Fate mapping the mouse embryo

The use of clonal analysis to obtain a fate map of the epiblast of the mouse embryo and to investigate cell distribution during gastrulation and early neurulation is described in a personal reminiscence. A revised fate map of the epiblast at 6.5 days gestation is provided, and the development of 3-dimensional, quantitative image analysis techniques outlined.     

Interval mapping methods for detecting QTL affecting survival and time-to-event phenotypes

Quantitative trait loci (QTL) are usually searched for using classical interval mapping methods which assume that the trait of interest follows a normal distribution. However, these methods cannot take into account features of most survival data such as a non-normal distribution and the presence of censored data. We propose two new QTL detection approaches which allow the consideration of censored data. One interval mapping method uses a Weibull model (W), which is popular in parametrical modelling of survival traits, and the other uses a Cox model (C), which avoids making any assumption on the trait distribution. Data were simulated following the structure of a published experiment. Using simulated data, we compare W, C and a classical interval mapping method using a Gaussian model on uncensored data (G) or on all data (G'=censored data analysed as though records were uncensored). An adequate mathematical transformation was used for all parametric methods (G, G' and W). When data were not censored, the four methods gave similar results. However, when some data were censored, the power of QTL detection and accuracy of QTL location and of estimation of QTL effects for G decreased considerably with censoring, particularly when censoring was at a fixed date. This decrease with censoring was observed also with G', but it was less severe. Censoring had a negligible effect on results obtained with the W and C methods.     

Parallel mapping of genotypes to phenotypes contributing to overall biological fitness

Laboratory selection is a powerful approach for engineering new traits in metabolic engineering applications. This approach is limited because determining the genetic basis of improved strains can be difficult using conventional methods. We have recently reported a new method that enables the measurement of fitness for all clones contained within comprehensive genomic libraries, thus enabling the genome-scale mapping of fitness altering genes. Here, we demonstrate a strategy for relating these measurements to the individual phenotypes selected for in a particular environment. We first provide a mathematical framework for decomposing fitness into selectable phenotypes. We then employed this framework to predict that single-batch selections would enrich primarily for library clones with increased growth rate, serial-batch would enrich for a broad collection of clones enhanced via a combination of increased growth rate and/or reduced lag times, and that overlap among selected clones would be minimal. We used the SCalar Analysis of Library Enrichments (SCALEs) method to test these predictions. We mapped all genomic regions for which increased copy number conferred a selective advantage to Escherichia coli when cultured via single- or serial-batch in the presence of 1-naphthol. We identified a surprisingly large collection (163 total) of tolerance regions, including all previously identified solvent tolerance genes in E. coli. We show that the majority of the identified regions were unique to the different selection strategies examined and that such differences were indeed due to differences among enriched clones in growth rate and lag times over the solvent concentrations examined. The combination of a framework for decomposing overall fitness into selectable phenotypes along with a genome-scale method for mapping genes to such phenotypes lays the groundwork for improving the rational design of laboratory selections.     

Fate mapping study of the endoderm of the 1.5-day-old chick embryo

Various portions of the endoderm between the levels of the first and the 10th somite of 1.5-day-old chick embryos were marked by local application of the vital dye Dil, and the fate of marked cells was analyzed after cultivation of the embryos for 2 days in vitro.The presumptive area of digestive tract ranging from the posterior pharynx to the jejunum was found to extend bilaterally from the midline of the 1.5-day embryo with a width two or three times as great as the distance between the midline and the lateral edge of the somite. Either side of this area contributed to the same side of the endodermal tube of digestive tract. The anterior and posterior portions generally contributed to the anterior and posterior regions of the digestive tract, respectively, and the cells originating from the portion farther from the midline took the more ventral and posterior position in the digestive tract endoderm. Most of the presumptive areas of the digestive organs in the endoderm of 1.5-day embryo were located in a more anterior position than those in the splanchnic mesoderm.     

Fate mapping study of the splanchnopleural mesoderm of the 1.5-day-old chick embryo

Various portions of the splanchnopleural mesoderm lateral to the somites of 1.5-day chick embryos were marked in ovo by local injection of Dil, and the distribution of the labelled cells in the digestive-tract mesoderm formed after 3 days' reincubation was analysed. The presumptive area of the digestive organs was confined to bands of splanchnic mesoderm lying lateral to the somites, on both sides, with a width two or three times that between the midline of the embryo and the lateral edge of the somite. Each band generally contributed cells to its own side of the digestive-tract mesoderm, except for the region around the bile duct. The anterior and posterior portion of the pre-gut area contributed cells to the anterior and posterior region of the digestive tract, respectively, but label originating from the portion furthest from the somite took the more ventral and posterior position. Thus, the presumptive areas of the respective digestive organs were located anteroposteriorly in the same order as in the digestive tract with their boundaries lying oblique to the embryonic axis.     

Fate mapping and cell lineage analysis of Hensen's node in the chick embryo.

Fate maps of chick Hensen's node were generated using DiI and the lineage of individual cells studied by intracellular injection of lysine-rhodamine-dextran (LRD). The cell types contained within the node are organized both spatially and temporally. At the definitive primitive streak stage (Hamburger and Hamilton stage 4), Hensen's node contains presumptive notochord cells mainly in its anterior midline and presumptive somite cells in more lateral regions. Early in development it also contains presumptive endoderm cells. At all stages studied (stages 3-9), some individual cells contribute progeny to more than one of these tissues. The somitic precursors in Hensen's node only contribute to the medial halves of the somites. The lateral halves of the somites are derived from a separate region in the primitive streak, caudal to Hensen's node.     

Fate mapping the avian epiblast with focal injections of a fluorescent-histochemical marker: ectodermal derivatives

A microinjection technique is described for fate mapping the epiblast of avian embryos. It consists of injecting the epiblast of cultured blastoderms with a fluorescent-histochemical marker, examining rhodamine fluorescence at the time of injection in living blastoderms, and assaying for horseradish peroxidase activity in histological sections obtained from the same embryos collected 24 h postinjection. Our results demonstrate that this procedure routinely marks cells, allowing their fates to be determined and prospective fate maps to be constructed. Two such maps are presented for ectodermal derivatives of the epiblast: one for late stages of Hensen's node progression (stages 3c through 4) and one for early stages of node regression (stages 4 + through 5). These new maps have six significant features. First, they show that regardless of whether the node is progressing or regressing, the flat neural plate extends at least 300 microns cranial to, 300 microns bilateral to and 1 mm caudal to the center of Hensen's node. Second, they confirm our previous fate mapping studies based on quail/chick chimeras. Namely, they show that the prenodal midline region of the epiblast forms the floor of the forebrain and the ventrolateral part of the optic vesicles as well as MHP cells (i.e., mainly wedge-shaped neurepithelial cells contained within the median hinge point of the bending neural plate); in contrast, paranodal and postnodal regions contribute L cells (i.e., mainly spindle-shaped neurepithelial cells constituting the lateral aspects of the neural plate). Third, they reveal a second source of MHP cells, Hensen's node, verifying previous studies of others based on tritiated thymidine labeling. Fourth, they demonstrate, in contrast to studies of other based on vital staining, carbon marking, and chorioallantoic grafting but in accordance with our previous studies based on quail/chick chimeras, that the cells contributing to the four craniocaudal subdivisions of the neural tube (i.e., forebrain, midbrain, hindbrain, and spinal cord) are not yet spatially segregated from one another at the flat neural plate stage, although more cranial neural plate cells tend to form more cranial subdivision and more caudal cells tend to form more caudal subdivisions. Thus, single injections routinely mark multiple neural tube subdivisions. Probable reasons for the discrepancy between our present results and the previous results of others is discussed. Fifth, they suggest that cells contributing to the surface ectoderm and neural plate are not yet completely spatially segregated from one another at the flat neural plate stage, particularly in caudal postnodal regions. Sixth, they delineate the locations of the otic placodes.(ABSTRACT TRUNCATED AT 400 WORDS)     

A logistic regression mixture model for interval mapping of genetic trait loci affecting binary phenotypes

Often in genetic research, presence or absence of a disease is affected by not only the trait locus genotypes but also some covariates. The finite logistic regression mixture models and the methods under the models are developed for detection of a binary trait locus (BTL) through an interval-mapping procedure. The maximum-likelihood estimates (MLEs) of the logistic regression parameters are asymptotically unbiased. The null asymptotic distributions of the likelihood-ratio test (LRT) statistics for detection of a BTL are found to be given by the supremum of a chi2-process. The limiting null distributions are free of the null model parameters and are determined explicitly through only four (backcross case) or nine (intercross case) independent standard normal random variables. Therefore a threshold for detecting a BTL in a flanking marker interval can be approximated easily by using a Monte Carlo method. It is pointed out that use of a threshold incorrectly determined by reading off a chi2-probability table can result in an excessive false BTL detection rate much more severely than many researchers might anticipate. Simulation results show that the BTL detection procedures based on the thresholds determined by the limiting distributions perform quite well when the sample sizes are moderately large.     

Two distinct high immune response phenotypes are both controlled byH-2 genes mapping inK orI-A

Murine responses to immunization with 2, 4, 6-trinitrophenyl (TNP) conjugated to autogenous mouse serum albumin (MSA) in complete Freund's adjuvant (CFA) are controlled by a gene(s) in theK orI-A region of theH-2 complex. High immune responses of bothH-2 ^d andH-2 ^b mice have been mapped to this region of the major histocompatibility complex. No modifying effects were observed from genes to the right ofI-A in either responder haplotype. High responsiveness controlled byK ^b orI-A ^b is inherited with complete or partial recessivity, depending on the route of immunization and the sex of the responder. However, high responsiveness controlled byK ^d orI-A ^d is inherited dominantly. This unusual pattern of inheritance of immune responsiveness to TNP-MSA is consistent with the genetic mapping toK orI-A. TNP-MSA-specific T-cell reactivity following immunization with TNP-MSA in vivo was examined utilizing a T-cell-dependent proliferation assay in vitro with cells obtained from high or low responder mice. Genetic mapping and mode of inheritance in this assay for antigen-specific T-cell reactivity corresponded with results obtained from a plaque-forming cell (PFC) assay measuring antibody production by B cells. Both the proliferative and PFC responses are probably under the sameIr gene control. Both gene dosage effects and Ir-gene-product interaction could influence the generation of specific immune responsiveness in F₁ hybrids between high and low responders to TNP-MSA.     

Fate mapping study of the endoderm in the posterior part of the 1.5-day-old chick embryo

Various endodermal sites posterior to the caudal-most somite were marked in ovo with the vital dye Dil, and the fate of marked endoderm was analyzed after 2 or 3 days' reincubation. The endoderm in this area became gut epithelium posterior to the caudal jejunum and yolk sac. The area occupied by the cells that were to contribute to the dorsal part of the digestive tube lay centrally around the area overlaid by axial and paraxial mesoderm, with the preventral digestive area lying outside with considerable overlapping, which was surrounded by the preyolk sac area. During the formation of the posterior digestive tube, the endoderm was elongated anteroposteriorly to a considerable degree. Cells that contributed to the cloaca and those that produced descendants in the large intestine occupied similar areas posterior to the center of the sinus rhomboidalis, which were included in the pre-ileal area extending more anteriorly. Prejejunal cells generally localized in a more anterior position than pre-ileal cells. Pre-allantoic cells were located in a rather small area around the posterior primitive streak.     

Genetically altered mice: phenotypes,no phenotypes,and Faux phenotypes

Phenotype means different things, but whatever the measure, phenotype can be profoundly influenced by genetic, environmental and infectious variables. The laboratory mouse is a complex multisystemic organism which, despite its genetically inbred nature, as highly variable pathophysiologic characteristics. Mouse strains have background characteristics that can influence genomics research. In addition to the mouse itself, different approaches toward creating mutant mice each create variables that influence phenotype. Different background strains of mice are utilized for these different approaches, and various strains are preferred among different laboratories. Background genotype significantly influences phenotype of gene mutations, as can insufficient genetic stabilization of a mutation. Research programs engaged in functional mouse genomics not only must use genetically well-defined mice, but also must incorporate environmental and infectious disease quality assurance/prevention programs. Laboratory mice are subject to over 60 different infectious disease agents, including a wide variety of viruses, bacteria, protozoa, and metazoa. Although these agents can be readily diagnosed and prevented, a number of forces are resulting in their rise in prevalence in mouse colonies. Infectious disease, including clinically silent infections, can and do influence phenotype, and can jeopardize research considerably through lost time, wasted effort, cost, and even loss of valuable strains.     

Fate mapping the avian neural plate with quail/chick chimeras: origin of prospective median wedge cells

The origin of prospective M cells, which are median neuroepithelial cells that become wedge-shaped during bending of the neural plate and eventually form the midline floor of the neural tube, was determined by constructing quail/chick chimeras and using the quail nucleolar marker to identify quail donor cells in chick host blastoderms. Two possible sites of prospective M-cell origin in the epiblast were examined: a single, midline rudiment located just rostral to Hensen's node and paired rudiments flanking the cranial part of the primitive streak. Our results suggest that M cells arise exclusively from the midline, prenodal rudiment. From this rudiment, M cells extend caudally throughout the entire length of the neuroepithelium. This new information on the origin of prospective M cells will aid in the analysis of their role in neurulation.     

Competition between phenotypes

Summary We present two models for phenotypic-dependent interspecific competition. In both cases the survivorship of individuals of one population depends on the entire phenotypic distribution of the other species. The first model considers a continuously varying metric trait, with assortative or random mating; the second model examines a character controlled by two alleles at a single locus. Pursuing the notion that each population maximizes its mean fitness we define a vector-optimum strategy using the concepts of cooperative and competitive optima. It is found that the dynamical constraints placed on the equations of motion by Mendelian genetics often prevent a population from evolving to a strategic optimum. However, for the single locus case with complete dominance, the competitive optimum always coincides with some dynamical equilibrium on the Hardy-Weinberg manifold.     

Murine catalase phenotypes

An examination of three inbred strains of mice differing with respect to liver and kidney catalase activity reveals two distinct genetic factors controlling the level of liver catalase activity. The first genetic factor controls the catalytic activity of the enzyme. Specific activity of purified enzyme from C57BL/6 and C57BL/Ha strains is 60% of that of the DBA/2 strain. The second factor controls the content of liver catalase. Liver catalase of C57BL/Ha is degraded in vivo at a rate one half that of liver catalase of DBA/2 and C57BL/6, resulting in the accumulation of twice as many catalase molecules in C57BL/Ha. The factor affecting turnover of catalase is apparently specific for catalase of liver since no differences exist in kidney catalase levels between C57BL/Ha and C57BL/6. Furthermore, this factor does not appear to alter the metabolism of total liver protein since no substantial difference in the turnover rate of liver protein is observed among the strains. It is particularly significant that the genetic factor affecting the amount of liver catalase does so by altering the rate of catalase degradation rather than the rate of synthesis, confirming the previously published report of Rechcigl and Heston (1967). Thus, these studies emphasize that the quantity of an enzyme in animal cells is a balance between the rate of synthesis and the rate of degradation of the enzyme.This paper was presented at a symposium entitled Genetic Control of Mammalian Metabolism held at The Jackson Laboratory, Bar Harbor, Maine, June 30–July 2, 1969. The symposium was supported in part by an allocation from NIH General Research Support Grant FR 05545 from the Division of Research Resources to The Jackson Laboratory.This investigation was supported by USPHS Research Grant GM 14931 from the Division of General Medical Sciences, and Grants PF-373 and P-427 from the American Cancer Society.