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PubMed1996

Inducible site-directed recombination in mouse embryonic stem cells.

The site-directed recombinase Cre can be employed to delete or express genes in cell lines or animals. Clearly, the ability to control remotely the activity of this enzyme would be highly desirable. To this end we have constructed expression vectors for fusion proteins consisting of the Cre recombinase and a mutated hormone-binding domain of the murine oestrogen receptor. The latter still binds the anti-oestrogen drug tamoxifen but no longer 17 beta-oestradiol. We show here that in embryonic stem cells expressing such fusion proteins, tamoxifen can efficiently induce Cre-mediated recombination, thereby activating a stably integrated LacZ reporter gene. In the presence of either 10 microM tamoxifen or 800 nM 4-hydroxy-tamoxifen, recombination of the LacZ gene is complete within 3-4 days. By placing a tamoxifen-binding domain on both ends of the Cre protein, the enzymatic activity of Cre can be even more tightly controlled. Transgenic mice expressing such an tamoxifen-inducible Cre enzyme may thus provide a new and useful genetic tool to mutate or delete genes at specific times during development or in adult animals.

Animals↗

PubMed2003

New antibiotic resistance cassettes suitable for genetic studies in Borrelia burgdorferi.

In this report we describe two distinct approaches to develop new antibiotic resistance cassettes that allow for efficient selection of Borrelia burgdorferi transformants. The first approach utilizes fusions of borrelial flagellar promoters to antibiotic resistance markers from other bacteria. The AACC1 gene, which encodes a gentamicin acetyltransferase, conferred a high level of gentamicin resistance in B. Burfdorferi when expressed from these promoters. No cross-resistance occurred between this cassette and the kanamycin resistance cassette, which was previously developed in an analogous fashion. A second and different approach was taken to develop an efficient selectable marker that confers resistance to the antibiotic coumermycin A1. A synthetic gene was designed from the GYRB301 allele of the coumermycin-resistant B. Burgdorferi strain B31-NGR by altering the coding sequence at the wobble position. The resulting gene, GYRB(SYN), encodes a protein identical to the product of GYRB301, but the genes share only 66% nucleotide identity. The nucleotide sequence of GYRB(SYN)is sufficiently divergent from the endogenous B. Burgdorferi GYRB gene to prevent recombination between them. The cassettes described in this paper improve our repertoire of genetic tools in B. Burgdorferi. These studies also provide insight into parameters governing recombination and gene expression in B. Burgdorferi.

Amino Acid Sequence↗

PubMed2004

A resource for large-scale RNA-interference-based screens in mammals.

Gene silencing by RNA interference (RNAi) in mammalian cells using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) has become a valuable genetic tool. Here, we report the construction and application of a shRNA expression library targeting 9,610 human and 5,563 mouse genes. This library is presently composed of about 28,000 sequence-verified shRNA expression cassettes contained within multi-functional vectors, which permit shRNA cassettes to be packaged in retroviruses, tracked in mixed cell populations by means of DNA 'bar codes', and shuttled to customized vectors by bacterial mating. In order to validate the library, we used a genetic screen designed to report defects in human proteasome function. Our results suggest that our large-scale RNAi library can be used in specific, genetic applications in mammals, and will become a valuable resource for gene analysis and discovery.

Animals↗

PubMed2004

In vitro shuttle mutagenesis using engineered mariner transposons.

Advances in our understanding of the protozoan parasite Leishmania have been facilitated by the development of molecular and genetic tools. One powerful approach for gene identification and analysis is transposon mutagenesis. This can be performed directly in vivo, but often it is more convenient to generate transpositions in vitro for subsequent analysis in vivo, in a process termed "shuttle mutagenesis." The Drosophila element mariner is well suited for application by either route. Minimal mariner elements containing cis-acting elements required for transposition have been generated, which can be further modified to suit the needs of the experimenter. Additional genetic markers and/or reporters can be introduced, which are useful for procedures such as insertional mutagenesis, shotgun sequencing, or the generation of protein and transcriptional fusions for subsequent analysis. Active transposase can readily be generated following expression in Escherichia coli, and efficiencies of 10-3/target can be obtained, allow-ing the generation of large transposon insertion libraries suitable for subsequent screening in vivo. This chapter explains the steps necessary to purify active Mos1 transposase and conduct an in vitro transposition reaction. We also discuss some of the considerations relevant to the design and application of functional mariner elements (donor plasmids) relevant to studies in Leishmania and other organisms.

Base Sequence↗

PubMed2005

Chicken genome: new tools and concepts.

Last spring, the Second International Chicken Genome Workshop was held at the Stowers Institute for Medical Research, less than 2 months after the first draft of the chicken genome was publicly released in March, 2004. This major event was highly anticipated by the chicken community, because of the invaluable resources that would be newly provided. In addition, from an evolutionary standpoint, birds are the species most closely related to mammals, whose genome has been sequenced. The meeting gathered both agricultural and academic chicken communities and provided the opportunity to discuss the status of the chicken genome sequencing, the preliminary analysis of the chicken genome sequences freshly available, and the impact on avian genetic tools.

Animals↗

PubMed2006

Modular neuropile organization in the Drosophila larval brain facilitates identification and mapping of central neurons.

Elucidating how neuronal networks process information requires identification of critical individual neurons and their connectivity patterns. For this purpose, we used the third-instar Drosophila larval brain and applied reverse-genetic tools, immunolabeling procedures, and 3D digital reconstruction software. Consistent topological definition of neuropile compartments in the larval brain can be obtained through simple fluorescence-immunolabeling methods. The modular neuropiles can be used as a fiducial framework for mapping the projection patterns of individual neurons labeled with green fluorescent protein (GFP). GFP-labeled neurons often exhibit dendrite-like arbors as well as clustered varicose terminals on neurite branches that innervate identifiable neuropile compartments. We identified candidate cholinergic interneurons in genetic mosaic brains that overlap with the larval optic nerve terminus. By using the neuropile framework, we demonstrate that the candidate visual interneurons are not a subset of the previously identified circadian pacemaker neurons that also contact the larval optic nerve terminus; they may represent parallel pathways in the processing of visual inputs. Thus, in the Drosophila larval brain, modular neuropiles can be used as a framework for systematically identifying, mapping, and classifying interneurons; understanding their roles in behavior can then be pursued further.

Animals↗

PubMed2003

Mice, microbes and models of infection.

We urgently need animal models to study infectious disease. Mice are susceptible to a similar range of microbial infections as humans. Marked differences between inbred strains of mice in their response to pathogen infection can be exploited to analyse the genetic basis of infections. In addition, the genetic tools that are available in the laboratory mouse, and new techniques to monitor the expression of bacterial genes in vivo, make it the principal experimental animal model for studying mechanisms of infection and immunity.

Animals↗

PubMed2004

Aberrant cardiolipin metabolism in the yeast taz1 mutant: a model for Barth syndrome.

In eukaryotic cells, the acyl species of the phospholipid cardiolipin (CL) are more highly unsaturated than those of the other membrane phospholipids. Defective acylation of CL with unsaturated fatty acids and decreased total CL are associated with Barth syndrome, an X-linked cardio- and skeletal myopathy attributed to a defect in the gene G4.5 (also known as tafazzin). We constructed a yeast mutant (taz1) containing a null mutation in the homologue of the human G4.5 gene. The yeast taz1Delta mutant was temperature sensitive for growth in ethanol as sole carbon source, but grew normally on glucose or glycerol plus ethanol. Total CL content was reduced in the taz1Delta mutant, and monolyso-CL accumulated. The predominant CL acyl species found in wild-type cells, C18:1 and C16:1, were markedly reduced in the mutant, whereas CL molecules containing saturated fatty acids were present. Interestingly, CL synthesis increased in the mutant, whereas expression of the CL structural genes CRD1 and PGS1 did not, suggesting that de novo biosynthetic enzyme activities are regulated by CL acylation. These results indicate that the taz1Delta mutant is an excellent genetic tool for the study of CL remodelling and may serve as a model system for the study of Barth syndrome.

Acyltransferases↗

PubMed2000

Interdigitated deletion complexes on mouse chromosome 5 induced by irradiation of embryonic stem cells.

Chromosome deletions have several applications in the genetic analysis of complex organisms. They can be used as reagents in region-directed mutagenesis, for mapping of simple or complex traits, or to identify biological consequences of segmental haploidy, the latter being relevant to human contiguous gene syndromes and imprinting. We have generated three deletion complexes in ES (Embryonic Stem) cells that collectively span approximately 40 cM of proximal mouse chromosome 5. The deletion complexes were produced by irradiation of F(1) hybrid ES cells containing herpes simplex virus thymidine kinase genes (tk) integrated at the Dpp6, Hdh (Huntington disease locus), or Gabrb1 loci, followed by selection for tk-deficient clones. Deletions centered at the adjacent Hdh and Dpp6 loci ranged up to approximately 20 cM or more in length and overlapped in an interdigitated fashion. However, the interval between Hdh and Gabrb1 appeared to contain a locus haploinsufficient for ES cell viability, thereby preventing deletions of either complex from overlapping. In some cases, the deletions resolved the order of markers that were previously genetically inseparable. A subset of the ES cell-bearing deletions was injected into blastocysts to generate germline chimeras and establish lines of mice segregating the deletion chromosomes. At least 11 of the 26 lines injected were capable of producing germline chimeras. In general, those that failed to undergo germline transmission bore deletions larger than the germline-competent clones, suggesting that certain regions of chromosome 5 contain haploinsufficient developmental genes, and/or that overall embryonic viability is cumulatively decreased as more genes are rendered hemizygous. Mice bearing deletions presumably spanning the semidominant hammertoe locus (Hm) had no phenotype, suggesting that the classic allele is a dominant, gain-of-function mutation. Overlapping deletion complexes generated in the fashion described in this report will be useful as multipurpose genetic tools and in systematic functional mapping of the mouse genome.

Animals↗

PubMed2006

pTcINDEX: a stable tetracycline-regulated expression vector for Trypanosoma cruzi.

BACKGROUND: Trypanosoma cruzi is a protozoan pathogen of major medical importance in Latin America. It is also an early diverging eukaryote that displays many unusual biochemical features. The completion of the T. cruzi genome project has highlighted the need to extend the range of techniques available to study gene function. To this end we report the development of a stable tetracycline-dependent expression vector applicable to this parasite and describe in detail the parameters of the system. RESULTS: We first produced T. cruzi cell lines that constitutively expressed bacteriophage T7 RNA polymerase and the tetracycline repressor protein from a multicopy episome. An integrative vector with an inducible expression site under the control of a tetracycline-regulatable T7 promoter (pTcINDEX) was targeted to the transcriptionally silent ribosomal RNA spacer region of these parasites and transformants selected using a T7 RNA polymerase-dependent hygromycin resistance gene. To test the system we used two marker proteins, luciferase and red fluorescent protein (RFP), and an endogenous parasite protein (a mitochondrial superoxide dismutase). In each case we found that induction was both time and dose-dependent. Luciferase mRNA could be induced by at least 100-fold, and luciferase activity up to 60-fold, within 24 hours of the addition of tetracycline. When we examined RFP induction by confocal microscopy and fluorescence activated cell sorter, we observed very high levels of expression (>1000-fold increase in fluorescence intensity), although this was not synchronous throughout clonal populations. Induction of superoxide dismutase resulted in an 18-fold increase in cellular activity. The observation that a tagged version of the enzyme was correctly targeted to the mitochondrion demonstrates that our expression system may also provide a high-throughput strategy for subcellular localisation. CONCLUSION: Our results show that pTcINDEX represents a valuable addition to the genetic tools available for T. cruzi. The vector system is sufficiently flexible that it should have widespread uses including inducible expression of tagged proteins, generation of conditional knockout cell lines and the application of dominant-negative approaches.

Animals↗

PubMed2006

Nourseothricin acetyltransferease: a positive selectable marker for Toxoplasma gondii.

Molecular analysis of parasite genomes will require new molecular genetic tools. The nat1 gene of Streptomyces noursei encodes nourseothricin acetyltransferase, conferring resistance to the aminoglycoside antibiotic nourseothricin. Electroporation of nat1 cassettes into RH or Prugniaud strains of Toxoplasma gondii allows for selection of stable nourseothricin-resistant clones.

Acetyltransferases↗

PubMed2004

The clinical relevance of new insights in iron transport and metabolism.

There have been major basic advances in the field of iron metabolism in recent years. These advances include the discoveries of the HFE-1 gene, a series of transmembrane iron transporters or cotransporters (eg, divalent metal transporter-1, duodenal cytochrome b, ferroportin-1, hephaestin, and transferrin receptor-2), and two key regulatory proteins named hepcidin and hemojuvelin. Several mutations of these various proteins have been linked to human diseases. These discoveries have led to major improvements in our understanding of iron physiology and have also profoundly modified and extended the pathologic iron field. Clinical applications have rapidly emerged with the appearance of new iron overload syndromes and the practical input of new genetic tools enabling the noninvasive diagnosis of HFE-1 hemochromatosis. These basic advances are paving the road for innovative therapeutic strategies not only in iron overload syndromes but also in the wide area of chronic disease-related anemia.

Antimicrobial Cationic Peptides↗

PubMed2000

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↗

PubMed2004

Active zone localization of presynaptic calcium channels encoded by the cacophony locus of Drosophila.

Presynaptic calcium channels play a central role in chemical synaptic transmission by providing the calcium trigger for evoked neurotransmitter release. These voltage-gated calcium channels are composed of a primary structural subunit, alpha1, as well as auxiliary beta and alpha2delta subunits. Our previous genetic, molecular, and functional analysis has shown that the cacophony (cac) gene encodes a primary presynaptic calcium channel alpha1 subunit in Drosophila. Here we report that transgenic expression of a cac-encoded alpha1 subunit fused with enhanced green fluorescent protein efficiently rescues cac lethal mutations and allows in vivo analysis of calcium channel localization at active zones. The results reported here further characterize the primary role of cac-encoded calcium channels in neurotransmitter release. In addition, these studies provide a unique genetic tool for live imaging of functional presynaptic calcium channels in vivo and define a molecular marker for immunolocalization of other presynaptic proteins relative to active zones. These findings are expected to facilitate additional analysis of synaptic development and function in this important model system.

Animals↗

PubMed2006

Genetics as a tool to improve cancer outcomes: ethics and policy.

Genetic research is rapidly increasing the opportunities for the detection of inherited cancer risk. Clinicians and policy makers must ensure the adequate evaluation of the benefits and harms of this new area of practice, address the challenges of family-based detection of individuals at risk and develop practice guidelines and educational strategies that are responsive to rapidly changing knowledge. When the benefits of testing are well established, efforts must also be made to ensure access to genetic services for all who can benefit.

Bioethics↗

PubMed1995

The urease locus of Mycobacterium tuberculosis and its utilization for the demonstration of allelic exchange in Mycobacterium bovis bacillus Calmette-Guérin.

The ureABC genes of Mycobacterium tuberculosis were cloned. By using a set of degenerate primers corresponding to a conserved region of the urease enzyme (EC 3.5.1.5), a fragment of the expected size was amplified by PCR and was used to screen a M. tuberculosis cosmid library. Three open reading frames with extensive similarity to the urease genes from other organisms were found. The locus was mapped on the chromosome, using an ordered M. tuberculosis cosmid library. A suicide vector containing a ureC gene disrupted by a kanamycin marker (aph) was used to construct a urease-negative Mycobacterium bovis bacillus Calmette-Guérin mutant by allelic exchange involving replacement of the ureC gene with the aph::ureC construct. To our knowledge, allelic exchange has not been reported previously in the slow-growing mycobacteria. Homologous recombination will be an invaluable genetic tool for deciphering the mechanisms of tuberculosis pathogenesis, a disease that causes 3 x 10(6) deaths a year worldwide.

Alleles↗

PubMed2004

[Thyroid cancer: prognostic factors and treatment].

Because most differentiated thyroid carcinomas have an excellent prognosis, some authors have claimed that these patients are suffering from over treatment. Grouping patient- and tumor-specific factors have been proposed for prognostic stratification, but no clinicopathologic staging was demonstrated to be useful at the present time. More recently, molecular genetic tools have been used to identify and understand how the primary tumor progresses and many molecular markers have been proposed in order to distinguish the subset of patients at risk of developing metastasis. Here we analyzed some of them, with emphasis on the expression of NIS, a determinant of prognosis since the functional integrity of the iodine transport is essential to assure an uptake of radioiodine high enough to detect and destroy any tumoral thyroid tissue. More recent observations on how some relevant molecular genetics aspects of thyroid cancer impact new potential therapeutic approaches are also discussed.

Adolescent↗

PubMed1988

B-lymphoid neoplasms: immunoglobulin genes as molecular determinants of clonality, lineage, differentiation, and translocation.

The basic rules of Ig gene recombination that were learned from examining clonal proliferations of B cells have paid enormous dividends in improving our understanding of B-cell malignancy. The DNA rearrangements of Ig genes creates a tumor-specific marker capable of establishing the clonality, cellular lineage, and stage of development of a lymphoid tumor. Most importantly, the Ig genes have proved to be the sites of interchromosomal translocations that contribute directly to the malignant phenotype. These genetic tools hold the promise of improving our classification schemes, providing sensitive and specific approaches to following the clinical course, and providing insights into pathogenesis that will prompt improved therapies.

B-Lymphocytes↗