Genetic study of plasmid integration into yeast chromosomes. VI. Patterns of the destabilization of chimeric chromosomes and their use in gene mapping

The 2 microns DNA-dependent destabilization of yeast chimeric chromosomes III, IV, V was analysed. The comparison of its peculiarities with the earlier localized sites of episomal plasmid integration allowed to derive genetic regularities of destabilization process. Two destabilization rules that describe patterns of the loss of genetic information in the chromosome were formulated. The usefulness of this for mitotic intrachromosomal gene mapping in yeast was demonstrated using plasmid integration site mapping in chromosome I.     

Genetic variation screening of TNNT2 gene in a cohort of patients with hypertrophic and dilated cardiomyopathy

Mutations in troponin T (TNNT2) gene represent the important part of currently identified disease-causing mutations in hypertrophic (HCM) and dilated (DCM) cardiomyopathy. The aim of this study was to analyze TNNT2 gene exons in patients with HCM and DCM diagnosis to improve diagnostic and genetic consultancy in affected families. All 15 exons and their flanking regions of the TNNT2 gene were analyzed by DNA sequence analysis in 174 patients with HCM and DCM diagnosis. We identified genetic variations in TNNT2 exon regions in 56 patients and genetic variations in TNNT2 intron regions in 164 patients. Two patients were found to carry unique mutations in the TNNT2 gene. Limited genetic screening analysis is not suitable for routine testing of disease-causing mutations in patients with HCM and DCM as only individual mutation-positive cases may be identified. Therefore, this approach cannot be recommended for daily clinical practice even though, due to financial constraints, it currently represents the only available strategy in a majority of cardio-centers.     

Genetic dynamics of population systems represented by small subpopulations: analytical modeling and numeric results

Genetic dynamics of population systems consisting of a finite number of small (Ne < 10(2)) semiisolated subpopulations was studied. A method of quantitative estimation of statistical parameters was developed for different types of population systems and different directions or intensities of selection. The following regularities were established: (1) optimal numbers of subpopulations, their effective size and rates of gene migration promoting continuous maintenance of genetic diversity can be chosen; (2) the genetic process in a population system is stationary only in the case of a specific structure of gene migrations corresponding to Wright's island model; (3) cyclic dynamics can stabilize the population system at high levels of gene diversity in a heterogeneous environment if gene migration and subpopulation size change in time. Similarities and differences between the concept of population system and the concept of metapopulation, which have been simultaneously proposed in Russia and abroad, are discussed in the final section.     

A proposal for using the ensemble approach to understand genetic regulatory networks

Understanding the genetic regulatory network comprising genes, RNA, proteins and the network connections and dynamical control rules among them, is a major task of contemporary systems biology. I focus here on the use of the ensemble approach to find one or more well-defined ensembles of model networks whose statistical features match those of real cells and organisms. Such ensembles should help explain and predict features of real cells and organisms. More precisely, an ensemble of model networks is defined by constraints on the "wiring diagram" of regulatory interactions, and the "rules" governing the dynamical behavior of regulated components of the network. The ensemble consists of all networks consistent with those constraints. Here I discuss ensembles of random Boolean networks, scale free Boolean networks, "medusa" Boolean networks, continuous variable networks, and others. For each ensemble, M statistical features, such as the size distribution of avalanches in gene activity changes unleashed by transiently altering the activity of a single gene, the distribution in distances between gene activities on different cell types, and others, are measured. This creates an M-dimensional space, where each ensemble corresponds to a cluster of points or distributions. Using current and future experimental techniques, such as gene arrays, these M properties are to be measured for real cells and organisms, again yielding a cluster of points or distributions in the M-dimensional space. The procedure then finds ensembles close to those of real cells and organisms, and hill climbs to attempt to match the observed M features. Thus obtains one or more ensembles that should predict and explain many features of the regulatory networks in cells and organisms.     

The genetic structure of the European breeding populations of a declining farmland bird,the ortolan bunting (<Emphasis Type="Italic">Emberiza hortulana</Emphasis>), reveals conservation priorities

Anthropogenic activities, such as agricultural intensification, caused large declines in biodiversity, including farmland birds. In addition to demographic consequences, anthropogenic activities can result in loss of genetic diversity, reduction of gene flow and altered genetic structure. We investigated the distribution of the genetic variation of a declining farmland and long-distance migratory bird, the ortolan bunting Emberiza hortulana, across its European breeding range to assess the impact of human-driven population declines on genetic diversity and structure in order to advise conservation priorities. The large population declines observed have not resulted in dramatic loss of genetic diversity, which is moderate to high and constant across all sampled breeding sites. Extensive gene flow occurs across the breeding range, even across a migratory divide, which contributes little to genetic structuring. However, gene flow is asymmetric, with the large eastern populations acting as source populations for the smaller western ones. Furthermore, breeding populations that underwent the largest declines, in Fennoscandia and Baltic countries, appear to be recently isolated, with no gene exchange occurring with the eastern or the western populations. These are signs for concern as declines in the eastern populations could affect the strength of gene flow and in turn affect the western populations. The genetic, and demographic, isolation of the northern populations make them particularly sensitive to loss of genetic diversity and to extinction as no immigration is occurring to counter-act the drastic declines. In such a situation, conservation efforts are needed across the whole breeding range: in particular, protecting the eastern populations due to their key role in maintaining gene flow across the range, and focussing on the northern populations due to their recent isolation and endangered status.     

Recent progress on the identity and characterization of factors that shape gene organization during eukaryotic evolution

Comparative genomics has identified regions of chromosomes susceptible to participate in rearrangements that modify gene order and genome architecture. Additionally, despite the high levels of genome rearrangement, unusually large regions that remain unaffected have also been uncovered. Functional constraints, such as long-range enhancers or local coregulation of neighboring genes, are thought to explain the maintenance of gene order (i.e., collinearity conservation) among distantly related species since the disruption of these protected regions would cause detrimental misregulation of gene expression. Local enrichment of certain genetic elements in regions of conserved collinearity has been used to support the existence of regulatory-based constraints, although the evidence is largely circumstantial. Indeed, a mechanism of chromosome evolution based only on the existence of fragile regions (i.e., those more susceptible to breaks) can also give rise to extended collinearity conservation, making it difficult to determine whether conserved gene organization is actually caused by functional constraints. Chromosome engineering coupled with genome wide expression profiling and phenotypic assays can provide unambiguous evidence for the presence of functional constraints acting on particular genomic regions. We have recently used this integrated approach to evaluate the presence and nature of putative constraints acting on one of the largest chromosomal regions conserved across nine species of Drosophila. We propose that regulatory-based constraints might not suffice to explain the maintenance of gene organization of some chromosome domains over evolutionary time.     

Structural systems identification of genetic regulatory networks

MOTIVATION: Reverse engineering of genetic regulatory networks from experimental data is the first step toward the modeling of genetic networks. Linear state-space models, also known as linear dynamical models, have been applied to model genetic networks from gene expression time series data, but existing works have not taken into account available structural information. Without structural constraints, estimated models may contradict biological knowledge and estimation methods may over-fit. RESULTS: In this report, we extended expectation-maximization (EM) algorithms to incorporate prior network structure and to estimate genetic regulatory networks that can track and predict gene expression profiles. We applied our method to synthetic data and to SOS data and showed that our method significantly outperforms the regular EM without structural constraints. AVAILABILITY: The Matlab code is available upon request and the SOS data can be downloaded from http://www.weizmann.ac.il/mcb/UriAlon/Papers/SOSData/, courtesy of Uri Alon. Zak's data is available from his website, http://www.che.udel.edu/systems/people/zak.     

Blur and disparity are complementary cues to depth

Estimating depth from binocular disparity is extremely precise, and the cue does not depend on statistical regularities in the environment. Thus, disparity is commonly regarded as the best visual cue for determining 3D layout. But depth from disparity is only precise near where one is looking; it is quite imprecise elsewhere. Away from fixation, vision resorts to using other depth cues-e.g., linear perspective, familiar size, aerial perspective. But those cues depend on statistical regularities in the environment and are therefore not always reliable. Depth from defocus blur relies on fewer assumptions and has the same geometric constraints as disparity but different physiological constraints. Blur could in principle fill in the parts of visual space where disparity is imprecise. We tested this possibility with a depth-discrimination experiment. Disparity was more precise near fixation and blur was indeed more precise away from fixation. When both cues were available, observers relied on the more informative one. Blur appears to play an important, previously unrecognized role in depth perception. Our findings lead to a new hypothesis about the evolution of slit-shaped pupils and have implications for the design and implementation of stereo 3D displays.     

Pleiotropic effects of environment-sensitive genes affecting fitness in relation to postmating reproductive isolation

With regard to speciation in sexually reproducing organisms, some population geneticists continue to argue about the relative merits of sympatry versus allopatry. However, all workers seem quite comfortable with the conventional scenario depicting how reproductive isolation arises between subpopulations in the state of incipient speciation. This view according to which the evolution of reproductive isolation mainly results from some genetic divergence consecutive to a substantial restriction in gene flow is questioned here. A verbal model is described in which gene flow is no longer seen as being first interrupted by a mere physical barrier. The model is based on limited genetic changes at loci influencing fitness but it places two important constraints on the properties of the genetic elements involved in it. One of them is concerned with the environment-sensitivity of the mutations implicated in the process, and the other with their presumed pleiotropic action on a behavioural trait.     

Network Features of the Mammalian Circadian Clock

The mammalian circadian clock is a cell-autonomous system that drives oscillations in behavior and physiology in anticipation of daily environmental change. To assess the robustness of a human molecular clock, we systematically depleted known clock components and observed that circadian oscillations are maintained over a wide range of disruptions. We developed a novel strategy termed Gene Dosage Network Analysis (GDNA) in which small interfering RNA (siRNA)-induced dose-dependent changes in gene expression were used to build gene association networks consistent with known biochemical constraints. The use of multiple doses powered the analysis to uncover several novel network features of the circadian clock, including proportional responses and signal propagation through interacting genetic modules. We also observed several examples where a gene is up-regulated following knockdown of its paralog, suggesting the clock network utilizes active compensatory mechanisms rather than simple redundancy to confer robustness and maintain function. We propose that these network features act in concert as a genetic buffering system to maintain clock function in the face of genetic and environmental perturbation.     

Constraints on the evolution of adaptive phenotypic plasticity in plants

The high potential fitness benefit of phenotypic plasticity tempts us to expect phenotypic plasticity as a frequent adaptation to environmental heterogeneity. Examples of proven adaptive plasticity in plants, however, are scarce and most plastic responses actually may be 'passive' rather than adaptive. This suggests that frequently requirements for the evolution of adaptive plasticity are not met or that such evolution is impeded by constraints. Here we outline requirements and potential constraints for the evolution of adaptive phenotypic plasticity, identify open questions, and propose new research approaches. Important open questions concern the genetic background of plasticity, genetic variation in plasticity, selection for plasticity in natural habitats, and the nature and occurrence of costs and limits of plasticity. Especially promising tools to address these questions are selection gradient analysis, meta-analysis of studies on genotype-by-environment interactions, QTL analysis, cDNA-microarray scanning and quantitative PCR to quantify gene expression, and two-dimensional gel electrophoresis to quantify protein expression. Studying plasticity along the pathway from gene expression to the phenotype and its relationship with fitness will help us to better understand why adaptive plasticity is not more universal, and to more realistically predict the evolution of plastic responses to environmental change.     

An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution

Studies of the evolution of development characterize the way in which gene regulatory dynamics during ontogeny constructs and channels phenotypic variation. These studies have identified a number of evolutionary regularities: (1) phenotypes occupy only a small subspace of possible phenotypes, (2) the influence of mutation is not uniform and is often canalized, and (3) a great deal of morphological variation evolved early in the history of multicellular life. An important implication of these studies is that diversity is largely the outcome of the evolution of gene regulation rather than the emergence of new, structural genes. Using a simple model that considers a generic property of developmental maps-the interaction between multiple genetic elements and the nonlinearity of gene interaction in shaping phenotypic traits-we are able to recover many of these empirical regularities. We show that visible phenotypes represent only a small fraction of possibilities. Epistasis ensures that phenotypes are highly clustered in morphospace and that the most frequent phenotypes are the most similar. We perform phylogenetic analyses on an evolving, developmental model and find that species become more alike through time, whereas higher-level grades have a tendency to diverge. Ancestral phenotypes, produced by early developmental programs with a low level of gene interaction, are found to span a significantly greater volume of the total phenotypic space than derived taxa. We suggest that early and late evolution have a different character that we classify into micro- and macroevolutionary configurations. These findings complement the view of development as a key component in the production of endless forms and highlight the crucial role of development in constraining biotic diversity and evolutionary trajectories.     

Genetic characterization of dipeptidase activity modifiers inDrosophila melanogaster from natural populations

An examination of Drosophila melanogaster from natural populations revealed genetic variation for dipeptidase-A (DIP-A) and dipeptidase-B (DIP-B) activities within sets of lines that differed from one another only in the second or the third chromosome. Analyses of diallel crosses indicate that both activities are inherited additively, and coordinate control of expression is suggested by the significant positive correlation between the two activities. Electrophoresis and thermal denaturation studies failed to detect structural differences among lines with different levels of DIP-A activity. No characteristic level of activity could be associated with any DIP-A allozyme. Mapping experiments revealed the presence of activity modifiers that are in tight linkage with the structural gene, as well as those that manifest their effects from a distance. The maximum genetic distance between a high-activity effect on DIP-A and the structural gene was determined to be 0.029 map unit. These results are in accordance with the prevalence of activity modifiers for various enzymes in Drosophila melanogaster.     

The genetic code constrains yet facilitates Darwinian evolution

An important goal of evolutionary biology is to understand the constraints that shape the dynamics and outcomes of evolution. Here, we address the extent to which the structure of the standard genetic code constrains evolution by analyzing adaptive mutations of the antibiotic resistance gene TEM-1 β-lactamase and the fitness distribution of codon substitutions in two influenza hemagglutinin inhibitor genes. We find that the architecture of the genetic code significantly constrains the adaptive exploration of sequence space. However, the constraints endow the code with two advantages: the ability to restrict access to amino acid mutations with a strong negative effect and, most remarkably, the ability to enrich for adaptive mutations. Our findings support the hypothesis that the standard genetic code was shaped by selective pressure to minimize the deleterious effects of mutation yet facilitate the evolution of proteins through imposing an adaptive mutation bias.     

New view on the population genetic structure of marine fish

The view on homogeneous population genetic structure in many marine fish with high mobility has changed significantly during the last ten years. Molecular genetic population studies over the whole ranges of such species as Atlantic herring and Atlantic cod showed a complex picture of spatial differentiation both on the macrogeographic and, in many areas, on the microgeographic scale, although the differentiation for neutral molecular markers was low. It was established that the migration activity of such fish is constrained in many areas of the species range by hydrological and physicochemical transition zones (environmental gradients), as well as gyres in the spawning regions. Natal homing was recorded in a number of marine fish species. Existing in marine fish constraints of gene migration and a very high variance of reproductive success determine a significantly smaller proportion of effective reproductive size of their populations in the total population size, which generates more complex abundance dynamics than assumed earlier. The various constraints on gene migration and natal homing in marine fish promote the formation of local adaptations at ecologically important phenotypic traits. Effects of selection underlying adaptations are actively investigated in marine fish on the genomic level, using approaches of population genomics. The knowledge of adaptive intraspecific structure enables understanding the ecological and evolutionary processes, that influence biodiversity and providing spatial frames for conservation of genetic resources under commercial exploitation. Contemporary views on the population genetic and adaptive structures or biocomplexity in marine fish support and develop the main principles of the conception of systemic organization of the species and its regional populations, which were advanced by Yu.P. Altukhov and Yu.G. Rychkov.     

Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions

The regulation of gene expression is mediated by interactions between chromatin and protein complexes. The importance of where and when these interactions take place in the nucleus is currently a subject of intense investigation. Increasing evidence indicates that gene activation or silencing is often associated with repositioning of the locus relative to nuclear compartments and other genomic loci. At the same time, however, structural constraints impose limits on chromatin mobility. Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation.     

The evolution of MHC diversity: evidence of intralocus gene conversion and recombination in a single-locus system

Gene conversion, the unidirectional exchange of genetic material between homologous sequences, is thought to strongly influence patterns of genetic diversity. The high diversity of major histocompatibility complex (MHC) genes in many species is thought to reflect a long history of gene conversion events both within and among loci. Theoretical work suggests that intra- and interlocus gene conversion leave characteristic signatures of nucleotide diversity, but empirical studies of MHC variation have rarely been able to analyze the effects of conversion events in isolation, due to the presence of multiple gene copies in most species. The potbellied seahorse (Hippocampus abdominalis), a species with a single copy of the MH class II beta-chain gene (MHIIb), provides an ideal system in which to explore predictions on the effects of intralocus gene conversion on patterns of genetic diversity. The genetic diversity of the MHIIb peptide binding region (PBR) is high in the seahorse, similar to other vertebrate species. In contrast, the remainder of the gene shows a total absence of synonymous variation and low levels of intronic sequence diversity, concentrated in 3 short repetitive regions and 1-12 SNPs per intron. The distribution of substitutions across the gene results in a patchwork pattern of shared polymorphism between otherwise divergent sequences. The pattern of nucleotide diversity observed in the seahorse MHIIb gene is congruent with theoretical expectations for intralocus gene conversion, indicating that this evolutionary mechanism has played an important role in MHC gene evolution, contributing to both the high diversity in the PBR and the low diversity outside this region. Neutral variation at this locus may be further reduced due to biases in nucleotide composition and functional constraints.     

Bacterial evolution through the selective loss of beneficial Genes. Trade-offs in expression involving two loci

The loss of preexisting genes or gene activities during evolution is a major mechanism of ecological specialization. Evolutionary processes that can account for gene loss or inactivation have so far been restricted to one of two mechanisms: direct selection for the loss of gene activities that are disadvantageous under the conditions of selection (i.e., antagonistic pleiotropy) and selection-independent genetic drift of neutral (or nearly neutral) mutations (i.e., mutation accumulation). In this study we demonstrate with an evolved strain of Escherichia coli that a third, distinct mechanism exists by which gene activities can be lost. This selection-dependent mechanism involves the expropriation of one gene's upstream regulatory element by a second gene via a homologous recombination event. Resulting from this genetic exchange is the activation of the second gene and a concomitant inactivation of the first gene. This gene-for-gene expression tradeoff provides a net fitness gain, even if the forfeited activity of the first gene can play a positive role in fitness under the conditions of selection.     

On replication of nucleic acids in relation to the evolution of the genetic code and of proteins

Some properties of transitions generated during an imprecise replication of nucleic acids are described here. A possible role of these transitions in the evolution of the genetic code with respect to the evolution of the tertiary structure of proteins is suggested. The data supporting this hypothesis are obtained from the analysis of certain regularities present in the genetic code and in the proportions of amino acid residues buried in the interior of globular proteins.