Ben Ewen-Campen

Harvard Medical School | HMS · Department of Genetics

The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA-system or QF-system. Here, we...

The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA-system or QF-system. Here, we...

The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA-system or QF-system. Here, we...

Having tools and resources for independent control of gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as LexA/LexAop or QF/QUAS...

The split-Gal4 system allows for intersectional genetic labeling of highly specific cell types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a gen...

The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a gen...

Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene perturbation, and there is a need...

Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene perturbation, and there is a need...

The frizzled (fz) and disheveled (dsh) genes are highly conserved members of the core planar cell polarity (PCP) pathway and of the Wnt signaling pathway. Given these dual functions, a number of studies have examined whether Wnt ligands may provide a global, tissue-scale orientation cue for PCP establishment during development, and these studies ha...

The Transgenic RNAi Project (TRiP), a Drosophila melanogaster functional genomics platform at Harvard Medical School, was initiated in 2008 to generate and distribute a genome-scale collection of RNAi fly stocks. To date, the TRiP has generated >15,000 RNAi fly stocks. As this covers most Drosophila genes, we have largely transitioned to developmen...

Screening for successful CRISPR/Cas9 editing events remains a time consuming technical bottleneck in the field of Drosophila genome editing. This step can be particularly laborious for events that do not cause a visible phenotype, or those which occur at relatively low frequency. A promising strategy to enrich for desired CRISPR events is to co-sel...

Significance We present flySAM, a potent system for Cas9-based transcriptional activation (CRISPRa) in Drosophila . flySAM greatly improves on existing in vivo CRISPRa techniques in terms of potency, scalability, and ease of use, and provides a simple and general method for conducting overexpression experiments and screens. flySAM will now serve as...

CRISPR/Cas9-based transcriptional activation (CRISPRa) has recently emerged as a powerful and scalable technique for systematic over-expression genetic analysis in Drosophila melanogaster. We present flySAM, a potent new tool for in vivo CRISPRa, which offers a major improvement over existing strategies in terms of effectiveness, scalability, and e...

Perturbation of genes in cultured cells is useful for gene function discovery, combinatorial screening, and other applications. In contrast to RNAi the CRISPR system targets genomic sequence. CRISPR can be used to make double strand breaks in genomic DNA to induce mutations in specific gene targets, including knockout mutations or more specific gen...

Single-gene knockout experiments can fail to reveal function in the context of redundancy, which is frequently observed among duplicated genes (paralogs) with overlapping functions. We discuss the complexity associated with studying paralogs and outline how recent advances in CRISPR will help address the "phenotype gap" and impact biomedical resear...

Significance Recently, a number of approaches have been developed to repurpose the CRISPR/Cas9 system as a sequence-specific transcriptional activator for gain-of-function experiments (CRISPR activators, or “CRISPRa”). While multiple CRISPRa strategies have been characterized in cell culture, little is known about their performance in vivo. We pres...

The rapid rise of CRISPR as a technology for genome engineering and related research applications has created a need for algorithms and associated online tools that facilitate design of on-target and effective guide RNAs (gRNAs). Here, we review the state-of-the-art in CRISPR gRNA design for research applications of the CRISPR-Cas9 system, includin...

Several programmable transcription factors exist based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare Cas9 activator systems and examine their ability to induce robust gene expression in several human, mouse, and fly cell lines. We also explore th...

A number of approaches for Cas9-mediated transcriptional activation have recently been developed, allowing target genes to be over-expressed from their endogenous genomic loci. However, these approaches have thus far been limited to cell culture, and this technique has not been demonstrated in vivo in any animal. The technique involving the fewest...

Significance Many model organisms specify germ cells using maternally supplied germ-line determinants. In contrast, mice rely on embryonic cell–cell signaling to induce cells to become germ cells. Molecular evidence for inductive germ-line specification had previously been provided only for the mouse. Here we provide functional evidence for inducti...

Primordial germ cell (PGC) formation in holometabolous insects like Drosophila melanogaster relies on maternally synthesised germ cell determinants that are asymmetrically localised to the oocyte posterior cortex. Embryonic nuclei that inherit this "germ plasm" acquire PGC fate. In contrast, historical studies of basally branching insects (Hemimeta...

Most genomic resources available for insects represent the Holometabola, which are insects that undergo complete metamorphosis like beetles and flies. In contrast, the Hemimetabola (direct developing insects), representing the basal branches of the insect tree, have very few genomic resources. We have therefore created a large and publicly availabl...

Background: Primordial germ cell (PGC) specification is a universal process across animals, but the molecular mechanisms specifying PGCs are remarkably diverse. In Drosophila, PGCs are specified by maternally provided, asymmetrically localized cytoplasmic factors (germ plasm). In contrast, historical literature on most other arthropods reports tha...

oskar is the only gene in the animal kingdom necessary and sufficient for specifying functional germ cells [1, 2]. However, oskar has only been identified in holometabolous ("higher") insects that specify their germline using specialized cytoplasm called germ plasm [3]. Here we show that oskar evolved before the divergence of higher insects and pro...

Arthropods are the most diverse animal phylum, but their genomic resources are relatively few. While the genome of the branchiopod Daphnia pulex is now available, no other large-scale crustacean genomic resources are available for comparison. In particular, genomic resources are lacking for the most tractable laboratory model of crustacean developm...

Arthropods and vertebrates display a segmental body organisation along all or part of the anterior-posterior axis. Whether this reflects a shared, ancestral developmental genetic mechanism for segmentation is uncertain. In vertebrates, segments are formed sequentially by a segmentation 'clock' of oscillating gene expression involving Notch pathway...

Most evolutionary developmental biology ("evo-devo") studies of emerging model organisms focus on small numbers of candidate genes cloned individually using degenerate PCR. However, newly available sequencing technologies such as 454 pyrosequencing have recently begun to allow for massive gene discovery in animals without sequenced genomes. Within...

Relatively little is known about Arctic Warblers (Phylloscopus borealis) that breed in central Alaska. We monitored Arctic Warbler populations in two adjacent but distinct habitat types in central Alaska (high elevation, ‘open shrub’ and lower elevation, ‘dense shrub’). We collected 95 nests over three breeding seasons to learn more about nest-buil...

Germ cells occupy a unique position in animal reproduction, development, and evolution. In sexually reproducing animals, only they can produce gametes and contribute genetically to subsequent generations. Nonetheless, germ line specification during embryogenesis is conceptually the same as the specification of any somatic cell type: germ cells must...

Many scarab beetles produce rigid projections from the body called horns. The exaggerated sizes of these structures and the staggering diversity of their forms have impressed biologists for centuries. Recent comparative studies using DNA sequence-based phylogenies have begun to reconstruct the historical patterns of beetle horn evolution. At the sa...