Metabolism and the other fat: a protocadherin in mitochondria.

The protocadherin Fat is known as a tumor suppressor regulating growth in Drosophila and for its conserved function during planar cell polarity establishment. McNeill and colleagues now identify an unsuspected role for a C-terminal proteolytic product of Fat in mitochondria: regulating the electron transport machinery and metabolism.

Author Correction: Emerging mechanisms of cell competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Emerging mechanisms of cell competition.

The growth and survival of cells within tissues can be affected by 'cell competition' between different cell clones. This phenomenon was initially recognized between wild-type cells and cells with mutations in ribosomal protein (Rp) genes in Drosophila melanogaster. However, competition also affects D. melanogaster cells with mutations in epithelial polarity genes, and wild-type cells exposed to 'super-competitor' cells with mutation in the Salvador-Warts-Hippo tumour suppressor pathway or expressing elevated levels of Myc. More recently, cell competition and super-competition were recognized in mammalian development, organ homeostasis and cancer. Genetic and cell biological studies have revealed that mechanisms underlying cell competition include the molecular recognition of 'different' cells, signalling imbalances between distinct cell populations and the mechanical consequences of differential growth rates; these mechanisms may also involve innate immune proteins, p53 and changes in translation.

A network of broadly expressed HLH genes regulates tissue-specific cell fates.

Spatial and temporal expression of specific basic-helix-loop-helix (bHLH) transcription factors defines many types of cellular differentiation. We find that a distinct mechanism regulates the much broader expression of the heterodimer partners of these specific factors and impinges on differentiation. In Drosophila, a cross-interacting regulatory network links expression of the E protein Daughterless (Da), which heterodimerizes with bHLH proteins to activate them, with expression of the Id protein Extramacrochaetae (Emc), which antagonizes bHLH proteins. Coupled transcriptional feedback loops maintain the widespread Emc expression that restrains Da expression, opposing bHLH-dependent differentiation while enhancing growth and cell survival. Where extracellular signals repress emc, Da expression can increase. This defines regions of proneural ectoderm independently from the proneural bHLH genes. Similar regulation is found in multiple Drosophila tissues and in mammalian cells and therefore is likely to be a conserved general feature of developmental regulation by HLH proteins.

Founding the Wnt gene family: How wingless was found to be a positional signal and oncogene homolog.

The Wnt family of developmental regulators were named after the Drosophila segmentation gene wingless and the murine proto-oncogene int-1. Homology between these two genes connected oncogenesis to cell-cell signals in development. I review how wingless was initially characterized, and cloned, as part of the quest to identify developmental cell-to-cell signals, based on predictions of the Positional Information Model, and on the properties of homeotic and segmentation gene mutants. The requirements and cell-nonautonomy of wingless in patterning multiple embryonic and adult structures solidified its status as a candidate signaling molecule. The physical location of wingless mutations and transcription unit defined the gene and its developmental transcription pattern. When the Drosophila homolog of int-1 was then isolated, and predicted to encode a secreted proto-oncogene homolog, it's identity to the wingless gene confirmed that a developmental cell-cell signal had been identified and connected cancer to development.

The CRL4 E3 ligase Mahjong/DCAF1 controls cell competition through the transcription factor Xrp1, independently of polarity genes.

Cell competition, the elimination of cells surrounded by more fit neighbors, is proposed to suppress tumorigenesis. Mahjong (Mahj), a ubiquitin E3 ligase substrate receptor, has been thought to mediate competition of cells mutated for lethal giant larvae (lgl), a neoplastic tumor suppressor that defines apical-basal polarity of epithelial cells. Here, we show that Drosophila cells mutated for mahjong, but not for lgl [l(2)gl], are competed because they express the bZip-domain transcription factor Xrp1, already known to eliminate cells heterozygous for ribosomal protein gene mutations (Rp/+ cells). Xrp1 expression in mahj mutant cells results in activation of JNK signaling, autophagosome accumulation, eIF2α phosphorylation and lower translation, just as in Rp/+ cells. Cells mutated for damage DNA binding-protein 1 (ddb1; pic) or cullin 4 (cul4), which encode E3 ligase partners of Mahj, also display Xrp1-dependent phenotypes, as does knockdown of proteasome subunits. Our data suggest a new model of mahj-mediated cell competition that is independent of apical-basal polarity and couples Xrp1 to protein turnover.

For deep networks, the whole equals the sum of the parts.

Deep convolutional networks exceed humans in sensitivity to local image properties, but unlike biological vision systems, do not discover and encode abstract relations that capture important properties of objects and events in the world. Coupling network architectures with additional machinery for encoding abstract relations will make deep networks better models of human abilities and more versatile and capable artificial devices.

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1.

Whereas complete loss of Rp function is generally lethal, most heterozygous Rp mutants grow more slowly and are subject to competitive loss from mosaics tissues that also contain wild type cells. The rpS12 gene has a special role in the cell competition of other Ribosomal Protein (Rp) mutant cells in Drosophila. Elimination by cell competition is promoted by higher RpS12 levels and prevented by a specific rpS12 mis-sense mutation, identifying RpS12 as a key effector of cell competition due to mutations in other Rp genes. Here we show that RpS12 is also required for other aspects of Rp mutant phenotypes, including hundreds of gene expression changes that occur in 'Minute' Rp heterozygous wing imaginal discs, overall translation rate, and the overall rate of organismal development, all through the bZip protein Xrp1 that is one of the RpS12-regulated genes. Our findings outline the regulatory response to mutations affecting essential Rp genes that controls overall translation, growth, and cell competition, and which may contribute to cancer and other diseases.

All in the family: proneural bHLH genes and neuronal diversity.

Proneural basic Helix-Loop-Helix (bHLH) proteins are required for neuronal determination and the differentiation of most neural precursor cells. These transcription factors are expressed in vastly divergent organisms, ranging from sponges to primates. Here, we review proneural bHLH gene evolution and function in the Drosophila and vertebrate nervous systems, arguing that the Drosophila gene atonal provides a useful platform for understanding proneural gene structure and regulation. We also discuss how functional equivalency experiments using distinct proneural genes can reveal how proneural gene duplication and divergence are interwoven with neuronal complexity.

Transcriptional and post-transcriptional regulation of extra macrochaetae during Drosophila adult peripheral neurogenesis.

Regulation of the Drosophila ID protein Extra macrochaetae (Emc) is important because reduced Emc levels have been proposed to favor proneural gene activity and thereby define a prepattern for neurogenesis. Recent studies suggest a major role for post-translational control of Emc levels. To further define the mechanisms of Emc regulation, we identified two redundant cis-regulatory regions by germline transformation-rescue experiments that make use of new molecularly-defined emc mutants. We distinguished the mechanisms by which Daughterless (Da) regulated Emc expression, finding post-translational regulation in most tissues, and additional transcriptional regulation in the eye imaginal disc posterior to the morphogenetic furrow. Dpp and Hh signaling pathways repressed Emc transcriptionally and post-translationally within the morphogenetic furrow of the eye disc, whereas Wg signaling repressed Emc expression at the anterior margin of the wing imaginal disc. Although the emc 3' UTR is potentially regulatory, no effect of miRNA pathways on Emc protein levels was discernible. Our work supports recent evidence that post-transcriptional mechanisms contribute more to regulation of Emc protein levels than transcriptional mechanisms do.

A potential link between p53, cell competition and ribosomopathy in mammals and in Drosophila.

The term cell competition has been used to describe the phenomenon whereby particular cells can be eliminated during tissue growth only when more competitive cells are available to replace them. Multiple examples implicate differential activity of p53 in cell competition in mammals, but p53 has not been found to have the same role in Drosophila, where the phenomenon of cell competition was first recognized. Recent studies now show that Drosophila cells harboring mutations in Ribosomal protein (Rp) genes, which are eliminated by cell competition with wild type cells, activate a p53 target gene, Xrp1. In Diamond Blackfan Anemia, human Rp mutants activate p53 itself, through a nucleolar stress pathway. These results suggest a link between mammalian and Drosophila Rp mutants, translation, and cell competition.

Higher lymph node harvest in patients with a pathologic complete response after neoadjuvant therapy for esophageal cancer is associated with improved survival.

BACKGROUND AND OBJECTIVES: Lymph node harvest during esophagectomy has been associated with improved survival for esophageal cancer but the value of enhanced lymph node harvest following complete pathologic response (pCR) is debated. This study investigated if increasing lymph node harvest in esophageal cancer patients with a pCR after neoadjuvant therapy and esophagectomy is associated with improved survival. METHODS: We queried the National Cancer Data Base for patients with esophageal cancer between 2004 and 2014 who underwent neoadjuvant chemotherapy or chemoradiation therapy followed by esophagectomy found to have pCR. Multivariable Cox modeling was utilized to evaluate the impact of increasing lymph node counts on overall survival (OS). RESULTS: A total of 1373 patients met inclusion criteria. A National Comprehensive Cancer Network compliant lymphadenectomy of ≥15 nodes was associated with improved survival (66.7% vs 51.1%; P < .001). Cox modeling showed that the first node cutoff to demonstrate a statistically significant improvement in OS was ≥7 nodes (hazard ratio [HR], 95% confidence interval [CI]: 0.81, 0.68-0.97; 5-year OS: 54.2%) with a trend of decreasing and statistically significant HRs until ≥25 nodes (HR, 95% CI: 0.52, 0.37-0.72; 5-year OS: 68.4%). CONCLUSIONS: High negative node counts after neoadjuvant therapy and esophagectomy are associated with improved survival in patients with pCR.

Assessment of Couple Relationships Standards in Same-Sex Attracted Adults.

Relationship standards are beliefs about what makes a good romantic relationship. To date, no research on relationship standards in same-sex relationships has been conducted. This paper describes development of the Rainbow Couples Relationship Standards Scale (Rainbow CRSS). In common with measures of relationship standards developed with heterosexuals, the Rainbow CRSS assesses the importance people attach to Couple Bond standards (expression of love, caring, intimacy), Family Responsibility standards (extended family relations, maintenance of face and harmony), Religion, and Relationship Effort standards. The Rainbow CRSS also assesses three standards hypothesized to be of particular importance to same-sex couples: Relationship Outness (public disclosure of the relationship), Sexual Openness (acceptance of open sexual relationship), and Dyadic Coping with Homophobic discrimination. Participants were 414 same-sex attracted men and women who completed the Rainbow CRSS online, plus some validation scales. The Rainbow CRSS showed a coherent two-level factor structure that was similar to that in heterosexual couples for the Couple Bond and Family Responsibility Scales. Same-sex attracted people's standards were similar for men and women, and for singles versus those in a relationship. Same-sex attracted people's standards were very similar in endorsement of Couple Bond, Family Responsibility, Religion, and Relationship Effort standards to those of heterosexuals. The Relationship Outness and Dyadic Coping with Homophobia scales assessed potentially important standards that reflect some distinctive challenges for same-sex couple relationships.

La terapia familiar generalmente se ha conceptualizado como un proceso conversacional por medio del cual los terapeutas y los pacientes generan nuevos significados. Basándose en un estudio de tres años de prácticas conversacionales observables en procesos satisfactorios de terapia familiar de familias chilenas con un niño/adolescente que tiene comportamientos disruptivos, buscamos ejemplos clínicos de patrones interpersonales transformadores (PIT). Estos patrones son un aspecto clave del "IPscope" o instrumento de evaluación de los patrones interpersonales (Tomm, St. George, Wulff, & Strong, 2014), un marco que usamos para analizar los procesos de creación de significado en la terapia familiar. Los patrones interpersonales transformadores constituyen un enfoque innovador para analizar los procesos terapéuticos mediante el reconocimiento de prácticas conversacionales fáciles de seguir empíricamente que participan en la generación de "significados nuevos". Los patrones interpersonales transformadores intervienen en la presentación y la articulación discursiva ("convencer de crear") de las manersa preferidas de los pacientes de relacionarse y vivir (p. ej.: preferencias relacionales o PR). Analizamos datos conversacionales de sesiones/tratamientos satisfactorios de terapia familiar y presentamos un modelo emergente de cinco categorías de prácticas conversacionales que constituyen patrones interpersonales transformadores, por ejemplo: PIT preparatorios, PIT identificadores, PIT localizadores, PIT transformadores y PIT consolidadores. Los hemos llamado "realizadores" porque estas prácticas conversacionales ayudan a las familias a convencerlas de crear (o a "hacer realidad") preferencias relacionales particulares. También ofrecemos descriptores fáciles de usar de las subcategorías de los realizadores (p. ej.: PIT de medición) que pueden ayudar a los profesionales a reconocer, aprender y llevar a cabo estas invitaciones conversacionales. Se debaten las consecuencias teóricas y las futuras líneas de investigación.

Deep convolutional networks do not classify based on global object shape.

Deep convolutional networks (DCNNs) are achieving previously unseen performance in object classification, raising questions about whether DCNNs operate similarly to human vision. In biological vision, shape is arguably the most important cue for recognition. We tested the role of shape information in DCNNs trained to recognize objects. In Experiment 1, we presented a trained DCNN with object silhouettes that preserved overall shape but were filled with surface texture taken from other objects. Shape cues appeared to play some role in the classification of artifacts, but little or none for animals. In Experiments 2-4, DCNNs showed no ability to classify glass figurines or outlines but correctly classified some silhouettes. Aspects of these results led us to hypothesize that DCNNs do not distinguish object's bounding contours from other edges, and that DCNNs access some local shape features, but not global shape. In Experiment 5, we tested this hypothesis with displays that preserved local features but disrupted global shape, and vice versa. With disrupted global shape, which reduced human accuracy to 28%, DCNNs gave the same classification labels as with ordinary shapes. Conversely, local contour changes eliminated accurate DCNN classification but caused no difficulty for human observers. These results provide evidence that DCNNs have access to some local shape information in the form of local edge relations, but they have no access to global object shapes.

Patterning the eye: A role for the cell cycle?

Although highly regulated cell cycle behavior accompanies specification of cell types in the Drosophila retina, no evidence has previously existed that cell cycle phase influences cell fate choice. Meserve and Duronio have now used genetic techniques to trace the fate of a sub-population of cells that accumulate in G2-phase of the cell cycle, discovering that they contribute to a particular fate, the precursor of the sensory inter-ommatidial bristles. Meserve and Duronio further show that G2 cells have an advantage acquiring inter-ommatidial bristle fate. This is the first evidence for a functional contribution of cell cycle phase to cell fate determination in the Drosophila eye and indicates that the fate of one population of retinal cells is established much earlier than previously recognized, during the larval stages when cell-cell interactions influence cell cycle phase. Inter-ommatidial bristle fate had been thought to arise much later, in the pupal stage, and models for how these neuronal eye structures arise will now have to be revised.

The Notch pathway regulates the Second Mitotic Wave cell cycle independently of bHLH proteins.

Notch regulates both neurogenesis and cell cycle activity to coordinate precursor cell generation in the differentiating Drosophila eye. Mosaic analysis with mitotic clones mutant for Notch components was used to identify the pathway of Notch signaling that regulates the cell cycle in the Second Mitotic Wave. Although S phase entry depends on Notch signaling and on the transcription factor Su(H), the transcriptional co-activator Mam and the bHLH repressor genes of the E(spl)-Complex were not essential, although these are Su(H) coactivators and targets during the regulation of neurogenesis. The Second Mitotic Wave showed little dependence on ubiquitin ligases neuralized or mindbomb, and although the ligand Delta is required non-autonomously, partial cell cycle activity occurred in the absence of known Notch ligands. We found that myc was not essential for the Second Mitotic Wave. The Second Mitotic Wave did not require the HLH protein Extra macrochaetae, and the bHLH protein Daughterless was required only cell-nonautonomously. Similar cell cycle phenotypes for Daughterless and Atonal were consistent with requirement for neuronal differentiation to stimulate Delta expression, affecting Notch activity in the Second Mitotic Wave indirectly. Therefore Notch signaling acts to regulate the Second Mitotic Wave without activating bHLH gene targets.

Hox5 interacts with Plzf to restrict Shh expression in the developing forelimb.

To date, only the five most posterior groups of Hox genes, Hox9-Hox13, have demonstrated loss-of-function roles in limb patterning. Individual paralog groups control proximodistal patterning of the limb skeletal elements. Hox9 genes also initiate the onset of Hand2 expression in the posterior forelimb compartment, and collectively, the posterior HoxA/D genes maintain posterior Sonic Hedgehog (Shh) expression. Here we show that an anterior Hox paralog group, Hox5, is required for forelimb anterior patterning. Deletion of all three Hox5 genes (Hoxa5, Hoxb5, and Hoxc5) leads to anterior forelimb defects resulting from derepression of Shh expression. The phenotype requires the loss of all three Hox5 genes, demonstrating the high level of redundancy in this Hox paralogous group. Further analyses reveal that Hox5 interacts with promyelocytic leukemia zinc finger biochemically and genetically to restrict Shh expression. These findings, along with previous reports showing that point mutations in the Shh limb enhancer lead to similar anterior limb defects, highlight the importance of Shh repression for proper patterning of the vertebrate limb.

A unified sensor architecture for isothermal detection of double-stranded DNA, oligonucleotides, and small molecules.

Pathogen detection is an important problem in many areas of medicine and agriculture, which can involve genomic or transcriptomic signatures or small-molecule metabolites. We report a unified, DNA-based sensor architecture capable of isothermal detection of double-stranded DNA targets, single-stranded oligonucleotides, and small molecules. Each sensor contains independent target detection and reporter modules, enabling rapid design. We detected gene variants on plasmids by using a straightforward isothermal denaturation protocol. The sensors were highly specific, even with a randomized DNA background. We achieved a limit of detection of ∼15 pM for single-stranded targets and ∼5 nM for targets on denatured plasmids. By incorporating a blocked aptamer sequence, we also detected small molecules using the same sensor architecture. This work provides a starting point for multiplexed detection of multi-strain pathogens, and disease states caused by genetic variants (e.g., sickle cell anemia).