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At least 955 records · Page 53Linked to original sources
PubMed2005

Drosophila, the golden bug, emerges as a tool for human genetics.

Drosophila melanogaster is emerging as one of the most effective tools for analyzing the function of human disease genes, including those responsible for developmental and neurological disorders, cancer, cardiovascular disease, metabolic and storage diseases, and genes required for the function of the visual, auditory and immune systems. Flies have several experimental advantages, including their rapid life cycle and the large numbers of individuals that can be generated, which make them ideal for sophisticated genetic screens, and in future should aid the analysis of complex multigenic disorders. The general principles by which D. melanogaster can be used to understand human disease, together with several specific examples, are considered in this review.

Animals↗
PubMed2006

Calculating petal tools by using genetic algorithms.

To pass from a spherical surface to a conic one, it is possible to use a petal tool or a small solid tool that is placed at different time intervals at several radial zones of the glass. Genetic algorithms are applied to calculate the angular sizes of the incomplete annular tools that make up the petal tools. We also present the desired wear results carried out with the petal tool that was designed on the basis of the dwell times of complete annular tools. These dwell times are calculated by using base functions that are generated with annular tools and by applying the genetic algorithms.

Journal Article↗
PubMed2004

A flexible data analysis tool for chemical genetic screens.

High-throughput assays generate immense quantities of data that require sophisticated data analysis tools. We have created a freely available software tool, SLIMS (Small Laboratory Information Management System), for chemical genetics which facilitates the collection and analysis of large-scale chemical screening data. Compound structures, physical locations, and raw data can be loaded into SLIMS. Raw data from high-throughput assays are normalized using flexible analysis protocols, and systematic spatial errors are automatically identified and corrected. Various computational analyses are performed on tested compounds, and dilution-series data are processed using standard or user-defined algorithms. Finally, published literature associated with active compounds is automatically retrieved from Medline and processed to yield potential mechanisms of actions. SLIMS provides a framework for analyzing high-throughput assay data both as a laboratory information management system and as a platform for experimental analysis.

Cyclic AMP Response Element-Binding Protein↗
PubMed2000

Development of endothelial cell lines from embryonic stem cells: A tool for studying genetically manipulated endothelial cells in vitro.

Totipotent embryonic stem cells can be induced to differentiate to endothelium in vitro. This may be a useful tool for obtaining cultures of genetically manipulated endothelial cells because embryonic stem cells are relatively easy to transfect and are commonly used for gene inactivation experiments in mice. However, embryonic stem cell-derived endothelial cells could not be easily separated from embryoid bodies and maintained in culture. In this study, we describe the isolation and characterization of immortalized endothelial cell lines obtained from embryonic stem cells differentiated in vitro. The cell lines were analyzed for expression of endothelial cell markers, including growth factor receptors and adhesion molecules, and compared with endothelial cells obtained from the yolk sac, the embryo proper, or the heart microcirculation of the adult. We propose that this approach may be useful for obtaining endothelial cells carrying gene mutations that are lethal at very early stages of development.

Animals↗
PubMed2000

Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: a tool for gene mapping and gene discovery.

A novel population consisted of a set of 99 near isogenic lines (NILs) and backcross recombinant inbred lines (BCRILs) derived from a cross between the cultivated tomato Lycopersicon esculentum cv. E6206 and L. hirsutum accession LA1777 is presented. Most of the lines contain a single defined introgression from L. hirsutum in the L. esculentum genetic background and together, the lines provide a coverage of more than the 85% of the L. hirsutum genome. These lines represent a new tool to uncover the genetic resources hidden in L. hirsutum as well as to study the genes responsible of its unique biology. Furthermore, the study of the allelic frequency and heterozygosity among BCRILs showed that specific genomic regions were likely subjected to unintentional selection pressures during the stock development. Genes involved in the reproductive behavior and (or) pollen viability are hypothesized to be responsible for these alterations.

Breeding↗
PubMed1990

[Antisense oligonucleotides: tools of molecular genetics and therapeutic agents].

The binding of an oligodeoxynucleotide, so-called anti-sense, to the complementary sequence of a messenger RNA can prevent the synthesis of the encoded protein. This approach constitutes a very efficient and specific means to artificially regulate gene expression. Numerous chemical modifications have been introduced into synthetic oligos in order to provide them with properties that unmodified molecules do not display. For instance, oligos built up with methylphosphonate, phosphorothioate and alpha-anomer units lead to molecules that are resistant to DNases. Acridine-linked oligos exhibit an increased affinity for the target sequence due to the intercalation of the dye into the oligo/RNA duplex. Two different mechanisms account for translation inhibition by antisense oligos. Inhibition of the elongation step results only from the induced cleavage of the target RNA by RNase-H. In contrast, oligos targeted upstream of the AUG initiation codon can block the initiation step through an RNase-H independent mechanism. As a consequence, methylphosphonate- and alpha-oligos, which do not elicit RNase-H activity, targeted to the 5' region, are efficient antisense; but they are inactive if targeted to the coding sequence. Experiments performed with antisense oligos in cell-free extracts supported the notion that the mini-exon sequence, acquired by trans-splicing, was present on every message in trypanosomatids and on some of them in nematodes. Furthermore, an acridine-linked oligo complementary to the mini-exon sequence of Trypanosoma brucei induced a lethal effect on cultured procyclics. Therefore these compounds constitute promising tools in molecular genetics and could open new routes to rationally tailor therapeutic agents.

Animals↗
PubMed2002

Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative.

The NIH Xenopus Initiative is establishing many of the genetic and genomic resources that have been recommended by the Xenopus research community. These resources include cDNA libraries, expressed sequence tags, full-length cDNA sequences, genomic libraries, pilot projects to mutagenize and phenotype X. tropicalis, and sequencing the X. tropicalis genome. This review describes the status of these projects and explains how to access their data and resources. Current information about these activities is available on the NIH Xenopus Web site (http://www.nih.gov/science/models/xenopus/).

Animals↗
PubMed2006

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.

Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.

Canada↗
PubMed1995

Genetically engineered mice: tools to understand craniofacial development.

In this review, we provide a survey of the experimental approaches used to generate genetically engineered mice. Two specific examples are presented that demonstrate the applicability of these approaches to craniofacial development. In the first, a promoter analysis of the Msx2 gene is presented which illustrates the cis regulatory interactions that defined cell-specific gene expression. In the second, a mouse model of the human disease craniosynostosis, Boston type, has been created by misregulation of the Msx2 gene product. Finally. we present a formulary of spontaneously occurring and genetically engineered mice that exhibit defects in developmental processes affecting the craniofacial complex. The purpose of this review is to provide insight into the experimental approaches that are used to create genetically engineered mice and to impress upon the reader that genetically engineered mice are well-suited to address fundamental questions pertaining to the development maintenance, and regeneration of tissues and organs.

Animals↗
PubMed2003

GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives.

The GeneFizz (http://pbga.pasteur.fr/GeneFizz) web tool permits the direct comparison between two types of segmentations for DNA sequences (possibly annotated): the coding/non-coding segmentation associated with genomic annotations (simple genes or exons in split genes) and the physics-based structural segmentation between helix and coil domains (as provided by the classical helix-coil model). There appears to be a varying degree of coincidence for different genomes between the two types of segmentations, from almost perfect to non-relevant. Following these two extremes, GeneFizz can be used for two purposes: ab initio physics-based identification of new genes (as recently shown for Plasmodium falciparum) or the exploration of possible evolutionary signals revealed by the discrepancies observed between the two types of information.

Algorithms↗
PubMed2003

Genetic and genomic tools for zebrafish research: the NIH zebrafish initiative.

The National Institutes of Health (NIH) has been a leading advocate of the zebrafish as a model organism for the study of vertebrate development, physiology, and disease. Genomic tools, developed with the support of NIH funding, have made zebrafish even more attractive as a genetic system and have stimulated research using this model. The NIH continues to provide support for new and existing community resources, such as the Zebrafish International Resource Center and the Zebrafish Information Network, research tool development and mutant screens, and a wide array of investigator-initiated studies that are using zebrafish to elucidate many aspects of vertebrate biology.

Animals↗
PubMed2024

Development of ptxD/Phi as a new dominant selection system for genetic manipulation in Cryptococcus neoformans.

Cryptococcus neoformans is a globally distributed pathogenic fungus posing a significant threat to immunocompromised individuals, particularly those with HIV/AIDS. Effective genetic manipulation tools are essential for understanding its biology and developing new therapies. However, current genetic tools, including the variation of versatile selectable markers, are limited. This study develops and validates the phosphite dehydrogenase gene (ptxD)/phosphite (Phi) selection system as a non-antibiotic selectable marker for genetic manipulation in C. neoformans. A codon-optimized ptxD gene from Pseudomonas stutzeri was cloned under the TEF promoter. Using the transient CRISPR-Cas9 coupled with electroporation system, we integrated the ptxD gene into the C. neoformans genome and assessed the impact of ptxD integration on cell growth and virulence factors. The ptxD/Phi system effectively selected transformed cells on Phi-containing media. Growth assays showed that ptxD integration did not adversely affect cell growth or key virulence factors, including pleomorphism, capsule size, and melanin production. Additionally, we successfully disrupted the ADE2 gene using this system, confirming its applicability for gene deletion. Taken together, the ptxD/Phi system provides a robust and versatile tool for genetic manipulation in C. neoformans, facilitating further research into its biology and pathogenicity.IMPORTANCECryptococcus neoformans is a type of fungus that can cause serious illnesses in people who have weakened immune systems, like those with HIV/AIDS. To better study this fungus and find new treatments, scientists need tools to change its genes in precise ways. However, the current tools available for this are somewhat limited. This research introduces a new tool called the phosphite dehydrogenase gene/phosphite system, which does not rely on antibiotics to work. It uses a gene from a different bacterium that helps select and grow only the fungus cells that have successfully incorporated new genetic information. This is particularly useful because it does not interfere with the normal growth of the fungus or the features that make it harmful (like its ability to change shape or produce protective coatings). By making it easier and more effective to manipulate the genetics of C. neoformans, this tool opens up new possibilities for understanding how this fungus operates and for developing therapies to combat its infections. This is crucial for improving the treatment of infections in vulnerable populations.

Cryptococcus neoformans↗
PubMedDate not supplied

Synthetic oligodeoxyribonucleotides as tools in molecular genetics: the characterization of the CYC1 (iso-1-cytochrome c encoding) locus of Saccharomyces cerevisiae.

The use of synthetic oligodeoxyribonucleotides as tools for the isolation, characterization and mutagenesis of eukaryote genes has played a major role in the molecular definition of the CYC1 locus of Saccharomyces cerevisiae, which is the structural gene for the apoprotein of iso-1-cytochrome c. Thus, the possibility of using a synthetic oligodeoxyribonucleotide as a probe to identify and monitor the isolation of a specific gene was first established by model studies which defined the melting temperatures (TmS) for duplexes of oligonucleotides of different lengths and base compositions. This led to the isolation of the CYC1 locus using a synthetic 13 nucleotide probe. A more convenient strategy for determination of DNA sequences by the Sanger method was provided by using synthetic oligodeoxyribonucleotides as primers with denatured double-strand plasmid DNA as template. By this means, the sequence of the CYC1 locus was determined by "walking" along the gene without isolating restriction fragments of the DNA or separating DNA strands. Synthetic oligodeoxyribonucleotides, used as primers for reverse transcriptase with mRNA as template, were also used to precisely define the 5'- and 3'-ends of the iso-1-cytochrome c mRNA. Yet another application of synthetic oligodeoxyribonucleotides is their use as specific mutagens after in vitro incorporation into double-stranded DNA. In the case of iso-1-cytochrome c, this mutagenic strategy is being used to define the role of conserved amino-acids in cytochrome function.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosome Mapping↗
PubMed2025

HCSeeker: A classification tool for human genetic variant hot and cold spots designed for PM1 and benign criteria in the ACMG-AMP guideline.

PURPOSE: The PM1 criterion, which states that a variant is located in a mutational hot spot and/or critical and well-established functional domain without benign variation (such as the active site of an enzyme), is considered moderate evidence for assessing its pathogenicity. Although guidelines from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology are widely adopted, the PM1 criterion remains limited from lacking a reliable database of variant hot spots. Compared with hot spots, cold spots are neglected by the guidelines. To improve variant classification, we suggest including cold spots for supporting benign classifications. Consequently, we have developed the HCSeeker to provide data support for PM1 and the "Benign" criteria. METHODS: HCSeeker uses the Kernel Density Estimation and the Expectation-Maximization algorithm to identify hot- and cold-spot regions. RESULTS: Through HCSeeker, we identified 988 hot spots and 682 cold spots across 889 genes and provided a public database (http://www.genemed.tech/hcseeker/) for researchers and clinicians to query variant locations, facilitating the application of American College of Medical Genetics and Genomics and the Association for Molecular Pathology PM1 or "Benign" criteria. CONCLUSION: We developed the HCSeeker tool, which can effectively identify variant hot and cold spots within genes to enhance the interpretability of gene variants.

Humans↗