The molecular biology capstone assessment: a concept assessment for upper-division molecular biology students

Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α=0.80) and test-retest stability (r=0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs.

Timing and mechanism of the initial cue establishing handed left–right asymmetry in Caenorhabditis elegans embryos

By the six-cell stage, embryos of Caenorhabditis elegans are morphologically L–R asymmetric with an invariant handedness that persists throughout development. We used intracellular markers to ask whether breaking of L–R symmetry could be observed at earlier stages. Observation of two- to three-cell embryos carrying intracellular markers indicated that L–R symmetry is broken concomitantly with establishment of D–V axis polarity during division of the anterior AB cell. The AB cleavage furrow initiates asymmetrically and always from the left, suggesting L–R differences in the AB cell cortex. An invariantly handed cortical rotation observed earlier during first cleavage implies that the one-cell embryo has an intrinsic chirality. We propose that L–R differences in the cortex could result from mechanical forces on asymmetric components of a chiral cortical network during the off-axis elongation of the AB-cell spindle prior to AB cleavage.

What's Downstream? A Set of Classroom Exercises to Help Students Understand Recessive Epistasis

Undergraduate students in genetics and developmental biology courses often struggle with the concept of epistasis because they are unaware that the logic of gene interactions differs between enzymatic pathways and signaling pathways. If students try to develop and memorize a single simple rule for predicting epistatic relationships without taking into account the nature of the pathway under consideration, they can become confused by cases where the rule does not apply. To remedy this problem, we developed a short pre-/post-test, an in-class activity for small groups, and a series of clicker questions about recessive epistasis in the context of a signaling pathway that intersects with an enzymatic pathway. We also developed a series of homework problems that provide deliberate practice in applying concepts in epistasis to different pathways and experimental situations. Students show significant improvement from pretest to posttest, and perform well on homework and exam questions following this activity. Here we describe these materials, as well as the formative and summative assessment results from one group of students to show how the activities impact student learning.

Combining peer discussion with instructor explanation increases student learning from in-class concept questions

Use of in-class concept questions with clickers can transform an instructor-centered "transmissionist" environment to a more learner-centered constructivist classroom. To compare the effectiveness of three different approaches using clickers, pairs of similar questions were used to monitor student understanding in majors' and nonmajors' genetics courses. After answering the first question individually, students participated in peer discussion only, listened to an instructor explanation only, or engaged in peer discussion followed by instructor explanation, before answering a second question individually. Our results show that the combination of peer discussion followed by instructor explanation improved average student performance substantially when compared with either alone. When gains in learning were analyzed for three ability groups of students (weak, medium, and strong, based on overall clicker performance), all groups benefited most from the combination approach, suggesting that peer discussion and instructor explanation are synergistic in helping students. However, this analysis also revealed that, for the nonmajors, the gains of weak performers using the combination approach were only slightly better than their gains using instructor explanation alone. In contrast, the strong performers in both courses were not helped by the instructor-only approach, emphasizing the importance of peer discussion, even among top-performing students.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMOCOCCAL PNEUMONIA : IV. THE MECHANISM OF PHAGOCYTOSIS IN THE ABSENCE OF ANTIBODY

1. Evidence has been presented in previous publications that the phagocytosis of pneumococci in the pneumonic lung during chemotherapy is due neither to specific opsonins nor to capsular injury (1, 2). The present studies have shown that the phagocytosis taking place in the lung is independent of any sort of intermediary factor and results from a direct action of the phagocytic cells upon the pneumococci. 2. Phagocytosis in the absence of antibody has been demonstrated not only in the lungs of living rats but in formalin-fixed lungs, on the surfaces of a variety of tissues (both freshly removed from the animal and previously "killed" with heat), and on the surfaces of such inert materials as moistened filter paper, cloth, and fiber glass. On the other hand, smooth materials such as glass, cellophane, albumin, and paraffin have failed to support the phagocytic reaction. This latter observation indicates that the physical character of the surface to which the leucocytes have access constitutes a determining factor in the non-antibody mechanism of phagocytosis. 3. Further experiments have defined the relationship of "surface phagocytosis" to that induced by specific opsonins. The non-antibody mechanism was found to operate only upon surfaces of suitable physical properties, whereas opsonins enabled phagocytes floating freely in a fluid medium to engulf the fully encapsulated organisms. 4. Direct visualization of the surface phenomenon in the lung revealed that leucocytes phagocyte the virulent organisms in the absence of antibody only after having trapped them against the alveolar walls. Once the encapsulated pneumococci have been ingested, they can be seen to undergo digestion within a few hours. The discovery of the phenomenon of surface phagocytosis affords clarification of previously unanswered problems concerning the mechanism of recovery in pneumococcal pneumonia.

STUDIES ON THE ANTIBACTERIAL ACTION OF THE SULFONAMIDE DRUGS : II. THE POSSIBLE RELATION OF DRUG ACTIVITY TO SUBSTANCES OTHER THANp-AMINOBENZOIC ACID

1. In cultures of Staphylococus aureus in a synthetic medium nicotinamide and cozymase were shown to block the bacteriostatic action of chemically unrelated sulfonamide drugs as well as the chemically related compound sulfapyridine. The antibacterial properties of organic dyes totally unrelated to the sulfonamide compounds (methylene blue and thionine) were also nullified by the addition of cozymase to the culture medium. 2. The antagonistic action of the pyridine-containing coenzyme, cozymase, was found, by quantitative study, to be no greater against sulfapyridine than against other structurally dissimilar sulfonamide compounds. 3. The antidrug effects of nicotinamide and cozymase in staphylococcus cultures were observed to be directly proportional to their ability to stimulate the growth of the organism in the synthetic medium. When tested in cultures of B. coli in which they failed to accelerate bacterial growth, these same substances failed to influence the bacteriostatic action of the sulfonamide drugs. 4. The in vitro action of the coenzyme, cocarboxylase, as measured in the Warburg respirometer, was shown to be unaffected by the chemically related drug, sulfathiazole, even when the latter was present in great excess. The above observations fail to support the theory that sulfapyridine, sulfathiazole, and sulfadiazine prevent bacterial growth by interfering with the functioning of the chemically related coenzymes, cozymase, and cocarboxylase. The mode of action of sulfanilamide and its more common derivatives is discussed in the light of these observations, and a tentative theory is offered to explain the differences in bacteriostatic potency exhibited by the various sulfonamide compounds.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMONIA DUE TO FRIEDLANDER'S BACILLUS : I. THE PATHOGENESIS OF EXPERIMENTAL FRIEDLANDER'S BACILLUS PNEUMONIA

Experimental pneumonia due to Friedländer's bacillus was produced in white rats by the intrabronchial inoculation of the bacilli suspended in mucin. The pneumonia was lobar in type, was almost uniformly fatal, and simulated the acute form of the natural disease in human beings. The pathogenesis of the pneumonic lesion was studied by examination of microscopic sections of the lungs of animals killed at frequent intervals during the course of the infection. The histologic characteristics of the various stages of the pneumonia were essentially the same as those previously described in experimental pneumococcal (Type I) pneumonia except for the following differences: (1) In isolated areas of the lung in Friedländer's pneumonia many more bacteria were encountered in the alveoli than were ever noted in experimental pneumococcal pneumonia. (2) Abscess formation was common in the late stages of Friedländer's infection, whereas it was not noted in the pneumococcal lesion. (3) Organization of the alveolar exudate, rarely observed in experimental pneumococcal pneumonia, was a prominent feature of the pneumonia due to Friedländer's bacillus. The mechanism of spread of Friedländer's lesion appeared to be the same as that of pneumococcal pneumonia. Likewise there was noted the same phagocytosis of organisms in the lungs of even bacteremic animals dying of the infection.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMONIA DUE TO FRIEDLANDER'S BACILLUS : II. THE EFFECT OF SULFONAMIDE CHEMOTHERAPY UPON THE PULMONARY LESION OF EXPERIMENTAL FRIEDLANDER'S BACILLUS PNEUMONIA

Sulfonamide chemotherapy was found to cure rats of an otherwise fatal form of experimental Friedländer's bacillus pneumonia when treatment was begun 6 hours after inoculation. Most of the pneumonic lesions cleared completely, but an occasional animal exhibited small residual abscesses in the previously consolidated lung. The recovery process taking place in the lungs was studied histologically at various intervals during therapy. As in the case of pneumococcal pneumonia, the principal action of the sulfonamide was upon the bacteria in the advancing edema zone at the periphery of the pneumonic lesion. The bacteriostatic action of the drug appeared to stop the spread of the pneumonia, and the Friedländer bacilli were ultimately ingested and destroyed by the phagocytic cells in the alveolar exudate. The phagocytosis of bacteria in the lung was shown to be unrelated to the presence of antibody in the blood.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMONIA DUE TO FRIEDLADER'S BACILLUS : III. THE ROLE OF "SURFACE PHAGOCYTOSIS" IN THE DESTRUCTION OF THE MICROORGANISMS IN THE LUNG

Phagocytosis of encapsulated Friedländer's bacilli has been demonstrated in the lungs of rats in the absence of both circulating and local antibody. The mechanism of phagocytosis independent of antibody has been shown to be due to the same surface factors that operate in the phagocytosis of Type I pneumococcus under similar conditions. Direct observation of the phagocytic process reveals that leucocytes in the lung can phagocyte unopsonized Friedländer's bacilli only by trapping them against the surfaces of alveolar walls or bronchi, or by pinning them against the surfaces of adjacent leucocytes. Evidence is presented that Friedländer's bacilli thus phagocyted are rapidly killed in the cytoplasm of the phagocytic cells. Reasons are discussed for the failure of prolonged chemotherapy to cure lung abscesses that not infrequently complicate the pneumonia due to Friedländer's bacillus.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMOCOCCAL PNEUMONIA : III. FACTORS INFLUENCING THE PHAGOCYTOSIS OF PNEUMOCOCCI IN THE LUNG DURING SULFONAMIDE THERAPY

The phagocytosis which occurs in the lungs of rats receiving sulfonamide is due neither to an opsonizing action of the sulfonamides nor to type-specific antibody. The evidence presented indicates that the destruction of the pneumococci is brought about by a phagocytic mechanism independent of both opsonization and capsular injury.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMOCOCCAL PNEUMONIA : II. THE EFFECT OF SULFONAMIDE THERAPY UPON THE PULMONARY LESION OF EXPERIMENTAL PNEUMONIA

Experimental pneumococcal pneumonia was produced in albino rats by intrabronchial inoculation of Type I pneumococci suspended in mucin. The resulting pneumonia was uniformly fatal in untreated rats. Eighty per cent of the animals so infected and treated with sulfonamide drugs 6 hours after inoculation survived the pneumonia. At the end of 1 week the surviving animals were sacrificed, and examination of the lungs showed sharply demarcated localized pulmonary lesions containing no pneumococci. Microscopic study of the lungs of treated animals sacrificed at 6, 18, 42, 66, 96, and 168 hours after the start of treatment revealed the following sequence of events. During the first 18 hours the drug apparently had little effect upon the pneumonic lesion, but at the end of 18 hours pneumococci in the edema zone began to show striking changes in their morphology, indicating bacteriostesis. Forty-two hours after the start of treatment the edema zone had disappeared, the pneumonia had ceased to spread, and the pneumococci at the margin of the lesion had been overtaken by leucocytes. Careful examination of the exudate in the periphery of the lesion revealed definite phagocytosis of pneumococci. By the 4th day no pneumococci could be found in the stained sections, and after 1 week there remained only macrophages in the rapidly clearing alveoli. In order to demonstrate the phagocytic reaction more clearly the effect of sulfonamide drugs was studied in pneumonic rats previously rendered leucopenic by exposure to x-ray. The pneumonia in these animals was relatively acellular, and the few macrophages present in each alveolus could be seen to have phagocyted large numbers of pneumococci after 18 to 42 hours of treatment. The macrophages not only phagocyted the pneumococci but ultimately destroyed them, the pneumonic lesion later going on to complete resolution. The fact that this phagocytic reaction was observed in the lungs of animals with bacteremia suggests that the phagocytosis is independent of circulating type-specific opsonins.

STUDIES ON THE ANTIBACTERIAL ACTION OF THE SULFONAMIDE DRUGS : I. THE RELATION OFp-AMINOBENZOIC ACID TO THE MECHANISM OF BACTERIOSTASIS

The following observations have been made which substantiate the theory that the sulfonamide drugs used in the treatment of bacterial infections exert their bacteriostatic effect by competing with the essential metabolite, p-amino-benzoic acid, for an important enzyme site on the bacterial cell. 1. p-Aminobenzoic acid was shown to nullify the bacteriostatic effect of all of the six sulfonamide compounds studied even though the drugs exhibited marked differences in chemical structure. 2. The bacteriostatic potency of each sulfonamide drug was found to be directly proportional to its ability to counteract the antibacteriostatic action of p-aminobenzoic acid. 3. In the case of each drug tested over a wide range of concentrations the minimum amount of p-aminobenzoic acid needed to prevent bacteriostasis was such that the ratio of p-aminobenzoic acid to drug was constant. 4. The linear relationship between p-aminobenzoic acid and drug was interpreted as indicating the competitive inhibition of an essential enzyme reaction by a substance chemically related to the substrate. This interpretation was supported by the fact that the equation derived on purely theoretical grounds relating drug and acid expressed the same linear relationship as that observed experimentally.

STUDIES ON THE MECHANISM OF RECOVERY IN PNEUMOCOCCAL PNEUMONIA : I. THE ACTION OF TYPE SPECIFIC ANTIBODY UPON THE PULMONARY LESION OF EXPERIMENTAL PNEUMONIA

A uniformly fatal lobar pneumonia was produced in white rats by inoculation of the left main bronchus with virulent Type I pneumococci suspended in mucin. All of the animals succumbed in less than 5 days, half of them dying within 48 hours. In only 5 of 40 rats was the lesion confined to the left lung, and all but one developed pleurisy, pericarditis, or both. All had bacteriemia at the time of death. The pathogenesis of the pulmonary lesion was studied by examining the lungs of 35 rats killed at various intervals following inoculation. The pneumonic process spread rapidly until most of the left lung was involved in 36 hours. Frequent blood cultures showed invasion of the blood stream in a few rats at 6 hours and in over 90 per cent at the end of the first day. The first signs of pleurisy usually appeared at 18 hours. Microscopic examination of the actively spreading lesion revealed three characteristic zones: (1) an outer "edema zone" in which the alveoli contained many pneumococci floating freely in edema fluid, (2) a middle zone where both leucocytes and organisms were present, many of the latter being phagocytized, and (3) an inner zone of advanced consolidation in which the alveoli contained many leucocytes but no organisms and where there were already local areas of early resolution. Study of numerous lesions, at intervals of from 12 to 36 hours after inoculation, indicated that the pneumococci spread into normal alveoli principally by way of the infected edema fluid in the outer zone. Pneumococcus-laden edema fluid in large bronchi and in alveoli beneath the pleura suggested the mode of spread of the infection to other lobes and possibly to the pleural cavity. No adequate explanation could be found for the presence of active phagocytosis in the lungs of animals with bacteriemia and presumably without circulating antibodies, but this conspicuous phagocytic reaction was obviously responsible for the clearing of the central part of the spreading lesion. The action of type specific antibody upon the pulmonary lesion of experimental lobar pneumonia was studied in rats similarly infected but treated with antipneumococcal serum. When injected intravenously in a single dose within 18 hours after inoculation the antiserum was found to protect all of the rats against the otherwise fatal pneumonia. It stopped the spread of the pneumonic lesion, cleared the blood stream of organisms, and prevented the extension of early pleurisy. The antibody caused agglutination and capsular swelling of the pneumococci in the lung, particularly in the edema zone at the margin of the lesion where they were most numerous. Apparently immobilized by agglutination the organisms were overtaken by leucocytes and destroyed by phagocytosis. The phagocytic reaction was greatly accelerated by the specific opsonins of the antiserum, and the pneumococci were destroyed by polymorphonuclear leucocytes before many macrophages appeared in the alveolar exudate. Within a week after treatment resolution of the pulmonary lesion was well in progress. Both horse and rabbit antibody were shown to penetrate the lung, and immune bodies were demonstrated in the alveoli within 10 minutes after the start of treatment. The relation of the observed phenomena to the curative action of anti-pneumococcal serum has been briefly discussed, and it is pointed out that the principal effect of antiserum is to cause immobilization of the pneumococci in the advancing edema zone. Experiments to be reported in a later publication have shown that sulfapyridine exerts a similar effect through a different mechanism.

Innovations in teaching undergraduate biology and why we need them

A growing revolution is under way in the teaching of introductory science to undergraduates. It is driven by concerns about American competitiveness as well as results from recent educational research, which explains why traditional teaching approaches in large classes fail to reach many students and provides a basis for designing improved methods of instruction. Discipline-based educational research in the life sciences and other areas has identified several innovative promising practices and demonstrated their effectiveness for increasing student learning. Their widespread adoption could have a major impact on the introductory training of biology students.

A diagnostic assessment for introductory molecular and cell biology

We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed for use as a pre- and posttest to measure student learning gains. To develop the assessment, we first worked with faculty to create a set of learning goals that targeted important concepts in the field and seemed likely to be emphasized by most instructors teaching these subjects. We interviewed students using open-ended questions to identify commonly held misconceptions, formulated multiple-choice questions that included these ideas as distracters, and reinterviewed students to establish validity of the instrument. The assessment was then evaluated by 25 biology experts and modified based on their suggestions. The complete revised assessment was administered to more than 1300 students at three institutions. Analysis of statistical parameters including item difficulty, item discrimination, and reliability provides evidence that the IMCA is a valid and reliable instrument with several potential uses in gauging student learning of key concepts in molecular and cell biology.

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.