Requirements for Mediator Complex Subunits Distinguish Three Classes of Notch Target Genes at the Drosophila Wing Margin

Spatial and temporal gene regulation relies on a combinatorial code of sequence-specific transcription factors that must be integrated by the general transcriptional machinery. A key link between the two is the mediator complex, which consists of a core complex that reversibly associates with the accessory kinase module. We show here that genes activated by Notch signaling at the dorsal-ventral boundary of the Drosophila wing disc fall into three classes that are affected differently by the loss of kinase module subunits. One class requires all four kinase module subunits for activation, while the others require only Med12 and Med13, either for activation or for repression. These distinctions do not result from different requirements for the Notch coactivator Mastermind or the corepressors Hairless and Groucho. We propose that interactions with the kinase module through distinct cofactors allow the DNA-binding protein Suppressor of Hairless to carry out both its activator and repressor functions

The retinal determination gene dachshund restricts cell proliferation by limiting the activity of the Homothorax-Yorkie complex

The Drosophila transcriptional co-activator protein Yorkie and its vertebrate orthologs YAP and TAZ are potent oncogenes, whose activity is normally kept in check by the upstream Hippo kinase module. Upon its translocation into the nucleus, Yorkie forms complexes with several tissue-specific DNA-binding partners, which help to define the tissue-specific target genes of Yorkie. In the progenitor cells of the eye imaginal disc, the DNA-binding transcription factor Homothorax is required for Yorkie-promoted proliferation and survival through regulation of the bantam microRNA (miRNA). The transit from proliferating progenitors to cell cycle quiescent precursors is associated with the progressive loss of Homothorax and gain of Dachshund, a nuclear protein related to the Sno/Ski family of co-repressors. We have identified Dachshund as an inhibitor of Homothorax-Yorkie-mediated cell proliferation. Loss of dachshund induces Yorkie-dependent tissue overgrowth. Conversely, overexpressing dachshund inhibits tissue growth, prevents Yorkie or Homothorax-mediated cell proliferation of disc epithelia and restricts the transcriptional activity of the Yorkie-Homothorax complex on the bantam enhancer in Drosophila cells. In addition, Dachshund collaborates with the Decapentaplegic receptor Thickveins to repress Homothorax and Cyclin B expression in quiescent precursors. The antagonistic roles of Homothorax and Dachshund in Yorkie activity, together with their mutual repression, ensure that progenitor and precursor cells are under distinct proliferation regimes. Based on the crucial role of the human dachshund homolog DACH1 in tumorigenesis, our work suggests that DACH1 might prevent cellular transformation by limiting the oncogenic activity of YAP and/or TAZ.Spanish Ministry of Economy and Competitiveness (MINECO), EU Feder Funds: (BFU2012-34324), Consolider 'From Genes to Shape' (MICINN), FCT fellowships: (SFRH/BPD/46983/2008, IF/01031/2012)

dachshund Potentiates Hedgehog Signaling during Drosophila Retinogenesis

Proper organ patterning depends on a tight coordination between cell proliferation and differentiation. The patterning of Drosophila retina occurs both very fast and with high precision. This process is driven by the dynamic changes in signaling activity of the conserved Hedgehog (Hh) pathway, which coordinates cell fate determination, cell cycle and tissue morphogenesis. Here we show that during Drosophila retinogenesis, the retinal determination gene dachshund (dac) is not only a target of the Hh signaling pathway, but is also a modulator of its activity. Using developmental genetics techniques, we demonstrate that dac enhances Hh signaling by promoting the accumulation of the Gli transcription factor Cubitus interruptus (Ci) parallel to or downstream of fused. In the absence of dac, all Hh-mediated events associated to the morphogenetic furrow are delayed. One of the consequences is that, posterior to the furrow, dac- cells cannot activate a Roadkill-Cullin3 negative feedback loop that attenuates Hh signaling and which is necessary for retinal cells to continue normal differentiation. Therefore, dac is part of an essential positive feedback loop in the Hh pathway, guaranteeing the speed and the accuracy of Drosophila retinogenesis.MINECO Spain grants: (BFU2012-34324, BFU2015- 66040); Research Foundation—Flanders FWO grants: (G.0640.13, G.0791.14, PhD fellowship); Fundação para a Ciência e Tecnologia grant: (IF/01031/2012)

The Big Bang of tissue growth: Apical cell constriction turns into tissue expansion

How tissue growth is regulated during development and cancer is a fundamental question in biology. In this issue, Tsoumpekos et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201705104) and Forest et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201705107) identify Big bang (Bbg) as an important growth regulator of the Drosophila melanogaster wing imaginal disc.Research in the Janody laboratory is supported by funds from Fundação para a Ciência e Tecnologia (FCT; PTDC/BIA-BCM/121455/ 2010) and from FCT cofinanced by European Regional Development Fund through Programa Operacional Competitividade e Internacional-ização (POCI-01-0145-FEDER-016390). Florence Janody is the recipient of Fundação para a Ciência e Tecnologia IF/01031/2012

From one-day to multiday activity scheduling: Extending the OASIS framework

Applications of activity-based models for the estimation of transport demand have demonstrated to achieve greater behavioural realism than traditional trip-based models. However, state-of-the art models focus on single-day schedules as focal points to their estimations, thus ignoring fundamental dynamics that explain individual behaviour over longer periods of time. Several authors have highlighted the importance of multiday analyses in activity-travel contexts, which are still lacking in many state-of-the-art framework. In this paper, we present an extension of the OASIS framework, an integrated model for the simulation of single day schedules, to include intrapersonal interactions influencing longer term decisions. We formulate the multiday problem as a multiobjective optimisation problem where each day d is associated with a utility Ud. We consider an activity-based set up where individuals maximise the total utility of their schedules over multiple days (e.g. week). We discuss implications and requirements of this formulation, and illustrate the methodology with chosen examples

OASIS: Optimisation-based Activity Scheduling with Integrated Simultaneous choice dimensions

Activity-based models offer the potential of a far deeper understanding of daily mobility behaviour than trip-based models. However, activity-based models used both in research and practice have often relied on applying sequential choice models between subsequent choices, oversimplifying the scheduling process. In this paper we introduce OASIS, an integrated framework to simulate activity schedules by considering all choice dimensions simultaneously. We present a methodology for the estimation of the parameters of an activity-based model from historic data, allowing for the generation of realistic and consistent daily mobility schedules. The estimation process has two main elements: (i) choice set generation, using the Metropolis-Hasting algorithm, and (ii) estimation of the maximum likelihood estimators of the parameters. We test our approach by estimating parameters of multiple utility specifications for a sample of individuals from a Swiss nationwide travel survey, and evaluating the output of the OASIS model against realised schedules from the data. The results demonstrate the ability of the new framework to simulate realistic distributions of activity schedules, and estimate stable and significant parameters from historic data that are consistent with behavioural theory. This work opens the way for future developments of activity-based models, where a great deal of constraints can be explicitly included in the modelling framework, and all choice dimensions are handled simultaneously

Choice set generation for activity-based models

Activity-based models have seen a significant increase in research focus in the past decade. Based on the fundamental assumption that travel demand is derived from the need to do activities and time and space constraints (Hägerstraand, 1970, Chapin, 1974). ABM offer a more flexible and behaviourally centred alternative to traditional trip-based approaches. Econometric — or utility-based — activity-based models (e.g., Adler and Ben-Akiva, 1979, Bowman and BenAkiva, 2001) postulate that the process of activity generation and scheduling can be modelled as discrete choices. Individuals derive a utility from performing activities, and they schedule them as to maximise the total utility of the schedule. In classical discrete choice model applications, the parameters of the utility functions can be estimated by deriving their maximum likelihood estimators. As the likelihood function is defined over a full enumeration of the alternatives in the choice set, this approach is limited for activity-based applications: the set of possible activities and their spatio-temporal sequence is combinatorial and not fully observed by either the decision-maker or the modeller. While discrete choice models can be estimated over samples of alternatives (e.g., Guevara and Ben-Akiva, 2013) an appropriate definition of such sample is as crucial as it is challenging. This paper presents a methodology to sample a choice set of full daily schedules for a given individual and a list of activities. The Metropolis-Hastings algorithm allows us to explore the space efficiently and draw both high and lower probability alternatives for consistent estimation of the parameters. The methodology is tested on a sample of individuals from the 2015 Swiss Mobility and Transport Microcensus (Office fédéral de la statistique and Office fédéral du développement Territorial, 2017)

Archive et folie

Archive et folie se donnent volontiers comme incompatibles, que ce soit selon un discours normatif qui vide la folie pour mieux la faire taire, ou selon un discours alternatif qui entend valoriser ce vide. Dans une perspective clinique, toutefois, la question se déplace. Le fou ne s’y aborde pas comme celui qui serait indemne de la fonction d’archive, mais bien plutôt comme celui qui en est trop proche, comme celui qui y est pris, qui la supporte littéralement. On envisagera ici, pour une situation donnée, comment le clinicien autant que le patient se trouvent impliqués dans un parcours qui va du symptôme à son devenir archive.The archive and madness are often said to be incompatible, whether according to a normative discourse that empties madness in order to silence it all the more, or according to an alternative discourse that intends to validate this gap. From a clinical perspective, however, the question shifts. The madman does not approached it as someone who is unharmed by the function of the archive, but rather as someone who is too close to it, someone who is caught up by it, who endures it, literally. What will be considered here, for a given situation, is how the clinician, as much as the patient, finds himself involved on a course that goes from symptom to becoming archive

The spectraplakin Dystonin antagonizes YAP activity and suppresses tumourigenesis

Aberrant expression of the Spectraplakin Dystonin (DST) has been observed in various cancers, including those of the breast. However, little is known about its role in carcinogenesis. In this report, we demonstrate that Dystonin is a candidate tumour suppressor in breast cancer and provide an underlying molecular mechanism. We show that in MCF10A cells, Dystonin is necessary to restrain cell growth, anchorage-independent growth, self-renewal properties and resistance to doxorubicin. Strikingly, while Dystonin maintains focal adhesion integrity, promotes cell spreading and cell-substratum adhesion, it prevents Zyxin accumulation, stabilizes LATS and restricts YAP activation. Moreover, treating DST-depleted MCF10A cells with the YAP inhibitor Verteporfin prevents their growth. In vivo, the Drosophila Dystonin Short stop also restricts tissue growth by limiting Yorkie activity. As the two Dystonin isoforms BPAG1eA and BPAG1e are necessary to inhibit the acquisition of transformed features and are both downregulated in breast tumour samples and in MCF10A cells with conditional induction of the Src proto-oncogene, they could function as the predominant Dystonin tumour suppressor variants in breast epithelial cells. Thus, their loss could deem as promising prognostic biomarkers for breast cancer.The authors acknowledge the support of the Bloomington Drosophila Stock Centre, the National Institute of Genetics (NIG-Fly) the services of the Animal, Imaging and Cytometry and Genomics facilities at Instituto Gulbenkian de Ciência, and of the i3S Scientific Platforms, including the Cell Culture and Genotyping (CCGen) and the Genomics (GenCore) platforms, as well as the Bioimaging and the Advanced Light Microscopy platforms. We are also grateful to M. J. Amorim and N. Tapon for reagents and to A. Monteiro for fly food preparation. We specially thank K. Struhl for providing the TAM-inducible ER-Src and PBabe cell lines and Rafeeq Mir, Eurico Morais-de-Sá, Archana Pawar and Carla Oliveira for comments on the manuscript. This work was supported by funds from Fundação para a Ciência e Tecnologia (FCT), co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) through Programa Operacional Competitividade e Internacionalização (POCI) (POCI-01-0145-FEDER-016390) and the Laço Grant in breast cancer 2015 to F.J. The i3S Bioimaging and Advanced Light Microscopy scientific platforms are both member of the national infrastructure PPBI-Portuguese Platform of BioImaging, supported by POCI-01-0145-FEDER-022122. P.J. was the recipient of fellowships from FCT (PD/ BD/52439/2013). F.J. was the recipient of IF/01031/2012

Representing location choice within activity-based models

Since the 70s, there has been a growing interest in activity-based modelling. This approach models the need to travel as a result of performing daily activities (Bowman and BenAkiva, 2001). Nevertheless, the activities need to be scheduled which involves a lot of variables and results in a huge number of unique alternatives (Pougala et al., 2021). Among these variables, the number of possible locations is usually bigger than other variables, motivating the use of a choice set for locations. However, this choice set of locations is usually not known by the modeller (Pagliara and Timmermans, 2009), so there is a need to recreate it. In addition, it would be useful for two purposes: simulation of daily schedules, and estimation of the parameters of an activity-based model based on an underlying choice model. For the first one, alternatives in the choice set must be competitive, to generate realistic schedules, as for the latter one, it should also contain unlikely alternatives to estimate unbiased parameters. In this paper, a methodology to generate a choice set of destinations suitable for both purposes is presented. The choice set is generated with a choice model and can be transformed afterwards to include unlikely alternatives. The methodology is validated using the 2015 Swiss Mobility and Transport Microsensus (fédéral de la statistique and fédéral du développement Territorial, 2017) dataset