published Kaplan-Meier Survival Curves for Economic Evaluations: A Simulation Study

Background

In general, the individual patient-level data (IPD) collected in clinical trials are not available to independent researchers to conduct economic evaluations; researchers only have access to published survival curves and summary statistics. Thus, methods that use published survival curves and summary statistics to reproduce statistics for economic evaluations are essential. Four methods have been identified: two traditional methods 1) least squares method, 2) graphical method; and two recently proposed methods by 3) Hoyle and Henley, 4) Guyot et al. The four methods were first individually reviewed and subsequently assessed regarding their abilities to estimate mean survival through a simulation study.

Methods

A number of different scenarios were developed that comprised combinations of various sample sizes, censoring rates and parametric survival distributions. One thousand simulated survival datasets were generated for each scenario, and all methods were applied to actual IPD. The uncertainty in the estimate of mean survival time was also captured.

Results

All methods provided accurate estimates of the mean survival time when the sample size was 500 and a Weibull distribution was used. When the sample size was 100 and the Weibull distribution was used, the Guyot et al. method was almost as accurate as the Hoyle and Henley method; however, more biases were identified in the traditional methods. When a lognormal distribution was used, the Guyot et al. method generated noticeably less bias and a more accurate uncertainty compared with the Hoyle and Henley method.

Conclusions

The traditional methods should not be preferred because of their remarkable overestimation. When the Weibull distribution was used for a fitted model, the Guyot et al. method was almost as accurate as the Hoyle and Henley method. However, if the lognormal distribution was used, the Guyot et al. method was less biased compared with the Hoyle and Henley method.     

The evolution of proteins from random amino acid sequences: II. Evidence from the statistical distributions of the lengths of modern protein sequences

This paper continues an examination of the hypothesis that modern proteins evolved from random heteropeptide sequences. In support of the hypothesis, White and Jacobs (1993, J Mol Evol 36:79–95) have shown that any sequence chosen randomly from a large collection of nonhomologous proteins has a 90% or better chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. The goal of the present study was to investigate the possibility that the random-origin hypothesis could explain the lengths of modern protein sequences without invoking specific mechanisms such as gene duplication or exon splicing. The sets of sequences examined were taken from the 1989 PIR database and consisted of 1,792 super-family proteins selected to have little sequence identity, 623 E. coli sequences, and 398 human sequences. The length distributions of the proteins could be described with high significance by either of two closely related probability density functions: The gamma distribution with parameter 2 or the distribution for the sum of two exponential random independent variables. A simple theory for the distributions was developed which assumes that (1) protoprotein sequences had exponentially distributed random independent lengths, (2) the length dependence of protein stability determined which of these protoproteins could fold into compact primitive proteins and thereby attain the potential for biochemical activity, (3) the useful protein sequences were preserved by the primitive genome, and (4) the resulting distribution of sequence lengths is reflected by modern proteins. The theory successfully predicts the two observed distributions which can be distinguished by the functional form of the dependence of protein stability on length.The theory leads to three interesting conclusions. First, it predicts that a tetra-nucleotide was the signal for primitive translation termination. This prediction is entirely consistent with the observations of Brown et al. (1990a,b, Nucleic Acids Res 18:2079–2086 and 18: 6339-6345) which show that tetra-nucleotides (stop codon plus following nucleotide) are the actual signals for termination of translation in both prokaryotes and eukaryotes. Second, the strong dependence of statistical length distributions on sequence-termination signaling codes implies that the evolution of stop codons and translation-termination processes was as important as gene splicing in early evolution. Third, because the theory is based upon a simple no-exon stochastic model, it provides a plausible alternative to a limited universe of exons from which all proteins evolved by gene duplication and exon splicing (Dorit et al. 1990, Science 250:1377–1382).     

A survey of unequal crossover systems and their mathematical properties

We present a model of gene duplication by means of unequal crossover (UCO) where the probability of any given pairing between homologous sequences scales as a penalty factor p ^z ≤ 1, with z the number of mismatches due to asymmetric sequence alignment. From this general representation, we derive several limiting case models of UCO, some of which have been treated elsewhere in the literature. One limiting case is random unequal crossover (RUCO), obtained by setting p = 1 (corresponding to equiprobable pairings at each site). Another limiting case scenario (the ‘Krueger-Vogel’ model) proposes an optimal ‘endpoint’ alignment which strongly penalizes both overhang and deviations from endpoint matching positions. For both of these scenarios, we make use of the symmetry properties of the transition operator (together with the more general UCO properties of copy number conservation and equal parent-offspring mean copy number) to derive the stationary distribution of gene copy number generated by UCO. For RUCO, the stationary distribution of genotypes is shown to be a negative binomial, or alternatively, a convolution of geometric distributions on ‘haplotype’ frequencies. A different type of model derived from the general representation only allows recombination without overhang (internal UCO or IntUCO). This process has the special property of converging to a single copy length or a distribution on a pair of copy lengths in the absence of any other evolutionary forces. For UCO systems in general, we also show that selection can readily act on gene copy number in all of the UCO systems we investigate due to the perfect heritability (h ² = 1) imposed by conservation of copy number. Finally, some preliminary work is presented which suggests that the more general models based on misalignment probabilities seem to also converge to stationary distributions, which are most likely functions of parameter value p. An erratum to this article is available at .     

Synthesis and application of dipeptides; current status and perspectives

The functions and applications of l-α-dipeptides (dipeptides) have been poorly studied compared with proteins or amino acids. Only a few dipeptides, such as aspartame (l-aspartyl-l-phenylalanine methyl ester) and l-alanyl-l-glutamine (Ala-Gln), are commercially used. This can be attributed to the lack of an efficient process for dipeptide production though various chemical or chemoenzymatic method have been reported. Recently, however, novel methods have arisen for dipeptide synthesis including a nonribosomal peptide-synthetase-based method and an l-amino acid α-ligase-based method, both of which enable dipeptides to be produced through fermentative processes. Since it has been revealed that some dipeptides have unique physiological functions, the progress in production methods will undoubtedly accelerate the applications of dipeptides in many fields. In this review, the functions and applications of dipeptides, mainly in commercial use, and methods for dipeptide production including already proven processes as well as newly developed ones are summarized. As aspartame and Ala-Gln are produced using different industrial processes, the manufacturing processes of these two dipeptides are compared to clarify the characteristics of each procedure.     

Stochastic dynamic study of optical transition properties of single GFP-like molecules

Due to high fluctuations and quantum uncertainty, the processes of single-molecules should be treated by stochastic methods. To study fluorescence time series and their statistical properties, we have applied two stochastic methods, one of which is an analytic method to study the off-time distributions of certain fluorescence transitions and the other is Gillespie’s method of stochastic simulations. These methods have been applied to study the optical transition properties of two single-molecule systems, GFPmut2 and a Dronpa-like molecule, to yield results in approximate agreement with experimental observations on these systems. Rigorous oscillatory time series of GFPmut2 before it unfolds in the presence of denaturants have not been obtained based on the stochastic method used, but, on the other hand, the stochastic treatment puts constraints on the conditions under which such oscillatory behavior is possible. Furthermore, a sensitivity analysis is carried out on GFPmut2 to assess the effects of transition rates on the observables, such as fluorescence intensities.     

Establishing insecticide-resistant phytoseiid mite predators in deciduous tree fruit orchards

A summary of basic biological, ecological and toxicological characteristics of 3 phytoseiid mite predatorsTyphlodromus occidentalis Nesbitt,Amblyseius fallacis Garman andTyphlodromus pyri Scheuten which have developed resistances to certain insecticides commonly used in commercial fruit orchards is presented. Methods of culturing and mass-rearing these mites are reviewed. Also the cultural and pesticidal measures which should be maintained to facilitate effective biological control of spider mite pest of deciduous fruit crops by these predators and to maximally provide for their establishment in areas of the world where resistance has not developed or they do not occur naturally are discussed.

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Résumé L'auteur résume les caractéristiques fondamentles biologiques, écologiques et toxicologiques de 3 phytoséiides prédateurs d'acariens,Typhlodromus occidentalis Nesbitt,Amblyseius fallacis Garman etTyphlodromus pyri Scheuter, qui ont acquis une résistance à certains insecticides généralement utilisés dans les vergers de fruits commerciaux. Les méthodes d'élevage et de multiplication massive de ces acariens sont rappelées. Sont également discutées les techniques culturales et phytosanitaires qui sont à employer pour favoriser ces prédateurs comme agents de lutte biologique efficace contre les acariens nuisibles aux vergers et pour procéder à leur implantation dans les régions du monde où la résistance ne s'est pas manifestée ou bien où ces prédateurs n'existent pas naturellement.

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This publication was supported in part by a NSF-EPA grant GB-34718 to the University of California. The findings, opinions and recommendations expressed herein are those of the author and not necessarily those of the University of California, NSF or EPA. Published as Journal Article N. 1559 of the Michigan State University Agricultural Experiment Station.     

Somatotypes in Spanish children

Using the Heath-Carter (1972) method modified byHebbelinck et al. (1973), the somatotypes ina Spanish school-age population were determined. The study shows an evolution in the components of the somatotype with age, and a distribution of somatoplots in the somatochart which presnts peculiar characteristics in both sexes.     

A Stochastic Process and Generalized Distributions for the Study of Oviposition Evolution of a Parasite

This paper considers a generalized birth process {X^m(t), t > 0} and presents a new stochastic model for the number of eggs laid by a parasite on a host. Also, given an underlying distribution for the number of visits between parasites and a host, this distribution is generalized by the distribution of the number of eggs per visit laid on the host. If a certain number of eggs are already present on the host, a parasite such as a Japanese weevil, may avoid oviposition in subsequent visits (see JANARDAN (1980)) to the same host. A class of generalized distributions are presented to model such situations. The case of a single egg laying parasite and a Poisson distribution for the number of visits of the parasite to the same host yields a distribution of particular interest. In order to develop this model, certain lemmas are derived. Finally a characteristic property of this stochastic model is presented.     

Ein neues Interferenzmodell zur Aufstellung von Tetraden-Kartierungsfunktionen

Summary In order to construct chromosome maps from tetrad data a new mapping function has been devised from a model of interfence characterized by an exactly defined factor of interferencei. In tetrads of a rank greater zero this factor indicates the value of inhibition of the next crossing-over. These mapping functions are of some advantage, biological as mathermatical, compared with similar functions given byBarrett et al. (1954). The mapping functions enable to evaluate interference in a two-point test cross.

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Mit 3 Textabbildungen

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Mit Mitteln der Deutschen Forschungsgemeinschaft.