From yeast genetics to biotechnology

Roots of classical yeast genetics go back to the early work of Lindegreen in the 1930s, who studied thallism, sporulation and inheritance of wine yeast strains belonging to S. cerevisiae. Consequent mutation and hybridization of heterothallic S. cerevisae strains resulted in the discovery of life cycle and mating type system, as well as construction of the genetic map. Elaboration of induced mutation and controlled hybridization of yeast strains opened up new possibilities for the genetic analysis of technologically important properties and for the production of improved industrial strains, but a big drawback was the widely different genetic properties of laboratory and industrial yeast strains. Genetic analysis and mapping of industrial strains were generally hindered because of homothallism, poor sporulation and/or low spore viability of brewing and wine yeast strains [1, 2]. In spite of this, there are a few examples of the application of sexual hybridization in the study of genetic control of important technological properties, e.g. sugar utilization, flocculation and flavor production in brewing yeast strains [3] or in the improvement of ethanol producing S. cerevisiae strains [4]. Rare mating and application of karyogamy deficient (kar-) mutants also proved useful in strain improvement [5]. Importance of yeasts in biotechnology is enormous. This includes food and beverage fermentation processes where a wide range of yeast species are playing role, but S. cerevisiae is undoubtedly the most important species among them. New biotechnology is aiming to improve these technologies, but besides this, a completely new area of yeast utilization has been emerged, especially in the pharmaceutical and medical areas. Without decreasing the importance of S. cerevisiae, numerous other yeast species, e.g. Kluyveromyces lactis, Hansenula polymorpha, Pichia pastoris, Schizosaccharomyces pombe and Yarrowia lipolytica have gained increasing potentialities in the modern fermentation biotechnology [6]. Developments in yeast genetics, biochemistry, physiology and process engineering provided bases of rapid development in modern biotechnology, but elaboration of the recombinant DNA technique is far the most important milestone in this field. Other molecular genetic techniques, as molecular genotyping of yeast strains proved also very beneficial in yeast fermentation technologies, because dynamics of both the natural and inoculated yeast biota could be followed by these versatile DNA-based techniques.     

From inflammation to pain: experimental gene therapy

Chronic pain is frequently associated with profound alterations of neuronal systems involved in pain processing and should be considered as a real disease state of the nervous system. Unfortunately, some forms of chronic pain remain difficult to be satisfactorily treated. In the search for new therapeutic strategies, the gene-based approaches are of potential interest as they offer the possibility to introduce a therapeutic protein into some relevant structures and to drive its continuous production in the near vicinity of targeted cells. Recently, these techniques have been experimented in several animal models of chronic pain, showing that transfer at the spinal level of some genes, in particular those of opioid precursors proopiomelanocortin or proenkephalin A, leading to the overproduction of products that they encode, attenuated persistent pain of both inflammatory and neuropathic origin. Thus, in polyarthritic rat, a model of chronic inflammatory pain, we demonstrated that herpes simplex virus vector mediated overexpression of proenkephalin A in primary sensory neurons at the lumbar level elicited both antihyperalgesic and anti-inflammatory activities. Apart from opioids, numerous other molecules involved in pain processing are of potential therapeutic interest for gene-based protocols. For instance, targeting some molecules involved in pain induction and perpetuation, such as proinflammatory cytokines, raises an interesting possibility to block the "development" of pain. The clinical application of these approaches remains to be established, and, presently, one of the main problems to be solved is the innocuity of virus-derived vectors. However, the experimental use of gene-based techniques might be particularly useful for the evaluation of the therapeutic interest of some recently identified molecules involved in pain processing and might finally lead to the development of new "classical" pharmacological tools.     

From genetics of intraspecific differences to genetics of intraspecific similarity

Based on the Mendelian approach to heredity, modern genetics describes inheritance of characters belonging to the category of intraspecific difference. The other large category of characters, intraspecific similarity, stays out of investigation. In this review, the genome part responsible for intraspecific similarity is considered as invariant and regulatory. An approach to studying the invariant part of the Drosophila melanogaster genome is formulated and the results of examining this genome part are presented. The expression of mutations at genes in the invariant genome part is different from that of Mendelian genes. We conclude that these genes are present in the genome in multiple copies and they are functionally haploid in the diploid genome. Severe abnormalities of development appearing in the progeny of mutant parents suggest that the mutant genes are genes regulating ontogeny. A hypothesis on an elementary ontogenetic event is advanced and the general scheme of ontogeny is presented. A concept on two types of gene allelism (cis- and trans-allelism) is formulated. This approach opens a possibility for studying genetic material responsible for the formation of intraspecific similarity characters at different taxonomic levels on the basis of crossing individuals of the same species.     

From classical genetics to quantitative genetics to systems biology: modeling epistasis

Gene expression data has been used in lieu of phenotype in both classical and quantitative genetic settings. These two disciplines have separate approaches to measuring and interpreting epistasis, which is the interaction between alleles at different loci. We propose a framework for estimating and interpreting epistasis from a classical experiment that combines the strengths of each approach. A regression analysis step accommodates the quantitative nature of expression measurements by estimating the effect of gene deletions plus any interaction. Effects are selected by significance such that a reduced model describes each expression trait. We show how the resulting models correspond to specific hierarchical relationships between two regulator genes and a target gene. These relationships are the basic units of genetic pathways and genomic system diagrams. Our approach can be extended to analyze data from a variety of experiments, multiple loci, and multiple environments.     

From hybrids to hermaphrodites in population genetics

A report on the 46th annual PopGroup conference, Glasgow, UK, December 18-21,2012.     

Systems genetics: From GWAS to disease pathways

Most common diseases are complex, involving multiple genetic and environmental factors and their interactions. In the past decade, genome-wide association studies (GWAS) have successfully identified thousands of genetic variants underlying susceptibility to complex diseases. However, the results from these studies often do not provide evidence on how the variants affect downstream pathways and lead to the disease. Therefore, in the post-GWAS era the greatest challenge lies in combining GWAS findings with additional molecular data to functionally characterize the associations. The advances in various ~omics techniques have made it possible to investigate the effect of risk variants on intermediate molecular levels, such as gene expression, methylation, protein abundance or metabolite levels. As disease aetiology is complex, no single molecular analysis is expected to fully unravel the disease mechanism. Multiple molecular levels can interact and also show plasticity in different physiological conditions, cell types and disease stages. There is therefore a great need for new integrative approaches that can combine data from different molecular levels and can help construct the causal inference from genotype to phenotype. Systems genetics is such an approach; it is used to study genetic effects within the larger scope of systems biology by integrating genotype information with various ~omics datasets as well as with environmental and physiological variables. In this review, we describe this approach and discuss how it can help us unravel the molecular mechanisms through which genetic variation causes disease. This article is part of a Special Issue entitled: From Genome to Function.     

From sequence to phenotype: reverse genetics in Drosophila melanogaster

There has been a long history of innovation and development of tools for gene discovery and genetic analysis in Drosophila melanogaster. This includes methods to induce mutations and to screen for those mutations that disrupt specific processes, methods to map mutations genetically and physically, and methods to clone and characterize genes at the molecular level. Modern genetics also requires techniques to do the reverse to disrupt the functions of specific genes, the sequences of which are already known. This is the process referred to as reverse genetics. During recent years, some valuable new methods for conducting reverse genetics in Drosophila have been developed.     

From brain function to therapy

<正>During the 20th century,biological sciences developed enormously and uncovered many mysteries of life.With one exception,we have now understood very well the various systems of our body,such as the digestive,circulatory and reproductive systems.This one exception is the nervous system,mainly the brain.The scientific study of the nervous     

From Mendelian to molecular genetics: the Xiphophorus melanoma model

In human tumor biopsies it is almost impossible to pinpoint the particular molecular abnormalities that determine neoplasia. In animal models where tumorigenesis is initiated by clearly defined genetic events, it is possible to study the genes and their functions that make a normal cell become a fully malignant cancer cell. In the fish Xiphophorus, melanoma can be initiated by simple crossings, and the signaling pathways that govern tumor growth and progression can be delineated. This model offers the prospect of obtaining a complete picture of the molecular changes and regulatory networks underlying tumor formation, which should contribute to a better understanding of some general principles of cancer biology, and identify new targets for melanoma research in particular.     

From genetics to epigenetics: new insights into keloid scarring

Keloid scarring is a dermal fibroproliferative response characterized by excessive and progressive deposition of collagen; aetiology and molecular pathology underlying keloid formation and progression remain unclear. Genetic predisposition is important in the pathogenic processes of keloid formation, however, environmental factors and epigenetic mechanisms may also play pivotal roles. Epigenetic modification is a recent area of investigation in understanding the molecular pathogenesis of keloid scarring and there is increasing evidence that epigenetic changes may play a role in induction and persistent activation of fibroblasts in keloid scars. Here we have reviewed three epigenetic mechanisms: DNA methylation, histone modification and the role of non‐coding RNAs. We also review the evidence that these mechanisms may play a role in keloid formation ‐ in future, it may be possible that epigenetic markers may be used instead of prognostic or diagnostic markers here. However, there is a significant amount of work required to increase our current understanding of the role of epigenetic modification in keloid disease.     

A mouse model of the fragile gene FHIT: From carcinogenesis to gene therapy and cancer prevention

Mouse models of tumor suppressors are increasingly useful to investigate biomedical aspects of cancer genetics. Some tumor suppressor genes are located at common fragile sites that are specific chromosomal regions highly susceptible to DNA lesions. The tumor suppressor gene FHIT, at the fragile site FRA3B, is the first fragile gene with a developed and characterized mouse knockout model. The human gene FHIT is frequently deleted in cancers and cancer cell lines of many epithelial tissues, and Fhit protein is absent or reduced in most cancers. The mouse Fhit ortholog is also located at a common fragile site, Fra14A2 on murine chromosome 14, and sustains homozygous deletions in murine cancer cell lines. The Fhit knockout mouse is, therefore, an adequate model to study human FHIT function. To establish an animal model and to explore the role of FHIT in tumorigenesis, we have developed a mouse strain carrying one or two inactivated Fhit alleles. Insights into Fhit mouse genetics that have emerged in the last 7 years, and are reviewed in the present article, allowed for development of new tools in carcinogenesis and gene delivery studies.     

From protoplasts to gene clusters

Advances in protoplast technology underpinned many crucial developments in our understanding of the molecular biology of filamentous fungi. This review follows one of these developments, namely the discovery and analysis of difuran toxin gene clusters. Our understanding of the biosynthetic pathway of the agriculturally important toxin, aflatoxin, has been dramatically enhanced by the use of protoplasts and protoplast-based gene transformation methods. Since the identification of the first pathway genes by complementation of mutants with transforming DNA, transformation has continued to play a critical role in the elucidation of gene function and regulation. But despite the wealth of knowledge accumulated so far some fundamental questions remain to be answered. How did these gene clusters evolve? What is the biological role of aflatoxin? The discovery of homologues of aflatoxin genes in other fungal species such as the pine needle pathogen Dothistroma septosporum may help to shed some light on these questions.     

候选基因策略在植物遗传学中的应用

随着遗传学研究技术的快速发展和后基因组学时代的来临,候选基因的概念和研究方法越来越多地被人们所应用,成 为功能克隆、图位克隆、表型克隆、插入突变等方法之外的又一重要基因克隆策略。候选基因策略的基本原理和主要步骤,以 及其在植物遗传学中具有重要的应用实例。