The Genetics Concept Assessment: a new concept inventory for gauging student understanding of genetics

We have designed, developed, and validated a 25-question Genetics Concept Assessment (GCA) to test achievement of nine broad learning goals in majors and nonmajors undergraduate genetics courses. Written in everyday language with minimal jargon, the GCA is intended for use as a pre- and posttest to measure student learning gains. The assessment was reviewed by genetics experts, validated by student interviews, and taken by >600 students at three institutions. Normalized learning gains on the GCA were positively correlated with averaged exam scores, suggesting that the GCA measures understanding of topics relevant to instructors. Statistical analysis of our results shows that differences in the item difficulty and item discrimination index values between different questions on pre- and posttests can be used to distinguish between concepts that are well or poorly learned during a course.

Teaching concepts versus facts in developmental biology

Points of View (POV) address issues faced by many people within the life science education community. CBE—Life Sciences Education (CBE-LSE) publishes the POV Feature to present two or more opinions published side-by-side on a common topic. We consider POVs to be “Op-Ed” pieces designed to stimulate thought and dialogue on significant educational issues. They are not meant to be exhaustive treatments of a subject. In this issue, we ask the question, “What are key concepts in developmental biology?” We present three POVs. The first is by CBE-LSE Editor-in-Chief, William Wood, and it is in part based on his experience teaching developmental biology to undergraduates at the University of Colorado, Boulder, including his collaborative experiments in the classroom with Jennifer Knight, the first results of which have been published in CBE-LSE (Knight and Wood, 2005). The second, a partially tongue-in-cheek list of key concepts to convey to students about embryonic development, is by Scott Gilbert (Swarthmore College), author of the leading textbook worldwide for teaching developmental biology, Developmental Biology, 8th ed. (Sinauer Associates, Inc.). The third is by Jeff Hardin (University of Wisconsin–Madison), who has produced Web-based educational materials for teaching developmental biology that are used nationally and internationally for conveying dynamic events during early development (see the WWW feature in this issue by Stark for more details), and who deals with the vexing problem of trying to convey the essential four-dimensional nature of embryonic development to introductory students.

Handed asymmetry, handedness reversal and mechanisms of cell fate determination in nematode embryos

Embryos of the nematode Caenorhabditis elegans exhibit left-right asymmetry with an invariant handedness. The embryonic cell lineage is asymmetrical: although the animal is generally bilaterally symmetrical with only a few left-right asymmetries, many of its contralaterally analogous cells arise via different lineages on the two sides of the embryo. Larvae and adults also exhibit left-right asymmetries with a handedness that is normally invariant. The frequency of animals with opposite handedness was increased among the progeny of adults exposed to the mutagen ethyl methanesulphonate and among animals that developed from embryos treated in early cleavage with chitinase to destroy the egg shell. Reversal of embryonic handedness was accomplished directly by micromanipulation at the 6-cell stage, resulting in mirror-image but otherwise normal development into healthy, fertile animals with all the usual left-right asymmetries reversed. This demonstrates that (1) the handedness of cell positions in the 6-cell embryo dictates handedness throughout development; (2) at this stage the pair of anterior blastomeres on the right is equivalent to the pair on the left; and (3) the extensive differences in fates of lineally homologous cells on the two sides of the animal must be dictated by cellular interactions, most of which are likely to occur early in embryogenesis and appear to have been conserved in widely diverged nematode species.

Teaching more by lecturing less

We carried out an experiment to determine whether student learning gains in a large, traditionally taught, upper-division lecture course in developmental biology could be increased by partially changing to a more interactive classroom format. In two successive semesters, we presented the same course syllabus using different teaching styles: in fall 2003, the traditional lecture format; and in spring 2004, decreased lecturing and addition of student participation and cooperative problem solving during class time, including frequent in-class assessment of understanding. We used performance on pretests and posttests, and on homework problems to estimate and compare student learning gains between the two semesters. Our results indicated significantly higher learning gains and better conceptual understanding in the more interactive course. To assess reproducibility of these effects, we repeated the interactive course in spring 2005 with similar results. Our findings parallel results of similar teaching-style comparisons made in other disciplines. On the basis of this evidence, we propose a general model for teaching large biology courses that incorporates interactive engagement and cooperative work in place of some lecturing, while retaining course content by demanding greater student responsibility for learning outside of class.

The left-right polarity puzzle: determining embryonic handedness

Whenever symmetry is broken in nature to yield only one of two equally probable outcomes, there is an intriguing problem to be solved.

Embryonic handedness choice in C. elegans involves the Galpha protein GPA-16

The mechanism by which polarity of the left-right (LR) axis is initially established with the correct handedness is not understood for any embryo. C. elegans embryos exhibit LR asymmetry with an invariant handedness that is first apparent at the six-cell stage and persists throughout development. We show here that a strong loss-of-function mutation in a gene originally designated spn-1 affects early spindle orientations and results in near randomization of handedness choice. This mutation interacts genetically with mutations in three par genes that encode localized cortical components. We show that the spn-1 gene encodes the Galpha protein GPA-16, which appears to be required for centrosomal association of a Gbeta protein. We will henceforth refer to this gene as gpa-16. These results demonstrate for the first time involvement of heterotrimeric G proteins in establishment of embryonic LR asymmetry and suggest how they might act.

Expression of the C. elegans labial orthologue ceh-13 during male tail morphogenesis

Hox genes are transcriptional regulators of metazoan body regionalization along the anteroposterior axis that act by specifying positional identity in differentiating cells. ceh-13, the labial orthologue in Caenorhabditis elegans, is expressed both during embryogenesis and post- embryonic development. Using GFP reporter analysis and immunocytochemistry, we discovered a spatiotemporal pattern of gene expression in the male tail during the L3 and L4 larval stages that is TGF-beta pathway-dependent. Analysis of reporter activity in transgenic animals identified a distinct promoter region driving male tail-specific ceh-13 expression. We also report the interspecies conservation of sequence motifs within this region and speculate that, in the course of evolutionary diversification, ceh-13 may have acquired new functionality while conserving its homeotic role.

Inquiry-based undergraduate teaching in the life sciences at large research universities: a perspective on the Boyer Commission Report

The 1998 Boyer Commission Report advocated improvement of undergraduate education at large research universities through large-scale participation of undergraduates in the universities' research mission. At a recent conference sponsored by the Reinvention Center, which is dedicated to furthering the goals of the Boyer Commission, participants discussed progress toward these goals and recommendations for future action. A breakout group representing the life sciences concluded that independent research experience for every undergraduate may not be feasible or desirable but that transformation of lecture courses to more inquiry-based and interactive formats can effectively further the Commission's goals.

A cuticle collagen encoded by the lon-3 gene may be a target of TGF-beta signaling in determining Caenorhabditis elegans body shape

The signaling pathway initiated by the TGF-beta family member DBL-1 in Caenorhabditis elegans controls body shape in a dose-dependent manner. Loss-of-function (lf) mutations in the dbl-1 gene cause a short, small body (Sma phenotype), whereas overexpression of dbl-1 causes a long body (Lon phenotype). To understand the cellular mechanisms underlying these phenotypes, we have isolated suppressors of the Sma phenotype resulting from a dbl-1(lf) mutation. Two of these suppressors are mutations in the lon-3 gene, of which four additional alleles are known. We show that lon-3 encodes a collagen that is a component of the C. elegans cuticle. Genetic and reporter-gene expression analyses suggest that lon-3 is involved in determination of body shape and is post-transcriptionally regulated by the dbl-1 pathway. These results support the possibility that TGF-beta signaling controls C. elegans body shape by regulating cuticle composition.

Roles of the Homothorax/Meis/Prep homolog UNC-62 and the Exd/Pbx homologs CEH-20 and CEH-40 in C. elegans embryogenesis

Co-factor homeodomain proteins such as Drosophila Homothorax (Hth)and Extradenticle (Exd) and their respective vertebrate homologs, the Meis/Prep and Pbx proteins, can increase the DNA-binding specificity of Hox protein transcription factors and appear to be required for many of their developmental functions. We show that the unc-62 gene encodes theC. elegans ortholog of Hth, and that maternal-effect unc-62mutations can cause severe posterior disorganization during embryogenesis (Nob phenotype), superficially similar to that seen in embryos lacking function of either the two posterior-group Hox genes nob-1 and php-3 or the caudal homolog pal-1. Other zygotically actingunc-62 alleles cause earlier embryonic arrest or incompletely penetrant larval lethality with variable morphogenetic defects among the survivors, suggesting that unc-62 functions are required at several stages of development. The differential accumulation of four unc-62transcripts is consistent with multiple functions. The C. elegans exdhomologs ceh-20 and ceh-40 interact genetically withunc-62 and may have overlapping roles in embryogenesis: neither CEH-20 nor CEH-40 appears to be required when the other is present, but loss of both functions causes incompletely penetrant embryonic lethality in the presence of unc-62(+) and complete embryonic lethality in the presence of an unc-62 hypomorphic allele.

Extragenic suppressors of a dominant masculinizing her-1 mutation in C. elegans identify two new genes that affect sex determination in different ways

SUMMARY

The her-1 regulatory switch gene in C. elegans sex determination is normally active in XO animals, resulting in male development, and inactive in XX animals, allowing hermaphrodite development. The her-1(n695gf) mutation results in the incomplete transformation of XX animals into phenotypic males. We describe four extragenic mutations that suppress the masculinized phenotype of her-1(n695gf) XX. They define two previously undescribed genes, sup-26 and sup-27. All four mutations exhibit semidominance of suppression and by themselves have no visible effects on sex determination in otherwise genotypically wild-type XX or XO animals. Analysis of interactions with mutations in the major sex-determining genes show that sup-26 and sup-27 influence sex determination in fundamentally different ways. sup-26 appears to act independently of her-1 to negatively modulate synthesis or function of tra-2 in both XX and XO animals. sup-27 may play a role in X-chromosome dosage compensation and influence sex determination indirectly.

Assembly and use of a broadly applicable neural cDNA microarray

cDNA microarrays provide an efficient method to analyze gene expression patterns in thousands of genes in parallel. In some cases, large unfocused collections of cDNAs have been used in hybridization studies, in others small logically defined collections of tissue specific arrays have been used. Here we describe the bioinformatic selection of 1152 named human cDNAs specifically designed for neuroscience applications, arrayed on nylon membranes at high density. cDNAs were chosen which represent all the major cellular types of the brain including; neurons, astrocytes, microglia, and oligodendrocytes. Gene families chosen include cell type specific markers, ion-channels, transporters, receptors, and cell adhesion molecules among many others. These arrays were used with region specific samples from human brain to determine MRNA expression profiles for each region. Used with 33p labeled complex probes, this is a low cost, highly sensitive approach for tbc investigator to focus on tissue specific genes of interest where samples of limiting amounts of RNA are used. This selected set of brain-relevant cDNAs should be widely useful in the analysis of gene expression patterns from brain tissues as well as neural cell lines.

A Caenorhabditis elegans TGF-beta, DBL-1, controls the expression of LON-1, a PR-related protein, that regulates polyploidization and body length

Using cDNA-based array analysis combined with double-stranded RNA interference (dsRNAi), we have identified yk298h6 as a target gene of Caenorhabditis elegans TGF-beta signaling. Worms overexpressing dbl-1, a TGF-beta ligand, are 16% longer than wild type. Array analysis shows yk298h6 to be one of several genes suppressed in such worms. Disruption of yk298h6 function by dsRNAi also resulted in long worms, suggesting that it is a negative regulator of body length. yk298h6 was then mapped to, and shown to be identical to, lon-1, a known gene that affects body length. lon-1 encodes a 312 amino acid protein with a motif sequence that is conserved from plants to humans. Expression studies confirm that LON-1 is repressed by DBL-1, suggesting that LON-1 is a novel downstream component of the C.elegans TGF-beta growth regulation pathway. Consistent with this, LON-1 is expressed mainly in the larval and adult hypodermis and has dose-dependent effects on body length associated with changes in hypodermal ploidy, but not hypodermal cell proliferation.

Advanced high school biology in an era of rapid change: a summary of the biology panel report from the NRC Committee on Programs for Advanced Study of Mathematics and Science in American High Schools

A recently released National Research Council (NRC) report, Learning and Understanding: Improving Advanced Study of Mathematics and Science in U.S. High Schools, evaluated and recommended changes in the Advanced Placement (AP), International Baccalaureate (IB), and other advanced secondary school science programs. As part of this study, discipline-specific panels were formed to evaluate advanced programs in biology, chemistry, physics, and mathematics. Among the conclusions of the Content Panel for Biology were that AP courses in particular suffer from inadequate quality control as well as excessive pressure to fulfill their advanced placement function, which encourages teachers to attempt coverage of all areas of biology and emphasize memorization of facts rather than in-depth understanding. In this essay, the Panel's principal findings are discussed, with an emphasis on its recommendation that colleges and universities should be strongly discouraged from using performance on either the AP examination or the IB examination as the sole basis for automatic placement out of required introductory courses for biology majors and distribution requirements for nonmajors.

Zygotic expression of the caudal homolog pal-1 is required for posterior patterning in Caenorhabditis elegans embryogenesis

Previous work has shown that the Caenorhabditis elegans gene pal-1, a homolog of Drosophila caudal, is required maternally for blastomere specification in the early embryo and postembryonically for tail development in males. We show here that embryonic (zygotic) transcription of pal-1 is also required for posterior patterning during later embryogenesis. Embryos homozygous for strong loss-of-function mutations arrest as nonviable L1 larvae with gross posterior defects. PAL-1 protein produced from zygotic transcripts is expressed dynamically during gastrulation and morphogenesis in specific cells of all major lineages except the germ line. Most expressing cells are undergoing cell movements or forming midline structures or both. Mutant embryos exhibit defects involving most of the expressing cells. Aberrant early cell positions are observed in posterior hypodermis, both in the C-lineage cells that express pal-1 and in the neighboring hypodermal seam cell precursors, which do not, as well as in posterior muscle derived from the C and D lineages. Defects in late gastrulation, ventral hypodermal enclosure, and formation of the rectum result from failures of cell movements of ABp and MS descendants. Limited mosaic analysis supports the view that most of the required pal-1 functions are cell autonomous.