Carmen R. Domingo

Cell behaviors associated with somite segmentation and rotation in Xenopus laevis.

During vertebrate development the formation of somites is a critical step, as these structures will give rise to the vertebrae, muscle, and dermis. In Xenopus laevis, somitogenesis consists of the partitioning of the presomitic mesoderm into somites, which undergo a 90‐degree rotation to become aligned parallel to the notochord. Using a membrane‐targeted green fluorescent protein to visualize cell outlines, we examined the individual cell shape changes occurring during somitogenesis. We show that this process is the result of specific, coordinated cell behaviors beginning with the mediolateral elongation of cells in the anterior presomitic mesoderm and then the subsequent bending of these elongated cells to become oriented parallel with the notochord. By labeling a clonal population of paraxial mesoderm cells, we show that cells bend around their dorsoventral axis. Moreover, this cell bending correlates with an increase in the number of filopodial protrusions, which appear to be posteriorly directed toward the newly formed segmental boundary. By examining the formation of somites at various positions along the anteroposterior axis, we show that the general sequence of cell behaviors is the same; however, somite rotation in anterior somites is slower than in posterior somites. Lastly, this coordinated set of cell behaviors occurs in a dorsal‐to‐ventral progression within each somite such that cells in the dorsal aspect of the somite become aligned along the anteroposterior axis before cells in other regions of the same somite. Together, our data further define how these cell behaviors are temporally and spatially coordinated during somite segmentation and rotation. Developmental Dynamics 235:3268–3279, 2006.

Signals that instruct somite and myotome formation persist in Xenopus laevis early tailbud stage embryos

Somite formation is a lengthy process that begins at gastrulation and continues through tailbud stages to form approximately 50 pairs of somites in the frog, Xenopus laevis. In Xenopus, the somite primarily gives rise to myotome. We sought to determine whether the formation of somites and myotome requires a transient signal active during gastrulation or a constitutive signal active throughout development to instruct dorsal mesodermal cells to form the posterior somites. Previous work from our lab revealed that cells from the neural ectoderm are capable of responding to mesoderm-inducing signals [Domingo and Keller: Dev Biol 2000;225:226–240]. Thus, to test for the presence of somite-inducing signals, we performed a series of grafting experiments in which we used gastrula cells from the anterior neural ectoderm (ANE). Fluorescently labeled ANE cells were grafted to the posterior paraxial mesoderm of progressively older host embryos between stages 11 (mid gastrula) and 23 (early tailbud). Our results showed that signals within the paraxial mesoderm can instruct prospective ANE cells, which normally give rise to head structures, to instead differentiate into myotome cells. We found that the grafted cells adopted the local paraxial mesoderm cell behaviors, which consists of mediolateral intercalation, segmentation, somite cell rotation, and differentiation to myotome. In addition, we show that the grafted ANE cells that adopt a myotome morphology also express the muscle-specific marker, 12/101. Through a series of heterochronic grafts, we determined that the duration of somite-inducing signals extends from the early gastrula (stage 11) through the early tailbud (stage 23) stage embryos. These results demonstrate that somite induction is not a transient event that occurs during gastrulation, but that it is instead a continuous event that can occur as new somites are added to the posterior axis.

The Role of Sdf‐1α signaling in Xenopus laevis somite morphogenesis

Background: Stromal derived factor‐1α (sdf‐1α), a chemoattractant chemokine, plays a major role in tumor growth, angiogenesis, metastasis, and in embryogenesis. The sdf‐1α signaling pathway has also been shown to be important for somite rotation in zebrafish (Hollway et al., 2007). Given the known similarities and differences between zebrafish and Xenopus laevis somitogenesis, we sought to determine whether the role of sdf‐1α is conserved in Xenopus laevis. Results: Using a morpholino approach, we demonstrate that knockdown of sdf‐1α or its receptor, cxcr4, leads to a significant disruption in somite rotation and myotome alignment. We further show that depletion of sdf‐1α or cxcr4 leads to the near absence of β‐dystroglycan and laminin expression at the intersomitic boundaries. Finally, knockdown of sdf‐1α decreases the level of activated RhoA, a small GTPase known to regulate cell shape and movement. Conclusion: Our results show that sdf‐1α signaling regulates somite cell migration, rotation, and myotome alignment by directly or indirectly regulating dystroglycan expression and RhoA activation. These findings support the conservation of sdf‐1α signaling in vertebrate somite morphogenesis; however, the precise mechanism by which this signaling pathway influences somite morphogenesis is different between the fish and the frog. Developmental Dynamics 243:509–526, 2014.

Temporal and spatial patterning of axial myotome fibers in Xenopus laevis

Somites give rise to the vertebral column and segmented musculature of adult vertebrates. The cell movements that position cells within somites along the anteroposterior and dorsoventral axes are not well understood. Using a fate mapping approach, we show that at the onset of Xenopus laevis gastrulation, mesoderm cells undergo distinct cell movements to form myotome fibers positioned in discrete locations within somites and along the anteroposterior axis. We show that the distribution of presomitic cells along the anteroposterior axis is influenced by convergent and extension movements of the notochord. Heterochronic and heterotopic transplantations between presomitic gastrula and early tail bud stages show that these cells are interchangeable and can form myotome fibers in locations determined by the host embryo. However, additional transplantation experiments revealed differences in the competency of presomitic cells to form myotome fibers, suggesting that maturation within the tail bud presomitic mesoderm is required for myotome fiber differentiation. Developmental Dynamics 239:1162–1177, 2010.© 2010 Wiley‐Liss, Inc.

Classroom sound can be used to classify teaching practices in college science courses

Significance Although the United States needs to expand its STEM (science, technology, engineering, mathematics) workforce, United States postsecondary institutions struggle to retain and effectively teach students in STEM disciplines. Using teaching techniques beyond lecture, such as pair discussions and reflective writing, has been shown to boost student learning, but it is unknown what proportion of STEM faculty use these active-learning pedagogies. Here we describe DART: Decibel Analysis for Research in Teaching, a machine-learning–derived algorithm that analyzes classroom sound to predict with high accuracy the learning activities used in classrooms, and its application to thousands of class session recordings. DART can be used for large-scale examinations of STEM teaching practices, evaluating the extent to which educators maximize opportunities for effective STEM learning. Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning–derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.

Making muscle: Morphogenetic movements and molecular mechanisms of myogenesis in Xenopus laevis.

Xenopus laevis offers unprecedented access to the intricacies of muscle development. The large, robust embryos make it ideal for manipulations at both the tissue and molecular level. In particular, this model system can be used to fate map early muscle progenitors, visualize cell behaviors associated with somitogenesis, and examine the role of signaling pathways that underlie induction, specification, and differentiation of muscle. Several characteristics that are unique to X. laevis include myogenic waves with distinct gene expression profiles and the late formation of dermomyotome and sclerotome. Furthermore, myogenesis in the metamorphosing frog is biphasic, facilitating regeneration studies. In this review, we describe the morphogenetic movements that shape the somites and discuss signaling and transcriptional regulation during muscle development and regeneration. With recent advances in gene editing tools, X. laevis remains a premier model organism for dissecting the complex mechanisms underlying the specification, cell behaviors, and formation of the musculature system.

Collectively Improving Our Teaching: Attempting Biology Department–wide Professional Development in Scientific Teaching

A collaborative professional development program that engaged nearly 90% of faculty in a biology department in more than 40 hours of training on scientific teaching was instituted. Participating instructors integrated active learning in their courses, as shown through a variety of methods, and reported positive effects on teaching and departmental community.

Muscle specification in the Xenopus laevis gastrula-stage embryo

Recent fate maps of the Xenopus laevis gastrula show that mesodermal tissue surrounding the blastopore gives rise to muscle (Keller [ 1991 ] Methods Cell Biol 36:61–113; Lane and Smith [ 1999 ] Development 126:423–434). In a significant deviation from earlier data, the new maps demonstrate that cells in the ventral half of the gastrula are precursors to a significant portion of trunk somites. However, these posterior somites are not formed until tadpole stages (stages 38–44). We therefore set out to determine the timing of muscle specification within the ventral half of the gastrula. Our approach was to generate a series of tissue explants from gastrula‐stage embryos and then culture them to either stage 28 (tailbud) or stage 44 (tadpole). At each endpoint, the presence of muscle in explants was assessed with a muscle‐specific antibody. Interestingly, we found that muscle tissue is detected in ventral explants. However, these explants must be cultured to the tadpole stage. This is perhaps not unexpected, as this is the point at which this tissue normally gives rise to muscle. We further show that muscle specification of the involuting marginal zone does not change over the course of gastrulation. Together, these results suggest that dorsalizing signals emanating from the midline during gastrulation are not necessary for muscle specification of the ventral half of the involuting marginal zone. Developmental Dynamics 233:1348–1358, 2005.

Embryonic cells depleted of β-catenin remain competent to differentiate into dorsal mesodermal derivatives

Disruption of axis specification leads to defects in dorsal tissue patterning and cell movements. Here, we examine how β‐catenin coordinately affects gastrulation movements and dorsal mesoderm differentiation. The reduction of β‐catenin protein levels by morpholino oligonucleotides complementary to β‐catenin mRNA causes a disruption in gastrulation movements. Time‐lapse imaging of β‐catenin morphants during gastrulation reveals that involution occurs simultaneously around the blastopore in the absence of convergent extension cell movements. Transplantation experiments show that morphant cells grafted from the marginal zone into wild‐type hosts differentiate into notochord and muscle. However, wild‐type mesoderm cells grafted to the marginal zone of β‐catenin morphants do not form dorsal tissues. These data argue that β‐catenin is not required for the initial establishment of dorsal mesoderm cell competency, but it is required for the maintenance of that competency. We propose that tissue interactions that occur during convergent extension movements are necessary for maintaining dorsal tissue competency. Developmental Dynamics 236:3007–3019, 2007.

Promoting diversity in computing

In this paper we present a pilot program at San Francisco State University, Promoting INclusivity in Computing (PINC), that is designed to achieve two goals simultaneously: (i) improving diversity in computing, and (ii) increasing computing literacy in data-intensive fields. To achieve these goals, the PINC program enrolls undergraduate students from non Computer Science (non-CS) fields, such as, Biology, that have become increasingly data-driven, and that traditionally attract diverse student population. PINC incorporates several well-established pedagogical practices, such as, cohort-based program structure, near-peer mentoring, and project-driven learning, to attract, retain, and successfully graduate a highly diverse and interdisciplinary student body. On successful completion of the program, students are awarded a minor in Computing Applications. Since its inception 18 months ago, 60 students have participated in this program. Of these 73% are women, and 51% are underrepresented minorities (URM). 74% of the participating students had nominal or no exposure to computer programming before PINC. Findings from student surveys show that majority of the PINC students now feel less intimidated about computer programming, and vividly see its utility and necessity. For several students, participation in the PINC program has already opened up career pathways (industry and academic summer internships) that were not available to them before.