Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

Competing hypotheses seek to explain the evolution of oxygenic and anoxygenic processes of photosynthesis. Since chlorophyll is less reduced and precedes bacteriochlorophyll on the modern biosynthetic pathway, it has been proposed that chlorophyll preceded bacteriochlorophyll in its evolution. However, recent analyses of nucleotide sequences that encode chlorophyll and bacteriochlorophyll biosynthetic enzymes appear to provide support for an alternative hypothesis. This is that the evolution of bacteriochlorophyll occurred earlier than the evolution of chlorophyll. Here we demonstrate that the presence of invariant sites in sequence datasets leads to inconsistency in tree building (including maximum-likelihood methods). Homologous sequences with different biological functions often share invariant sites at the same nucleotide positions. However, different constraints can also result in additional invariant sites unique to the genes, which have specific and different biological functions. Consequently, the distribution of these sites can be uneven between the different types of homologous genes. The presence of invariant sites, shared by related biosynthetic genes as well as those unique to only some of these genes, has misled the recent evolutionary analysis of oxygenic and anoxygenic photosynthetic pigments. We evaluate an alternative scheme for the evolution of chlorophyll and bacteriochlorophyll.

Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution.

Although the evolutionary success of polyploidy in higher plants has been widely recognized, there is virtually no information on how polyploid genomes have evolved after their formation. In this report, we used synthetic polyploids of Brassica as a model system to study genome evolution in the early generations after polyploidization. The initial polyploids we developed were completely homozygous, and thus, no nuclear genome changes were expected in self-fertilized progenies. However, extensive genome change was detected by 89 nuclear DNA clones used as probes. Most genome changes involved loss and/or gain of parental restriction fragments and appearance of novel fragments. Genome changes occurred in each generation from F2 to F5, and the frequency of change was associated with divergence of the diploid parental genomes. Genetic divergence among the derivatives of synthetic polyploids was evident from variation in genome composition and phenotypes. Directional genome changes, possibly influenced by cytoplasmic-nuclear interactions, were observed in one pair of reciprocal synthetics. Our results demonstrate that polyploid species can generate extensive genetic diversity in a short period of time. The occurrence and impact of this process in the evolution of natural polyploids is unknown, but it may have contributed to the success and diversification of many polyploid lineages in both plants and animals.

Parallel evolution of sexual isolation in sticklebacks

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

Specialization in pyramidal cell structure in the cingulate cortex of the Chacma baboon (Papio ursinus): An intracellular injection study of the posterior and anterior cingulate gyrus with comparative notes on the macaque and vervet monkeys

This study forms part of an ongoing investigation of pyramidal cell structure in the cingulate cortex of primates. Recently we have demonstrated that layer III pyramidal cells in the anterior cingulate gyrus are considerably larger, more branched and more spinous than those in the posterior cingulate gyrus (areas 24 and 23, respectively) in the macaque and vervet monkeys. Moreover, the extent of the interareal difference in specialization in pyramidal cell structure differed between the two species. These data suggest that pyramidal cell circuitry may have evolved differently in these closely related species. Presently there are too few data to speculate on what is selecting for this specialization in structure. Here we extend the basis for comparison by studying pyramidal cell structure in cingulate gyrus of the Chacma baboon (Papio ursinus). Methodology used here is the same as that for our previous studies: intracellular injection of Lucifer Yellow in flat-mounted cortical slices. We found that pyramidal cells in anterior cingulate gyrus (area 24) were more branched and more spinous than those in posterior cingulate gyrus (area 23). Moreover, the complexity in pyramidal cell structure in both the anterior and posterior cingulate gyrus of the baboon differed to that in the corresponding regions in either the macaque or vervet monkeys. (C) 2005 Elsevier Ireland Ltd. All rights reserved.

Pyramidal cell specialization in the occipitotemporal cortex of the Chacma baboon (Papio ursinus)

Pyramidal cell structure varies systematically in occipitotemporal visual areas in monkeys. The dendritic trees of pyramidal cells, on average, become larger, more branched and more spinous with progression from the primary visual area (V1) to the second visual area (V2), the fourth (V4, or dorsolateral DL visual area) and inferotemporal (IT) cortex. Presently available data reveal that the extent of this increase in complexity parallels the expansion of occipitotemporal cortex. Here we extend the basis for comparison by studying pyramidal cell structure in occipitotemporal cortical areas in the chacma baboon. We found a systematic increase in the size of and branching complexity in the basal dendritic trees, as well as a progressive increase in the spine density along the basal dendrites of layer III pyramidal cells through V1, V2 and V4. These data suggest that the trend for more complex pyramidal cells with anterior progression through occipitotemporal visual areas is not a feature restricted to monkeys and prosimians, but is a widespread feature of occipitotemporal cortex in primates.

Syntactic complexity measures and their relation to oral proficiency in Japanese as a foreign language

The study reported in this article is a part of a large-scale study investigating syntactic complexity in second language (L2) oral data in commonly taught foreign languages (English, German, Japanese, and Spanish; Ortega, Iwashita, Rabie, & Norris, in preparation). In this article, preliminary findings of the analysis of the Japanese data are reported. Syntactic complexity, which is referred to as syntactic maturity or the use of a range of forms with degrees of sophistication (Ortega, 2003), has long been of interest to researchers in L2 writing. In L2 speaking, researchers have examined syntactic complexity in learner speech in the context of pedagogic intervention (e.g., task type, planning time) and the validation of rating scales. In these studies complexity is examined using measures commonly employed in L2 writing studies. It is assumed that these measures are valid and reliable, but few studies explain what syntactic complexity measures actually examine. The language studied is predominantly English, and little is known about whether the findings of such studies can be applied to languages that are typologically different from English. This study examines how syntactic complexity measures relate to oral proficiency in Japanese as a foreign language. An in-depth analysis of speech samples from 33 learners of Japanese is presented. The results of the analysis are compared across proficiency levels and cross-referenced with 3 other proficiency measures used in the study. As in past studies, the length of T-units and the number of clauses per T-unit is found to be the best way to predict learner proficiency; the measure also had a significant linear relation with independent oral proficiency measures. These results are discussed in light of the notion of syntactic complexity and the interfaces between second language acquisition and language testing. Adapted from the source document

Applications of ultralong Raman fibre lasers in photonics

This thesis presents a numerical and experimental investigation on applications of ultralong Raman fibre lasers in optical communications, supercontinuum generation and soliton transmission. The research work is divided in four main sections. The first involves the numerical investigation of URFL intra-cavity power and the relative intensity noise transfer evolution along the transmission span. The performance of the URFL is compared with amplification systems of similar complexity. In the case of intracavity power evolution, URFL is compared with a first order Raman amplification system. For the RIN transfer investigation, URFL is compared with a bi-directional dual wavelength pumping system. The RIN transfer function is investigated for several cavity design parameters such as span length, pump distribution and FBG reflectivity. The following section deals with experimental results of URFL cavities. The enhancement of the available spectral bandwidth in the C-band and its spectral flatness are investigated for single and multi-FBGs cavity system. Further work regarding extended URFL cavity in combination with Rayleigh scattering as random distributed feedback produced a laser cavity with dual wavelength outputs independent to each other. The last two sections relate to URFL application in supercontinuum (SC) generation and soliton transmission. URFL becomes an enhancement structure for SC generation. This thesis shows successful experimental results of SC generation using conventional single mode optical fibre and pumped with a continuous wave source. The last section is dedicated to soliton transmission and the study of soliton propagation dynamics. The experimental results of exact soliton transmission over multiple soliton periods using conventional single mode fibre are shown in this thesis. The effect of the input signal, pump distribution, span length and FBGs reflectivity on the soliton propagation dynamics is investigated experimentally and numerically.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

Decision Trees for Applicability of Evolution Rules in Transition P Systems

Transition P Systems are a parallel and distributed computational model based on the notion of the cellular membrane structure. Each membrane determines a region that encloses a multiset of objects and evolution rules. Transition P Systems evolve through transitions between two consecutive configurations that are determined by the membrane structure and multisets present inside membranes. Moreover, transitions between two consecutive configurations are provided by an exhaustive non-deterministic and parallel application of active evolution rules subset inside each membrane of the P system. But, to establish the active evolution rules subset, it is required the previous calculation of useful and applicable rules. Hence, computation of applicable evolution rules subset is critical for the whole evolution process efficiency, because it is performed in parallel inside each membrane in every evolution step. The work presented here shows advantages of incorporating decision trees in the evolution rules applicability algorithm. In order to it, necessary formalizations will be presented to consider this as a classification problem, the method to obtain the necessary decision tree automatically generated and the new algorithm for applicability based on it.

Fast Linear Algorithm for Active Rules Application in Transition P Systems

Transition P systems are computational models based on basic features of biological membranes and the observation of biochemical processes. In these models, membrane contains objects multisets, which evolve according to given evolution rules. In the field of Transition P systems implementation, it has been detected the necessity to determine whichever time are going to take active evolution rules application in membranes. In addition, to have time estimations of rules application makes possible to take important decisions related to the hardware / software architectures design. In this paper we propose a new evolution rules application algorithm oriented towards the implementation of Transition P systems. The developed algorithm is sequential and, it has a linear order complexity in the number of evolution rules. Moreover, it obtains the smaller execution times, compared with the preceding algorithms. Therefore the algorithm is very appropriate for the implementation of Transition P systems in sequential devices.

Stochastic anti-resonance in a fibre Raman amplifier

Stochastic anti-resonance, that is resonant enhancement of randomness caused by polarization mode beatings, is analyzed both numerically and analytically on an example of fibre Raman amplifier with randomly varying birefringence. As a result of such anti-resonance, the polarization mode dispersion growth causes an escape of the signal state of polarization from a metastable state corresponding to the pulling of the signal to the pump state of polarization.This phenomenon reveals itself in abrupt growth of gain fluctuations as well as in dropping of Hurst parameter and Kramers length characterizing long memory in a system and noise induced escape from the polarization pulling state. The results based on analytical multiscale averaging technique agree perfectly with the numerical data obtained by direct numerical simulations of underlying stochastic differential equations. This challenging outcome would allow replacing the cumbersome numerical simulations for real-world extra-long high-speed communication systems.

A coherent master equation for active mode locking in lasers

We present the derivation of a new master equation for active mode locking in lasers that fully takes into account the coherent effects of the light matter interaction through a peculiar adiabatic elimination technique. The coherent effects included in our model could be relevant to describe properly mode-locked semiconductor lasers where the standard Haus' Master Equation predictions show some discrepancy with respect to the experimental results and can be included in the modelling of other mode locking techniques too.

Anderson localization of light in synthetic photonic lattices

We make an comprehensive experimental and theoretical study of an effect of localization of light in photonic lattices realized in time domain with random optical potential. We show that localization occurs in whole range of disorder strength in full agreement with Anderson localization in 1D model. The disorder influence on modes structure is also discussed.

Revealing spatio-temporal regimes of generation in Raman fiber lasers

We present here experimental observation of different spatio-temporal generation regimes in quasi-CW Raman fiber laser in the most simple experimental configuration. The generation regimes depend on pump power and range from partial mode-locking to turbulent, and a generation of short-lived pulses. While in temporal domain transitions could be described in quantitative way, in spatio-temporal domain they represent qualitative change in observed dynamics.

Optimization of pavement maintenance and rehabilitation programming using shuffled complex evolution algorithm

The major barrier to practical optimization of pavement preservation programming has always been that for formulations where the identity of individual projects is preserved, the solution space grows exponentially with the problem size to an extent where it can become unmanageable by the traditional analytical optimization techniques within reasonable limit. This has been attributed to the problem of combinatorial explosion that is, exponential growth of the number of combinations. The relatively large number of constraints often presents in a real-life pavement preservation programming problems and the trade-off considerations required between preventive maintenance, rehabilitation and reconstruction, present yet another factor that contributes to the solution complexity. In this research study, a new integrated multi-year optimization procedure was developed to solve network level pavement preservation programming problems, through cost-effectiveness based evolutionary programming analysis, using the Shuffled Complex Evolution (SCE) algorithm.^ A case study problem was analyzed to illustrate the robustness and consistency of the SCE technique in solving network level pavement preservation problems. The output from this program is a list of maintenance and rehabilitation treatment (M&R) strategies for each identified segment of the network in each programming year, and the impact on the overall performance of the network, in terms of the performance levels of the recommended optimal M&R strategy. ^ The results show that the SCE is very efficient and consistent in the simultaneous consideration of the trade-off between various pavement preservation strategies, while preserving the identity of the individual network segments. The flexibility of the technique is also demonstrated, in the sense that, by suitably coding the problem parameters, it can be used to solve several forms of pavement management programming problems. It is recommended that for large networks, some sort of decomposition technique should be applied to aggregate sections, which exhibit similar performance characteristics into links, such that whatever M&R alternative is recommended for a link can be applied to all the sections connected to it. In this way the problem size, and hence the solution time, can be greatly reduced to a more manageable solution space. ^ The study concludes that the robust search characteristics of SCE are well suited for solving the combinatorial problems in long-term network level pavement M&R programming and provides a rich area for future research. ^