Complex Dynamics of defective interfering baculoviruses during serial passage in insect cells

Defective interfering (DI) viruses are thought to cause oscillations in virus levels, known as the ‘Von Magnus effect’. Interference by DI viruses has been proposed to underlie these dynamics, although experimental tests of this idea have not been forthcoming. For the baculoviruses, insect viruses commonly used for the expression of heterologous proteins in insect cells, the molecular mechanisms underlying DI generation have been investigated. However, the dynamics of baculovirus populations harboring DIs have not been studied in detail. In order to address this issue, we used quantitative real-time PCR to determine the levels of helper and DI viruses during 50 serial passages of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in Sf21 cells. Unexpectedly, the helper and DI viruses changed levels largely in phase, and oscillations were highly irregular, suggesting the presence of chaos. We therefore developed a simple mathematical model of baculovirus-DI dynamics. This theoretical model reproduced patterns qualitatively similar to the experimental data. Although we cannot exclude that experimental variation (noise) plays an important role in generating the observed patterns, the presence of chaos in the model dynamics was confirmed with the computation of the maximal Lyapunov exponent, and a Ruelle-Takens-Newhouse route to chaos was identified at decreasing production of DI viruses, using mutation as a control parameter. Our results contribute to a better understanding of the dynamics of DI baculoviruses, and suggest that changes in virus levels over passages may exhibit chaos.

Functional domains of Bacillus subtilis transcription factor AraR and identification of aminoacids important for nucleoprotein complex assembly and effector-binding.

Journal of Bacteriology (Apr 2006) 3024-3036

Habitat preferences, diet, feeding strategy and social organization of the black spider monkey [Ateles paniscus paniscus Linnaeus 1758] in Surinam

A Socioecological Field Study.This monograph reports on a 26 month socioecological study of black spider monkeys (Ateles paniscus paniscus)in the Raleigh-vallen — Voltzberg Nature Reserve, Surinam. It recognizes the fundamental importance of food to the behavior and the regulation of population density fox this primate. It clarifies the complex temporal and spatial effects of tropical rain forest food sources on the behavior of a group of spider monkeys, concentrating on food category, food plant identity and phenology, and quantity, density and dispersion of the most important food sources. In addition, the present study describes habitat choice, optimal feeding strategy and sexual behavior of the spider monkey, and discusses implications of diet for social behavior. This study is also fundamental to conservation. Specialized in eating mature fruits, the spider monkey is a very important dispersal agent for many trees and lianes, particularly canopy species. However, the spider monkey is probably the most vulnerable monkey species in Surinam and it is disappearing rapidly throughout the remainder of its range. Unfortunately, it is large and noisy and can be easily tracked and hunted. It is largely restricted to undisturbed high forest, and consequently habitat destruction has more effect on it than on most other species. Together with its slow reproductive rate (a female gives birth only once every four or five years), this means that the species is poorly adapted to recover from exploitation. In order to implement proper measures for conservation, data on forest type preferences, diet and social behavior of the species, or on closely related species, in undisturbed areas, such as the one described in this monograph, are essential tools for assessing the potential of proposed protected areas.

Storing Data in the Trial of Complex Technical Products

The article considers the ways of organization of databases for the storage of the results obtained during testing. A new variant of the organization of the data to ensure the ability to write to the database different sets of parameters in the form of chronological series. The required set of parameters depends on the modification of the tested technical installation.

A simple genetic basis for complex social behaviour mediates widespread gene expression differences.

A remarkable social polymorphism is controlled by a single Mendelian factor in the fire ant Solenopsis invicta. A genomic element marked by the gene Gp-9 determines whether workers tolerate one or many fertile queens in their colony. Gp-9 was recently shown to be part of a supergene with two nonrecombining variants, SB and Sb. SB/SB and SB/Sb queens differ in how they initiate new colonies, and in many physiological traits, for example odour and maturation rate. To understand how a single genetic element can affect all these traits, we used a microarray to compare gene expression patterns between SB/SB and SB/Sb queens of three different age classes: 1-day-old unmated queens, 11-day-old unmated queens and mated, fully reproductive queens collected from mature field colonies. The number of genes that were differentially expressed between SB/SB and SB/Sb queens of the same age class was smallest in 1-day-old queens, maximal in 11-day-old queens and intermediate in reproductive queens. Gene ontology analysis showed that SB/SB queens upregulate reproductive genes faster than SB/Sb queens. For all age classes, genes inside the supergene were overrepresented among the differentially expressed genes. Consistent with the hypothesized greater number of transposons in the Sb supergene, 13 transposon genes were upregulated in SB/Sb queens. Viral genes were also upregulated in SB/Sb mature queens, consistent with the known greater parasite load in colonies headed by SB/Sb queens compared with colonies headed by SB/SB queens. Eighteen differentially expressed genes between reproductive queens were involved in chemical signalling. Our results suggest that many genes in the supergene are involved in regulating social organization and queen phenotypes in fire ants.

Structural organization of Trypanosoma cruzi

Since the initial description of Trypanosoma cruzi by Carlos Chagas in 1909, several research groups have used different microscopic techniques to obtain detailed information about the various developmental stages found in the life cycle of this intracellular parasite. This review describes the present knowledge on the organization of the most important structures and organelles found in the protozoan, such as the cell surface, flagellum, cytoskeleton, kinetoplast-mitochondrion complex, glycosome, acidocalcisome, contractile vacuole, lipid inclusions, the secretory pathway, endocytic pathway and the nucleus.

Genomic organization and gene expression in a chromosomal region of Leishmania major.

Little is known about the relation between the genome organization and gene expression in Leishmania. Bioinformatic analysis can be used to predict genes and find homologies with known proteins. A model was proposed, in which genes are organized into large clusters and transcribed from only one strand, in the form of large polycistronic primary transcripts. To verify the validity of this model, we studied gene expression at the transcriptional, post-transcriptional and translational levels in a unique locus of 34kb located on chr27 and represented by cosmid L979. Sequence analysis revealed 115 ORFs on either DNA strand. Using computer programs developed for Leishmania genes, only nine of these ORFs, localized on the same strand, were predicted to code for proteins, some of which show homologies with known proteins. Additionally, one pseudogene, was identified. We verified the biological relevance of these predictions. mRNAs from nine predicted genes and proteins from seven were detected. Nuclear run-on analyses confirmed that the top strand is transcribed by RNA polymerase II and suggested that there is no polymerase entry site. Low levels of transcription were detected in regions of the bottom strand and stable transcripts were identified for four ORFs on this strand not predicted to be protein-coding. In conclusion, the transcriptional organization of the Leishmania genome is complex, raising the possibility that computer predictions may not be comprehensive.

Towards robust network based complex systems : from evolutionary cellular automata to biological models

Abstract Sitting between your past and your future doesn't mean you are in the present. Dakota Skye Complex systems science is an interdisciplinary field grouping under the same umbrella dynamical phenomena from social, natural or mathematical sciences. The emergence of a higher order organization or behavior, transcending that expected of the linear addition of the parts, is a key factor shared by all these systems. Most complex systems can be modeled as networks that represent the interactions amongst the system's components. In addition to the actual nature of the part's interactions, the intrinsic topological structure of underlying network is believed to play a crucial role in the remarkable emergent behaviors exhibited by the systems. Moreover, the topology is also a key a factor to explain the extraordinary flexibility and resilience to perturbations when applied to transmission and diffusion phenomena. In this work, we study the effect of different network structures on the performance and on the fault tolerance of systems in two different contexts. In the first part, we study cellular automata, which are a simple paradigm for distributed computation. Cellular automata are made of basic Boolean computational units, the cells; relying on simple rules and information from- the surrounding cells to perform a global task. The limited visibility of the cells can be modeled as a network, where interactions amongst cells are governed by an underlying structure, usually a regular one. In order to increase the performance of cellular automata, we chose to change its topology. We applied computational principles inspired by Darwinian evolution, called evolutionary algorithms, to alter the system's topological structure starting from either a regular or a random one. The outcome is remarkable, as the resulting topologies find themselves sharing properties of both regular and random network, and display similitudes Watts-Strogtz's small-world network found in social systems. Moreover, the performance and tolerance to probabilistic faults of our small-world like cellular automata surpasses that of regular ones. In the second part, we use the context of biological genetic regulatory networks and, in particular, Kauffman's random Boolean networks model. In some ways, this model is close to cellular automata, although is not expected to perform any task. Instead, it simulates the time-evolution of genetic regulation within living organisms under strict conditions. The original model, though very attractive by it's simplicity, suffered from important shortcomings unveiled by the recent advances in genetics and biology. We propose to use these new discoveries to improve the original model. Firstly, we have used artificial topologies believed to be closer to that of gene regulatory networks. We have also studied actual biological organisms, and used parts of their genetic regulatory networks in our models. Secondly, we have addressed the improbable full synchronicity of the event taking place on. Boolean networks and proposed a more biologically plausible cascading scheme. Finally, we tackled the actual Boolean functions of the model, i.e. the specifics of how genes activate according to the activity of upstream genes, and presented a new update function that takes into account the actual promoting and repressing effects of one gene on another. Our improved models demonstrate the expected, biologically sound, behavior of previous GRN model, yet with superior resistance to perturbations. We believe they are one step closer to the biological reality.

Entrepreneurship, organization and economic performance among Spanish firms, 1930-1975. The case of the motor industry

Before the Civil War (1936-1939), Spain had seen the emergence offirms of complex organizational forms. However, the conflict andthe postwar years changed this pattern. The argument put forwardin this paper is based on historical experience, the efforts willbe addressed to explain the development of Spanish entrepreneurshipduring the second half of the twentieth century. To illustrate thechange in entrepreneurship and organizational patterns among theSpanish firms during the Francoist regime we will turn to the caseof the motor vehicle industry.

Flexible social organization and high incidence of drifting in the sweat bee, Halictus scabiosae.

The very diverse social systems of sweat bees make them interesting models to study social evolution. Here we focus on the dispersal behaviour and social organization of Halictus scabiosae, a common yet poorly known species of Europe. By combining field observations and genetic data, we show that females have multiple reproductive strategies, which generates a large diversity in the social structure of nests. A detailed microsatellite analysis of 60 nests revealed that 55% of the nests contained the offspring of a single female, whereas the rest had more complex social structures, with three clear cases of multiple females reproducing in the same nest and frequent occurrence of unrelated individuals. Drifting among nests was surprisingly common, as 16% of the 122 nests in the overall sample and 44% of the nests with complex social structure contained females that had genotypes consistent with being full-sisters of females sampled in other nests of the population. Drifters originated from nests with an above-average productivity and were unrelated to their nestmates, suggesting that drifting might be a strategy to avoid competition among related females. The sex-specific comparison of genetic differentiation indicated that dispersal was male-biased, which would reinforce local resource competition among females. The pattern of genetic differentiation among populations was consistent with a dynamic process of patch colonization and extinction, as expected from the unstable, anthropogenic habitat of this species. Overall, our data show that H. scabiosae varies greatly in dispersal behaviour and social organization. The surprisingly high frequency of drifters echoes recent findings in wasps and bees, calling for further investigation of the adaptive basis of drifting in the social insects.

Isolation and characterization of major histocompatibility complex (MHC) class II B genes in the Barn owl (Aves: Tyto alba)

We isolated major histocompatibility complex class II B (MHCIIB) genes in the Barn owl (Tyto alba). A PCR-based approach combined with primer walking on genomic and complementary DNA as well as Southern blot analyses revealed the presence of two MHCIIB genes, both being expressed in spleen, liver, and blood. Characteristic structural features of MHCIIB genes as well as their expression and high non-synonymous substitution rates in the region involved in antigen binding suggest that both genes are functional. MHC organization in the Barn owl is simple compared to passerine species that show multiple duplications, and resembles the minimal essential MHC of chicken.

Regulation of protein transport from the Golgi complex to the endoplasmic reticulum by CDC42 and N-WASP.

Actin is involved in the organization of the Golgi complex and Golgi-to-ER protein transport in mammalian cells. Little, however, is known about the regulation of the Golgi-associated actin cytoskeleton. We provide evidence that Cdc42, a small GTPase that regulates actin dynamics, controls Golgi-to-ER protein transport. We located GFP-Cdc42 in the lateral portions of Golgi cisternae and in COPI-coated and noncoated Golgi-associated transport intermediates. Overexpression of Cdc42 and its activated form Cdc42V12 inhibited the retrograde transport of Shiga toxin from the Golgi complex to the ER, the redistribution of the KDEL receptor, and the ER accumulation of Golgi-resident proteins induced by the active GTP-bound mutant of Sar1 (Sar1[H79G]). Coexpression of wild-type or activated Cdc42 and N-WASP also inhibited Golgito-ER transport, but this was not the case in cells expressing Cdc42V12 and N-WASP(AWA), a mutant form of N-WASP that lacks Arp2/3 binding. Furthermore, Cdc42V12 recruited GFP-NWASP to the Golgi complex. We therefore conclude that Cdc42 regulates Golgi-to-ER protein transport in an N-WASP¿dependent manner.

Convergent genetic architecture underlies social organization in ants.

Complex adaptive polymorphisms are common in nature, but what mechanisms maintain the underlying favorable allelic combinations [1-4]? The convergent evolution of polymorphic social organization in two independent ant species provides a great opportunity to investigate how genomes evolved under parallel selection. Here, we demonstrate that a large, nonrecombining "social chromosome" is associated with social organization in the Alpine silver ant, Formica selysi. This social chromosome shares architectural characteristics with that of the fire ant Solenopsis invicta [2], but the two show no detectable similarity in gene content. The discovery of convergence at two levels-the phenotype and the genetic architecture associated with alternative social forms-points at general genetic mechanisms underlying transitions in social organization. More broadly, our findings are consistent with recent theoretical studies suggesting that suppression of recombination plays a key role in facilitating coordinated shifts in coadapted traits [5, 6].

Trail pheromones: an integrative view of their role in social insect colony organization.

Trail pheromones do more than simply guide social insect workers from point A to point B. Recent research has revealed additional ways in which they help to regulate colony foraging, often via positive and negative feedback processes that influence the exploitation of the different resources that a colony has knowledge of. Trail pheromones are often complementary or synergistic with other information sources, such as individual memory. Pheromone trails can be composed of two or more pheromones with different functions, and information may be embedded in the trail network geometry. These findings indicate remarkable sophistication in how trail pheromones are used to regulate colony-level behavior, and how trail pheromones are used and deployed at the individual level.

Social and temporal organization in an ant colony

Ant colonies are known for their complex and efficient social organization that com-pletely lacks hierarchical structure. However, due to methodological difficulties in follow¬ing all ants of a colony, it was until now impossible to investigate the social and temporal organization of colonies. We developed a tracking system that allows tracking the posi¬tions and orientations of several hundred individually labeled ants continuously, providing for the first time quantitative long term data on all individuals of a colony. These data permit reconstructing trajectories, activity patterns and social networks of all ants in a colony and enable us to investigate ant behavior quantitatively in previously unpreceded ways. By analyzing the spatial positions and social interactions of all ants in six colonies for 41 days we show that ant colonies are organized in groups of nurses, nest patrollers and foragers. Workers of each group were highly interconnected and occupied similar spa¬tial locations in the nest. Groups strongly segregated spatially, and were characterized by unique behavioral signatures. Nurses spent most of their time on the brood. Nest patrollers frequently visited the rubbish pile, and foragers frequently visited the forag¬ing arena. In addition nurses were on average younger than nest patrollers who were, in turn, younger than foragers. We further show that workers had a preferred behav¬ioral trajectory and moved from nursing to nest patrolling, and from nest patrolling to foraging. By analyzing the activity patterns of all ants we show that only a third of all workers in a colony exhibit circadian rhythms and that these rhythms shortened by on av¬erage 42 minutes in constant darkness, thereby demonstrating the presence of a functional endogenous clock. Most rhythmic workers were foragers suggesting that rhythmicity is tightly associated with task. Nurses and nest patrollers were arrhythmic which most likely reflects plasticity of the circadian clock, as isolated workers in many species exhibit circadian rhythmicity. Altogether our results emphasize that ant colonies, despite their chaotic appearance, repose on a strong underlying social and temporal organization. - Les colonies de fourmis sont connues pour leur organisation sociale complexe et effi-cace, charactérisée par un manque absolu de structure hiérarchique. Cependant, puisqu'il est techniquement très difficile de suivre toutes les fourmis d'une colonie, il a été jusqu'à maintenant impossible d'étudier l'organisation sociale et temporelle des colonies de four-mis. Nous avons développé un système qui permet d'extraire en temps réel à partir d'images vidéo les positions et orientations de plusieurs centaines de fourmis marquées individuellement. Nous avons pu ainsi générer pour la première fois des données quanti-tatives et longitudinales relatives à des fourmis appartenant à une colonie. Ces données nous ont permis de reconstruire la trajectoire et l'activité de chaque fourmi ainsi que ses réseaux sociaux. Ceci nous a permis d'étudier de manière exhaustive et objective le com-portement de tous les individus d'une colonie. En analysant les données spatiales et les interactions sociales de toutes les fourmis de six colonies qui ont été filmées pendant 41 jours, nous montrons que les fourmis d'une même colonie se répartissent en trois groupes: nourrices, patrouilleuses et approvisionneuses. Les fourmis d'un même groupe interagis-sent fréquemment et occupent le même espace à l'intérieur du nid. L'espace propre à un groupe se recoupe très peu avec celui des autres. Chaque groupe est caractérisé par un comportement typique. Les nourrices s'affairent surtout autour du couvain. Les pa-trouilleuses font de fréquents déplacements vers le tas d'ordures, et les approvisionneuses sortent souvent du nid. Les nourrices sont en moyenne plus jeunes que les patrouilleuses qui, à leur tour, sont plus jeunes que les approvisionneuses. De plus, nous montrons que les ouvrières changent de tâche au cours de leur vie, passant de nourrice à patrouilleuse puis à approvisionneuse. En analysant l'activité de chaque fourmi, nous montrons que seulement un tiers des ouvrières d'une colonie présente des rythmes circadiens et que ces rythmes diminuent en moyenne de 42 minutes lorsqu'il y a obscurité constante, ce qui démontre ainsi la présence d'une horloge endogène. De plus, la plupart des approvi¬sionneuses ont une activité rythmique alors que les nourrices et patrouilleuses présentent une activité arythmique, ce qui suggère que la rythmicité est étroitement associée à la tâche. L'arythmie des nourrices et patrouilleuses repose probablement sur une plasticité de l'horloge endogène car des ouvrières de nombreuses espèces font preuve d'une ryth¬micité circadienne lorsqu'elles sont isolées de la colonie. Dans l'ensemble nos résultats révèlent qu'une colonie de fourmis se fonde sur une solide organisation sociale et tem¬porelle malgré son apparence chaotique.