Site-specific transgenesis by Cre-mediated recombination in Drosophila

Transposons such as P elements are routinely used to stably transfer exogenous DNA (transgenes) into the Drosophila genome. Transgene insertion events, however, are essentially random and are subject to 'position effects' from nearby endogenous regulatory elements. Here we describe a microinjection-based system that uses Cre-mediated recombination to insert transgenes into precise genomic 'landing sites'. The system is simple and efficient, and will permit precise comparisons between multiple transgenic constructs.     

A yeast-based recombinogenic targeting toolset for transgenic analysis of human disease genes

Transgenic mouse models are valuable resources for analyzing functions of genes involved in human diseases. Mouse models provide critical insights into biological processes, including in vivo visualization of vasculature critical to our understanding of the immune system. Generating transgenic mice requires the capture and modification of large-insert DNAs representing genes of interest. We have developed a methodology using a yeast-bacterial shuttle vector, pClasper, that enables the capture and modification of bacterial artificial chromosomes (BAC)-sized DNA inserts. Numerous improvements and technical advances in the original pClasper vector have allowed greater flexibility and utility in this system. Examples of such pClasper mediated gene modifications include: Claspette-mediated capture of large-insert genomic fragments from BACs-human polycystic kidney disease-1 (PKD1); modification of pClasperA clones by the RareGap method-PKD1 mutations; Claspette-mediated modification of pClasper clones-mouse albumin-1 gene; and, of most relevance to our interest in lymph node vasculature-Claspimer-mediated modification of pClasper clones-high endothelial venule and lymphatic vessel genes. Mice that have been generated with these methods include mice with fluorescent high endothelial venules.     

GeneCluster 2.0: an advanced toolset for bioarray analysis

SUMMARY: GeneCluster 2.0 is a software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding classification, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting and k-nearest neighbor algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater. AVAILABILITY: http://www.broad.mit.edu/cancer/software     

Cytogenetic analysis of recombination in males of Drosophila ananassae

Cytogenetic studies of recombination in males of Drosophila ananassae were carried out by examining F₁ males derived from the mating of marker females, b se; bri ru of the BS stock, with males of two wild strains, TNG and L8. The male recombination values in both sections b-se (chromosome 2) and bri-ru (chromosome 3) are high in TNG F₁ but extremely low in L8 F₁ We demonstrate the presence of chiasmata in TNG F₁ males at a frequency capable of accounting for the observed recombination values. A unique series of “iso-site aberrations” was also observed in TNG F₁ males. Because of a parallelism in the distribution pattern between the chiasmata and the isosite aberrations, we propose that recombination in males of D. ananassae is meiotic in origin and that the iso-site aberrations are related to chiasma formation.     

Insights into brain development and disease from neurogenetic analyses in Drosophila melanogaster

Groundbreaking work by Obaid Siddiqi has contributed to the powerful genetic toolkit that is now available for studying the nervous system of Drosophila. Studies carried out in this powerful neurogenetic model system during the last decade now provide insight into the molecular mechanisms that operate in neural stem cells during normal brain development and during abnormal brain tumorigenesis. These studies also provide strong support for the notion that conserved molecular genetic programs act in brain development and disease in insects and mammals including humans.     

Mutational analysis of the Drosophila DNA repair and recombination gene mei-9

Drosophila mei-9 is essential for several DNA repair and recombination pathways, including nucleotide excision repair (NER), interstrand crosslink repair, and meiotic recombination. To better understand the role of MEI-9 in these processes, we characterized 10 unique mutant alleles of mei-9. These include a P-element insertion that disrupts repair functions but not the meiotic function; three nonsense mutations, one of which has nearly wild-type levels of protein; three missense mutations, one of which disrupts the meiotic function but not repair functions; two small in-frame deletions; and one frameshift.     

Efficiency of feedback selection for recombination in Drosophila

A number of theoretical models have been developed in population genetics to explain the evolution of recombination system under natural selection for adaptive traits. Using Drosophila cage populations of large size the effect of selection for resistance to daily temperature fluctuations on the rec-system was studied in this work. It is established that selection for population adaptability to extreme conditions leads during several tens of generations to significant increase in crossing-over rate within various parts of the genome (especially in b-cn and ru-h of chromosomes 2 and 3), as well as to relaxation of exchange interference for adjacent and non-adjacent segments. The Fisher's theoretical prognosis about tightening of linkage in optimal constant conditions was experimentally confirmed for the first time.     

Selection and recombination in Drosophila melanogaster

Summary Artificial selection for wing length in Drosophila melanogaster resulted in changed crossing-over frequencies between three marker genes on the 2nd chromosome, b, cn and vg.The results suggest that artificial selection is a causal agent in producing the observed changes; moreover it is suggested that the modifications in cross-over frequency are controlled by extra-nuclear factors.Research supported by C.N.R. Consiglio Nazionale delle Ricerche Roma, Grant n. 115.2298.4791.     

A versatile vector set for animal transgenesis

Genetic manipulation of a series of diverged arthropods is a highly desirable goal for a better understanding of developmental and evolutionary processes. A major obstacle so far has been the difficulty in obtaining marker genes that allow easy and reliable identification of transgenic animals. Here, we present a versatile vector set for germline transformation based on the promiscuous transposons mariner, Hermes and piggyBac. Into these vectors, we introduced a potentially universal marker system that is comprised of an artificial promoter containing three Pax-6 homodimer binding sites. This promoter drives strong expression of spectral variants of the enhanced green fluorescent protein (EGFP) in larval, pupal, and adult photoreceptors. Using special filter sets, the yellow (EYFP) and cyan (ECFP) variant are fully distinguishable and therefore represent a separable pair of markers. Furthermore, we adapted a simple plasmid-based transposition assay system to enable quick functional tests of our vectors in different arthropod species before employing them in more laborious germline transformation experiments. Using this system we demonstrate that our vectors transpose in both Drosophila melanogaster and Drosophila virilis. Received: 11 July 2000 / Accepted: 27 July 2000     

A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis

The first step in the generation of genetically tagged human embryonic stem cell (HESC) reporter lines is the isolation of cells that contain a stably integrated copy of the reporter vector. These cells are identified by their continued growth in the presence of a specific selective agent, usually conferred by a cassette encoding antibiotic resistance. In order to mitigate potential interference between the regulatory elements driving expression of the antibiotic resistance gene and those controlling the reporter gene, it is advisable to remove the positive selection cassette once the desired clones have been identified. This report describes a protocol for the removal of loxP-flanked selection cassettes from genetically modified HESCs by transient transfection with a vector expressing Cre recombinase. An integrated procedure for the clonal isolation of these genetically modified lines using single-cell deposition flow cytometry is also detailed. When performed sequentially, these protocols take approximately 1 month.     

A site specific increase in recombination in Drosophila ananassae

The e65 pi; bri ru stock of Drosophila ananassae produced an extremely high rate of recombination in males when made heterozygous with any one of the wild type stocks. We analyzed and characterized the genetic factors which caused this phenomenon. We show that the second chromosome of the e65 pi; bri ru stock carries an enhancer of male recombination. The enhancer, En(2)-ep, is located between Om(2C) and Arc. The enhancement of meiotic recombination both in males and females was also observed at the specific region between Om(2C) and Arc on 2L. The magnitude of increased recombination was 30-40 fold in males and 13-30 fold in females. The relation between the hotspot of recombination in both sexes and the enhancer of male recombination is discussed.     

Optomotor-blind of Drosophila melanogaster: a neurogenetic approach to optic lobe development and optomotor behaviour

The gene optomotor-blind (omb) plays a crucial role in Drosophila optic lobe development. Various mutations in omb lead to different structural defects in the adult optic lobes with correlated behavioural phenotypes. Molecular analysis of omb allows one to trace back behavioural defects to the spatio-temporal misexpression of the gene in mutant development.     

A general modular framework for gene set enrichment analysis

Background  

Analysis of microarray and other high-throughput data on the basis of gene sets, rather than individual genes, is becoming more important in genomic studies. Correspondingly, a large number of statistical approaches for detecting gene set enrichment have been proposed, but both the interrelations and the relative performance of the various methods are still very much unclear.     

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

High-throughput technologies are now used to generate more than one type of data from the same biological samples. To properly integrate such data, we propose using co-modules, which describe coherent patterns across paired data sets, and conceive several modular methods for their identification. We first test these methods using in silico data, demonstrating that the integrative scheme of our Ping-Pong Algorithm uncovers drug-gene associations more accurately when considering noisy or complex data. Second, we provide an extensive comparative study using the gene-expression and drug-response data from the NCI-60 cell lines. Using information from the DrugBank and the Connectivity Map databases we show that the Ping-Pong Algorithm predicts drug-gene associations significantly better than other methods. Co-modules provide insights into possible mechanisms of action for a wide range of drugs and suggest new targets for therapy.     

Genetic recombination and steroid metabolism in Drosophila]

A double-species ecologo-genetical model, including Drosophila and yeast, has been used as a new methodological instrument for investigation of the physiological mechanism of recombination. Incubation of Drosophila females in the medium containing yeast of the strain mutant for ergosterol synthesis leads to suppression of temperature-induced crossing over. The mass-spectrum analysis of steroid fraction from Drosophila females has shown that incubation of the yeast medium without ergosterol results in arrest of ecdysterone synthesis. These data are explained by the absence of ecdysterone synthesis precursor in the fly organism. The endocrinal control of crossing over is discussed in the light of hormonal regulation of meiosis.