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PubMed2002

Erratum to "Lactobacillus sakei: recent developments and future prospects" [Research in Microbiology 152 (2001) 839].

Lactobacillus sakei is one of the most important bacterial species involved in meat preservation and meat fermentation. In the last fifteen years, numerous studies have focused on this species due to its important role in food microbiology. The present paper reviews current knowledge of this emerging species in the fields of taxonomy, phylogeny and physiology, and metabolism. Recent developments in genetic tools and molecular genetics will also be emphasized to evaluate future prospects.

Animals↗
PubMed2002

Random amplified polymorphic DNA markers for discriminating Cochliomyia hominivorax from C. macellaria (Diptera: Calliphoridae).

The screwworm, Cochliomyia hominivorax (Coquerel), is one of the most important pests of livestock in the Western Hemisphere. During early immature stages it is morphologically very similar (first instars are virtually indistinguishable) to the secondary screwworm, C. macellaria (Fabricius). Here, the utility of the random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) was explored as a technique for developing molecular genetic markers for these two species. Of the 120 arbitrary primers screened, 21 primers produced markers that were further investigated. Seven of the 21 primers produced clear and reproducible markers that were tested with DNA of five individuals from four populations of each species; five of these primers showed 12 RAPD markers that differentiated the species in all populations. Analyses of data from these seven primers also suggested that intraspecific polymorphisms exist that could be useful in distinguishing populations of screwworms. Some population genetic tools, such as genetic distance, cluster analysis and bootstrapping, were used to statistically explore these polymorphisms. The resulting statistics showed 100% support for the ability of RAPD-PCR to discriminate between the two species. Bootstrapping with data from one of the genetic distance calculations produced a tree with all individual screwworms in the correct populations, indicating that RAPD-PCR has promise for displaying intraspecific genetic variation that could be used in establishing the general geographic origin of screwworm samples.

Animals↗
PubMed1998

Genetic models for non insulin dependent diabetes mellitus in rodents.

Efforts to identify human genes with major effects on insulin resistance and type II diabetes have yet to be successful because of the technical difficulties associated with the analysis of complex traits in humans. Animal models, particularly the rodent models with their well developed genetic tools, and their genetic similarity to humans, offer an alternate approach to access genes important in the etiology of diabetes. This approach is validated by the remarkable progress that has been made in the identification and characterization of the genes mutated in five monogenic mouse models of obesity. Identification of these genes has led to new insights into the etiology of obesity and provided promising targets for therapeutic intervention. Arguably, genetic animal models could do the same for our understanding of diabetes. In this brief review, we introduce rodent models of type II diabetes and report on the state of their genetic analyses.

Animals↗
PubMed1989

Listeria monocytogenes. A model system for the molecular study of intracellular parasitism.

Listeria monocytogenes is a facultative intracellular bacterium which, in its mammalian host, can infect enterocytes and mononuclear phagocytes. It is responsible for severe infections in humans and animals. Recovery from infection and resistance depends on the development of a T-cell response, antibodies not being protective. Several features of L. monocytogenes make it particularly suitable for the study of genetic and molecular aspects of invasion and intracellular parasitism. First, L. monocytogenes not only multiplies rapidly in bacterial broth but also easily infects macrophages and other cells in culture. Second, since it infects primarily immunocompromised individuals or pregnant women, its manipulation does not require extensive containment. Third, the genus Listeria includes several nonpathogenic species, facilitating the identification of species-specific genes and products required for pathogenicity. This identification is now possible due to the parallel development of powerful genus-specific genetic tools (transposons, plasmids, genetic transformation) and improvement of recombinant DNA techniques. Finally, the in vivo relevance of the putative virulence genes or gene products can be tested in the experimental murine infection, which has already proved invaluable in the study of the induction and expression of T-cell-mediated immune response. This review discusses current knowledge concerning these particular features, with an emphasis on listeriolysin O, a major virulence factor, and the only bacterial gene product known to be absolutely required for intracellular growth.

Animals↗
PubMed2005

First steps towards the genetic manipulation of Mycoplasma agalactiae and Mycoplasma bovis using the transposon Tn4001mod.

Mycoplasma agalactiae and M. bovis rank amongst the most serious pathogenic mycoplasmas infecting small ruminants and cattle, respectively. Despite considerable advances made in Mycoplasma molecular genetics in the past decade, there is still a complete lack of genetic tools to assess the pathogenic mechanisms of these two species. Studies were undertaken to develop a genetic system for the analysis of potential virulence factors of these pathogens. Transposon Tn4001mod was successfully introduced into various chromosomal sites of M. agalactiae and M. bovis with an optimal frequency of 10(-6) per viable colony-forming unit (CFU). This is the first report that demonstrates the amenability of these agents to transformation and to genetic manipulation. Furthermore, Tn4001 is implicated as the first potential genetic tool available for these ruminant pathogens.

Animals↗
PubMed2006

Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp.

The spirochetes of the Leptospira genus contain saprophytic and pathogenic members, the latter being responsible for leptospirosis. Despite the recent sequencing of the genome of the pathogen L. interrogans, the slow growth of these bacteria, their virulence in humans, and a lack of genetic tools make it difficult to work with these pathogens. In contrast, the development of numerous genetic tools for the saprophyte L. biflexa enables its use as a model bacterium. Leptospira spp. require iron for growth. In this work, we show that Leptospira spp. can acquire iron from different sources, including siderophores. A comparative genome analysis of iron uptake systems and their regulation in the saprophyte L. biflexa and the pathogen L. interrogans is presented in this study. Our data indicated that, for instance, L. biflexa and L. interrogans contain 8 and 12 genes, respectively, whose products share homology with proteins that have been shown to be TonB-dependent receptors. We show that some genes involved in iron uptake were differentially expressed in response to iron. In addition, we were able to disrupt several putative genes involved in iron acquisition systems or iron regulation in L. biflexa. Comparative genomics, in combination with gene inactivation, gives us significant functional information on iron homeostasis in Leptospira spp.

Amino Acid Sequence↗
PubMed2000

Starting a new genetic system: lessons from bacteroides.

Despite the fact that genetic manipulation is an essential adjunct of studies of microbial physiology, many important bacterial species are still not accessible to genetic manipulation. In many cases, the people who know the organism best and have studied its physiology extensively have little experience with genetic techniques and are uncertain how to set up a new system. In this article, we describe what we have learned in the process of developing a genetic system for Bacteroides spp. and helping to develop genetic tools for two related species of bacteria: Porphromonas gingivalis and Prevotella ruminicola. We discuss the relative usefulness of different types of genetic tools and make some suggestions about how to construct them.

Bacteroides↗
PubMed1998

Ribozymes as therapeutic tools for genetic disease.

The discovery that RNA can act as a biological catalyst, as well as a genetic molecule, indicated that there was a time when biological reactions were catalysed in the absence of protein-based enzymes. It also provided the platform to develop those catalytic RNA molecules, called ribozymes, as trans -acting tools for RNA manipulation. Viral diseases or diseases due to genetic lesions could be targeted therapeutically through ribozymes, provided that the sequence of the genetic information involved in the disease is known. The hammerhead ribozyme, one of the smallest ribozymes identified, is able to induce site-specific cleavage of RNA, with ribozyme and substrate being two different oligoribonucleotides with regions of complementarity. Its ability to down-regulate gene expression through RNA cleavage makes the hammerhead ribozyme a candidate for genetic therapy. This could be particularly useful for dominant genetic diseases by down-regulating the expression of mutant alleles. The group I intron ribozyme, on the other hand, is capable of site-specific RNA trans -splicing. It can be engineered to replace part of an RNA with sequence attached to its 3' end. Such application may have importance in the repair of mutant mRNA molecules giving rise to genetic diseases. However, to achieve successful ribozyme-mediated RNA-directed therapy, several parameters including ribozyme stability, activity and efficient delivery must be considered. Ribozymes are promising genetic therapy agents and should, in the future, play an important role in designing strategies for the therapy of genetic diseases.

Animals↗
PubMed2003

Genetic authentication of ginseng and other traditional Chinese medicine.

The main objective of this paper is to review the chemical and genetic methods used in authentication of ginseng, especially the recent advances in microsatellite genotyping and its application to the authentication of other traditional Chinese medicines (TCM). The standardization and modernization of TCM hinge on the authentication of their botanical identities. Analysis of well-characterized marker compounds is now the most popular method for identifying the herbal materials and quality control of TCM, eg, ginsenoside profiling for authentication of Panax species. However, in many herbal species the chemical composition of the plant changes with the external environment and processing conditions, which lowers the reliability of these authentication methods. In the light of the advances in molecular biotechnology in the past few decades, genetic tools are now considered to provide more standardized and reliable methods for authentication of herbal materials at the DNA level. These genetic tools include random amplified polymorphic DNA (RAPD), DNA fingerprinting using multi-loci probes, restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and microsatellite marker technology. The practicality of these methods varies in terms of their sensitivity, reliability, reproducibility, and running cost. Using ginseng as an example, we reviewed the advantages and limitations of these molecular techniques in TCM authentication. We have developed a set of microsatellite markers from American ginseng that are able to differentiate Panax ginseng and Panax quinquetolius with the resolution down to farm level, ie, confirmation of its botanical identity and origin. Compared with other molecular techniques, microsatellite marker technology is more robust, accurate, reproducible, reliable, and sensitive. This is essential for large-scale TCM authentication centers.

DNA Fingerprinting↗
PubMed1999

Mouse genetics: a tool to help unlock the mechanisms of glaucoma.

Gene characterization holds great promise for understanding molecular mechanisms of disease. Although glaucoma gene identification is very valuable and allows assessment of an individual's genetic risk, it is not by itself sufficient to answer detailed questions about pathogenesis. Despite the recent identification of a number of glaucoma genes, there are still many questions regarding the ways in which mutations in these genes cause disease. The mouse system, including the ability to alter specific genes, provides a powerful experimental system for hypothesis testing and molecular dissection of pathogenesis subsequent to gene identification. The ability to control both genetic and environmental factors will allow the use of mice to identify modifier genes that alter complex glaucoma phenotypes and that are especially difficult to identify in human families. By providing a bridge between gene identification and tests of gene function, mouse studies will be an important complement to those in humans and other species. This article summarizes the recent use of mice and the future potential of applying approaches of mouse genetics to intraocular pressure and glaucoma research.

Animals↗
PubMed2001

Recombinant congenic strains derived from A/J and C57BL/6J: a tool for genetic dissection of complex traits.

Complex genetic traits can be dissected in mice, using well-defined sets of recombinant inbred strains, congenic strains, and recombinant congenic strains (RCS). We report the creation of a series of 37 independent RCS derived from the commonly used inbred strains of laboratory mouse A/J (A) and C57BL/6J (B6). These RCS were derived by systematic inbreeding of independent pairs of animals from a (F1 x A) x A and a (F1 x B) x B double backcross (N3), to create AcB and BcA strains, respectively. Fifteen AcB strains and 22 BcA strains at between 18 and 30 generations of inbreeding have been generated, are healthy, and show stable breeding performance. These strains have been genotyped for a total of 625 informative microsatellite DNA markers covering the entire genome, with an average spacing of 2.6 cM. Haplotype analyses indicate that on average, AcB and BcA strains contain 13.25% of the donor genome, a value close to the 12.5% expected from the breeding scheme used in their creation. In the AcB set, approximately 79% of the B6 genome has been transferred in independent strains, while in the BcA set approximately 84% of the A genome is represented on the B6 background. This represents an excellent coverage of congenic segments from both parental genomes in the two sets of strains, which can now be used to map simple and complex traits in a genome-wide fashion. As an example of the power of AcB/BcA strains as a mapping tool, the 37 strains were typed for susceptibility to infection with Legionella pneumophila, a monogenic trait controlled by the Lgn1 locus on Chromosome 13. Analysis of the strain distribution pattern of L. pneumophila susceptibility allowed direct mapping of Lgn1 to a 3-cM interval. The AcB/BcA set should prove a useful tool with which to investigate the complex genetic basis of known interstrain differences between A and B6 for many important diseases.

Animals↗
PubMed2001

Genetic transformation systems in insects.

The past 5 years have witnessed the emergence of techniques that permit the stable genetic transformation of a number of non-drosophilid insect species. These transposable-element-based strategies, together with virus-based techniques that allow the expression of genes to be quickly examined in insects, provide insect scientists with a first generation of genetic tools that can begin to be harnessed to further increase our understanding of gene function and regulation in insects. We review and compare the characteristics of these gene transfer systems and conclude that, although significant progress has been made, these systems still do not meet the requirements of robust genetic tools. We also review risk assessment issues arising from the generation and probable release of genetically engineered insects.

Animals↗
PubMed1997

Recent advances in genetic analyses of hyperthermophilic archaea and bacteria.

Hyperthermophilic Archaea and Bacteria are an extraordinarily important class of organisms for which genetic tools remain to be developed. Unique technological obstacles to this goal are posed by the thermophilic and, in some cases, strictly anaerobic nature of these organisms. However, recent advances in the cultivation of hyperthermophiles, in the discovery of genetic elements for vector development, and in the construction of genetic markers point toward the achievement of this goal in the near future. Transformation protocols have already been reported for Sulfolobus and Pyrococcus, and plasmid-mediated conjugation was recently found in Sulfolobus. Plasmids are available for Sulfolobus, Pyrococcus, and the bacterial hyperthermophile Thermotoga, and these provide the bases for vector construction in these hosts. A Desulfurococcus mobile intron may provide a novel means to introduce genes into a variety of archaeal hosts. With full genome sequences of several hyperthermophiles available soon, genetic tools will allow full exploitation of this information to study these organisms in depth and to utilize their unique properties in biotechnological applications.

Archaea↗
PubMed1992

Hearing on the possible uses and misuses of genetic information.

In summary, I will reiterate the five points I would like to leave with you today: First, the biological revolution has extraordinary power to do good. As long as the use of our new genetic knowledge is guided by the traditional ideals of the healing professions--to help improve the human condition without doing harm--we can expect real benefits to come of it. Second, however, we need to prepare for the fact that, like all powerful tools, genetic information can be misused and abused. As I hope to have illustrated, NIH has the will and ability to work with the American public and the scientific community in preparing for the responsible use of genetic information for now and the future. To date, the best example of that will is the precedent-setting work being conducted in concert with the human genome program through our ELSI program. Third, as a part of that work, it will be imperative to continue to protect the voluntary nature of genetic services. The rights of people to determine for themselves whether or not to pursue genetic information about themselves must be defended, even from the forced choices that discriminatory social practices may create. Fourth, in order to allow those who choose to do so to benefit from our new genetic tools, discrimination based on genotype must be prohibited as a matter of basic civil rights. And finally, in the bright light of the Human Genome Project and its ELSI program, it is important not to let genetics eclipse the important ethical, legal and social issues that attend other biomedical advances. It is the purpose of NIH's new center for science policy studies to illuminate this broader view of the road ahead. Thank you. I will be happy to answer any questions you might have.

Biomedical Research↗
PubMed2004

RNAi in functional genomics.

There has been a lack of powerful tools for systematic analysis of mammalian gene function, but RNA interference (RNAi) may now provide such a strategy. Stable transcription of RNAi triggers from suitable expression cassettes integrated into the host cell genome by viral gene transfer can induce long-term and heritable gene silencing in mammalian cells. However, the use of RNAi as a genetic tool is limited by difficulties in identifying efficient RNAi triggers, the problem of effective delivery and off-target effects, as well as potential genotoxic side effects of viral gene transfer strategies. Recent insights into the molecular mechanisms of silencing processes mediated by either siRNA or miRNA will allow further optimization of RNAi triggers as genetic tools.

Animals↗
PubMed2026

Zebrafish relatives as models for functional comparative genetics and genomics.

Closely related species, such as danionin fishes of the Danio, Danionella and Devario genera, often differ in their biology despite their shared evolutionary history, providing a platform for defining the molecular basis for the divergence of phenotypic traits. Such an approach requires the availability of large-scale genomic data, which have been provided by recent reports detailing the genomes of several danionins. Facilitated by the large number of genetic tools that are available for manipulation of the most studied member of this subgroup - the zebrafish, Danio rerio - the danionins have emerged as a useful comparative model system. Here we review their phylogeny and outline the phenotypic traits that are distinct to individual species or genera. We highlight how functional genetic tools such as interspecies hybridization, mutagenesis and transgenesis, as well as the recently reported genome assemblies, have enabled new avenues for hypothesis-driven and technology-driven exploration that collectively establish danionins as important genetic models for understanding a wide range of evolutionary innovations.

Journal Article↗