Evolutionary Significance of Self-acylation Property in Acyl Carrier Proteins

Acyl carrier protein is an integral component of many cellular metabolic processes. A number of studies have reported self-acylation behavior in acyl carrier proteins. Although AM exhibit high levels of similarity in their primary and tertiary structures, self-acylation behavior is restricted to only some ACPs that can be classified into two major families based on their function. The first family of ACPs is involved in polyketide biosynthesis, whereas the second family participates in fatty acid synthesis. Facilitated by the growing number of genome sequences available for analyses, large-scale phylogenetic studies were used in these studies to uncover as to how self-acylation behavior of acyl carrier proteins is linked with the evolution of metabolic pathways in organisms. These studies show that self-acylation behavior in acyl carrier proteins was lost during the course of evolution, with certain organisms and organelles viz. plastids, retaining it for specified functions. (C) 2009 IUBMB IUBMB Life, 61(8): 853-859, 2009

Efficient computation of volume fractions for multi-material cell complexes in a grid by slicing

The paper presents a novel slicing based method for computation of volume fractions in multi-material solids given as a B-rep whose faces are triangulated and shared by either one or two materials. Such objects occur naturally in geoscience applications and the said computation is necessary for property estimation problems and iterative forward modeling. Each facet in the model is cut by the planes delineating the given grid structure or grid cells. The method, instead of classifying the points or cells with respect to the solid, exploits the convexity of triangles and the simple axis-oriented disposition of the cutting surfaces to construct a novel intermediate space enumeration representation called slice-representation, from which both the cell containment test and the volume-fraction computation are done easily. Cartesian and cylindrical grids with uniform and non-uniform spacings have been dealt with in this paper. After slicing, each triangle contributes polygonal facets, with potential elliptical edges, to the grid cells through which it passes. The volume fractions of different materials in a grid cell that is in interaction with the material interfaces are obtained by accumulating the volume contributions computed from each facet in the grid cell. The method is fast, accurate, robust and memory efficient. Examples illustrating the method and performance are included in the paper.

Time and Energy Complexity of Distributed Computation of a Class of Functions in Wireless Sensor Networks

We consider a scenario in which a wireless sensor network is formed by randomly deploying n sensors to measure some spatial function over a field, with the objective of computing a function of the measurements and communicating it to an operator station. We restrict ourselves to the class of type-threshold functions (as defined in the work of Giridhar and Kumar, 2005), of which max, min, and indicator functions are important examples: our discussions are couched in terms of the max function. We view the problem as one of message-passing distributed computation over a geometric random graph. The network is assumed to be synchronous, and the sensors synchronously measure values and then collaborate to compute and deliver the function computed with these values to the operator station. Computation algorithms differ in (1) the communication topology assumed and (2) the messages that the nodes need to exchange in order to carry out the computation. The focus of our paper is to establish (in probability) scaling laws for the time and energy complexity of the distributed function computation over random wireless networks, under the assumption of centralized contention-free scheduling of packet transmissions. First, without any constraint on the computation algorithm, we establish scaling laws for the computation time and energy expenditure for one-time maximum computation. We show that for an optimal algorithm, the computation time and energy expenditure scale, respectively, as Theta(radicn/log n) and Theta(n) asymptotically as the number of sensors n rarr infin. Second, we analyze the performance of three specific computation algorithms that may be used in specific practical situations, namely, the tree algorithm, multihop transmission, and the Ripple algorithm (a type of gossip algorithm), and obtain scaling laws for the computation time and energy expenditure as n rarr infin. In particular, we show that the computation time for these algorithms scales as Theta(radicn/lo- g n), Theta(n), and Theta(radicn log n), respectively, whereas the energy expended scales as , Theta(n), Theta(radicn/log n), and Theta(radicn log n), respectively. Finally, simulation results are provided to show that our analysis indeed captures the correct scaling. The simulations also yield estimates of the constant multipliers in the scaling laws. Our analyses throughout assume a centralized optimal scheduler, and hence, our results can be viewed as providing bounds for the performance with practical distributed schedulers.

The phylogeny and evolutionary timescale of muscoide (Diptera: Brachycera: Calyptratae) inferred from mitochondrial genomes

Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene

Evolutionary and conservation biology of the Finnish house sparrow

Recently it has been recognized that evolutionary aspects play a major role in conservation issues of a species. In this thesis I have combined evolutionary research with conservation studies to provide new insight into these fields. The study object of this thesis is the house sparrow, a species that has features that makes it interesting for this type of study. The house sparrow has been ubiquitous almost all over the world. Even though being still abundant, several countries have reported major declines. These declines have taken place in a relatively short time covering both urban and rural habitats. In Finland this species has declined by more than two thirds in just over two decades. In addition, as the house sparrow lives only in human inhabited areas it can also raise public awareness to conservation issues. I used both an extensive museum collection of house sparrows collected in 1980s from all over Finland as well as samples collected in 2009 from 12 of the previously collected localities. I used molecular techniques to study neutral genetic variation within and genetic differentiation between the study populations. This knowledge I then combined with data gathered on morphometric measurements. In addition I analyzed eight heavy metals from the livers of house sparrows that lived in either rural or urban areas in the 1980s and evaluated the role of heavy metal pollution as a possible cause of the declines. Even though dispersal of house sparrows is limited I found that just as the declines started in 1980s the house sparrows formed a genetically panmictic population on the scale of the whole Finland. When compared to Norway, where neutral genetic divergence has been found even with small geographic distances, I concluded that this difference would be due to contrasting landscapes. In Finland the landscape is rather homogeneous facilitating the movements of these birds and maintaining gene flow even with the low dispersal. To see whether the declines have had an effect on the neutral genetic variation of the populations I did a comparison between the historical and contemporary genetic data. I showed that even though genetic diversity has not decreased due to the drastic declines the populations have indeed become more differentiated from each other. This shows that even in a still quite abundant species the declines can have an effect on the genetic variation. It is shown that genetic diversity and differentiation may approach their new equilibriums at different rates. This emphasizes the importance of studying both of them and if the latter has increased it should be taken as a warning sign of a possible loss of genetic diversity in the future. One of the factors suggested to be responsible for the house sparrow declines is heavy metal pollution. When studying the livers of house sparrows from 1980s I discovered higher levels of heavy metal concentrations in urban than rural habitats, but the levels of the metals were comparatively low and based on that heavy metal pollution does not seem to be a direct cause for the declines in Finland. However, heavy metals are known to decrease the amount of insects in urban areas and thus in the cities heavy metals may have an indirect effect on house sparrows. Although neutral genetic variation is an important tool for conservation genetics it does not tell the whole story. Since neutral genetic variation is not affected by selection, information can be one-sided. It is possible that even neutral genetic differentiation is low, there can be substantial variation in additive genetic traits indicating local adaptation. Therefore I performed a comparison between neutral genetic differentiation and phenotypic differentiation. I discovered that two traits out of seven are likely to be under directional selection, whereas the others could be affected by random genetic drift. Bergmann s rule may be behind the observed directional selection in wing length and body mass. These results highlight the importance of estimating both neutral and adaptive genetic variation.

Profligate Descent : The Cultural Transformations of Evolutionary Narrative

This dissertation traces a set of historical transformations the Darwinian evolutionary narrative has undergone toward the end of the twentieth century, especially as reflected in Anglo-American popular science books and novels. The study has three objectives. First, it seeks to understand the organizing logic of evolutionary narratives and the role that assumptions about gender and sexuality play in that logic. Second, it asks what kinds of cultural anxieties evolutionary theory raises and how evolutionary narratives negotiate them. Third, it examines the possibilities and limits of narrative transformation both as a historical phenomenon and as a theoretical question. This interdisciplinary dissertation is situated at the intersection of science studies, cultural studies, literary studies, and gender studies. Its understanding of science as a cultural practice that both emerges from and contributes to cultural expectations and institutional structures follows the tradition of science studies. Its focus on the question of popular appeal and the mechanisms of cultural change arises from cultural studies. Its view of narrative as a structural phenomenon is grounded in literary studies in general and feminist narrative theory in particular. Its understanding of gender and sexuality as implicated in discourses of epistemic authority builds on the view of gender and sexuality as contingent cultural categories central to gender studies. The primary material consists of over 25 British and American popular science books and novels, published roughly between 1990 and 2005. In order to highlight historical transformations, these texts are read in the context of Darwin s The Origin of Species and The Descent of Man, on the one hand, and such sociobiological classics as E. O. Wilson s On Human Nature and Richard Dawkins s The Selfish Gene, on the other. The research method combines feminist narrative analysis with cultural and historical contextualization, emphasizing discursive abruptions, recurrent narrative patterns, and underlying continuities. The dissertation demonstrates that the relationship between Darwin s evolutionary narrative and late twentieth-century evolutionary narratives is characterized by reemphasis, omissions, and continuous rewriting. In particular, contemporary evolutionary discourse extends the role assigned to reproduction both sexual and narrative in Darwin s writing, generating a narrative logic that imagines the desire to reproduce as the driving force of evolution and posits the reproductive sex act as the endlessly repeated narrative event that keeps the story going. The study argues that the popular appeal of evolutionary accounts of gender, sexuality, and human nature may arise, to an extent, from this reproductive narrative dynamic. This narrative dynamic, however, is not logically invulnerable. Since the continuation of the evolutionary narrative relies on successful reproduction, the possibility of reproductive failure poses a constant risk to narrative futurity, arousing cultural anxieties that evolutionary narratives need to address. The study argues that evolutionary narratives appease such anxieties by evoking a range of cultural narratives, especially romantic, religious, and national narratives. Furthermore, the study shows that the event-based logic of evolutionary narratives privileges observable acts over emotions, pleasures, identities, and desires, thus engendering a set of conceptual exclusions that limits the imaginative scope of evolution as a cultural narrative.

Analysis of the beta-glucoside utilization (bgl) genes of Shigella sonnei: evolutionary implications for their maintenance in a cryptic state

The pattern of expression of the genes involved in the utilization of aryl beta-glucosides such as arbutin and salicin is different in the genus Shigella compared to Escherichia coli. The results presented here indicate that the homologue of the cryptic bgl operon of E. coli is conserved in Shigella sonnei and is the primary system involved in beta-glucoside utilization in the organism. The organization of the bgl genes in 5. sonnei is similar to that of E. coli; however there are three major differences in terms of their pattern of expression. (i) The bglB gene, encoding phospho-beta-glucosidase B, is insertionally inactivated in 5. sonnei. As a result, mutational activation of the silent bgl promoter confers an Arbutin-positive (Arb(+)) phenotype to the cells in a single step; however, acquiring a Salicin-positive (Sal(+)) phenotype requires the reversion or suppression of the bglB mutation in addition. (ii) Unlike in E. coli, a majority of the activating mutations (conferring the Arb(+) phenotype) map within the unlinked hns locus, whereas activation of the E. coli bgl operon under the same conditions is predominantly due to insertions within the bglR locus. (iii) Although the bgl promoter is silent in the wild-type strain of 5. sonnei (as in the case of E. coli), transcriptional and functional analyses indicated a higher basal level of transcription of the downstream genes. This was correlated with a 1 bp deletion within the putative Rho-independent terminator present in the leader sequence preceding the homologue of the bglG gene. The possible evolutionary implications of these differences for the maintenance of the genes in the cryptic state are discussed.

Geometric quantum computation using fictitious spin-1/2 subspaces of strongly dipolar coupled nuclear spins

Geometric phases have been used in NMR to implement controlled phase shift gates for quantum-information processing, only in weakly coupled systems in which the individual spins can be identified as qubits. In this work, we implement controlled phase shift gates in strongly coupled systems by using nonadiabatic geometric phases, obtained by evolving the magnetization of fictitious spin-1/2 subspaces, over a closed loop on the Bloch sphere. The dynamical phase accumulated during the evolution of the subspaces is refocused by a spin echo pulse sequence and by setting the delay of transition selective pulses such that the evolution under the homonuclear coupling makes a complete 2 pi rotation. A detailed theoretical explanation of nonadiabatic geometric phases in NMR is given by using single transition operators. Controlled phase shift gates, two qubit Deutsch-Jozsa algorithm, and parity algorithm in a qubit-qutrit system have been implemented in various strongly dipolar coupled systems obtained by orienting the molecules in liquid crystal media.

Computation-Based Reliability Analysis in Real Time Applications

Reliability analysis for computing systems in aerospace applications must account for actual computations the system performs in the use environment. This paper introduces a theoretical nonhomogeneous Markov model for such applications.

An efficient reduction algorithm for computation of interconnect delay variability for statistical timing analysis in clock tree planning

In this paper, we propose a novel and efficient algorithm for modelling sub-65 nm clock interconnect-networks in the presence of process variation. We develop a method for delay analysis of interconnects considering the impact of Gaussian metal process variations. The resistance and capacitance of a distributed RC line are expressed as correlated Gaussian random variables which are then used to compute the standard deviation of delay Probability Distribution Function (PDF) at all nodes in the interconnect network. Main objective is to find delay PDF at a cheaper cost. Convergence of this approach is in probability distribution but not in mean of delay. We validate our approach against SPICE based Monte Carlo simulations while the current method entails significantly lower computational cost.

Nucleotide sequence of the 3terminal region of belladonna mottle virus (renamed Physalis mottle virus) RNA and analysis of the evolutionary relationships among tymoviral coat proteins

The 3' terminal 1255 nt sequence of Physalis mottle virus (PhMV) genomic RNA has been determined from a set of overlapping cDNA clones. The open reading frame (ORF) at the 3' terminus corresponds to the amino acid sequence of the coat protein (CP) determined earlier except for the absence of the dipeptide, Lys-Leu, at position 110-111. In addiition, the sequence upstream of the CP gene contains the message coding for 178 amino acid residues of the C-terminus of the putative replicase protein (RP). The sequence downstream of the CP gene contains an untranslated region whose terminal 80 nucleotides can be folded into a characteristic tRNA-like structure. A phylogenetic tree constructed after aligning separately the sequence of the CP, the replicase protein (RP) and the tRNA-like structure determined in this study with the corresponding sequences of other tymoviruses shows that PhMV wrongly named belladonna mottle virus [BDMV(I)] is a separate tymovirus and not another strain of BDMV(E) as originally envisaged. The phylogenetic tree in all the three cases is identical showing that any subset of genomic sequence of sufficient length can be used for establishing evolutionary relationships among tymoviruses.

In-Network Computation in Random Wireless Networks: A PAC Approach to Constant Refresh Rates with Lower Energy Costs

We propose a method to compute a probably approximately correct (PAC) normalized histogram of observations with a refresh rate of Theta(1) time units per histogram sample on a random geometric graph with noise-free links. The delay in computation is Theta(root n) time units. We further extend our approach to a network with noisy links. While the refresh rate remains Theta(1) time units per sample, the delay increases to Theta(root n log n). The number of transmissions in both cases is Theta(n) per histogram sample. The achieved Theta(1) refresh rate for PAC histogram computation is a significant improvement over the refresh rate of Theta(1/log n) for histogram computation in noiseless networks. We achieve this by operating in the supercritical thermodynamic regime where large pathways for communication build up, but the network may have more than one component. The largest component however will have an arbitrarily large fraction of nodes in order to enable approximate computation of the histogram to the desired level of accuracy. Operation in the supercritical thermodynamic regime also reduces energy consumption. A key step in the proof of our achievability result is the construction of a connected component having bounded degree and any desired fraction of nodes. This construction may also prove useful in other communication settings on the random geometric graph.

Interior Medial Axis Transform computation of 3D objects bound by free-form surfaces

This paper presents an algorithm for generating the Interior Medial Axis Transform (iMAT) of 3D objects with free-form boundaries. The algorithm proposed uses the exact representation of the part and generates an approximate rational spline description of the iMAT. The algorithm generates the iMAT by a tracing technique that marches along the object's boundary. The level of approximation is controlled by the choice of the step size in the tracing procedure. Criteria based on distance and local curvature of boundary entities are used to identify the junction points and the search for these junction points is done in an efficient way. The algorithm works for multiply-connected objects as well. Results of the implementation are provided. (C) 2010 Elsevier Ltd. All rights reserved.