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Computer Software of Eukaryotic Promoter Analysis

Since the initiation of the Human Genome Project (1–3), project originators have envisioned a need for the development of computer software programs to analyze and annotate the massive amount of sequence data expected to be produced as a result of sequencing efforts (4). Efforts directed tow ...

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Aggregation Chimeras: Combining ES Cells, Diploid and Tetraploid Embryos

In recent years, chimeras have been providing a powerful way to study mouse development (1) in combination with invention and improvement of other techniques and materials, including embryonic stem (ES) cells (2) and tetraploid embryos (3,4). ES cells are pluripotent cell lines derived from ...

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How to Study Pathologic Phenotypes of Knockout Mice

It has become increasingly clear that when one knocks out a gene it is almost always impossible to predict the resultant phenotype. One must be prepared to look at every organ at every stage of development, from earliest embryonic life to old age. With any luck the knockout (KO) mice will have an obvious phen ...

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Analysis of Hematopoietic Phenotypes in Knockout Mouse Models

The hematopoietic and vascular system of the developing embryo share a common mesodermal precursor, the hemangioblast (1–3). The primitive hematopoietic system arises in the extraembryonic blood islands of the yolk sac and the aorta-gonad-mesonephros (AGM) region of the embryo. Mul ...

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Isolation of Embryonic Fibroblasts and Their Use in the In Vitro Characterization of Gene Function

The use of primary-embryo-derived fibroblasts and established cell lines derived from them has played an important role in the characterization of gene function in knockout and overexpression transgenic mice. This is for several reasons. First, these have been widely used for a variety of ...

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Influence of Genetic Background on Knockout Mouse Phenotypes

Once a knockout allele generated by gene targeting has been introduced into the germline of a mouse, the primary concern is to efficiently screen the animal for mutant phenotypes. This is not necessarily a trivial exercise given the high frequency of unexpected or lack of phenotypes. With the num ...

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Generation of Double-Knockout Embryonic Stem Cells

The inactivation of selected genes in the prokaryotic and eukaryotic genome is a powerful tool in studying their function both at the level of individual cells and in the context of a complete organism. The method of gene inactivation relies on the ability of virtually every cell type to exchange DNA ...

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Lineage Allocation During Early Embryogenesis: Mapping of the Neural Primordia and Application to the Analysis of Mouse Mutants

Fate-mapping and lineage-tracing studies that were performed on mouse embryos maintained in culture have provided a unique insight into the morphogenetic processes that take place during gastrulation and early organogenesis. These experiments allow the analysis of the develo ...

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Embryonic Stem Cells in the Study of Hematopoiesis

The hematopoietic system is a complex mix of stem cells, committed progenitors, and mature effector cells of at least nine different lineages. Although these cells perform very different functions, they arise from a common ancestor, the hematopoietic stem cell (HSC) (1–8). HSCs may be defined ...

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In Vitro Differentiation of Embryonic Stem Cells and Analysis of Cellular Phenotypes

Embryonic stem (ES) cells, the totipotent cells of early embryos established as permanent lines (1,2) retain their developmental capacity in vivo (3) as well as in vitro (see 4–6). The totipotent properties of ES cells are the basis of the gene-targeting technology to create mutant mice strains wi ...

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Interferon-Inducible ES Cell Expression Systems

The ability to culture homogeneous populations of pluripotent embryonic stem (ES) cells in the presence of leukemia inhibitory factor (LIF) or IL-6 (interleukin) family cytokines provides an experimentally tractable system for the investigation of gene function in pluripotent c ...

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Overview: Gene Knockouts

The ability to generate a mouse with a targeted mutation in a desired gene has been one of the most important advances in understanding the function of gene products. Not only can gene disruption demonstrate the function of genes, but by disrupting cell development or survival it can also demonstra ...

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Transgenic Studies in the Mouse: Improving the Technology Towards a Conditional Temporal and Spatial Approach

The biological consequences of altered gene expression as a result of gain of function mutations or gene dosage remains an important question in molecular biology and molecular medicine. This is of particular interest in medical research due to the many clinically relevant diseases that ...

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Parametric Linkage Analysis

“Linkage” describes the situation in which two syntenic loci are inherited together. More specifically, two loci are said to be linked if they are close enough to each other on a chromosome that recombination during meiosis is uncommon enough for their cosegregation to be detectable within fa ...

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Association Studies

A classical case-control study design is frequently used in genetic epidemiology to investigate the association between genotype and the presence or absence of disease. Association studies can also be useful in the investigation of quantitative traits. The aim of such studies is to test f ...

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Nonparametric Linkage Analysis: I. Haseman-Elston

The original nonparametric (or model-free) method of linkage analysis that was described by Haseman and Elston in 1972 (1) was designed for analysis of quantitative traits using the sib-pair study design. In the following subheading, a brief introduction to linear regression precedes a de ...

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Nonparametric Linkage Analysis: II. Variance Components

R. A. Fisher combined Galtonian biometrics with Mendelian inheritance to establish what is known today as biometrical genetics. In his article “The Correlation Between Relatives on the Supposition of Mendelian Inheritance” (1), Fisher demonstrated that the normal distribution ob ...

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Linkage and Association: The Transmission/Disequilibrium Test for QTLs

Usually, the probability of observing a particular allele at one locus is independent of the alleles observed at another locus. However, this is not the case when two alleles are ‘associated.’ For instance, let the frequency of allele 1 at locus 1 by p 1 and the frequency of allele 2 at locus 2 be p 2 . If the two alleles are n ...

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Joint Linkage and Segregation Analysis Using Markov Chain Monte Carlo Methods

Complex genetic traits are some of the most challenging in human studies. Such traits, which are characterized by genetic and etiologic heterogeneity, typically show evidence of familial influences, but do not follow simple Mendelian patterns of inheritance. Of interest in this chapt ...

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Approaches to the Analysis of QTL Data in Mice, Using the Nonobese Diabetic Mouse as an Example

One route to the identification of genes involved in human complex disease is to exploit an animal model such as the rodent model of human type 1 diabetes, the nonobese diabetic (NOD) mouse. Although the genes predisposing to disease in an animal model may not be identical to those in the human, the underly ...

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