Chemosensory control of surface antigen switching in the nematode Caenorhabditis elegans.

Nematodes change their surface compositions in response to environmental signals, which may allow them to survive attacks from microbial pathogens or host immune systems. In the free-living species Caenorhabditis elegans, wild-type worms are induced to display an L1 (first larval stage) surface epitope at later larval stages when grown on an extract of spent culture medium (Inducible Larval Display or ILD). Before this study, it was not known whether ILD was regulated by the well-characterized, neurologically based chemical senses of C. elegans, which mediate other behavioural and developmental responses to environmental signals such as chemotaxis and formation of the facultatively arrested dauer larva stage. We show here that ILD requires the activities of three genes that are essential for the function of the C. elegans chemosensory neurons. ILD was abolished in chemotaxis-defective che-3, osm-3 and tax-4 mutants. In contrast, chemotaxis-defective mutants altered in a different gene, srf-6, show constitutive display of the L1 epitope on all four larval stages. The ILD-defective che-3, osm-3 and tax-4 mutations blocked the constitutive larval display of an srf-6 mutant. Combining srf-6 and certain dauer-constitutive mutations in double mutants enhanced constitutive dauer formation, consistent with the idea that srf-6 acts in parallel with specific components of the dauer formation pathway. These results taken together are consistent with the hypothesis that ILD is triggered by environmental signals detected by the nematode's chemosensory neurons.

Statistics: detecting differences among groups.

Some of the statistical tests most commonly used (and misused) in biological research are presented here. The tests discussed are those used for comparisons among groups (e.g., t test and ANOVA). The purpose of this appendix is to enable the investigator to determine rapidly the most appropriate way to analyze data, and to point out some of the most common errors to avoid.

Statistics for the molecular biologist: group comparisons.

In this appendix, some of the statistical tests most commonly used (and misused) in biological research are discussed. These tests are used for comparisons among groups (e.g., t test and ANOVA). A number of other important areas (e.g., linear regression, correlation, and goodness-of-fit testing) are not covered. The purpose is to enable the reader to determine rapidly the most appropriate way to analyze data, and to point out some of the most common errors to avoid.

Computational methods for single-point and multipoint analysis of genetic variants associated with a simulated complex disorder in a general population.

Several techniques for association analysis have been applied to simulated genetic data for a general population. We describe and compare the performance of three single-point methods and two multipoint approaches rooted in machine learning and data mining.

Graphical simulation of early development of the cerebral cortex.

Much experimental data exists concerning the development of the cerebral cortex. There is a need for a common vehicle to integrate this data and to allow the testing of hypotheses concerning development. Computer simulation and visualization are powerful mechanisms for hypothesis testing. Our long-term goal is to create a robust, extensible, portable tool for simulation and visualization of cortical development to serve both research and educational purposes. This paper describes a simulation program, SimCortex, which models the early stages of development of the cerebral cortex of the mouse. Version 1.0 of SimCortex models the proliferation of progenitor cells in the pseudostratified ventricular epithelium (PVE), the generation of young neurons and their migration into the cortical plate, which is the forerunner of cell layers II through VI of the adult cortex. We present an overview of the design and implementation of SimCortex, sample output of the system and a comparison of our results with experimental data. We conclude with a brief overview of proposed future enhancements of the system.

Clonal analysis in the chicken retina reveals tangential dispersion of clonally related cells.

Development of the chicken retina was investigated through clonal analysis using retroviral vectors. Replication-incompetent retroviral vectors encoding either human placental alkaline phosphatase, beta-galactosidase, or a viral core protein were used in paired combinations to infect retinal progenitor cells from Embryonic Days 2.5-7.0. Labeled clones were analyzed late in embryonic development after retinal histogenesis was complete. The early accessibility of the chicken retina, combined with its large final size, resulted in the labeling of much larger clones than had been reported previously in other species. The clones were composed of many cell types, supporting previous conclusions from other vertebrates that the progenitor cells of developing retina are multipotent. The majority of clones derived from early infections consisted of multiple tightly clustered arrays of cells accompanied by dispersed individual cells. Clonal complexity and tangential dispersion were greater in peripheral than central retina and decreased considerably with increasing age of infection. These observations suggest that early during retinal development, shortly after optic cup formation, there is considerable mixing of progenitor cells.

Migration patterns of clonally related granule cells and their progenitors in the developing chick cerebellum.

During cerebellar development, granule neurons and their progenitors undergo complex migrations. To define these migratory paths better, we used replication-incompetent retroviruses to label dividing cells early in cerebellar development. Clonally related granule cells were widely dispersed in both rostrocaudal and mediolateral planes; clones often spanned the midline. The data suggest that granule cell progenitors originate from the ventricular zone along the entire mediolateral extent of the caudal edge of the cerebellum. After reaching the cerebellar surface, progenitors move primarily rostrally and proliferate in the superficial external granule layer. Postmitotic granule cells then migrate long distances medially and laterally in the transverse plane in the deep external granule layer, where previously they had been thought simply to extend transverse processes.

Establishment and characterization of multipotent neural cell lines using retrovirus vector-mediated oncogene transfer.

Neural cell lines were produced by retroviral vector-mediated transduction of the avian myc oncogene. Target cells were mitotic progenitor cells of postnatal mouse olfactory bulb and cerebellum, and postnatal rat cerebral cortex. Infection of the first two areas, where neurogenesis and gliogenesis occur postnatally, produced multipotent clonal lines that exhibited phenotypes of both neuronal and glial cells, and one line with a stable neuronal phenotype. Infection of cerebral cortex, where gliogenesis, but not neurogenesis, occurs postnatally, generated mortal clones that exhibited cells of glial phenotype. These lines should prove valuable for both in vitro and in vivo studies aimed at understanding the control of cell fate and differentiation of neural progenitors.

A program which determines mutagenic concentrations of chemical carcinogens via a diffusion bioassay.

A computer program implementing a mathematical model for determining mutagenic concentrations of chemical carcinogens was developed. The mathematical model describes the experiment in which a droplet of a suspected carcinogen is put at the center of a petri dish containing a bacterial lawn in an agar gel. After a period of incubation during which the chemical diffuses outward, one observes a concentric ring of mutants around the center. The largest radius at which mutation occurs, r mut, corresponds to the lowest (threshold) concentration of the chemical sufficient to produce bacterial mutation. Given a series of initial concentrations of a chemical and the resulting r mut's, the program computes and reports the threshold concentration and the decay time of the chemical. The program is also used as a method to determine the lowest mutagenic concentration for a particular time of exposure.