93,888 research outputs found
Perspectives on Case-based Multimedia Web Projects in Science
This article discusses the merits of case-based learning in an interactive online environment. Researchers used both qualitative and quantitative research over a 2-year period to examine the learning that occurred in a high school context when students were engaged in a case-based multimedia project. Part of the Case It! project, students played both the role of laboratory technician performing and presenting research as well as professionals using the information in their practice. Students were required to use three types of simulation software developed exclusively for the Case It! project. Results were measured using both pre- and post-tests, artifacts students created such as Web posters, records of Internet conferences, and interviews from both the students and the teacher involved in this project. Researches found the online format of the lesson fostered a higher level of questioning and problem solving skills, as well as extended explanations and discussions of ethics in science. Educational levels: Graduate or professional
Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus
Background During the last years the quantification of immune response under immunological challenges, e.g. parasitation, has been a major focus of research. In this context, the expression of immune response genes in teleost fish has been surveyed for scientific and commercial purposes. Despite the fact that it was shown in teleostei and other taxa that the gene for beta-actin is not the most stably expressed housekeeping gene (HKG), depending on the tissue and experimental treatment, the gene has been us Results To establish a reliable method for the measurement of immune gene expression in Gasterosteus aculeatus, sequences from the now available genome database and an EST library of the same species were used to select oligonucleotide primers for HKG, in order to perform quantitative reverse-transcription (RT) PCR. The expression stability of ten candidate reference genes was evaluated in three different tissues, and in five parasite treatment groups, using the three algorithms BestKeeper, geNorm and N Conclusion As they were the most stably expressed genes in all tissues examined, we suggest using the genes for the L13a ribosomal binding protein and ubiquitin as alternative or additional reference genes in expression analysis in Gasterosteus aculeatus.
Multiple tests of association with biological annotation metadata
We propose a general and formal statistical framework for multiple tests of
association between known fixed features of a genome and unknown parameters of
the distribution of variable features of this genome in a population of
interest. The known gene-annotation profiles, corresponding to the fixed
features of the genome, may concern Gene Ontology (GO) annotation, pathway
membership, regulation by particular transcription factors, nucleotide
sequences, or protein sequences. The unknown gene-parameter profiles,
corresponding to the variable features of the genome, may be, for example,
regression coefficients relating possibly censored biological and clinical
outcomes to genome-wide transcript levels, DNA copy numbers, and other
covariates. A generic question of great interest in current genomic research
regards the detection of associations between biological annotation metadata
and genome-wide expression measures. This biological question may be translated
as the test of multiple hypotheses concerning association measures between
gene-annotation profiles and gene-parameter profiles. A general and rigorous
formulation of the statistical inference question allows us to apply the
multiple hypothesis testing methodology developed in [Multiple Testing
Procedures with Applications to Genomics (2008) Springer, New York] and related
articles, to control a broad class of Type I error rates, defined as
generalized tail probabilities and expected values for arbitrary functions of
the numbers of Type I errors and rejected hypotheses. The resampling-based
single-step and stepwise multiple testing procedures of [Multiple Testing
Procedures with Applications to Genomics (2008) Springer, New York] take into
account the joint distribution of the test statistics and provide Type I error
control in testing problems involving general data generating distributions
(with arbitrary dependence structures among variables), null hypotheses, and
test statistics.Comment: Published in at http://dx.doi.org/10.1214/193940307000000446 the IMS
Collections (http://www.imstat.org/publications/imscollections.htm) by the
Institute of Mathematical Statistics (http://www.imstat.org
Using Avida to test the effects of natural selection on phylogenetic reconstruction methods
Phylogenetic trees group organisms by their ancestral relationships. There are a number of distinct algorithms used to reconstruct these trees from molecular sequence data, but different methods sometimes give conflicting results. Since there are few precisely known phylogenies, simulations are typically used to test the quality of reconstruction algorithms. These simulations randomly evolve strings of symbols to produce a tree, and then the algorithms are run with the tree leaves as inputs. Here we use Avida to test two widely used reconstruction methods, which gives us the chance to observe the effect of natural selection on tree reconstruction. We find that if the organisms undergo natural selection between branch points, the methods will be successful even on very large time scales. However, these algorithms often falter when selection is absent
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