Merlin and expanded integrate cell signaling that regulates cyst stem cell proliferation in the Drosophila testis niche.

The Drosophila testis is a model organism stem cell niche in which two stem cell populations coordinate together to produce sperm; thus, these stem cells must be balanced in the niche. Merlin, a tumor-suppressor and human disease gene required for contact inhibition of proliferation, is known to limit the proliferation of the somatic cyst stem cells in the testis niche. Expanded encodes a protein that is structurally similar to Merlin in Drosophila, and is semi-redundant with Merlin in multiple tissues. We found that expanded depletion caused similar cyst lineage cell over-proliferation as observed with Merlin, and double mutants showed more severe phenotypes than either gene individually. Thus, these genes have partially redundant functions in the cyst lineage cells of this niche. We also expressed non-phosphorylatable constitutively "tumor suppressing" alleles of Merlin in cyst lineage cells, and surprisingly, we observed a similar cyst lineage over-proliferation phenotype. Merlin is known to impact multiple different signaling pathways to exert its effect on proliferation. We found that the Merlin loss of function phenotype was associated with an increase in MAPK/ERK signaling, consistent with Merlin's established role in transmembrane receptor inhibition. Constitutive Merlin displayed a reduction in both MAPK/ERK signaling and PI3K/Tor signaling. PI3K/Tor signaling is required for cyst cell differentiation, and inhibition of this pathway by Merlin activation phenocopied the Tor cyst lineage loss of function phenotype. Thus, Merlin impacts and integrates the activity of multiple signaling pathways in the testis niche. The ability of Merlin to dynamically change its activity via phosphorylation in response to local contact cues provides an intriguing mechanism whereby the signaling pathways that control these stem cells might be dynamically regulated in response to the division of a neighboring germ cell.

The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates.

The era of 'big data' is also the era of abundant data, creating new opportunities for student-scientist research partnerships. By coordinating undergraduate efforts, the Genomics Education Partnership produces high-quality annotated data sets and analyses that could not be generated otherwise, leading to scientific publications while providing many students with research experience.

Pvr regulates cyst stem cell division in the Drosophila testis niche, and has functions distinct from Egfr.

Regulation of the rate of stem cell division is one of the key determinants of the abundance of differentiating progeny in stem cell-supported tissues, and mis-regulation can lead to tumorigenesis. The well-studied Drosophila testis niche is an excellent model system to study the regulation of stem cell division in vivo. This niche supports two stem cell populations-the germline stem cells (GSCs) and cyst stem cells (CySCs), which cluster around a group of cells called the hub. The differentiating cells of these two stem cell populations cooperate together to produce sperm. Signal transduction initiated by the epidermal growth factor receptor (Egfr) is a key regulatory pathway in the cyst lineage, and much of the study of this stem cell population has centered around understanding the complexities of the requirements for Egfr signaling. We examined another receptor tyrosine kinase, Pvr, the sole Drosophila PDGF/VEGF homolog, and found that it accumulates in the cyst lineage cells of the testis, while its ligand Pvf1 accumulates in the hub. Pvr inhibition caused a reduction in both CySC numbers and the proportion of CySCs in S phase, similar to Egfr inhibition. However, testes with Pvr inhibition exhibited a low-penetrance non-autonomous germ cell differentiation defect distinct from that observed with Egfr inhibition. Cyst cells with constitutively activated Pvr failed to support germ cell differentiation, as observed with constitutively activated Egfr. However, constitutively activated Pvr promoted tumorous accumulation of cyst cells outside of the niche, a phenotype not observed with constitutively activated Egfr. Thus, Egfr and Pvr have some receptor-specific functions and some shared functions in the cyst lineage cells of the testis.

Student Attitudes Contribute to the Effectiveness of a Genomics CURE.

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience.

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.

germ cell-less acts to repress transcription during the establishment of the Drosophila germ cell lineage.

Previously, it has been shown that, during early Drosophila and C. elegans development, the germ cell precursors undergo a period of transcriptional quiescence. Here, we report that Germ cell-less (GCL), a germ plasm component necessary for the proper formation of "pole cells," the germ cell precursors in Drosophila, is required for the establishment of this transcriptional quiescence. While control embryos silence transcription prior to pole cell formation in the pole cell-destined nuclei, this silencing does not occur in embryos that lack GCL activity. The failure to establish quiescence is tightly correlated with failure to form the pole cells. Furthermore, we show that GCL can repress transcription of at least a subset of genes in an ectopic context, independent of other germ plasm components. Our results place GCL as the earliest gene known to act in the transcriptional repression of the germline. GCL's subcellular distribution on the nucleoplasmic surface of the nuclear envelope and its effect on transcription suggest that it may act to repress transcription in a manner similar to that proposed for transcriptional silencing of telomeric regions.

Examining the process of de novo gene birth: an educational primer on "integration of new genes into cellular networks, and their structural maturation".

New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database.

A course-based research experience: how benefits change with increased investment in instructional time.

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Stem cells supporting other stem cells.

Adult stem cell therapies are increasingly prevalent for the treatment of damaged or diseased tissues, but most of the improvements observed to date are attributed to the ability of stem cells to produce paracrine factors that have a trophic effect on existing tissue cells, improving their functional capacity. It is now clear that this ability to produce trophic factors is a normal and necessary function for some stem cell populations. In vivo adult stem cells are thought to self-renew due to local signals from the microenvironment where they live, the niche. Several niches have now been identified which harbor multiple stem cell populations. In three of these niches - the Drosophila testis, the bulge of the mammalian hair follicle, and the mammalian bone marrow - one type of stem cell has been found to produce factors that contribute to the maintenance of a second stem cell population in the shared niche. In this review, I will examine the architecture of these three niches and discuss the molecular signals involved. Together, these examples establish a new paradigm for stem cell behavior, that stem cells can promote the maintenance of other stem cells.

Germline self-renewal requires cyst stem cells and stat regulates niche adhesion in Drosophila testes.

Adults maintain tissue-specific stem cells through niche signals. A model for niche function is the Drosophila melanogaster testis, where a small cluster of cells called the hub produce locally available signals that allow only adjacent cells to self-renew. We show here that the principal signalling pathway implicated in this niche, chemokine activation of STAT, does not primarily regulate self-renewal of germline stem cells (GSCs), but rather governs GSC adhesion to hub cells. In fact, GSC renewal does not require hub cell contact, as GSCs can be renewed solely by contact with the second resident stem cell population, somatic cyst stem cells (CySCs), and this involves BMP signalling. These data suggest a modified paradigm whereby the hub cells function as architects of the stem cell environment, drawing into proximity cellular components necessary for niche function. Self-renewal functions are shared by the hub cells and the CySCs. This work also reconciles key differences in GSC renewal between Drosophila testis and ovary niches, and highlights how a niche can coordinate the production of distinct lineages by having one stem cell type rely on a second.

Zfh-1 controls somatic stem cell self-renewal in the Drosophila testis and nonautonomously influences germline stem cell self-renewal.

The ability of adult stem cells to maintain their undifferentiated state depends upon residence in their niche. While simple models of a single self-renewal signal are attractive, niche-stem cell interactions are likely to be more complex. Many niches have multiple cell types, and the Drosophila testis is one such complex niche with two stem cell types, germline stem cells (GSCs) and somatic cyst progenitor cells (CPCs). These stem cells require chemokine activation of Jak/STAT signaling for self-renewal. We identified the transcriptional repressor Zfh-1 as a presumptive somatic target of Jak/STAT signaling, demonstrating that it is necessary and sufficient to maintain CPCs. Surprisingly, sustained zfh-1 expression or intrinsic STAT activation in somatic cells caused neighboring germ cells to self-renew outside their niche. In contrast, germline-intrinsic STAT activation was insufficient for GSC renewal. These data reveal unexpected complexity in cell interactions in the niche, implicating CPCs in GSC self-renewal.

Transcriptional silencing and translational control: key features of early germline development.

The germ lineage has been studied for a long time because of its crucial role in the propagation and survival of a species. While this lineage, in contrast to the soma, is clearly unique in its totipotent ability to produce a new organism, it has now been found also to have specific features at the cellular level. One feature, a period of transcriptional quiescence in the early germ cell precursors, has been observed in both Drosophila and C. elegans, where it is essential for the formation and the survival of the germline. In addition, there are numerous instances where these early germ cells are reliant on translational regulation, especially in Drosophila. The genes that are important for these two functions, the mechanisms of their action, and studies in vertebrate organisms that reveal similarities as well as some potential differences in early germ cell development are discussed.