Search

The tragic murder of Mr. George Floyd brought to the head long-standing issues of racial justice and equity in the United States and beyond. This prompted many institutions of higher education, including professional organizations and societies, to engage in long-overdue conversations about the role of scientific institutions in perpetuating racism. Similar to many professional societies and organizations, the Society for the Advancement of Biology Education Research (SABER), a leading international professional organization for discipline-based biology education researchers, has long struggled with a lack of representation of People of Color (POC) at all levels within the organization. The events surrounding Mr. Floyd’s death prompted the members of SABER to engage in conversations to promote self-reflection and discussion on how the society could become more antiracist and inclusive. These, in turn, resulted in several initiatives that led to concrete actions to support POC, increase their representation, and amplify their voices within SABER. These initiatives included: a self-study of SABER to determine challenges and identify ways to address them, a year-long seminar series focused on issues of social justice and inclusion, a special interest group to provide networking opportunities for POC and to center their voices, and an increase in the diversity of keynote speakers and seminar topics at SABER conferences. In this article, we chronicle the journey of SABER in its efforts to become more inclusive and antiracist. We are interested in increasing POC representation within our community and seek to bring our resources and scholarship to reimagine professional societies as catalyst agents towards an equitable antiracist experience. Specifically, we describe the 12 concrete actions that SABER enacted over a period of a year and the results from these actions so far. In addition, we discuss remaining challenges and future steps to continue to build a more welcoming, inclusive, and equitable space for all biology education researchers, especially our POC members. Ultimately, we hope that the steps undertaken by SABER will enable many more professional societies to embark on their reflection journeys to further broaden scientific communities.

Writing is an active learning strategy strongly linked to student engagement. Student-authored learning narratives can reveal powerful self-beliefs that can either activate or inhibit success. In this targeted study of the aspect of student engagement most associated with self-beliefs (i.e., self-efficacy), students in separate sections of an introductory college biology course taught by the same professor were divided into experimental and control groups. The experimental group participated in an additional 1-unit required study skills component featuring writing-to-learn and self-efficacy development strategies. One hundred forty “pre” and “post” student self-efficacy narratives written in both cohorts were scored and also thematically coded. Scoring revealed a Cohen’s effect size d = 0.63 for the experimental group, but only d = 0.28 for control. Thus, writing appears to activate student self-efficacy most if it is part of a deliberate and sustained campaign. Gains seemed particularly impactful for struggling students, as the experimental group also saw significantly fewer students, with unmet fundamental skills, earning Ds and Fs in the course than those in the control group. Subsequent student interviews were also analyzed and informed recommendations for future research and pedagogical practice.

The origin of the vertebrates was a major event in the evolution of morphological diversity and the genetic mechanisms responsible for this diversity, once purely theoretical, can now be approached experimentally in the genome era.With a prototypical chordate genome, vertebrate-like development and simple morphology, amphioxus provides the appropriate model for investigating the origin of the vertebrates. Comparative genomics is revealing that both conservation and divergence of genes and cis -regulatory elements involved in developmental regulatory networks are required to shape different animal body plans. This article reviews the cis -regulatory studies performed in amphioxus, the discovery of conserved non-coding elements (CNEs) across the metazoans and the examination of amphioxus CNEs. Emerging ideas on the evolution of CNEs after large-scale genome duplication events and the state of cephalochordate genomics are also discussed.

Amphioxus and vertebrates are the only deuterostomes to exhibit unequivocal somitic segmentation. The relative simplicity of the amphioxus genome makes it a favorable organism for elucidating the basic genetic network required for chordate somite development. Here we describe the developmental expression of the somite marker, AmphiTbx15/18/22, which is first expressed at the mid-gastrula stage in dorsolateral mesendoderm. At the early neurula stage, expression is detected in the first three pairs of developing somites. By the mid-neurula stage, expression is downregulated in anterior somites, and only detected in the penultimate somite primordia. In early larvae, the gene is expressed in nascent somites before they pinch off from the posterior archenteron (tail bud). Integrating functional, phylogenetic and expression data from a variety of triploblast organisms, we have reconstructed the evolutionary history of the Tbx15/18/22 subfamily. This analysis suggests that the Tbx15/18/22 gene may have played a role in patterning somites in the last common ancestor of all chordates, a role that was later conserved by its descendents following gene duplications within the vertebrate lineage. Furthermore, the comparison of expression domains within this gene subfamily reveals similarities in the genetic bases of trunk and cranial mesoderm segmentation. This lends support to the hypothesis that the vertebrate head evolved from an ancestor possessing segmented cranial mesoderm.

PHA-4 is a forkhead/winged helix transcription factor that acts as an organ identity factor in the development of the Caenorhabditis elegans pharynx. PEB-1 is a novel DNA-binding protein also involved in pharyngeal morphogenesis. PHA-4 and PEB-1 bind at overlapping sites on the C183 sequence element that controls pharynx-specific expression of the C. elegans myo-2 gene. It has been suggested that PHA-4 and PEB-1 act cooperatively on the C183 sequence. In this study, we test this model and assess the C183-dependent transcriptional activity of PHA-4 and PEB-1, both individually and in combination. We show that PHA-4 and PEB-1 are both modest transcriptional activators in yeast but that co-expression of the two factors does not result in significantly increased expression of a C183-regulated reporter gene. Electrophoretic mobility-shift assays provide no evidence for the formation of a PHA-4/PEB-1 complex in vitro but rather show that PHA-4 and PEB-1 cannot bind C183 simultaneously. As we have reported previously, ectopic expression of PHA-4 in C. elegans causes ectopic expression of a C183-regulated reporter gene. We show that ectopic expression of PEB-1 cannot cause ectopic expression of the same reporter but rather ectopic PEB-1 inhibits reporter gene activation by PHA-4. Overall, our results do not support a model in which PHA-4 and PEB-1 synergize in vivo but rather support a model in which PEB-1 may negatively modulate PHA-4's ability to activate transcription through C183 during formation of the C. elegans pharynx.

Gene expression in the Caenorhabditis elegans pharynx is regulated in part by organ-specific signals, which in the myo-2 gene target a regulatory sequence called the C subelement. C subelement activity requires the organ specification factor PHA-4, a winged-helix transcription factor expressed in all pharyngeal cells. To identify additional factors involved in pharyngeal organogenesis, we performed a yeast one-hybrid screen for C subelement binding proteins. Here we describe the novel factor PEB-1, which is coexpressed with PHA-4 in many pharyngeal cell types, including muscles, epithelial cells, marginal cells, and glands, but is undetectable in the pharyngeal nervous system. PEB-1 is also detected outside the pharynx in cells surrounding the rectum and vulva, as well as in the germ line. Reduction of peb-1 function using RNAi results in morphological defects in the somatic tissues in which peb-1 is expressed. We have mapped the PEB-1 DNA-binding domain to a 158-residue region, which is unrelated to known DNA-binding proteins but shares some sequence similarity to the Drosophila Mod(mdg4) proteins. PEB-1 specifically recognizes a site in the C subelement that partially overlaps the PHA-4 binding site. Both the PEB-1 and the PHA-4 binding sites are necessary for strong C subelement enhancer activity in some cells in which these factors are coexpressed. In contrast the PEB-1 site is dispensable for C subelement activity in pharyngeal neurons. We propose that PEB-1 functions with PHA-4 to activate target gene expression in cells in which they are coexpressed.

In the basal chordate amphioxus (Branchiostoma), somites extend the full length of the body. The anteriormost somites segment during the gastrula and neurula stages from dorsolateral grooves of the archenteron. The remaining ones pinch off, one at a time, from the tail bud. These posterior somites appear to be homologous to those of vertebrates, even though the latter pinch off from the anterior end of bands of presomitic mesoderm rather than directly from the tail bud. To gain insights into the evolution of mesodermal segmentation in chordates, we determined the expression of ten genes in nascent amphioxus somites. Five (Uncx4.1, NeuroD/atonal-related, IrxA, Pcdhdelta2-17/18, and Hey1) are expressed in stripes in the dorsolateral mesoderm at the gastrula stage and in the tail bud while three (Paraxis, Lcx, and Axin) are expressed in the posterior mesendoderm at the gastrula and neurula stages and in the tail bud at later stages. Expression of two genes (Pbx and OligA) suggests roles in the anterior somites that may be unrelated to initial segmentation. Together with previous data, our results indicate that, with the exception that Engrailed is only segmentally expressed in the anterior somites, the genetic mechanisms controlling formation of both the anterior and posterior somites are probably largely identical. Thus, the fundamental pathways for mesodermal segmentation involving Notch-Delta, Wnt/beta-catenin, and Fgf signaling were already in place in the common ancestor of amphioxus and vertebrates although budding of somites from bands of presomitic mesoderm exhibiting waves of expression of Notch, Wnt, and Fgf target genes was likely a vertebrate novelty. Given the conservation of segmentation gene expression between amphioxus and vertebrate somites, we propose that the clock mechanism may have been established in the basal chordate, while the wavefront evolved later in the vertebrate lineage.

The amphioxus genome has a single Delta gene (AmphiDelta) encoding a protein 766 amino acids long. Comparison of Delta proteins of amphioxus and other animals indicates that AmphiDelta retains features of a basal bilaterian Delta protein—in having nine epidermal growth factor (EGF) repeats and also in having characteristic numbers of amino acids separating successive cysteines between and within EGF repeats. During development, AmphiDelta is expressed in the forming somites, in some regions of pharyngeal endoderm, and in cells (presumably differentiating neurons) scattered in both the neural plate and ectoderm. Expression is strongly associated with cells initiating movements to separate themselves from parent epithelia, either en masse by evagination (endoderm and mesoderm) or by delamination as isolated cells (ectoderm). The AmphiDelta-expressing cells delaminating from the ectoderm apparently migrate beneath it as they begin differentiating into probable sensory neurons, suggesting a scenario for the evolutionary origin of the placode-derived neurons of vertebrate cranial ganglia. genesis 45:113–122, 2007. Published 2007 Wiley-Liss, Inc.

To gain insights into the relation between evolution of cis -regulatory DNA and evolution of gene function, we identified tissue-specific enhancers of the engrailed gene of the basal chordate amphioxus ( Branchiostoma floridae ) and compared their ability to direct expression in both amphioxus and its nearest chordate relative, the tunicate Ciona intestinalis. In amphioxus embryos, the native engrailed gene is expressed in three domains – the eight most anterior somites, a few cells in the central nervous system (CNS) and a few ectodermal cells. In contrast, in C. intestinalis , in which muscle development is highly divergent, engrailed expression is limited to the CNS. To characterize the tissue-specific enhancers of amphioxus engrailed , we first showed that 7.8 kb of upstream DNA of amphioxus engrailed directs expression to all three domains in amphioxus that express the native gene. We then identified the amphioxus engrailed muscle-specific enhancer as the 1.2 kb region of upstream DNA with the highest sequence identity to the mouse en-2 jaw muscle enhancer. This amphioxus enhancer directed expression to both the somites in amphioxus and to the larval muscles in C. intestinalis . These results show that even though expression of the native engrailed has apparently been lost in developing C. intestinalis muscles, they express the transcription factors necessary to activate transcription from the amphioxus engrailed enhancer, suggesting that gene networks may not be completely disrupted if an individual component is lost.

Caenorhabditis elegans PEB-1 is a novel protein containing a DNA-binding domain in its N terminus, which includes a Cys/His-rich FLYWCH motif also found in Drosophila Mod(mdg4) proteins, and a large C-terminal domain of unknown function. PEB-1 is expressed in most pharyngeal cell types, but its molecular function remains unclear. Here we describe comparative and functional analyses of PEB-1. Characterization of the PEB-1 sequence from C. briggsae indicates highest conservation in the DNA-binding domain (including the FLYWCH motif) and the C terminus, suggesting two functional domains. The PEB-1 FLYWCH motif is essential for DNA-binding and in vivo function; however, it does not bind detectable metal. Likewise, the PEB-1 C terminus is necessary for full activity in vivo, although the DNA-binding domain alone is sufficient for partial function. Both the FLYWCH motif and the C-terminal domain are required for efficient nuclear localization, suggesting PEB-1 must bind DNA and other components to remain in the nucleus. Analysis of binding sites revealed a YDTGCCRW PEB-1 consensus-binding site, and matches to this consensus are widespread in the C. elegans genome.

The amphioxus genome has a single Delta gene (AmphiDelta) encoding a protein 766 amino acids long. Comparison of Delta proteins of amphioxus and other animals indicates that AmphiDelta retains features of a basal bilaterian Delta protein—in having nine epidermal growth factor (EGF) repeats and also in having characteristic numbers of amino acids separating successive cysteines between and within EGF repeats. During development, AmphiDelta is expressed in the forming somites, in some regions of pharyngeal endoderm, and in cells (presumably differentiating neurons) scattered in both the neural plate and ectoderm. Expression is strongly associated with cells initiating movements to separate themselves from parent epithelia, either en masse by evagination (endoderm and mesoderm) or by delamination as isolated cells (ectoderm). The AmphiDelta-expressing cells delaminating from the ectoderm apparently migrate beneath it as they begin differentiating into probable sensory neurons, suggesting a scenario for the evolutionary origin of the placode-derived neurons of vertebrate cranial ganglia. genesis 45:113–122, 2007. Published 2007 Wiley-Liss, Inc.