The Base of the Animal Tree?: The identity of the most basal lineages of the animal kingdom evolutionary tree has long been contested. Ryan et al. (p. 10.1126/science.1242592 ; see the Perspective by Rokas ) sequenced the genome of the ctenophore the warty comb jelly or sea walnut, Mnemiopsis leidyi , and conclude that ctenophores alone, not sponges or the clade consisting of both ctenophores and cnidarians, are the most basal extant animals. The results suggest a specific evolutionary process that likely occurred—including repeated gains and loss of mesoderm, expansion of genes associated with the cell cycle, growth signaling, apoptosis, and epithelial and neural cell types. Furthermore, previous hypotheses regarding the evolution of animals may require re-evaluation.

Mapping Hydra development cell by cell: Hydra continually renews all cells in its body using three stem cell populations. This feature of Hydra allowed Siebert et al. to identify the transcriptional signatures of stem cells, progenitors, and terminally differentiated cells using single-cell RNA sequencing of adult Hydra (see the Perspective by Reddien). From these data, they built differentiation trajectories for all cell lineages, identified gene modules expressed along these trajectories, and identified putative regulators of genes within these modules. In addition, they identified candidate markers for elusive cell populations (such as multipotent stem cells and germline stem cells) and built a molecular map of the nervous system. Science , this issue p. eaav9314 ; see also p. 314

Production of amyloid-β protein (Aβ) is initiated by a β-secretase that cleaves the Aβ precursor protein (APP) at the N terminus of Aβ (the β site). A recently identified aspartyl protease, BACE, cleaves the β site and at residue 11 within the Aβ region of APP. Here we show that BACE2, a BACE homolog, cleaves at the β site and more efficiently at a different site within Aβ. The Flemish missense mutation of APP, implicated in a form of familial Alzheimer's disease, is adjacent to this latter site and markedly increases Aβ production by BACE2 but not by BACE. BACE and BACE2 respond identically to conservative β-site mutations, and alteration of a common active site Arg inhibits β-site cleavage but not cleavage within Aβ by both enzymes. These data suggest that BACE2 contributes to Aβ production in individuals bearing the Flemish mutation, and that selective inhibition of these highly similar proteases may be feasible and therapeutically advantageous.

Cnidarian bleaching results from the breakdown in the symbiosis between the host cnidarian and its dinoflagellate symbiont. Coral bleaching in recent years has increasingly caused degradation and mortality of coral reefs on a global scale. Although much is understood about the environmental causes of bleaching, the underlying cellular mechanisms of symbiont release that drive the process are just beginning to be described. In this study, we investigated the roles of two cellular pathways, host cell apoptosis and autophagy, in the bleaching process of the symbiotic anemone Aiptasia pallida . Host cell apoptosis was experimentally manipulated using gene knockdown of an anemone caspase by RNA interference, chemical inhibition of caspase using ZVAD-fmk and an apoptosis-inducer wortmannin. Autophagy was manipulated by chemical inhibition using wortmannin or induction using rapamycin. The applications of multiple single treatments resulted in some increased bleaching in anemones under control conditions but no significant drop in bleaching in individuals subjected to a hyperthermic stress. These results indicated that no single pathway is responsible for symbiont release during bleaching. However, when multiple inhibitors were applied simultaneously to block both apoptosis and autophagy, there was a significant reduction in bleaching in heat-stressed anemones. Our results allow us to formulate a model for cellular processes involved in the control of cnidarian bleaching where apoptosis and autophagy act together in a see-saw mechanism such that if one is inhibited the other is induced. Similar interconnectivity between apoptosis and autophagy has previously been shown in vertebrates including involvement in an innate immune response to pathogens and parasites. This suggests that the bleaching response could be a modified immune response that recognizes and removes dysfunctional symbionts.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.