Non-random Structure Research Articles

Probabilistic Versus Deterministic Algebraic Cryptanalysis—A Performance Comparison

In this work, the performance of probabilistic algebraic attacks is compared to classical (fast) algebraic attacks in the context of their application to certain linear feedback shift register (LFSR)-based stream ciphers. Using some results from coding theory it is shown that in terms of time complexity classical deterministic algebraic attacks are in general a more efficient cryptanalytic tool, unless the filtering function F : GF (2)n rarr GF (2)m has such a nonrandom structure that its cryptographic use is presumably refutable anyway.

Thermodynamics of Loop Formation in the Denatured State of Rhodopseudomonas palustris Cytochrome c′: Scaling Exponents and the Reconciliation Problem

The observation that denatured proteins yield scaling exponents, ν, consistent with random-coil behavior and yet can also have pockets of residual or nonrandom structure has been termed the “reconciliation problem”. To provide greater insight into the denatured state of a foldable sequence, we have measured histidine–heme loop formation equilibria in the denatured state of a class II c-type cytochrome, cytochrome c′ from Rhodopseudomonas palustris. We have prepared a series of variants that provide His–heme loop stabilities, p K loop(His), for loop sizes ranging from 10 to 111 residues at intervals of 7 to 11 residues along the sequence of the protein. We observe a scaling exponent for loop formation, ν 3, of 2.5 ± 0.3. Theoretical values for ν 3 range from 1.8 to 2.4; thus, the observed ν 3 is consistent with random-coil behavior. However, in contrast to data for loop formation as a function of loop size obtained with peptides of homogeneous sequence, we observe considerable scatter about the linear dependence of loop stability on loop size. Thus, foldable sequences behave very differently from homogeneous peptide sequences. The observed scatter suggests that there is considerable variation in the conformational properties along the backbone of a foldable sequence, consistent with alternating compact and extended regions. With regard to the reconciliation problem, it is evident that a scaling exponent consistent with a random coil is necessary but not sufficient to demonstrate random-coil behavior.

Probing the urea dependence of residual structure in denatured human α-lactalbumin

Backbone 15N relaxation parameters and 15N–1HN residual dipolar couplings (RDCs) have been measured for a variant of human α-lactalbumin (α-LA) in 4, 6, 8 and 10 M urea. In the α-LA variant, the eight cysteine residues in the protein have been replaced by alanines (all-Ala α-LA). This protein is a partially folded molten globule at pH 2 and has been shown previously to unfold in a stepwise non-cooperative manner on the addition of urea. 15N R2 values in some regions of all-Ala α-LA show significant exchange broadening which is reduced as the urea concentration is increased. Experimental RDC data are compared with RDCs predicted from a statistical coil model and with bulkiness, average area buried upon folding and hydrophobicity profiles in order to identify regions of non-random structure. Residues in the regions corresponding to the B, D and C-terminal 310 helices in native α-LA show R2 values and RDC data consistent with some non-random structural propensities even at high urea concentrations. Indeed, for residues 101–106 the residual structure persists in 10 M urea and the RDC data suggest that this might include the formation of a turn-like structure. The data presented here allow a detailed characterization of the non-cooperative unfolding of all-Ala α-LA at higher concentrations of denaturant and complement previous studies which focused on structural features of the molten globule which is populated at lower concentrations of denaturant.Electronic supplementary materialThe online version of this article (doi:10.1007/s10858-009-9342-y) contains supplementary material, which is available to authorized users.

Avoiding spurious findings of nonrandom social structure in association data

Researchers studying animal societies often begin by testing whether a population shows nonrandom social structure, by comparing observed social associations with the predictions of a null model. Association data comprises observations of individuals in groups, which are observed through repeated surveys. Each survey is conducted on a discrete occasion, for example, within 1 day or 1 week. Current null models randomize the interactions among individuals, while preserving two key elements of the data: the number of times that each individual has been seen, and the sizes of observed groups. A critical assumption of existing permutation methods is that each observed group is independent. However, this assumption is often violated. Typically, researchers search a large study area, relative to the distances moved by animals within the sampling occasion. Thus, most individuals will not have had opportunity to change their group associations during a sampling occasion. We show how randomization tests should be modified to account for this nonindependence of group membership. We generated association data sets in which we randomly assigned individuals to groups. We tested these data sets for nonrandom structure using the generally accepted ‘trial swap’ algorithm. We found that spurious conclusions of nonrandom structure occur when we allowed permutation of individuals across sampling occasions, but not when we ‘blocked’ the data by sampling occasion, and constrained our randomizations to permute individuals only among groups within each block.

The use of Monte Carlo method in significance tests of Ripley's function outcome or how to avoid false discovery of nonrandom spatial structure of tree stand

Metoda Monte Carlo w badaniu istotności wyników funkcji Ripleya, czyli jak się ustrzec fałszywego stwierdzenia nielosowości struktury przestrzennej drzewostanu

Extraction and Characterization of Essential Discharge Patterns from Multisite Recordings of Spiking Ongoing Activity

BackgroundNeural activation patterns proceed often by schemes or motifs distributed across the involved cortical networks. As neurons are correlated, the estimate of all possible dependencies quickly goes out of control. The complex nesting of different oscillation frequencies and their high non-stationariety further hamper any quantitative evaluation of spiking network activities. The problem is exacerbated by the intrinsic variability of neural patterns.Methodology/Principal FindingsOur technique introduces two important novelties and enables to insulate essential patterns on larger sets of spiking neurons and brain activity regimes. First, the sampling procedure over N units is based on a fixed spike number k in order to detect N-dimensional arrays (k-sequences), whose sum over all dimension is k. Then k-sequences variability is greatly reduced by a hierarchical separative clustering, that assigns large amounts of distinct k-sequences to few classes. Iterative separations are stopped when the dimension of each cluster comes to be smaller than a certain threshold. As threshold tuning critically impacts on the number of classes extracted, we developed an effective cost criterion to select the shortest possible description of our dataset. Finally we described three indexes (C,S,R) to evaluate the average pattern complexity, the structure of essential classes and their stability in time.Conclusions/SignificanceWe validated this algorithm with four kinds of surrogated activity, ranging from random to very regular patterned. Then we characterized a selection of ongoing activity recordings. By the S index we identified unstable, moderatly and strongly stable patterns while by the C and the R indices we evidenced their non-random structure. Our algorithm seems able to extract interesting and non-trivial spatial dynamics from multisource neuronal recordings of ongoing and potentially stimulated activity. Combined with time-frequency analysis of LFPs could provide a powerful multiscale approach linking population oscillations with multisite discharge patterns.

Structured association patterns and their energetic benefits in female eastern grey kangaroos, Macropus giganteus

Little is known about the determinants of females' social interactions in species with fission–fusion social organization, in which individuals associate with different individuals at different times. Even less is known about social organization in marsupials. We investigated the association patterns of wild female eastern grey kangaroos in southeast Queensland. Female kangaroos had a nonrandom social structure and we present a new methodology for analysing social structure that accounts for the amount of spatial overlap shared by pairs of female kangaroos. This simulation model showed that patterns of association among our female kangaroos were not simply those predicted by their patterns of spatial overlap. Females that associated frequently with certain associates were able to graze for longer because they were less vigilant, and thus were able to benefit from having frequent associates. Female kangaroo social structure was affected by the loss of key members of the society during a period of unusually high predation. Information-theoretical modelling showed that the factors affecting grazing behaviour changed after partial population turnover, with the strength of association between nearest neighbours having a positive effect on grazing behaviour before population turnover and group size having a positive effect on grazing behaviour after population turnover. We propose that social organization within this marsupial is more structured than previously thought.

Exceptional error minimization in putative primordial genetic codes

BackgroundThe standard genetic code is redundant and has a highly non-random structure. Codons for the same amino acids typically differ only by the nucleotide in the third position, whereas similar amino acids are encoded, mostly, by codon series that differ by a single base substitution in the third or the first position. As a result, the code is highly albeit not optimally robust to errors of translation, a property that has been interpreted either as a product of selection directed at the minimization of errors or as a non-adaptive by-product of evolution of the code driven by other forces.ResultsWe investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage as the measure of a code's robustness to mistranslation. It is shown that, when the 16-supercodon table is populated with 10 putative primordial amino acids, inferred from the results of abiotic synthesis experiments and other evidence independent of the code's evolution, and with minimal assumptions used to assign the remaining supercodons, the resulting 2-letter codes are nearly optimal in terms of the error minimization level.ConclusionThe results of the computational experiments with putative primordial genetic codes that contained only two meaningful letters in all codons and encoded 10 to 16 amino acids indicate that such codes are likely to have been nearly optimal with respect to the minimization of translation errors. This near-optimality could be the outcome of extensive early selection during the co-evolution of the code with the primordial, error-prone translation system, or a result of a unique, accidental event. Under this hypothesis, the subsequent expansion of the code resulted in a decrease of the error minimization level that became sustainable owing to the evolution of a high-fidelity translation system.ReviewersThis article was reviewed by Paul Higgs (nominated by Arcady Mushegian), Rob Knight, and Sandor Pongor. For the complete reports, go to the Reviewers' Reports section.

GABAergic hub neurons orchestrate synchrony in developing hippocampal networks

Event Abstract Back to Event GABAergic hub neurons orchestrate synchrony in developing hippocampal networks Rosa Cossart1* 1 INMED-INSERM, France Network theory predicts that scale-free power law distributed topologies, which include “hubs” i.e. super-connected nodes, are an effective design regarding synchronization. Although the non-random structure of cortical networks has been largely described, the existence of functional hubs in living brain networks lacked experimental evidence. We have recently developed a method for online analysis of network dynamics based on two-photon imaging that enables to localize during an experiment, neurons driving population activity without any a priori assumption. Using network dynamics imaging, online reconstruction of functional connectivity and targeted intracellular recordings, we observed that developing hippocampal networks follow a scale-free topology and performed recordings from functional hubs. Morphometric analysis revealed that recorded hippocampal hubs driving early network synchronizations are a fraction of GABAergic interneurons displaying remarkably widespread axonal projections. In other words, we found superconnected neurons (circuit-hubs) orchestrating network synchrony in developing hippocampal slices. I will explain how we found them and describe their specific morpho-physiological properties as well as show how they control network dynamics. Conference: INMED Satellite Conference of SFN - Neuroscience 2009, Multiple Facets of GABA in Brain Development, Chicago, United States, 16 Oct - 16 Oct, 2009. Presentation Type: Oral Presentation Topic: Abstracts Citation: Cossart R (2009). GABAergic hub neurons orchestrate synchrony in developing hippocampal networks. Conference Abstract: INMED Satellite Conference of SFN - Neuroscience 2009, Multiple Facets of GABA in Brain Development. doi: 10.3389/conf.neuro.03.2009.13.011 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 23 Jul 2009; Published Online: 23 Jul 2009. * Correspondence: Rosa Cossart, INMED-INSERM, 13331 Marseille, France, cossart@inmed.univ-mrs.fr Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Rosa Cossart Google Rosa Cossart Google Scholar Rosa Cossart PubMed Rosa Cossart Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Habitat niche community-level analysis of an amphibian assemblage at Lake Nabugabo, Uganda

Abstract. Community structure was studied across six different habitat types in an amphibian assemblage constituted by 24 species belonging to five families, from Lake Nabugabo, Uganda. We employed a suite of different statistical methods, including univariate, multivariate, and Monte Carlo procedures to investigate the randomness/nonrandomness and the seasonal effects (wet versus dry season) of the community assembly. We calculated for each species in each habitat type an index of relative abundance by using a time constrained counting technique, with 48 1-h counts for each habitat type. Co-occurrence was analysed by C score with 30 000 simulations; resource partitioning patterns by RA2 and RA3 algorithms with 30 000 simulations; and apparent dissimilarity among species in terms of habitat use by UPGMA dendrograms. After pooling data from wet and dry seasons, it resulted that the amphibian community was non-randomly assembled according to C-score analyses, but both RA2 and RA3 were unable to uncover any competitive structure for the dataset. Seasonal effects were evident, and although C score analyses confirmed a nonrandom structure for the community under study (particularly in wet season), RA3 showed that species with high relative abundance tended to significantly concentrate in one habitat type (swamp forest) rather than to partition the habitat resource. UPGMA dendrograms grouped the species differently in dry versus wet seasons. Overall, the comparative evidence of 1) non-random community structure according to C-score analysis, and 2) absence of resource partitioning according to niche overlap null models analysis, suggests that community organization in Lake Nabugabo amphibians is generated by habitat affinities rather than by interspecific competition.

Simulated power spectral density (PSD) of background electrocorticogram (ECoG)

The ECoG background activity of cerebral cortex in states of rest and slow wave sleep resembles broadband noise. The power spectral density (PSD) then may often conform to a power-law distribution: a straight line in coordinates of log power vs. log frequency. The exponent, x, of the distribution, 1/f(x), ranges between 2 and 4. These findings are explained with a model of the neural source of the background activity in mutual excitation among pyramidal cells. The dendritic response of a population of interactive excitatory neurons to an impulse input is a rapid exponential rise and a slow exponential decay, which can be fitted with the sum of two exponential terms. When that function is convolved as the kernel with pulses from a Poisson process and summed, the resulting "brown" or "black noise conforms to the ECoG time series and the PSD in rest and sleep. The PSD slope is dependent on the rate of rise. The variation in the observed slope is attributed to variation in the level of the background activity that is homeostatically regulated by the refractory periods of the excitatory neurons. Departures in behavior from rest and sleep to action are accompanied by local peaks in the PSD, which manifest emergent nonrandom structure in the ECoG, and which prevent reliable estimation of the 1/f(x) exponents in active states. We conclude that the resting ECoG truly is low-dimensional noise, and that the resting state is an optimal starting point for defining and measuring both artifactual and physiological structures emergent in the activated ECoG.

The importance of the compound community on the parasite infracommunity structure in a small benthic fish

The extent to which the structure of parasite infracommunities and component communities is determined by the composition of the compound community was assessed by determining the importance of unspecific larval parasites relative to the other guilds (ectoparasites and adult endoparasites). This was analyzed under the hypothesis that the infracommunities harbored by any fish species in coastal waters of the northern Argentine sea will be dominated by unspecific larval stages, which also will be the determinants of the infracommunity structure. These predictions were tested in the Atlantic sea robin, Prionotus nudigula. A total of 1,570 metazoans belonging to 11 species were found in the overall sample (total prevalence = 98%). Larval endoparasites, especially Corynosoma australe and Grillotia sp., were the best represented species, with a deep influence on the infracommunity structure, accounting for the highest proportion of individuals, dominating about 60% of the infracommunities, greatly determining all infracommunity descriptors, and producing marked changes in the similarity among infracommunities. Given the abundance and broad distribution of unspecific larval parasites in the compound community, infracommunities can be considered as subsets of the species available regionally. They are obtained by passive sampling of infective stages as fish feed, and lead to predictable assemblages, with a non-random composition and structure modeled mainly by ecological filters.

Long-term social structure of long-finned pilot whales (Globicephala melas) in the Strait of Gibraltar

The Strait of Gibraltar is inhabited by around 216 pilot whales, which are present all year round, and nothing is known about their social structure. The aim of this study is to analyse the inter-individual association patterns within this pilot whales community to (1) provide an insight on their long-term social system and (2) to assess the relationship between sexes within this social system. Between 1999 and 2006, 23,004 km was sampled in the Strait of Gibraltar, and 4,887 images of dorsal fins of pilot whales were taken from 226 groups. The sex of 56 of the individuals could be determined genetically. The strength of the behavioural relationships between dyads of individuals was calculated, and the temporal aspects of the social structure were evaluated, showing in a non-random social structure made by constant companions. The preferred associations between individuals consisted in associations of males–females. Eight long-term units could be found with different degrees of association rates. Consequently, we propose that, in the Strait, the pilot whales exhibit a hierarchical social system composed of a population encompassing several clans of pilot whales each containing several pods. Pods will then be formed by several line units, similar to killer whale matrilineal units.

Non-parametric smoothing of multivariate genetic distances in the analysis of spatial population structure at fine scale

Species dispersal studies provide valuable information in biological research. Restricted dispersal may give rise to a non-random distribution of genotypes in space. Detection of spatial genetic structure may therefore provide valuable insight into dispersal. Spatial structure has been treated via autocorrelation analysis with several univariate statistics for which results could dependent on sampling designs. New geostatistical approaches (variogram-based analysis) have been proposed to overcome this problem. However, modelling parametric variograms could be difficult in practice. We introduce a non-parametric variogram-based method for autocorrelation analysis between DNA samples that have been genotyped by means of multilocus-multiallele molecular markers. The method addresses two important aspects of fine-scale spatial genetic analyses: the identification of a non-random distribution of genotypes in space, and the estimation of the magnitude of any non-random structure. The method uses a plot of the squared Euclidean genetic distances vs. spatial distances between pairs of DNA-samples as empirical variogram. The underlying spatial trend in the plot is fitted by a non-parametric smoothing (LOESS, Local Regression). Finally, the predicted LOESS values are explained by segmented regressions (SR) to obtain classical spatial values such as the extent of autocorrelation. For illustration we use multivariate and single-locus genetic distances calculated from a microsatellite data set for which autocorrelation was previously reported. The LOESS/SR method produced a good fit providing similar value of published autocorrelation for this data. The fit by LOESS/SR was simpler to obtain than the parametric analysis since initial parameter values are not required during the trend estimation process. The LOESS/SR method offers a new alternative for spatial analysis.

Resource partitioning in freshwater turtle communities: A null model meta-analysis of available data

Resource partitioning is one of the most intensely studied issues in ecology since the mid-1900s, nonetheless this issue has never been examined in detail for several important animal groups, including the freshwater turtles. In this paper I re-analyze by null models several studies on resource partitioning by freshwater turtles published in the peer-reviewed literature. These studies originated from all continents and from a variety of climatic and habitat conditions. I used data given in the original papers to recalculate dietary overlap between species. Then, the true datasets were compared to randomly generated datasets produced by 3 × 10 4 Monte Carlo permutations, by using two different randomization algorithms (RA2 and RA3 of Lawlor, 1980). Datasets were inspected to find non-random structure of the various communities along four resource dimensions: macro-habitat, micro-habitat, food, and time. Based on my meta-analysis, I concluded that the micro-habitat resource is the most important dimension (it was the resource partitioned in nearly 80% of the study cases), followed by the food resource dimension (nearly 70%), whereas macro-habitat and time were clearly less important. In relation to micro-habitat dimension, the selection of basking site typology is perhaps the main aspect of the microhabitat niche to be partitioned. Logistic regression models indicated that the presence of a resource partitioning structure in the dataset was influenced only by matrix size, and not by number of species, continent, presence of substantial body size differences among coexisting species, or tropical versus non-tropical origin. A combination of causes may explain the observed patterns: interspecific competition is likely important in shaping several turtle communities, but intrinsic and extrinsic constraints and predation are also relevant.

Effects of stand, landscape, and spatial variables on bird communities in larch plantations and deciduous forests in central Japan

We examined the effects of stand, landscape, and spatial variables on bird communities in deciduous forests and Japanese larch ( Larix leptolepis (Sieb & Zucc.) Gord.) plantations in a montane region of Nagano Prefecture, central Japan. We used plot-transect methods at 97 sites: 33 in winter 2003 and 18 sites were added in the 2004 breeding season in deciduous forests, and 32 in winter 2004 and 14 sites were added in the 2005 breeding season in larch plantations. Bird–environment relationships were explored using partial redundancy analysis and partial regression analysis. We used spatial variables derived from principal coordinates of neighbor matrices as explanatory variables to detect nonrandom spatial structure of bird communities. Variation in bird communities was mainly explained by stand and spatial variables for both forest types, whereas the effects of landscape variables were small. In plantations, important stand variables for both seasons included stand height, elevation, and the basal area of vines, whereas shrubs, dwarf bamboo ( Sasa senanensis (Franch. & Savat.) Rehd.), and larch snags were important in the breeding season. In deciduous forests, the most important stand variable for both seasons was the basal area of northern Japanese hemlock ( Tsuga diversifolia (Maxim.) Mast.) and Nikko fir ( Abies homolepis Sieb. & Zucc.) trees. Spatial variables showed that bird communities had large-scale (>10 km) spatial variation that could not be explained by stand or landscape variables.

Do aquatic macrophytes co-occur randomly? An analysis of null models in a tropical floodplain

One of the main issues in community ecology is the detection of structure and the identification of its related causes. In this study, co-occurrence null models were used to identify possible spatio-temporal patterns in the assemblage of aquatic macrophytes in the Upper Paraná River floodplain. The samples were obtained through the Long Term Ecological Research (LTER) Program at two different grains: (1) a coarser spatial grain in January and August 2001 (entire floodplain lagoons); (2) and a finer spatial grain in November 2006 (1 m(2) quadrats). The study was conducted in 36 lagoons, both connected and disconnected to the main river channel, located in the sub-basins of the Baía, Ivinheima and Paraná rivers. Two null models of species co-occurrence, the C-Score and Checkerboard indices, were used to test the null hypothesis of random structure of the aquatic macrophyte assemblages. The null models showed that the aquatic macrophyte assemblages were spatially structured in the distinct spatial grains. However, despite this general pattern, macrophyte assemblages are organized differently depending on the degree of connectivity, seasonal period and, at a finer grain, depth. Species co-occurrences were random in the disconnected lagoons during flood periods, in deep zones of the lagoons of the Baía River and in the shallow littoral zone in the lagoons of the Paraná River. Analysis of the patterns of co-occurrence indicated that competition and/or habitat preferences are probably important influences on the nonrandom structure of assemblages. However, we suppose that at least three important factors (disturbances by water level fluctuation, dispersion and facilitation) counteract potential effects of competition in specific situations, leading macrophyte assemblages to assume random structure.

Fibril Growth Kinetics Reveal a Region of β2-microglobulin Important for Nucleation and Elongation of Aggregation

Amyloid is a highly ordered form of aggregate comprising long, straight and unbranched proteinaceous fibrils that are formed with characteristic nucleation-dependent kinetics in vitro. Currently, the structural molecular mechanism of fibril nucleation and elongation is poorly understood. Here, we investigate the role of the sequence and structure of the initial monomeric precursor in determining the rates of nucleation and elongation of human β2-microglobulin (β2m). We describe the kinetics of seeded and spontaneous (unseeded) fibril growth of wild-type β2m and 12 variants at pH 2.5, targeting specifically an aromatic-rich region of the polypeptide chain (residues 62–70) that has been predicted to be highly amyloidogenic. The results reveal the importance of aromatic residues in this part of the β2m sequence in fibril formation under the conditions explored and show that this region of the polypeptide chain is involved in both the nucleation and the elongation phases of fibril formation. Structural analysis of the conformational properties of the unfolded monomer for each variant using NMR relaxation methods revealed that all variants contain significant non-random structure involving two hydrophobic clusters comprising regions 29–51 and 58–79, the extent of which is critically dependent on the sequence. No direct correlation was observed, however, between the extent of non-random structure in the unfolded state and the rates of fibril nucleation and elongation, suggesting that the early stages of aggregation involve significant conformational changes from the initial unfolded state. Together, the data suggest a model for β2m amyloid formation in which structurally specific interactions involving the highly hydrophobic and aromatic-rich region comprising residues 62–70 provide a complementary interface that is key to the generation of amyloid fibrils for this protein at acidic pH.

Small-scale spatial genetic structure in an ant species with sex-biased dispersal

In a population of the monogynous, polyandrous ant Cataglyphis cursor, we analysed the spatial genetic structure of queens, colony fathers and workers at a microgeographical scale to infer the extent of sex-biased dispersal and to assess the impact of limited dispersal on the patterns of relatedness within the colony. To this end, four microsatellite markers were scored for the queen and an average of 26 workers from each of 35 mapped colonies. We used pair-wise kinship coefficients between all pairs of genotypes, including the reconstructed colony father genotypes (1) to test and quantify isolation by distance patterns within each sex or caste through the analysis of kinship–distance curves, and (2) to compute the average relatedness between categories of colony members. The kinship–distance curve was much steeper for colony queens than colony fathers, indicating male-biased dispersal. However, colony fathers also displayed a non-random spatial genetic structure, so that even males show some dispersal limitation at the scale of the population, which extends over less than 250 m. The degree of relatedness between the different sexes and castes of colonies was well predicted from the number of mates per queen and the inbreeding of queens, and the impact of limited dispersal was very weak at this scale of observation. We discuss the interest of kinship–distance curves to assess sex-biased dispersal on a local scale and we compare our results with large-scale analyses of genetic structure in Cataglyphis cursor and other monogynous ant species.

Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products.

Products of the umuD gene in Escherichia coli play key roles in coordinating the switch from accurate DNA repair to mutagenic translesion DNA synthesis (TLS) during the SOS response to DNA damage. Homodimeric UmuD(2) is up-regulated 10-fold immediately after damage, after which slow autocleavage removes the N-terminal 24 amino acids of each UmuD. The remaining fragment, UmuD'(2), is required for mutagenic TLS. The small proteins UmuD(2) and UmuD'(2) make a large number of specific protein-protein contacts, including three of the five known E. coli DNA polymerases, parts of the replication machinery, and RecA recombinase. We show that, despite forming stable homodimers, UmuD(2) and UmuD'(2) have circular dichroism (CD) spectra with almost no alpha-helix or beta-sheet signal at physiological concentrations in vitro. High protein concentrations, osmolytic crowding agents, and specific interactions with a partner protein can produce CD spectra that resemble the expected beta-sheet signature. A lack of secondary structure in vitro is characteristic of intrinsically disordered proteins (IDPs), many of which act as regulators. A stable homodimer that lacks significant secondary structure is unusual but not unprecedented. Furthermore, previous single-cysteine cross-linking studies of UmuD(2) and UmuD'(2) show that they have a nonrandom structure at physiologically relevant concentrations in vitro. Our results offer insights into structural characteristics of relatively poorly understood IDPs and provide a model for how the umuD gene products can regulate diverse aspects of the bacterial SOS response.