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Development of genetic systems for the mycobacteria.

Requisite to a detailed understanding of the molecular basis of bacterial pathogenesis is a genetic system which allows for the transfer, mutation, and expression of specific genes. Genetic analysis of mycobacteria has been exceedingly difficult since the mycobacteria grow slowly and no natural efficient method of gene transfer within the pathogenic has thus far been found. Using a molecular genetic approach, we have developed both the vectors and the methodology for efficient gene transfer in the mycobacteria. Initially, a novel of type of mycobacteriophage vector was developed, termed a shuttle phasmid. This hybrid shuttle vector replicates in Escherichia coli as a plasmid and in mycobacteria as a phage, capable of introducing foreign DNA into a wide variety of mycobacterial species. A set of shuttle phasmids, constructed from a temperate mycobacteriophage, retained their ability to lysogenize their mycobacterial hosts and could thus introduce foreign DNA stably into mycobacterial cells. An E. coli gene conferring kanamycin-resistance was cloned into these vectors and shown to express in the mycobacteria, thus providing the first selectable marker gene for subsequent genetic studies. Using kanamycin-resistance gene as a selection, the M. fortuitum plasmid pAL5000 replicon, and electroporation; a plasmid transformation system has been developed for both M. smegmatis and BCG. We now plan to use these phage and plasmid systems to analyze, genetically, the virulence attributes of the pathogenic mycobacteria. In addition, by introducing and expressing foreign antigens in BCG, we hope to develop a novel recombinant multi-vaccine vehicle capable of conferring immunity to a variety of bacterial, viral, and parasitic pathogens.

BCG Vaccine↗

The role of reverse genetics systems in studying viral hemorrhagic fevers.

Viral hemorrhagic fever (VHF) is an infectious syndrome in humans often associated with high fatality rates. For most VHFs there are no specific and effective therapies or vaccines available and, in general, there is a lack of knowledge regarding the biology and pathogenesis of the causative agents. Therefore, a more detailed understanding of the molecular basis of VHF pathogenesis, including the identification of viral virulence determinants and host interactions and responses, will be important to enhance our ability to control VHF infections. The recently developed "reverse genetics systems" for several VHF causing viruses have allowed the generation of infectious viruses from cloned cDNA and thus, the generation of virus mutants. Here we review the existing reverse genetics systems for VHF causing viruses and discuss their use in studying viral replication, pathogenesis, and the development of antivirals and vaccines.

Animals↗

Hybridization, transgressive segregation and evolution of new genetic systems in Drosophila.

Introgressive hybridization facilitates incorporation of genes from one species into the gene pool of another. Studies on long-term effects of introgressive hybridization in animal systems are sparse. Drosophila nasuta (2n = 8) and D. albomicans (2n = 6)-a pair of allopatric, morphologically almost identical, cross-fertile members of the nasuta subgroup of the immigrans species group-constitute an excellent system to analyse the impact of hybridization followed by transgressive segregation of parental characters in the hybrid progeny. Hybrid populations of D. nasuta and D. albomicans maintained for over 500 generations in the laboratory constitute new recombinant hybrid genomes, here termed cytoraces. The impact of hybridization, followed by introgression and transgressive segregation, on chromosomal constitution and karyotypes, some fitness parameters, isozymes, components of mating behaviour and mating preference reveals a complex pattern of interracial divergence among parental species and cytoraces. This assemblage of characters in different combinations in a laboratory hybrid zone allows us to study the emergence of new genetic systems. Here, we summarize results from our ongoing studies comparing these hybrid cytoraces with the parental species, and discuss the implications of these findings for our understanding of the evolution of new genetic systems.

Animals↗

Genetic systems of West Nile virus and their potential applications.

Prevention and treatment of West Nile virus (WNV) and other flavivirus infections have become a global public health priority. This fact is highlighted by the recent epidemic of WNV in the US. Since the first outbreak of WNV in the US in 1999, the virus has caused over 4000 known human cases and at least 263 human deaths. The epidemic of WNV in the US in 2002 represents the largest meningoencephalitis outbreak in the western hemisphere, and the largest WNV outbreak ever reported. Reverse genetic systems of WNV are extremely useful tools for studying many aspects of the virus, including viral replication, pathogenesis, antiviral therapy and vaccine development. In this review the current status of the reverse genetic systems of WNV and their potential applications are discussed.

Antiviral Agents↗

[Diversity of genetic systems responsible for biodegradation of naphthalene in Pseudomonas fluorescens strains].

The genetic systems that are responsible for naphthalene catabolism were analyzed in 18 naphthalene-degrading Pseudomonas fluorescens strains isolated from oil-contaminated soils in different regions of Russia. It was found that thirteen strains contain plasmids, from 20 to 120 kb in size, at least five of which are conjugative and bear the catabolic genes responsible for the complete utilization of naphthalene and salicylate. Five plasmids belong to the P-7 incompatibility group, and two plasmids belong to the P-9 incompatibility group. The naphthalene biodegradation genes of P. fluorescens are highly homologous to each other. The study revealed a new group of the nahAc genes and two new variants of the nahG gene. The suggestion is made that the key genes of naphthalene biodegradation, nahAc and nahG, evolve independently and occur in P. fluorescens strains in different combinations.

Cluster Analysis↗

Molecular genetic systems to study the role of poly(ADP-ribosyl)ation in the cellular response to DNA damage.

To study biological functions of poly(ADP-ribose) polymerase (PARP), low-molecular-mass inhibitors have been used extensively, and the experimental results obtained led to the view that PARP plays a role in DNA repair as well as in other cellular processes, eg DNA replication, cell proliferation, and differentiation. Accumulating evidence that these inhibitors have side effects on other metabolic pathways prompted us to develop two molecular genetic systems for the modulation of poly(ADP-ribosyl)ation in living cells: i) the first approach is centered on the DNA-binding domain (DBD) of PARP, which recognizes DNA strand breaks through its zinc fingers, leading to enzyme activation. We have established stable cell culture systems for either constitutive or inducible overexpression of the DBD. In these cells we observe a drastic trans-dominant inhibition of poly(ADP-ribosyl)ation which is associated with sensitization of cells to gamma-irradiation; and ii) in an attempt to specifically increase the poly(ADP-ribose) formation capacity in living cells, the hamster cell line CO60 was stably transfected to obtain constitutive overexpression of full-length human PARP. These molecular genetic systems may be useful for the elucidation of the precise role of poly(ADP-ribosyl)ation in the biological response to DNA damage.

Animals↗

Developing a genetic system in Deinococcus radiodurans for analyzing mutations.

We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the beta-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif(r) system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif(r) in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N'-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

Amino Acid Sequence↗

A molecular genetic system for the pathogenic yeast Candida dubliniensis.

Candida dubliniensis is a recently described pathogenic yeast of the genus Candida that is closely related to Candida albicans but differs from it in several phenotypic and genotypic characteristics, including putative virulence traits, which may explain differences in the spectrum of diseases caused by the two species. In contrast to C. albicans, a molecular genetic system to study virulence of C. dubliniensis is lacking. We have developed a system for the genetic transformation of C. dubliniensis that is based on the use of the dominant selection marker MPA(R) from C. albicans that confers resistance to mycophenolic acid (MPA). Using this transformation system, a GFP (green fluorescent protein) reporter gene that was genetically engineered for functional expression in C. albicans and placed under control of the inducible C. albicans SAP2 (secreted aspartic proteinase) promoter was integrated into the C. dubliniensis genome. MPA-resistant transformants containing the SAP2P-GFP fusion fluoresced under SAP2-inducing conditions but not under SAP2-repressing conditions. These results demonstrate that the MPA(R) selection marker is useful for transformation of C. dubliniensis wild-type strains, that the GFP reporter gene is functionally expressed in C. dubliniensis, and that the C. albicans SAP2 promoter can be used for controlled gene expression in C. dubliniensis. These genetic tools will allow the dissection of the differences in virulence characteristics between the two pathogenic yeast species at the molecular level.

Aspartic Acid Endopeptidases↗

Assessing linkage disequilibrium in a complex genetic system. I. Overall deviation from random association.

Linkage disequilibrium is an important tool both at the end stages of positional cloning studies to map genes of particular interest and in reconstruction of population histories. With advances in molecular biology, complex genetic systems involving multiple highly polymorphic markers are becoming more commonly used to study linkage disequilibrium. These systems contain much more genetic information than simple two marker systems. In this article, we introduce a measure to summarize the overall deviation from random association and propose a permutation-based estimate for this measure. The performance of the proposed estimation procedure is studied through simulations. The methods proposed in this paper are then applied to population data at the dopamine D2 receptor locus (DRD2) and at the homeobox B (HOXB) gene cluster.

Alleles↗

The relation of birth rank and parental age to the phenotype distributions of 14 genetic systems in an Australian population sample.

The mean birth ranks and parental ages at birth of persons of known phenotype were determined for a sample of 421 Australian residents characterized with respect to 14 genetic systems. Sex was found to influence birth rank but no variation with parity among 38 sets of phenotypes or factors was found. Differences were observed among the maternal ages of subjects possessing MM, MN and NN phenotypes and M+ and M- factors. Persons of type PGM1 1, 2-1 and 2 possessed significantly different paternal ages; this was associated with a positive linear regression of paternal age on the PGM1-1 gene dosage. The relevance of this type of study to investigations of disorders occurring at advanced parental age is pointed out.

ABO Blood-Group System↗

Couplings of character and of chirality in the origin of the genetic system.

Data from the literature and new data presented here suggest that the genetic system (coding and protein synthesis) is based on relationships of character and structure between amino acids and nucleic acids. Character relationships seem to be anticodonic and structurally the greatest preferences are seen between the heteropair, L-amino acids and D-ribose nucleic acids. However, living systems using the other heteropair must have been equally likely. Homopairing (L-L and D-D) in living systems seems unlikely. Awareness of the heterocoupling of steric forms narrows somewhat the problem of understanding the origin of chirality.

Adenosine↗

[The genetic systems of the type and rate of development in soft wheat].

25 years studying of particular genetics of wheat growth habit and rate development in Plant Breeding and Genetics Institute of UAAS was summed up. The main genetic systems involved in control of flowering response differences and possibility of application in breeding of genetic diversity of Vrn, Ppd genes, ear-lines per se and duration vernalization requirement were pointed out.

Alleles↗

A genetic system to study the in vivo role of transcriptional regulators in Escherichia coli.

A genetic system for studying in vivo the interactions between a transcriptional regulatory protein and its target DNA has been developed for Escherichia coli. It is composed of two compatible plasmids: one high-copy-number promoter-probe vector, and one low-copy-number vector in which the gene encoding the desired protein is cloned under the control of an inducible promoter. The system was successfully tested for its specificity and for dosage analysis by using a combination of the plasmid pLS1-encoded RepA repressor and its target DNA.

Bacterial Proteins↗

Evaluation of Thimet 10-G for mutagenicity by 4 different genetic systems.

The insecticide Thimet 10-G was tested for mutagenic activity by 4 different genetic systems. It was unable to induce gene mutation in Salmonella, transfection inhibition in Mycobacterium, micronuclei formation in mice, and sister-chromatid exchange (SCE) in human lymphocytes were evaluated. It caused in mice an increase in the ratio of normochromatic to polychromatic erythrocytes and in human lymphocytes a decrease in mitotic index and delay in cell cycle. The results indicate that the insecticide is not mutagenic in the 4 test systems used at present.

Animals↗

A model genetic system for testing the in vivo function of peptide toxins.

We have developed a model genetic system for analyzing the function of peptide toxins from animal venoms. We engineered and propagated strains of Drosophila melanogaster expressing heat-inducible transgenes encoding either kappa-ACTX-Hv1c or omega-ACTX-Hv1a, two insect-specific neurotoxic peptides found in the venom of the Australian funnel-web spider Hadronyche versuta. Heat induction of transgene expression for 20 min was sufficient to kill all transgenic flies, indicating that the ion channels targeted by these toxins are viable insecticide targets. The unusual phenotype of flies induced to express omega-ACTX-Hv1a recapitulates that of a hypomorphic allele of the high-voltage-activated calcium channel Dmca1D, suggesting that this is likely to be the target of omega-ACTX-Hv1a.

Amino Acid Sequence↗

Construction of Reverse Genetics System for Feline Calicivirus FCV-BJ616 and Proteomic Analysis.

Feline calicivirus (FCV) is a primary cause of upper respiratory tract infections and oral ulcerative disease in cats and exhibits substantial genetic diversity that complicates prevention and control. In this study, we isolated the FCV-BJ616 strain, established a reverse-genetics system, and investigated its pathogenic mechanisms, thereby providing a foundation for antibody-based therapies and broad-spectrum vaccine development. The virus was purified by three rounds of plaque cloning, and its morphology was examined by electron microscopy. VP1 expression was confirmed by immunofluorescence and Western blotting. Using integrated systems-biology and reverse-genetics approaches, an infectious clone of rFCV-BJ616 was successfully assembled and rescued, exhibiting genetic stability comparable to that of the parental strain. In vivo infection experiments showed that rFCV-BJ616 retained wild-type virulence, causing persistent high fever, weight loss, and multiorgan pathology in infected cats. Proteomic analysis indicated that infection with FCV-BJ616 or rFCV-BJ616 markedly activated cytokine-mediated inflammatory signaling pathways. Both FCV-BJ616 and rFCV-BJ616 significantly upregulated the expression of IL-8, S100A8/A9, and TLR3, which are associated with acute inflammation and tissue damage. Furthermore, elevated IFN-β levels concomitant with STAT1 downregulation suggested a transient attenuation of antiviral signaling during early immune activation. These findings were corroborated by ELISA-based validation of serum cytokine profiles. Collectively, this study provides new insights into the molecular pathogenesis and evolution of FCV-BJ616 and establishes a robust reverse-genetics platform for precise genome manipulation and future vaccine development.

Animals↗

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↗

Distribution of gene frequencies and discrimination probabilities for 22 human blood genetic systems in four racial groups.

Gene frequencies were computed in four racial categories from 5956 blood donors from California, Hawaii, Mexico City, and Texas. Calculations were based on the phenotypic distribution of 22 blood genetic systems including 7 blood groups and 15 genetically controlled polymorphic proteins and enzymes. Matching probabilities for 20 systems were approximately 1 in 100 000 Asians, 1 in 200 000 blacks, 1 in 330 000 Mexicans, and 1 in 1 000 000 whites. The complementary discrimination probability, which measures the likelihood that two random individuals do not match, was, for practical purposes, unity. The combined new technology for blood grouping and electrophoresis using cellulose acetate membranes provides a powerful individualizing and discriminating tool for forensic science investigation.

Alanine Transaminase↗