Analysis of the fixation of discrete genetic structures by means of an integral model of evolution in a Mendelian one-locus population of diploid organisms

An integral model of the evolution of a Mendelian one-locus population of diploid organisms with continual allele diversity developing under density-limiting conditions or without density limitation has been proposed and analyzed. The model was used to study the mechanism of the appearance of discrete genetic structures, i.e., the fixation of a limited number of alleles. Local resistance of the resultant genetic distributions to homogeneous equiprobable mutations has been demonstrated.     

A model of evolution for accumulating genetic information

By taking into account recent knowledge of multigene families and other repetitive DNA sequences, a model of evolution by gene duplication for accumulating genetic information is studied. Genetic information is defined as the sum of distinct functions that the gene family can perform. A coefficient, "genetic diversity" is defined and used in this study, that is highly correlated with genetic information. Initially, a multigene family with a few gene copies is assumed, and natural selection starts to work on this gene family to increase genetic diversity contained in the gene family. As an important mechanism, unequal crossing-over is incorporated. Together with mutation, it is responsible for supplying genetic variability among individuals for selection to work. A specific model, in which individuals with less genetic diversity are selectively disadvantageous, has been studied in detail. Through approximate theoretical analysis and extensive Monte Carlo studies, it has been shown that the system is an extremely efficient way to accumulate genetic information. For attaining one gene, the genetic load is much smaller under this model than under the traditional model of natural selection. The model may be applied to the process of origin of multigene families with diverse copy members such as those of immunoglobulin or cytochrome P450. In general, the process of creating new genes by duplication might be somewhere between the present and the traditional models.     

Genetic modifiers of neurological disease

Genetic modifiers make an important contribution to neurological disease phenotypes. Significant progress has been made by studying genetic modifiers in model organisms. The ability to study complex genetic interactions in model systems contributes to our understanding of the genetic factors that influence neurological disease. This will lead to the development of novel therapeutic strategies and personalized treatment based on genetic risk.     

A quantitative genetics model for viability selection

Viability selection will change gene frequencies of loci controlling fitness. Consequently, the frequencies of marker loci linked to the viability loci will also change. In genetic mapping, the change of marker allelic frequencies is reflected by the departure from Mendelian segregation ratio. The non-Mendelian segregation of markers has been used to map viability loci along the genome. However, current methods have not been able to detect the amount of selection (s) and the degree of dominance (h) simultaneously. We developed a method to detect both s and h using an F2 mating design under the classical fitness model. We also developed a quantitative genetics model for viability selection by proposing a continuous liability controlling the viability of individuals. With the liability model, mapping viability loci has been formulated as mapping quantitative trait loci. As a result, nongenetic systematic environmental effects can be easily incorporated into the model and subsequently separated from the genetic effects of the viability loci. The quantitative genetic model has been verified with a series of Monte Carlo simulation experiments.     

REVIEW: Optimality models in the age of experimental evolution and genomics

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well‐researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well‐researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.     

Genetic control of migratory behaviour in birds

Although it has long been suspected that biannual migration in birds has a direct genetic basis, only in the last decade have details of the inheritance of behavioural traits such as migratory activity and directional preferences been demonstrated. A model has now been developed to estimate how inexperienced first-time migrants manage to reach their unknown winter quarters on the basis of inherited spatio-temporal programs. Furthermore, in obligate partial migrants the decision to migrate or not has been shown to have a strong genetic base. Migratoriness and sedentariness in partial migrants have been shown to have a high potential for rapid evolution. A recent set of results has suggested that novel migratory habits can evolve in less than 25 years. A possible consequence is that environmental changes, including 'greenhouse' effects, might considerably alter avian migration systems by acting on genetic variation for migratory tendencies.     

果蝇唾腺多线染色体研究进展及其在遗传学教学中的应用

果蝇唾腺多线染色体是细胞遗传学的3大经典染色体之一,从1934年至今因其具有显著的特点已经作为一个优异的模型用在不同的遗传学研究中。果蝇唾腺多线染色体最大的贡献就是为研究间期染色体结构和基因的表达调控提供了一个非凡的视角;另外,果蝇唾腺多线染色体还可以用于解释一些特殊的遗传现象,例如剂量补偿效应和花斑位置效应。文章一方面就以上进展作一简要总结,另一方面尝试将这一典型案例系统地用于遗传学教学中,引导和激发学生学习遗传学的兴趣。     

Computational characterization of double reduction in autotetraploid natural populations

Population genetic theory has been well developed for diploid species, but its extension to study genetic diversity, variation and evolution in autopolyploids, a class of polyploids derived from the genome doubling of a single ancestral species, requires the incorporation of multisomic inheritance. Double reduction, which is characteristic of autopolyploidy, has long been believed to shape the evolutionary consequence of organisms in changing environments. Here, we develop a computational model for testing and estimating double reduction and its genomic distribution in autotetraploids. The model is implemented with the expectation–maximization (EM) algorithm to dissect unobservable allelic recombinations among multiple chromosomes, enabling the simultaneous estimation of allele frequencies and double reduction in natural populations. The framework fills an important gap in the population genetic theory of autopolyploids.     

Genetic variance in temperature dependent adult size deriving from physiological genetic variation at temperature boundaries

An increase in genetic variation in body size has often been observed under stress; an increase in dominance variance and interaction variance as well as in additive genetic variance has been reported. The increase in genetic variation must be caused by physiological mechanisms that are specific to adverse environments. A model is proposed to explain the occurrence of an increase in genetic variation in body size in Drosophila at extreme temperatures. The model has parameters specific to the low- and high-temperature regions of the viable range. Additive genetic variation in the boundary temperatures leads to a marked increase in additive genetic variation in development rate and body size at extreme temperatures. Additive genetic variation in the temperature sensitivity in the low- and high-temperature regions adds non-additive genetic variation. Development rate shows patterns in additive genetic variation that differ from the patterns of genetic variation in body size; therefore, the genetic correlation between development rate and body size changes sign repeatedly as a function of temperature. The existence of dominance in the genetic variation in the boundary temperatures or in the low- and high-temperature sensitivities leads to a higher total genetic variance due to higher dominance and interaction variance, for both development rate and body size. This revised version was published online in July 2006 with corrections to the Cover Date.     

The systems of genetic control of the traits of branching and plant height in linseed

The genetic control of the traits "plant height", "the number of lateral shoots" and "the number of lateral stems" has been studied in 3 pure lines and 1 variety of linseed according to the model 1 of Hayman method. It has been shown that the traits under investigation are inherited according to the additive-dominant model of genetic control in the absence of any interloci interactions. The higher plant height and numerous lateral shoots are recessive traits controlled by 2 blocks of polymeric genes, whereas the trait of numerous lateral stems is a dominant trait influenced by 1 to 3 blocks of genes. The linseed lines have been ranked according to the number of dominant alleles they have. Suggestions for selection using these parental genotypes have been made.     

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.     

The rat as an animal model of Alzheimer's disease

As a disease model, the laboratory rat has contributed enormously to neuroscience research over the years. It has also been a popular animal model for Alzheimer's disease but its popularity has diminished during the last decade, as techniques for genetic manipulation in rats have lagged behind that of mice. In recent years, the rat has been making a comeback as an Alzheimer's disease model and the appearance of increasing numbers of transgenic rats will be a welcome and valuable complement to the existing mouse models. This review summarizes the contributions and current status of the rat as an animal model of Alzheimer's disease.     

Position effect and related phenomena.

Position-effect variegation in Drosophila, the mosaic expression of genes juxtaposed to heterochromatin, remains an enigmatic long-range phenomenon. While the chromatin-conformation model has been challenged, compelling contrary evidence is lacking. Nevertheless, progress has been made in the genetic and molecular analysis of genes involved in the process of heterochromatin formation and in the characterization of genetic elements normally located in pericentric heterochromatin. In addition, telomeric position effect in yeast provides a new model system for the study of the quasi-stable inheritance of an inactivated state.     

Transduction of chromosome and plasmid markers of bacteriophage P1 in pseudotuberculosis pathogen

A clone of bacteriophage P1 clr100 cml has been isolated capable of the general transduction in the cells of pseudotuberculosis causative agent. The genetic transfer of the 6 Md pesticinogenicity plasmid by the bacteriophage has been used as a model to demonstrate the possibility of transduction. The bacteriophage used has been shown to be efficient in interspecies transduction between yersinia.     

The impact of Arabidopsis research on plant biotechnology

Arabidopsis thaliana, a small annual weed belonging to the mustard family, has become a widely used model in plant genetic research. It has a small genome, short life cycle, and is easy to mutagenize. Identification of genes based on phenotype alone, often a rather difficult part of molecular genetic research, is easiest in this plant. Laboratories working on the "model" plant Arabidopsis thaliana have created a network for sharing resources and ideas, so progress has been rapid. The importance of this plant to biotechnology is that genes isolated from Arabidopsis can be used to find their homologs in crop plants. Likewise, fundamental mechanisms can be understood in a model plant, and applied in crop plants.     

The evolution of female mate choice by sexual conflict

Although empirical evidence has shown that many male traits have evolved via sexual selection by female mate choice, our understanding of the adaptive value of female mating preferences is still very incomplete. It has recently been suggested that female mate choice may result from females evolving resistance rather than attraction to males, but this has been disputed. Here, we develop a quantitative genetic model showing that sexual conflict over mating indeed results in the joint evolution of costly female mate choice and exaggerated male traits under a wide range of circumstances. In contrast to tradition explanations of costly female mate choice, which rely on indirect genetic benefits, our model shows that mate choice can be generated as a side-effect of females evolving to reduce the direct costs of mating.     

Histone deacetylases: a new class of efficient anti-tumor drugs

Circa twenty-five years ago, cancer research was dominated by the concept that the origin of cancer was genetic. Thousands of genetic alterations have indeed been identified involving more than hundred different genes in cancer development. Today, the model has evolved: it has been demonstrated that malignancies can be initiated not only through genetic alterations but also through epigenetic deregulations. By altering the expression of gene involved in cell regulation, epigenetic alterations, such as histone acetylation, play a key role in the initiation and progression of neoplasm. It has been shown that an imbalance between the acelylated and deacetylated status of chromatin is significantly involved in the acquisition of a malignant phenotype. Thus, the modulation of the histone acetylation level by histone deacetylase (HDAC) inhibitors could lead to a genetic re-programmation in cancer cells that would favor apoptosis and prevent proliferation. The potential therapeutic value of several HDAC inhibitors for cancer patients has been evaluated in clinical assays with very promising outcome. Indeed, the first inhibitors available for patients has been recently approved for cancer patients tracing the way for a new class of promising anti-cancer therapy modalities.     

Construction of stochastic context trees for genetic texts

A method has been developed for constructing a tree source model for genetic text generation. Model visualisation in the form of suffix (context) trees provides a new way of context analysis of symbol sequences. Estimation of the stochastic complexity of the data in the frame of the model serves as a criterion for the model's ascertainment. The model and complexity values are used for analysis of genetic texts. The software realisation of this algorithm enables to reveal statistical properties of genetic sequences based on an information measure. The program developed is available via Internet at http://wwwmgs.bionet.nsc.ru/mgs/programs/complexity/.     

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales

The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.     

杨树的组织培养及其基因工程研究

杨树是林木基因工程的模式植物,在其组织培养过程中,试管苗的再生不仅与植株的基因型,年龄及组织的来源,状态等有关,还受许多外界因素如盐浓度及激素的种类与配比的影响,在杨树的转化过程中,DNA直接转移法和农杆菌介导法都有应用,但后者较为常用,组织培养及转化技术的日趋成熟,为杨树基因工程奠定了良好基础,本文对杨树组织培养,DNA转化方法及其基因工程进行了较为系统的概述。